Re: [IPT] Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Dear John,
Please see our working revisions/comments/questions on the DNA/tissue extension for Darwin Core (highlighted in blue). We were able to work through the draft up through "class sample properties": https://docs.google.com/document/d/1RCgIPfu9gAPubjjbog-9vCJonvqcK1pLOaq6H8GS...
The document is also attached for your reference (just incase any of you are unable to access the document).
Please try to respond to our questions and comments prior to our meeting tomorrow (be sure to make these changes using a different color for tracking purposes).
Tomorrow we will like to 1) briefly recap our revisions on the extension so far (addressing questions and comments), 2) complete our review of the extension and 3) identify any remaining issues with DwC working with IPT (and identify if any changes in the IPT are required).
Thank you for your help on this!
Kind Regards,
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu" <tuco@berkeley.edumailto:tuco@berkeley.edu> Date: Sunday, October 21, 2012 10:52 PM To: Gabriele Droege <g.droege@bgbm.orgmailto:g.droege@bgbm.org> Cc: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au>, John Deck <jdeck@berkeley.edumailto:jdeck@berkeley.edu>, Robert Hanner <bob.hanner@gmail.commailto:bob.hanner@gmail.com>, Éamonn Tuama <eotuama@gbif.orgmailto:eotuama@gbif.org>, Robert Robbins <rjr8222@gmail.commailto:rjr8222@gmail.com>, "Guentsch, Anton" <a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org> Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Dear all,
I finished working on the Google Doc "DNA Tissue Extension Notes - TDWG 2012". Feel free to let this be a working document where comments and questions can be added. I've attached a Word Doc version for archival purposes.
I added the two template extension files (DNATissueExtension.txt and DNAAmplificationExtension.txt) to the shared TDWG GGBN working group folder linked below. They are in the form they need to be submitted to GBIF to be added to their extension registry. They would both need to be updated with the term descriptions, examples, and constraints.
https://drive.google.com/#folders/0BxEyFKwB7zY4WEs0WkdtUU5oVnM
Cheers,
John
On Sun, Oct 21, 2012 at 10:38 PM, John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> wrote: Ooops
...at http://goo.gl/kGHmb. Adding touches based on the files Gabi sent. Will tell you all when finished with that and will send it as a Word doc at that time in case there are any issues with Google docs. Should be soon. Let me know if I should share to any different addresses.
Cheers,
John
On Sun, Oct 21, 2012 at 10:34 PM, John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> wrote: That helps a lot, as it clears up some of my own misconceptions. I have shared a document where I have captured the thinking behind a couple of different ways forward with one or two extensions and an example of how the two-extension might look in the context of a Darwin Core Archive. The DNA Tissue Extension Notes Google doc can be found at
On Sun, Oct 21, 2012 at 9:23 PM, "Dröge, Gabriele" <g.droege@bgbm.orgmailto:g.droege@bgbm.org> wrote: Yes we do... Hi John,
Thanks for getting back to us. Attached are two csv files, one with some main DNA facts and the other with associated GenBank entries und publications (2 examples with 2 GenBank entries per DNA sample). I included only UnitID/CollCode/InstCode for the related voucher specimen and I excluded the tissue facts since they are quite similar to the DNA facts and should be mapped independently.
Best, Gabi
-----Original Message----- From: Barker, Katharine [mailto:BarkerK@si.edumailto:BarkerK@si.edu] Sent: Sunday, October 21, 2012 11:41 PM To: Paul Flemons; Dröge, Gabriele Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Paul and Gabi,
Do we have any sample data that John can use as a test case? I think he would like it today, if possible.
Thanks for your help (and the team work).
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>" <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Date: Sunday, October 21, 2012 12:03 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu>> Subject: Re: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Hi Katie,
Messages received. Will have the extension stuff ready within a few hours and hope to be able to attend remotely. One thing in the meantime. Do you have any example data that could be used as a test case to populate a core with this extension? Would like to try that with some realy data to test my assumptions.
Sorry for the delay.
Thanks,
John
On Sun, Oct 21, 2012 at 10:08 AM, Barker, Katharine <BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu>> wrote: Dear John,
I'm sorry that you were unable to attain a visa for China. I was really looking forward to working with you in person with the group. Paul mentioned that he had e-mailed you earlier this evening. Can you please send us the draft for the DarwinCore DNA/tissue extension as soon as possible for review during our working sessions? We have one tomorrow at 1:30 (Beijing time) and another on Tuesday at the same time. It would be really great if you could Skype into either both or one of the sessions.
Thanks for your help on this.
Kind Regards,
Katie
From: <Barker>, Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu><mailto:barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu>>> Date: Thursday, October 18, 2012 1:34 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu><mailto:barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu>>>, 'John Deck' <jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>>>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au><mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au>>>, "'"Dröge", Éamonn Tuama <eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org><mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>>, "Whitacre, Jamie" <WHITACREJ@si.edumailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edumailto:WHITACREJ@si.edu><mailto:WHITACREJ@si.edumailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edumailto:WHITACREJ@si.edu>>>, "'rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:'rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>'" <rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>>, "'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>'" <a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>>, "'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>'" <gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>>, "'tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:'tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>'" <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>> Cc: "'morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:'morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk>>'" <morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk>>>, "Parr, Cynthia" <parrc@si.edumailto:parrc@si.edu<mailto:parrc@si.edumailto:parrc@si.edu><mailto:parrc@si.edumailto:parrc@si.edu<mailto:parrc@si.edumailto:parrc@si.edu>>> Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Dear all,
This is a friendly reminder that we will be meeting next Tuesday afternoon at the TDWG 2012 Conference in order to finalize the draft DarwinCore-A DNA/tissue extension for GGBN. As you know, the immediate need for GGBN members is to publish information on tissues. This will happen through extensions to both ABCDDNA and DarwinCore-A. Here we are focused on developing the DarwinCore-A DNA/tissue extension.
An update on the timeline for developing the draft DarwinCore-A DNA/tissue extension is listed below.
1) Review content requirements for DarwinCore-A DNA/tissue extension (completed, see attached required DNA and tissue elements)
2) John Weiczorek will develop the draft DarwinCore-A DNA/tissue extension (to be completed for group review prior to our break out session on Tuesday afternoon, October 23).
3) Tuesday October 23, working meeting
· Questions to answer before final review of DNA/tissue extension
o How do we include repeatable elements of ABCDDNA into DwC-A-DNA (References to more than one sequence record/publication are mandatory)?
o How do we extend the "Basis of Record" in ABCD and DwC-A and how do we include an element similar to ABCD-"Kind of Unit" to DwC-A?
o What are the remaining issues for DwC-A working with IPT? Are any changes in the IPT required?
· Review and finalize draft DarwinCore-A DNA/tissue extension for posting to GBIF site.
Thank you again to everyone who is involved in this project. I look forward to seeing all of you in Beijing.
Kind Regards,
Katie
From: Barker, Katharine Sent: Friday, September 28, 2012 9:53 AM To: 'John Deck'; Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org><mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>; tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Dear all,
We will be meeting this Tuesday at 1pm U.S. Eastern time over Skype in order to discuss the actions required to develop the draft proposal for the Darwin Core tissue/DNA extension. A proposal for designing, testing, and implementing the GGBN data portal is attached for your reference. Please review the timeline and action items leading up to the TDWG 2012 Conference.
My Skype name is Katharine.Barker1. If possible, please forward me your skype account names prior to our meeting.
Kind Regards,
Katie
From:jdeck88@gmail.commailto:From%3Ajdeck88@gmail.com<mailto:From%3Ajdeck88@gmail.commailto:From%253Ajdeck88@gmail.com><mailto:jdeck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@gmail.commailto:jdeck88@gmail.com>> [mailto:jdeck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@gmail.commailto:jdeck88@gmail.com>] On Behalf Of John Deck Sent: Tuesday, September 25, 2012 4:04 PM To: Barker, Katharine Cc: Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org><mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>; tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Here is the wrapup of the bioCollections Ontology workshop from last week at GSC14:
http://biocodecommons.org/workshops/bioCollections/index.html
This is relevant to these discussions since we focussed on what constitutes a "sample" and also, probably more importantly, processes that work with samples.
We briefly discussed the DwC Tissue Extension and came up with a proposal for a quick-fix and a more substantial fix. The quick-fix is to create two new BasisOfRecord terms: TissueSubSample, DNAExtract (or some terms like that -- Tuco could provide more clarification on this too). Thus, theoretically we could override the dwc:Occurrence class to mean, for example, TissueSubSample the same way we do for Specimens and Observations. The bigger fix is to more fundamentally re-orient DwC around the notion of "Sample", involving adding/changing some properties although we didn't get into any specifics.
P.s. I can do the 12/1/2 timeslots for that monday or tuesday but not the 11.
John On Mon, Sep 24, 2012 at 12:39 PM, Barker, Katharine <BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu><mailto:BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu>>> wrote: Dear all,
We will have a telecon meeting early next week in order to discuss a draft proposal for the Darwin Core tissue/DNA extension. Gabi, Paul, and I will put together a first draft for discussion to be distributed prior to the telecon. As you know, the goal is to have a working draft ready for our working group to review at the TDWG meeting in Beijing this October.
These are our options for meeting next week: Monday 11am, 12pm, 1pm, 2pm US EDT Tuesday 11am, 12pm, 1pm, 2pm US EDT
Please let me know if you cannot make one of these times.
Thanks again to those of you who provided input last week at the GSC 14 meeting.
Kind Regards,
Katie
From: Barker, Katharine Sent: Wednesday, September 12, 2012 10:51 AM To: 'Paul Flemons'; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org><mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; 'rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>'; jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>>; 'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>'; 'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>'; 'tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>' Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core Importance: High
Dear all,
My name is Katie Barker and I am the Global Genome Biodiversity Network Coordinator. As you know from Paul Flemons, members of the GGBN Data Standards and Data Access Task Force are trying to pull together a task group, which you are all part of, for the upcoming TDWG meeting in Beijing this October in order to address a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members. I am contacting you to schedule a meeting in late September/early October to develop a draft proposal for this extension to be completed at the upcoming TDWG meeting.
Please let me know your availability for the last two weeks of September and first two weeks of October. There will be some scheduling issues, as there are task group members on the west and east coasts of the U.S., Europe and Australia.
Paul Flemons (in Australia) will be in the U.S. the first week of October, so maybe we can meet in the afternoon of the 1st, anytime on the second 2nd, or in the morning of the 3rd of October over teleconference (US Eastern Daylight Time). Please let me know if any of these time slots work for you.
Gabi, I believe that you and John Deck will be at the GSC 14 meeting next week. Is there any chance that you can start drawing up an outline for the proposed extension? We could review the outline during our group telecon and start drafting a proposal for review at the TDWG meeting in October.
Kind Regards,
Katie
Task Group Members:
John Weiczorek - Berkeley Éamonn O'Tuama - GBIF Jamie Whitacre - SI John Deck - Berkeley Robert Robbins - University of California, San Diego Anton Guentsch - BGBM Gabi Droege- BGBM Paul Flemons- AM
From: Paul Flemons [mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au>] Sent: Tuesday, August 07, 2012 2:50 AM To: tuco@berkley.edumailto:tuco@berkley.edu<mailto:tuco@berkley.edumailto:tuco@berkley.edu><mailto:tuco@berkley.edumailto:tuco@berkley.edu<mailto:tuco@berkley.edumailto:tuco@berkley.edu>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org<mailto:j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org><mailto:j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org<mailto:j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org>>; jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>> Cc: Barker, Katharine; Éamonn Ó Tuama [GBIF]; "Dröge, Gabriele" (g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG<mailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG><mailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG<mailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG>>) Subject: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core
Hi all, I am on the Data Standards and Access Task Force for the Global Genome Biodiversity Network (http://ggbn.org/) which is in need of a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members.
To this end I am writing to you to ask if you would be interested in participating in a small working group at TDWG in Beijing this year.
At this stage my plan would be to identify relevant fields for inclusion in the extension, using ABCDDNA as a reference. If sufficient progress is made then we would submit the extension for ratification by TDWG (is that how its done John?) The GGBN will use whatever comes out of the group to move towards having a suitable DwC based schema for data sharing.
So please let me know if you are willing to participate in the task group and/or if there is anyone else you feel would be beneficial to have involved.
How much time do you think we will need? I have been thinking that a day will be needed, so we could make that consist of either one full day or two half days. Im also thinking that during the week will be the best time for this.
Thanks for your time
Best Regards Paul
Paul K J Flemons Manager, Collection Informatics Team Lead, Atlas of Living Australia Biodiversity Volunteer Portalhttp://volunteer.ala.org.au Biodiversity Information Standards (TDWG) Representative for Oceania Australian Museum 6 College Street Sydney NSW 2010 Australia t 61 2 9320 6343 m 0413458649 f 61 2 9320 6021 Visit: http://www.australianmuseum.net.auhttp://www.australianmuseum.net.au/ Like: http://www.facebook.com/australianmuseum Follow: http://www.twitter.com/austmus Watch: http://www.youtube.com/austmus [cid:image001.png@01CDAD34.391DC790mailto:image001.png@01CDAD34.391DC790<mailto:image001.png@01CDAD34.391DC790mailto:image001.png@01CDAD34.391DC790>] Inspiring the exploration of nature and cultures
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-- John Deck (541) 321-0689tel:%28541%29%20321-0689tel:%28541%29%20321-0689
Hi all, I only quickly looked through the proposal, but it looks good, pragmatic and definitely to be working for the case when a DNASample equals a single taxon Occurrence.
Im not so sure how well it would work with environmental samples - would we have the sample flattened out and repeated to represent the individual taxa, sexes, ages, etc found in there? I was therefore wondering if anyone had thought about the attached setup before. Sample is at its core and occurrence & dna amplification as extensions with the amplifications (optionally?) refering to the occurrence they belong to.
Another quick observation is that we try to reuse existing terms in extensions as much as possible. Following that rule for example dwc:institutionCode should rather be used instead of dNACollectionCode and probably dc:source for the referenceCitation
until tomorrow, regards, Markus
On 22.10.2012, at 12:21, Barker, Katharine wrote:
Dear John,
Please see our working revisions/comments/questions on the DNA/tissue extension for Darwin Core (highlighted in blue). We were able to work through the draft up through "class sample properties": https://docs.google.com/document/d/1RCgIPfu9gAPubjjbog-9vCJonvqcK1pLOaq6H8GS...
The document is also attached for your reference (just incase any of you are unable to access the document).
Please try to respond to our questions and comments prior to our meeting tomorrow (be sure to make these changes using a different color for tracking purposes).
Tomorrow we will like to 1) briefly recap our revisions on the extension so far (addressing questions and comments), 2) complete our review of the extension and 3) identify any remaining issues with DwC working with IPT (and identify if any changes in the IPT are required).
Thank you for your help on this!
Kind Regards,
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu" <tuco@berkeley.edumailto:tuco@berkeley.edu> Date: Sunday, October 21, 2012 10:52 PM To: Gabriele Droege <g.droege@bgbm.orgmailto:g.droege@bgbm.org> Cc: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au>, John Deck <jdeck@berkeley.edumailto:jdeck@berkeley.edu>, Robert Hanner <bob.hanner@gmail.commailto:bob.hanner@gmail.com>, Éamonn Tuama <eotuama@gbif.orgmailto:eotuama@gbif.org>, Robert Robbins <rjr8222@gmail.commailto:rjr8222@gmail.com>, "Guentsch, Anton" <a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org> Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Dear all,
I finished working on the Google Doc "DNA Tissue Extension Notes - TDWG 2012". Feel free to let this be a working document where comments and questions can be added. I've attached a Word Doc version for archival purposes.
I added the two template extension files (DNATissueExtension.txt and DNAAmplificationExtension.txt) to the shared TDWG GGBN working group folder linked below. They are in the form they need to be submitted to GBIF to be added to their extension registry. They would both need to be updated with the term descriptions, examples, and constraints.
https://drive.google.com/#folders/0BxEyFKwB7zY4WEs0WkdtUU5oVnM
Cheers,
John
On Sun, Oct 21, 2012 at 10:38 PM, John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> wrote: Ooops
...at http://goo.gl/kGHmb. Adding touches based on the files Gabi sent. Will tell you all when finished with that and will send it as a Word doc at that time in case there are any issues with Google docs. Should be soon. Let me know if I should share to any different addresses.
Cheers,
John
On Sun, Oct 21, 2012 at 10:34 PM, John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> wrote: That helps a lot, as it clears up some of my own misconceptions. I have shared a document where I have captured the thinking behind a couple of different ways forward with one or two extensions and an example of how the two-extension might look in the context of a Darwin Core Archive. The DNA Tissue Extension Notes Google doc can be found at
On Sun, Oct 21, 2012 at 9:23 PM, "Dröge, Gabriele" <g.droege@bgbm.orgmailto:g.droege@bgbm.org> wrote: Yes we do... Hi John,
Thanks for getting back to us. Attached are two csv files, one with some main DNA facts and the other with associated GenBank entries und publications (2 examples with 2 GenBank entries per DNA sample). I included only UnitID/CollCode/InstCode for the related voucher specimen and I excluded the tissue facts since they are quite similar to the DNA facts and should be mapped independently.
Best, Gabi
-----Original Message----- From: Barker, Katharine [mailto:BarkerK@si.edumailto:BarkerK@si.edu] Sent: Sunday, October 21, 2012 11:41 PM To: Paul Flemons; Dröge, Gabriele Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Paul and Gabi,
Do we have any sample data that John can use as a test case? I think he would like it today, if possible.
Thanks for your help (and the team work).
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>" <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Date: Sunday, October 21, 2012 12:03 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu>> Subject: Re: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Hi Katie,
Messages received. Will have the extension stuff ready within a few hours and hope to be able to attend remotely. One thing in the meantime. Do you have any example data that could be used as a test case to populate a core with this extension? Would like to try that with some realy data to test my assumptions.
Sorry for the delay.
Thanks,
John
On Sun, Oct 21, 2012 at 10:08 AM, Barker, Katharine <BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu>> wrote: Dear John,
I'm sorry that you were unable to attain a visa for China. I was really looking forward to working with you in person with the group. Paul mentioned that he had e-mailed you earlier this evening. Can you please send us the draft for the DarwinCore DNA/tissue extension as soon as possible for review during our working sessions? We have one tomorrow at 1:30 (Beijing time) and another on Tuesday at the same time. It would be really great if you could Skype into either both or one of the sessions.
Thanks for your help on this.
Kind Regards,
Katie
From: <Barker>, Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu><mailto:barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu>>> Date: Thursday, October 18, 2012 1:34 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu><mailto:barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu>>>, 'John Deck' <jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>>>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au><mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au>>>, "'"Dröge", Éamonn Tuama <eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org><mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>>, "Whitacre, Jamie" <WHITACREJ@si.edumailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edumailto:WHITACREJ@si.edu><mailto:WHITACREJ@si.edumailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edumailto:WHITACREJ@si.edu>>>, "'rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:'rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>'" <rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>>, "'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>'" <a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>>, "'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>'" <gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>>, "'tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:'tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>'" <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>> Cc: "'morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:'morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk>>'" <morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk>>>, "Parr, Cynthia" <parrc@si.edumailto:parrc@si.edu<mailto:parrc@si.edumailto:parrc@si.edu><mailto:parrc@si.edumailto:parrc@si.edu<mailto:parrc@si.edumailto:parrc@si.edu>>> Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Dear all,
This is a friendly reminder that we will be meeting next Tuesday afternoon at the TDWG 2012 Conference in order to finalize the draft DarwinCore-A DNA/tissue extension for GGBN. As you know, the immediate need for GGBN members is to publish information on tissues. This will happen through extensions to both ABCDDNA and DarwinCore-A. Here we are focused on developing the DarwinCore-A DNA/tissue extension.
An update on the timeline for developing the draft DarwinCore-A DNA/tissue extension is listed below.
Review content requirements for DarwinCore-A DNA/tissue extension (completed, see attached required DNA and tissue elements)John Weiczorek will develop the draft DarwinCore-A DNA/tissue extension (to be completed for group review prior to our break out session on Tuesday afternoon, October 23).Tuesday October 23, working meeting· Questions to answer before final review of DNA/tissue extension
o How do we include repeatable elements of ABCDDNA into DwC-A-DNA (References to more than one sequence record/publication are mandatory)?
o How do we extend the "Basis of Record" in ABCD and DwC-A and how do we include an element similar to ABCD-"Kind of Unit" to DwC-A?
o What are the remaining issues for DwC-A working with IPT? Are any changes in the IPT required?
· Review and finalize draft DarwinCore-A DNA/tissue extension for posting to GBIF site.
Thank you again to everyone who is involved in this project. I look forward to seeing all of you in Beijing.
Kind Regards,
Katie
From: Barker, Katharine Sent: Friday, September 28, 2012 9:53 AM To: 'John Deck'; Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org><mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>; tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Dear all,
We will be meeting this Tuesday at 1pm U.S. Eastern time over Skype in order to discuss the actions required to develop the draft proposal for the Darwin Core tissue/DNA extension. A proposal for designing, testing, and implementing the GGBN data portal is attached for your reference. Please review the timeline and action items leading up to the TDWG 2012 Conference.
My Skype name is Katharine.Barker1. If possible, please forward me your skype account names prior to our meeting.
Kind Regards,
Katie
From:jdeck88@gmail.commailto:From%3Ajdeck88@gmail.com<mailto:From%3Ajdeck88@gmail.commailto:From%253Ajdeck88@gmail.com><mailto:jdeck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@gmail.commailto:jdeck88@gmail.com>> [mailto:jdeck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@gmail.commailto:jdeck88@gmail.com>] On Behalf Of John Deck Sent: Tuesday, September 25, 2012 4:04 PM To: Barker, Katharine Cc: Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org><mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>; tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Here is the wrapup of the bioCollections Ontology workshop from last week at GSC14:
http://biocodecommons.org/workshops/bioCollections/index.html
This is relevant to these discussions since we focussed on what constitutes a "sample" and also, probably more importantly, processes that work with samples.
We briefly discussed the DwC Tissue Extension and came up with a proposal for a quick-fix and a more substantial fix. The quick-fix is to create two new BasisOfRecord terms: TissueSubSample, DNAExtract (or some terms like that -- Tuco could provide more clarification on this too). Thus, theoretically we could override the dwc:Occurrence class to mean, for example, TissueSubSample the same way we do for Specimens and Observations. The bigger fix is to more fundamentally re-orient DwC around the notion of "Sample", involving adding/changing some properties although we didn't get into any specifics.
P.s. I can do the 12/1/2 timeslots for that monday or tuesday but not the 11.
John On Mon, Sep 24, 2012 at 12:39 PM, Barker, Katharine <BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu><mailto:BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu>>> wrote: Dear all,
We will have a telecon meeting early next week in order to discuss a draft proposal for the Darwin Core tissue/DNA extension. Gabi, Paul, and I will put together a first draft for discussion to be distributed prior to the telecon. As you know, the goal is to have a working draft ready for our working group to review at the TDWG meeting in Beijing this October.
These are our options for meeting next week: Monday 11am, 12pm, 1pm, 2pm US EDT Tuesday 11am, 12pm, 1pm, 2pm US EDT
Please let me know if you cannot make one of these times.
Thanks again to those of you who provided input last week at the GSC 14 meeting.
Kind Regards,
Katie
From: Barker, Katharine Sent: Wednesday, September 12, 2012 10:51 AM To: 'Paul Flemons'; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org><mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; 'rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>'; jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>>; 'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>'; 'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>'; 'tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>' Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core Importance: High
Dear all,
My name is Katie Barker and I am the Global Genome Biodiversity Network Coordinator. As you know from Paul Flemons, members of the GGBN Data Standards and Data Access Task Force are trying to pull together a task group, which you are all part of, for the upcoming TDWG meeting in Beijing this October in order to address a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members. I am contacting you to schedule a meeting in late September/early October to develop a draft proposal for this extension to be completed at the upcoming TDWG meeting.
Please let me know your availability for the last two weeks of September and first two weeks of October. There will be some scheduling issues, as there are task group members on the west and east coasts of the U.S., Europe and Australia.
Paul Flemons (in Australia) will be in the U.S. the first week of October, so maybe we can meet in the afternoon of the 1st, anytime on the second 2nd, or in the morning of the 3rd of October over teleconference (US Eastern Daylight Time). Please let me know if any of these time slots work for you.
Gabi, I believe that you and John Deck will be at the GSC 14 meeting next week. Is there any chance that you can start drawing up an outline for the proposed extension? We could review the outline during our group telecon and start drafting a proposal for review at the TDWG meeting in October.
Kind Regards,
Katie
Task Group Members:
John Weiczorek - Berkeley Éamonn O'Tuama - GBIF Jamie Whitacre - SI John Deck - Berkeley Robert Robbins - University of California, San Diego Anton Guentsch - BGBM Gabi Droege- BGBM Paul Flemons- AM
From: Paul Flemons [mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au>] Sent: Tuesday, August 07, 2012 2:50 AM To: tuco@berkley.edumailto:tuco@berkley.edu<mailto:tuco@berkley.edumailto:tuco@berkley.edu><mailto:tuco@berkley.edumailto:tuco@berkley.edu<mailto:tuco@berkley.edumailto:tuco@berkley.edu>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org<mailto:j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org><mailto:j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org<mailto:j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org>>; jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>> Cc: Barker, Katharine; Éamonn Ó Tuama [GBIF]; "Dröge, Gabriele" (g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG<mailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG><mailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG<mailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG>>) Subject: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core
Hi all, I am on the Data Standards and Access Task Force for the Global Genome Biodiversity Network (http://ggbn.org/) which is in need of a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members.
To this end I am writing to you to ask if you would be interested in participating in a small working group at TDWG in Beijing this year.
At this stage my plan would be to identify relevant fields for inclusion in the extension, using ABCDDNA as a reference. If sufficient progress is made then we would submit the extension for ratification by TDWG (is that how its done John?) The GGBN will use whatever comes out of the group to move towards having a suitable DwC based schema for data sharing.
So please let me know if you are willing to participate in the task group and/or if there is anyone else you feel would be beneficial to have involved.
How much time do you think we will need? I have been thinking that a day will be needed, so we could make that consist of either one full day or two half days. Im also thinking that during the week will be the best time for this.
Thanks for your time
Best Regards Paul
Paul K J Flemons Manager, Collection Informatics Team Lead, Atlas of Living Australia Biodiversity Volunteer Portalhttp://volunteer.ala.org.au Biodiversity Information Standards (TDWG) Representative for Oceania Australian Museum 6 College Street Sydney NSW 2010 Australia t 61 2 9320 6343 m 0413458649 f 61 2 9320 6021 Visit: http://www.australianmuseum.net.auhttp://www.australianmuseum.net.au/ Like: http://www.facebook.com/australianmuseum Follow: http://www.twitter.com/austmus Watch: http://www.youtube.com/austmus [cid:image001.png@01CDAD34.391DC790mailto:image001.png@01CDAD34.391DC790<mailto:image001.png@01CDAD34.391DC790mailto:image001.png@01CDAD34.391DC790>] Inspiring the exploration of nature and cultures
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<DNATissueExtensionNotes2-TDWG2012.docx>_______________________________________________ IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt
I like the approach of having a Sample Core, but the approach taken thus far was with the view of being pragmatic to put into practice by January 2013. What do you think could be the possibility of adding a new Core type to the IPT on that time scale? The Darwin Core archive specification can certainly handle it, but the proof is in the implementation.
On Mon, Oct 22, 2012 at 8:11 AM, "Markus Döring (GBIF)" mdoering@gbif.orgwrote:
Hi all, I only quickly looked through the proposal, but it looks good, pragmatic and definitely to be working for the case when a DNASample equals a single taxon Occurrence.
Im not so sure how well it would work with environmental samples - would we have the sample flattened out and repeated to represent the individual taxa, sexes, ages, etc found in there? I was therefore wondering if anyone had thought about the attached setup before. Sample is at its core and occurrence & dna amplification as extensions with the amplifications (optionally?) refering to the occurrence they belong to.
Another quick observation is that we try to reuse existing terms in extensions as much as possible. Following that rule for example dwc:institutionCode should rather be used instead of dNACollectionCode and probably dc:source for the referenceCitation
until tomorrow, regards, Markus
On 22.10.2012, at 12:21, Barker, Katharine wrote:
Dear John,
Please see our working revisions/comments/questions on the DNA/tissue extension for Darwin Core (highlighted in blue). We were able to work through the draft up through "class sample properties":
https://docs.google.com/document/d/1RCgIPfu9gAPubjjbog-9vCJonvqcK1pLOaq6H8GS...
The document is also attached for your reference (just incase any of you are unable to access the document).
Please try to respond to our questions and comments prior to our meeting tomorrow (be sure to make these changes using a different color for tracking purposes).
Tomorrow we will like to 1) briefly recap our revisions on the extension so far (addressing questions and comments), 2) complete our review of the extension and 3) identify any remaining issues with DwC working with IPT (and identify if any changes in the IPT are required).
Thank you for your help on this!
Kind Regards,
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu" <tuco@berkeley.edu mailto:tuco@berkeley.edu> Date: Sunday, October 21, 2012 10:52 PM To: Gabriele Droege <g.droege@bgbm.orgmailto:g.droege@bgbm.org> Cc: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au>, John Deck <jdeck@berkeley.edumailto:jdeck@berkeley.edu>, Robert Hanner < bob.hanner@gmail.commailto:bob.hanner@gmail.com>, Éamonn Tuama < eotuama@gbif.orgmailto:eotuama@gbif.org>, Robert Robbins < rjr8222@gmail.commailto:rjr8222@gmail.com>, "Guentsch, Anton" < a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org> Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Dear all,
I finished working on the Google Doc "DNA Tissue Extension Notes - TDWG 2012". Feel free to let this be a working document where comments and questions can be added. I've attached a Word Doc version for archival purposes.
I added the two template extension files (DNATissueExtension.txt and DNAAmplificationExtension.txt) to the shared TDWG GGBN working group folder linked below. They are in the form they need to be submitted to GBIF to be added to their extension registry. They would both need to be updated with the term descriptions, examples, and constraints.
https://drive.google.com/#folders/0BxEyFKwB7zY4WEs0WkdtUU5oVnM
Cheers,
John
On Sun, Oct 21, 2012 at 10:38 PM, John Wieczorek <tuco@berkeley.edu mailto:tuco@berkeley.edu> wrote: Ooops
...at http://goo.gl/kGHmb. Adding touches based on the files Gabi sent. Will tell you all when finished with that and will send it as a Word doc at that time in case there are any issues with Google docs. Should be soon. Let me know if I should share to any different addresses.
Cheers,
John
On Sun, Oct 21, 2012 at 10:34 PM, John Wieczorek <tuco@berkeley.edu mailto:tuco@berkeley.edu> wrote: That helps a lot, as it clears up some of my own misconceptions. I have shared a document where I have captured the thinking behind a couple of different ways forward with one or two extensions and an example of how the two-extension might look in the context of a Darwin Core Archive. The DNA Tissue Extension Notes Google doc can be found at
On Sun, Oct 21, 2012 at 9:23 PM, "Dröge, Gabriele" <g.droege@bgbm.org mailto:g.droege@bgbm.org> wrote: Yes we do... Hi John,
Thanks for getting back to us. Attached are two csv files, one with some main DNA facts and the other with associated GenBank entries und publications (2 examples with 2 GenBank entries per DNA sample). I included only UnitID/CollCode/InstCode for the related voucher specimen and I excluded the tissue facts since they are quite similar to the DNA facts and should be mapped independently.
Best, Gabi
-----Original Message----- From: Barker, Katharine [mailto:BarkerK@si.edumailto:BarkerK@si.edu] Sent: Sunday, October 21, 2012 11:41 PM To: Paul Flemons; Dröge, Gabriele Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Paul and Gabi,
Do we have any sample data that John can use as a test case? I think he would like it today, if possible.
Thanks for your help (and the team work).
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto: tuco@berkeley.edumailto:tuco@berkeley.edu>> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu<mailto: tuco@berkeley.edumailto:tuco@berkeley.edu>" <tuco@berkeley.edumailto: tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Date: Sunday, October 21, 2012 12:03 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto: barkerk@si.edumailto:barkerk@si.edu>> Subject: Re: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Hi Katie,
Messages received. Will have the extension stuff ready within a few hours and hope to be able to attend remotely. One thing in the meantime. Do you have any example data that could be used as a test case to populate a core with this extension? Would like to try that with some realy data to test my assumptions.
Sorry for the delay.
Thanks,
John
On Sun, Oct 21, 2012 at 10:08 AM, Barker, Katharine <BarkerK@si.edu mailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu>> wrote: Dear John,
I'm sorry that you were unable to attain a visa for China. I was really looking forward to working with you in person with the group. Paul mentioned that he had e-mailed you earlier this evening. Can you please send us the draft for the DarwinCore DNA/tissue extension as soon as possible for review during our working sessions? We have one tomorrow at 1:30 (Beijing time) and another on Tuesday at the same time. It would be really great if you could Skype into either both or one of the sessions.
Thanks for your help on this.
Kind Regards,
Katie
From: <Barker>, Katharine Barker <barkerk@si.edu<mailto:barkerk@si.edu
<mailto:barkerk@si.edumailto:barkerk@si.edu><mailto:barkerk@si.edu
mailto:barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu>>> Date: Thursday, October 18, 2012 1:34 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto: barkerk@si.edumailto:barkerk@si.edu><mailto:barkerk@si.edumailto: barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu>>>, 'John Deck' <jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto: jdeck@berkeley.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edu mailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto: jdeck@berkeley.edu>>>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto: Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.aumailto: Paul.Flemons@austmus.gov.au><mailto:Paul.Flemons@austmus.gov.aumailto: Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.aumailto: Paul.Flemons@austmus.gov.au>>>, "'"Dröge", Éamonn Tuama < eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto: eotuama@gbif.org><mailto:eotuama@gbif.org<mailto:eotuama@gbif.org
<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>>, "Whitacre, Jamie" <
WHITACREJ@si.edumailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edumailto: WHITACREJ@si.edu><mailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edu
<mailto:WHITACREJ@si.edumailto:WHITACREJ@si.edu>>>, "'rjr8222@gmail.com
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<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>'" <
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a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>>, "' gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:' gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>'" < gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>>, "' tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu mailto:tuco@berkeley.edu><mailto:'tuco@berkeley.edumailto: tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>'" <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu mailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto: tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>> Cc: "'morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto: morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:' morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto: morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk>>'" < morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto: morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto: morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto: morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk>>>, "Parr, Cynthia" < parrc@si.edumailto:parrc@si.edu<mailto:parrc@si.edu<mailto:parrc@si.edu
<mailto:parrc@si.edumailto:parrc@si.edu<mailto:parrc@si.edu<mailto:
parrc@si.edu>>>> Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Dear all,
This is a friendly reminder that we will be meeting next Tuesday afternoon at the TDWG 2012 Conference in order to finalize the draft DarwinCore-A DNA/tissue extension for GGBN. As you know, the immediate need for GGBN members is to publish information on tissues. This will happen through extensions to both ABCDDNA and DarwinCore-A. Here we are focused on developing the DarwinCore-A DNA/tissue extension.
An update on the timeline for developing the draft DarwinCore-A DNA/tissue extension is listed below.
Review content requirements for DarwinCore-A DNA/tissue extension(completed, see attached required DNA and tissue elements)
John Weiczorek will develop the draft DarwinCore-A DNA/tissueextension (to be completed for group review prior to our break out session on Tuesday afternoon, October 23).
Tuesday October 23, working meeting· Questions to answer before final review of DNA/tissue extension
o How do we include repeatable elements of ABCDDNA into DwC-A-DNA (References to more than one sequence record/publication are mandatory)?
o How do we extend the "Basis of Record" in ABCD and DwC-A and how do we include an element similar to ABCD-"Kind of Unit" to DwC-A?
o What are the remaining issues for DwC-A working with IPT? Are any changes in the IPT required?
· Review and finalize draft DarwinCore-A DNA/tissue extension for posting to GBIF site.
Thank you again to everyone who is involved in this project. I look forward to seeing all of you in Beijing.
Kind Regards,
Katie
From: Barker, Katharine Sent: Friday, September 28, 2012 9:53 AM To: 'John Deck'; Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.orgmailto: eotuama@gbif.org<mailto:eotuama@gbif.org<mailto:eotuama@gbif.org
<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:
eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto: rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org mailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto: a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>; tuco@berkeley.edu mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto: tuco@berkeley.edu><mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu
<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>
Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Dear all,
We will be meeting this Tuesday at 1pm U.S. Eastern time over Skype in order to discuss the actions required to develop the draft proposal for the Darwin Core tissue/DNA extension. A proposal for designing, testing, and implementing the GGBN data portal is attached for your reference. Please review the timeline and action items leading up to the TDWG 2012 Conference.
My Skype name is Katharine.Barker1. If possible, please forward me your skype account names prior to our meeting.
Kind Regards,
Katie
From:jdeck88@gmail.commailto:From%3Ajdeck88@gmail.com<mailto: From%3Ajdeck88@gmail.commailto:From%253Ajdeck88@gmail.com><mailto: jdeck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@gmail.com mailto:jdeck88@gmail.com>> [mailto:jdeck88@gmail.commailto: jdeck88@gmail.com<mailto:jdeck88@gmail.commailto:jdeck88@gmail.com>] On Behalf Of John Deck Sent: Tuesday, September 25, 2012 4:04 PM To: Barker, Katharine Cc: Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.orgmailto: eotuama@gbif.org<mailto:eotuama@gbif.org<mailto:eotuama@gbif.org
<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:
eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto: rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org mailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto: a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>; tuco@berkeley.edu mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto: tuco@berkeley.edu><mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu
<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>
Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Here is the wrapup of the bioCollections Ontology workshop from last week at GSC14:
http://biocodecommons.org/workshops/bioCollections/index.html
This is relevant to these discussions since we focussed on what constitutes a "sample" and also, probably more importantly, processes that work with samples.
We briefly discussed the DwC Tissue Extension and came up with a proposal for a quick-fix and a more substantial fix. The quick-fix is to create two new BasisOfRecord terms: TissueSubSample, DNAExtract (or some terms like that -- Tuco could provide more clarification on this too). Thus, theoretically we could override the dwc:Occurrence class to mean, for example, TissueSubSample the same way we do for Specimens and Observations. The bigger fix is to more fundamentally re-orient DwC around the notion of "Sample", involving adding/changing some properties although we didn't get into any specifics.
P.s. I can do the 12/1/2 timeslots for that monday or tuesday but not the 11.
John On Mon, Sep 24, 2012 at 12:39 PM, Barker, Katharine <BarkerK@si.edu mailto:BarkerK@si.edu<mailto:BarkerK@si.edu<mailto:BarkerK@si.edu
<mailto:BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edu
mailto:BarkerK@si.edu>>> wrote: Dear all,
We will have a telecon meeting early next week in order to discuss a draft proposal for the Darwin Core tissue/DNA extension. Gabi, Paul, and I will put together a first draft for discussion to be distributed prior to the telecon. As you know, the goal is to have a working draft ready for our working group to review at the TDWG meeting in Beijing this October.
These are our options for meeting next week: Monday 11am, 12pm, 1pm, 2pm US EDT Tuesday 11am, 12pm, 1pm, 2pm US EDT
Please let me know if you cannot make one of these times.
Thanks again to those of you who provided input last week at the GSC 14 meeting.
Kind Regards,
Katie
From: Barker, Katharine Sent: Wednesday, September 12, 2012 10:51 AM To: 'Paul Flemons'; "Dröge, Gabriele"; eotuama@gbif.orgmailto: eotuama@gbif.org<mailto:eotuama@gbif.org<mailto:eotuama@gbif.org
<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:
eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; ' rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto: rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>'; jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edu mailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto: jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>>; 'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org mailto:a.guentsch@bgbm.org>>'; 'gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com>>'; 'tuco@berkeley.edu<mailto:tuco@berkeley.edu
<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:
tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu mailto:tuco@berkeley.edu>>' Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core Importance: High
Dear all,
My name is Katie Barker and I am the Global Genome Biodiversity Network Coordinator. As you know from Paul Flemons, members of the GGBN Data Standards and Data Access Task Force are trying to pull together a task group, which you are all part of, for the upcoming TDWG meeting in Beijing this October in order to address a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members. I am contacting you to schedule a meeting in late September/early October to develop a draft proposal for this extension to be completed at the upcoming TDWG meeting.
Please let me know your availability for the last two weeks of September and first two weeks of October. There will be some scheduling issues, as there are task group members on the west and east coasts of the U.S., Europe and Australia.
Paul Flemons (in Australia) will be in the U.S. the first week of October, so maybe we can meet in the afternoon of the 1st, anytime on the second 2nd, or in the morning of the 3rd of October over teleconference (US Eastern Daylight Time). Please let me know if any of these time slots work for you.
Gabi, I believe that you and John Deck will be at the GSC 14 meeting next week. Is there any chance that you can start drawing up an outline for the proposed extension? We could review the outline during our group telecon and start drafting a proposal for review at the TDWG meeting in October.
Kind Regards,
Katie
Task Group Members:
John Weiczorek - Berkeley Éamonn O'Tuama - GBIF Jamie Whitacre - SI John Deck - Berkeley Robert Robbins - University of California, San Diego Anton Guentsch - BGBM Gabi Droege- BGBM Paul Flemons- AM
From: Paul Flemons [mailto:Paul.Flemons@austmus.gov.aumailto: Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.aumailto: Paul.Flemons@austmus.gov.au>] Sent: Tuesday, August 07, 2012 2:50 AM To: tuco@berkley.edumailto:tuco@berkley.edu<mailto:tuco@berkley.edu mailto:tuco@berkley.edu><mailto:tuco@berkley.edu<mailto:tuco@berkley.edu
<mailto:tuco@berkley.edumailto:tuco@berkley.edu>>; a.guentsch@bgbm.org
mailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto: a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto: a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org<mailto: j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org><mailto: j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org<mailto: j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org>>; jdeck@berkeley.edu mailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto: jdeck@berkeley.edu><mailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edu
<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>>
Cc: Barker, Katharine; Éamonn Ó Tuama [GBIF]; "Dröge, Gabriele" ( g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG<mailto:g.droege@BGBM.ORG mailto:g.droege@BGBM.ORG><mailto:g.droege@BGBM.ORGmailto: g.droege@BGBM.ORG<mailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG>>) Subject: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core
Hi all, I am on the Data Standards and Access Task Force for the Global Genome Biodiversity Network (http://ggbn.org/) which is in need of a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members.
To this end I am writing to you to ask if you would be interested in participating in a small working group at TDWG in Beijing this year.
At this stage my plan would be to identify relevant fields for inclusion in the extension, using ABCDDNA as a reference. If sufficient progress is made then we would submit the extension for ratification by TDWG (is that how its done John?) The GGBN will use whatever comes out of the group to move towards having a suitable DwC based schema for data sharing.
So please let me know if you are willing to participate in the task group and/or if there is anyone else you feel would be beneficial to have involved.
How much time do you think we will need? I have been thinking that a day will be needed, so we could make that consist of either one full day or two half days. Im also thinking that during the week will be the best time for this.
Thanks for your time
Best Regards Paul
Paul K J Flemons Manager, Collection Informatics Team Lead, Atlas of Living Australia Biodiversity Volunteer Portal< http://volunteer.ala.org.au%3E Biodiversity Information Standards (TDWG) Representative for Oceania Australian Museum 6 College Street Sydney NSW 2010 Australia t 61 2 9320 6343 m 0413458649 f 61 2 9320 6021 Visit: http://www.australianmuseum.net.au< http://www.australianmuseum.net.au/%3E Like: http://www.facebook.com/australianmuseum Follow: http://www.twitter.com/austmus Watch: http://www.youtube.com/austmus [cid:image001.png@01CDAD34.391DC790<mailto:image001.png@01CDAD34.391DC790
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<DNATissueExtensionNotes2-TDWG2012.docx> _______________________________________________ IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt
Adding a new core type to the IPT could be done in less than a day - more work for GBIF would be to support such a format in our indexing code. But if we think its a better solution to go with a new sample core type, I think its worth the extra cost of coding for it.
On 22.10.2012, at 17:53, John Wieczorek wrote:
I like the approach of having a Sample Core, but the approach taken thus far was with the view of being pragmatic to put into practice by January 2013. What do you think could be the possibility of adding a new Core type to the IPT on that time scale? The Darwin Core archive specification can certainly handle it, but the proof is in the implementation.
On Mon, Oct 22, 2012 at 8:11 AM, "Markus Döring (GBIF)" mdoering@gbif.org wrote: Hi all, I only quickly looked through the proposal, but it looks good, pragmatic and definitely to be working for the case when a DNASample equals a single taxon Occurrence.
Im not so sure how well it would work with environmental samples - would we have the sample flattened out and repeated to represent the individual taxa, sexes, ages, etc found in there? I was therefore wondering if anyone had thought about the attached setup before. Sample is at its core and occurrence & dna amplification as extensions with the amplifications (optionally?) refering to the occurrence they belong to.
Another quick observation is that we try to reuse existing terms in extensions as much as possible. Following that rule for example dwc:institutionCode should rather be used instead of dNACollectionCode and probably dc:source for the referenceCitation
until tomorrow, regards, Markus
<sample core.png>
On 22.10.2012, at 12:21, Barker, Katharine wrote:
Dear John,
Please see our working revisions/comments/questions on the DNA/tissue extension for Darwin Core (highlighted in blue). We were able to work through the draft up through "class sample properties": https://docs.google.com/document/d/1RCgIPfu9gAPubjjbog-9vCJonvqcK1pLOaq6H8GS...
The document is also attached for your reference (just incase any of you are unable to access the document).
Please try to respond to our questions and comments prior to our meeting tomorrow (be sure to make these changes using a different color for tracking purposes).
Tomorrow we will like to 1) briefly recap our revisions on the extension so far (addressing questions and comments), 2) complete our review of the extension and 3) identify any remaining issues with DwC working with IPT (and identify if any changes in the IPT are required).
Thank you for your help on this!
Kind Regards,
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu" <tuco@berkeley.edumailto:tuco@berkeley.edu> Date: Sunday, October 21, 2012 10:52 PM To: Gabriele Droege <g.droege@bgbm.orgmailto:g.droege@bgbm.org> Cc: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au>, John Deck <jdeck@berkeley.edumailto:jdeck@berkeley.edu>, Robert Hanner <bob.hanner@gmail.commailto:bob.hanner@gmail.com>, Éamonn Tuama <eotuama@gbif.orgmailto:eotuama@gbif.org>, Robert Robbins <rjr8222@gmail.commailto:rjr8222@gmail.com>, "Guentsch, Anton" <a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org> Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Dear all,
I finished working on the Google Doc "DNA Tissue Extension Notes - TDWG 2012". Feel free to let this be a working document where comments and questions can be added. I've attached a Word Doc version for archival purposes.
I added the two template extension files (DNATissueExtension.txt and DNAAmplificationExtension.txt) to the shared TDWG GGBN working group folder linked below. They are in the form they need to be submitted to GBIF to be added to their extension registry. They would both need to be updated with the term descriptions, examples, and constraints.
https://drive.google.com/#folders/0BxEyFKwB7zY4WEs0WkdtUU5oVnM
Cheers,
John
On Sun, Oct 21, 2012 at 10:38 PM, John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> wrote: Ooops
...at http://goo.gl/kGHmb. Adding touches based on the files Gabi sent. Will tell you all when finished with that and will send it as a Word doc at that time in case there are any issues with Google docs. Should be soon. Let me know if I should share to any different addresses.
Cheers,
John
On Sun, Oct 21, 2012 at 10:34 PM, John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> wrote: That helps a lot, as it clears up some of my own misconceptions. I have shared a document where I have captured the thinking behind a couple of different ways forward with one or two extensions and an example of how the two-extension might look in the context of a Darwin Core Archive. The DNA Tissue Extension Notes Google doc can be found at
On Sun, Oct 21, 2012 at 9:23 PM, "Dröge, Gabriele" <g.droege@bgbm.orgmailto:g.droege@bgbm.org> wrote: Yes we do... Hi John,
Thanks for getting back to us. Attached are two csv files, one with some main DNA facts and the other with associated GenBank entries und publications (2 examples with 2 GenBank entries per DNA sample). I included only UnitID/CollCode/InstCode for the related voucher specimen and I excluded the tissue facts since they are quite similar to the DNA facts and should be mapped independently.
Best, Gabi
-----Original Message----- From: Barker, Katharine [mailto:BarkerK@si.edumailto:BarkerK@si.edu] Sent: Sunday, October 21, 2012 11:41 PM To: Paul Flemons; Dröge, Gabriele Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Paul and Gabi,
Do we have any sample data that John can use as a test case? I think he would like it today, if possible.
Thanks for your help (and the team work).
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>" <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Date: Sunday, October 21, 2012 12:03 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu>> Subject: Re: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Hi Katie,
Messages received. Will have the extension stuff ready within a few hours and hope to be able to attend remotely. One thing in the meantime. Do you have any example data that could be used as a test case to populate a core with this extension? Would like to try that with some realy data to test my assumptions.
Sorry for the delay.
Thanks,
John
On Sun, Oct 21, 2012 at 10:08 AM, Barker, Katharine <BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu>> wrote: Dear John,
I'm sorry that you were unable to attain a visa for China. I was really looking forward to working with you in person with the group. Paul mentioned that he had e-mailed you earlier this evening. Can you please send us the draft for the DarwinCore DNA/tissue extension as soon as possible for review during our working sessions? We have one tomorrow at 1:30 (Beijing time) and another on Tuesday at the same time. It would be really great if you could Skype into either both or one of the sessions.
Thanks for your help on this.
Kind Regards,
Katie
From: <Barker>, Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu><mailto:barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu>>> Date: Thursday, October 18, 2012 1:34 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu><mailto:barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu>>>, 'John Deck' <jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>>>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au><mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au>>>, "'"Dröge", Éamonn Tuama <eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org><mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>>, "Whitacre, Jamie" <WHITACREJ@si.edumailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edumailto:WHITACREJ@si.edu><mailto:WHITACREJ@si.edumailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edumailto:WHITACREJ@si.edu>>>, "'rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:'rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>'" <rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>>, "'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>'" <a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>>, "'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>'" <gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>>, "'tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:'tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>'" <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>> Cc: "'morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:'morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk>>'" <morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk>>>, "Parr, Cynthia" <parrc@si.edumailto:parrc@si.edu<mailto:parrc@si.edumailto:parrc@si.edu><mailto:parrc@si.edumailto:parrc@si.edu<mailto:parrc@si.edumailto:parrc@si.edu>>> Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Dear all,
This is a friendly reminder that we will be meeting next Tuesday afternoon at the TDWG 2012 Conference in order to finalize the draft DarwinCore-A DNA/tissue extension for GGBN. As you know, the immediate need for GGBN members is to publish information on tissues. This will happen through extensions to both ABCDDNA and DarwinCore-A. Here we are focused on developing the DarwinCore-A DNA/tissue extension.
An update on the timeline for developing the draft DarwinCore-A DNA/tissue extension is listed below.
Review content requirements for DarwinCore-A DNA/tissue extension (completed, see attached required DNA and tissue elements)John Weiczorek will develop the draft DarwinCore-A DNA/tissue extension (to be completed for group review prior to our break out session on Tuesday afternoon, October 23).Tuesday October 23, working meeting· Questions to answer before final review of DNA/tissue extension
o How do we include repeatable elements of ABCDDNA into DwC-A-DNA (References to more than one sequence record/publication are mandatory)?
o How do we extend the "Basis of Record" in ABCD and DwC-A and how do we include an element similar to ABCD-"Kind of Unit" to DwC-A?
o What are the remaining issues for DwC-A working with IPT? Are any changes in the IPT required?
· Review and finalize draft DarwinCore-A DNA/tissue extension for posting to GBIF site.
Thank you again to everyone who is involved in this project. I look forward to seeing all of you in Beijing.
Kind Regards,
Katie
From: Barker, Katharine Sent: Friday, September 28, 2012 9:53 AM To: 'John Deck'; Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org><mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>; tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Dear all,
We will be meeting this Tuesday at 1pm U.S. Eastern time over Skype in order to discuss the actions required to develop the draft proposal for the Darwin Core tissue/DNA extension. A proposal for designing, testing, and implementing the GGBN data portal is attached for your reference. Please review the timeline and action items leading up to the TDWG 2012 Conference.
My Skype name is Katharine.Barker1. If possible, please forward me your skype account names prior to our meeting.
Kind Regards,
Katie
From:jdeck88@gmail.commailto:From%3Ajdeck88@gmail.com<mailto:From%3Ajdeck88@gmail.commailto:From%253Ajdeck88@gmail.com><mailto:jdeck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@gmail.commailto:jdeck88@gmail.com>> [mailto:jdeck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@gmail.commailto:jdeck88@gmail.com>] On Behalf Of John Deck Sent: Tuesday, September 25, 2012 4:04 PM To: Barker, Katharine Cc: Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org><mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>; tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Here is the wrapup of the bioCollections Ontology workshop from last week at GSC14:
http://biocodecommons.org/workshops/bioCollections/index.html
This is relevant to these discussions since we focussed on what constitutes a "sample" and also, probably more importantly, processes that work with samples.
We briefly discussed the DwC Tissue Extension and came up with a proposal for a quick-fix and a more substantial fix. The quick-fix is to create two new BasisOfRecord terms: TissueSubSample, DNAExtract (or some terms like that -- Tuco could provide more clarification on this too). Thus, theoretically we could override the dwc:Occurrence class to mean, for example, TissueSubSample the same way we do for Specimens and Observations. The bigger fix is to more fundamentally re-orient DwC around the notion of "Sample", involving adding/changing some properties although we didn't get into any specifics.
P.s. I can do the 12/1/2 timeslots for that monday or tuesday but not the 11.
John On Mon, Sep 24, 2012 at 12:39 PM, Barker, Katharine <BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu><mailto:BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu>>> wrote: Dear all,
We will have a telecon meeting early next week in order to discuss a draft proposal for the Darwin Core tissue/DNA extension. Gabi, Paul, and I will put together a first draft for discussion to be distributed prior to the telecon. As you know, the goal is to have a working draft ready for our working group to review at the TDWG meeting in Beijing this October.
These are our options for meeting next week: Monday 11am, 12pm, 1pm, 2pm US EDT Tuesday 11am, 12pm, 1pm, 2pm US EDT
Please let me know if you cannot make one of these times.
Thanks again to those of you who provided input last week at the GSC 14 meeting.
Kind Regards,
Katie
From: Barker, Katharine Sent: Wednesday, September 12, 2012 10:51 AM To: 'Paul Flemons'; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org><mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; 'rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>'; jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>>; 'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>'; 'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>'; 'tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>' Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core Importance: High
Dear all,
My name is Katie Barker and I am the Global Genome Biodiversity Network Coordinator. As you know from Paul Flemons, members of the GGBN Data Standards and Data Access Task Force are trying to pull together a task group, which you are all part of, for the upcoming TDWG meeting in Beijing this October in order to address a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members. I am contacting you to schedule a meeting in late September/early October to develop a draft proposal for this extension to be completed at the upcoming TDWG meeting.
Please let me know your availability for the last two weeks of September and first two weeks of October. There will be some scheduling issues, as there are task group members on the west and east coasts of the U.S., Europe and Australia.
Paul Flemons (in Australia) will be in the U.S. the first week of October, so maybe we can meet in the afternoon of the 1st, anytime on the second 2nd, or in the morning of the 3rd of October over teleconference (US Eastern Daylight Time). Please let me know if any of these time slots work for you.
Gabi, I believe that you and John Deck will be at the GSC 14 meeting next week. Is there any chance that you can start drawing up an outline for the proposed extension? We could review the outline during our group telecon and start drafting a proposal for review at the TDWG meeting in October.
Kind Regards,
Katie
Task Group Members:
John Weiczorek - Berkeley Éamonn O'Tuama - GBIF Jamie Whitacre - SI John Deck - Berkeley Robert Robbins - University of California, San Diego Anton Guentsch - BGBM Gabi Droege- BGBM Paul Flemons- AM
From: Paul Flemons [mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au>] Sent: Tuesday, August 07, 2012 2:50 AM To: tuco@berkley.edumailto:tuco@berkley.edu<mailto:tuco@berkley.edumailto:tuco@berkley.edu><mailto:tuco@berkley.edumailto:tuco@berkley.edu<mailto:tuco@berkley.edumailto:tuco@berkley.edu>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org<mailto:j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org><mailto:j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org<mailto:j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org>>; jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>> Cc: Barker, Katharine; Éamonn Ó Tuama [GBIF]; "Dröge, Gabriele" (g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG<mailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG><mailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG<mailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG>>) Subject: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core
Hi all, I am on the Data Standards and Access Task Force for the Global Genome Biodiversity Network (http://ggbn.org/) which is in need of a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members.
To this end I am writing to you to ask if you would be interested in participating in a small working group at TDWG in Beijing this year.
At this stage my plan would be to identify relevant fields for inclusion in the extension, using ABCDDNA as a reference. If sufficient progress is made then we would submit the extension for ratification by TDWG (is that how its done John?) The GGBN will use whatever comes out of the group to move towards having a suitable DwC based schema for data sharing.
So please let me know if you are willing to participate in the task group and/or if there is anyone else you feel would be beneficial to have involved.
How much time do you think we will need? I have been thinking that a day will be needed, so we could make that consist of either one full day or two half days. Im also thinking that during the week will be the best time for this.
Thanks for your time
Best Regards Paul
Paul K J Flemons Manager, Collection Informatics Team Lead, Atlas of Living Australia Biodiversity Volunteer Portalhttp://volunteer.ala.org.au Biodiversity Information Standards (TDWG) Representative for Oceania Australian Museum 6 College Street Sydney NSW 2010 Australia t 61 2 9320 6343 m 0413458649 f 61 2 9320 6021 Visit: http://www.australianmuseum.net.auhttp://www.australianmuseum.net.au/ Like: http://www.facebook.com/australianmuseum Follow: http://www.twitter.com/austmus Watch: http://www.youtube.com/austmus [cid:image001.png@01CDAD34.391DC790mailto:image001.png@01CDAD34.391DC790<mailto:image001.png@01CDAD34.391DC790mailto:image001.png@01CDAD34.391DC790>] Inspiring the exploration of nature and cultures
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-- John Deck (541) 321-0689tel:%28541%29%20321-0689tel:%28541%29%20321-0689
<DNATissueExtensionNotes2-TDWG2012.docx>_______________________________________________ IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt
Well, let's investigate one thing about your diagram first. Shouldn't there be a one-to-many relationship between Occurrence (specimen) and Sample rather than a many-to-one?
Specimen from the field = Occurrence + Event + Location + Identification + Taxon Sample from the specimen's liver = Sample Sample from the specimen's heart = Sample Sample from the specimen's gut = Sample
And all of the Samples could have multiple Amplifications.
If we want to model this with a Sample Core, then Occurrences may be repeated in the Occurrence extension in your diagram, but every sample would have no more than one Occurrence in the extension file and the sampleID relationship would be one-to-one. If so, then it is also possible to have a Sample Core (Sample rowType) with sampleID as the core record identifier, with "Sample" as basisOfRecord, and with all of the attributes of Sample and of the existing Occurrence Core. This would avoid having a distinct Occurrence extension for Samples, which could get confusing for those who are accustomed to mapping Occurrences already. This combined Sample/Occurrence Core could still have a one-to-many relationship to the Amplifications.
On Mon, Oct 22, 2012 at 1:33 PM, "Markus Döring (GBIF)" mdoering@gbif.orgwrote:
Adding a new core type to the IPT could be done in less than a day - more work for GBIF would be to support such a format in our indexing code. But if we think its a better solution to go with a new sample core type, I think its worth the extra cost of coding for it.
On 22.10.2012, at 17:53, John Wieczorek wrote:
I like the approach of having a Sample Core, but the approach taken thus
far was with the view of being pragmatic to put into practice by January 2013. What do you think could be the possibility of adding a new Core type to the IPT on that time scale? The Darwin Core archive specification can certainly handle it, but the proof is in the implementation.
On Mon, Oct 22, 2012 at 8:11 AM, "Markus Döring (GBIF)" <
mdoering@gbif.org> wrote:
Hi all, I only quickly looked through the proposal, but it looks good, pragmatic
and definitely to be working for the case when a DNASample equals a single taxon Occurrence.
Im not so sure how well it would work with environmental samples - would
we have the sample flattened out and repeated to represent the individual taxa, sexes, ages, etc found in there?
I was therefore wondering if anyone had thought about the attached setup
before. Sample is at its core and occurrence & dna amplification as extensions with the amplifications (optionally?) refering to the occurrence they belong to.
Another quick observation is that we try to reuse existing terms in
extensions as much as possible. Following that rule for example dwc:institutionCode should rather be used instead of dNACollectionCode and probably dc:source for the referenceCitation
until tomorrow, regards, Markus
<sample core.png>
On 22.10.2012, at 12:21, Barker, Katharine wrote:
Dear John,
Please see our working revisions/comments/questions on the DNA/tissue
extension for Darwin Core (highlighted in blue). We were able to work through the draft up through "class sample properties":
https://docs.google.com/document/d/1RCgIPfu9gAPubjjbog-9vCJonvqcK1pLOaq6H8GS...
The document is also attached for your reference (just incase any of
you are unable to access the document).
Please try to respond to our questions and comments prior to our
meeting tomorrow (be sure to make these changes using a different color for tracking purposes).
Tomorrow we will like to 1) briefly recap our revisions on the
extension so far (addressing questions and comments), 2) complete our review of the extension and 3) identify any remaining issues with DwC working with IPT (and identify if any changes in the IPT are required).
Thank you for your help on this!
Kind Regards,
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu" <
tuco@berkeley.edumailto:tuco@berkeley.edu>
Date: Sunday, October 21, 2012 10:52 PM To: Gabriele Droege <g.droege@bgbm.orgmailto:g.droege@bgbm.org> Cc: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu>, Paul
Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au>, John Deck <jdeck@berkeley.edumailto:jdeck@berkeley.edu>, Robert Hanner < bob.hanner@gmail.commailto:bob.hanner@gmail.com>, Éamonn Tuama < eotuama@gbif.orgmailto:eotuama@gbif.org>, Robert Robbins < rjr8222@gmail.commailto:rjr8222@gmail.com>, "Guentsch, Anton" < a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>
Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for
Darwin Core-draft reminder
Dear all,
I finished working on the Google Doc "DNA Tissue Extension Notes - TDWG
2012". Feel free to let this be a working document where comments and questions can be added. I've attached a Word Doc version for archival purposes.
I added the two template extension files (DNATissueExtension.txt and
DNAAmplificationExtension.txt) to the shared TDWG GGBN working group folder linked below. They are in the form they need to be submitted to GBIF to be added to their extension registry. They would both need to be updated with the term descriptions, examples, and constraints.
https://drive.google.com/#folders/0BxEyFKwB7zY4WEs0WkdtUU5oVnM
Cheers,
John
On Sun, Oct 21, 2012 at 10:38 PM, John Wieczorek <tuco@berkeley.edu
mailto:tuco@berkeley.edu> wrote:
Ooops
...at http://goo.gl/kGHmb. Adding touches based on the files Gabi
sent. Will tell you all when finished with that and will send it as a Word doc at that time in case there are any issues with Google docs. Should be soon. Let me know if I should share to any different addresses.
Cheers,
John
On Sun, Oct 21, 2012 at 10:34 PM, John Wieczorek <tuco@berkeley.edu
mailto:tuco@berkeley.edu> wrote:
That helps a lot, as it clears up some of my own misconceptions. I
have shared a document where I have captured the thinking behind a couple of different ways forward with one or two extensions and an example of how the two-extension might look in the context of a Darwin Core Archive. The DNA Tissue Extension Notes Google doc can be found at
On Sun, Oct 21, 2012 at 9:23 PM, "Dröge, Gabriele" <g.droege@bgbm.org
mailto:g.droege@bgbm.org> wrote:
Yes we do... Hi John,
Thanks for getting back to us. Attached are two csv files, one with
some main DNA facts and the other with associated GenBank entries und publications (2 examples with 2 GenBank entries per DNA sample).
I included only UnitID/CollCode/InstCode for the related voucher
specimen and I excluded the tissue facts since they are quite similar to the DNA facts and should be mapped independently.
Best, Gabi
-----Original Message----- From: Barker, Katharine [mailto:BarkerK@si.edumailto:BarkerK@si.edu] Sent: Sunday, October 21, 2012 11:41 PM To: Paul Flemons; Dröge, Gabriele Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for
Darwin Core-draft reminder
Paul and Gabi,
Do we have any sample data that John can use as a test case? I think
he would like it today, if possible.
Thanks for your help (and the team work).
Katie
From: John Wieczorek <tuco@berkeley.edu<mailto:tuco@berkeley.edu
<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>
Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:
tuco@berkeley.edumailto:tuco@berkeley.edu>" <tuco@berkeley.edumailto: tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>
Date: Sunday, October 21, 2012 12:03 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:
barkerk@si.edumailto:barkerk@si.edu>>
Subject: Re: FW: Meeting at TDWG 2012 to define a tissue/DNA extension
for Darwin Core-draft reminder
Hi Katie,
Messages received. Will have the extension stuff ready within a few
hours and hope to be able to attend remotely. One thing in the meantime. Do you have any example data that could be used as a test case to populate a core with this extension? Would like to try that with some realy data to test my assumptions.
Sorry for the delay.
Thanks,
John
On Sun, Oct 21, 2012 at 10:08 AM, Barker, Katharine <BarkerK@si.edu
mailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu>> wrote:
Dear John,
I'm sorry that you were unable to attain a visa for China. I was
really looking forward to working with you in person with the group. Paul mentioned that he had e-mailed you earlier this evening. Can you please send us the draft for the DarwinCore DNA/tissue extension as soon as possible for review during our working sessions? We have one tomorrow at 1:30 (Beijing time) and another on Tuesday at the same time. It would be really great if you could Skype into either both or one of the sessions.
Thanks for your help on this.
Kind Regards,
Katie
From: <Barker>, Katharine Barker <barkerk@si.edu<mailto:barkerk@si.edu
<mailto:barkerk@si.edumailto:barkerk@si.edu><mailto:barkerk@si.edu
mailto:barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu>>>
Date: Thursday, October 18, 2012 1:34 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:
barkerk@si.edumailto:barkerk@si.edu><mailto:barkerk@si.edumailto: barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu>>>, 'John Deck' <jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto: jdeck@berkeley.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edu mailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto: jdeck@berkeley.edu>>>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto: Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.aumailto: Paul.Flemons@austmus.gov.au><mailto:Paul.Flemons@austmus.gov.aumailto: Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.aumailto: Paul.Flemons@austmus.gov.au>>>, "'"Dröge", Éamonn Tuama < eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto: eotuama@gbif.org><mailto:eotuama@gbif.org<mailto:eotuama@gbif.org
<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>>, "Whitacre, Jamie" <
WHITACREJ@si.edumailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edumailto: WHITACREJ@si.edu><mailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edu
<mailto:WHITACREJ@si.edumailto:WHITACREJ@si.edu>>>, "'rjr8222@gmail.com
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<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>'" <
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a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>>, "' gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:' gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>'" < gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>>, "' tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu mailto:tuco@berkeley.edu><mailto:'tuco@berkeley.edumailto: tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>'" <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu mailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto: tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>>
Cc: "'morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:
morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:' morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto: morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk>>'" < morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto: morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto: morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto: morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk>>>, "Parr, Cynthia" < parrc@si.edumailto:parrc@si.edu<mailto:parrc@si.edu<mailto:parrc@si.edu
<mailto:parrc@si.edumailto:parrc@si.edu<mailto:parrc@si.edu<mailto:
parrc@si.edu>>>>
Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for
Darwin Core//Telecon next week
Dear all,
This is a friendly reminder that we will be meeting next Tuesday
afternoon at the TDWG 2012 Conference in order to finalize the draft DarwinCore-A DNA/tissue extension for GGBN. As you know, the immediate need for GGBN members is to publish information on tissues. This will happen through extensions to both ABCDDNA and DarwinCore-A. Here we are focused on developing the DarwinCore-A DNA/tissue extension.
An update on the timeline for developing the draft DarwinCore-A
DNA/tissue extension is listed below.
Review content requirements for DarwinCore-A DNA/tissueextension (completed, see attached required DNA and tissue elements)
John Weiczorek will develop the draft DarwinCore-A DNA/tissueextension (to be completed for group review prior to our break out session on Tuesday afternoon, October 23).
Tuesday October 23, working meeting· Questions to answer before final review of DNA/tissue
extension
o How do we include repeatable elements of ABCDDNA into DwC-A-DNA
(References to more than one sequence record/publication are mandatory)?
o How do we extend the "Basis of Record" in ABCD and DwC-A and how do
we include an element similar to ABCD-"Kind of Unit" to DwC-A?
o What are the remaining issues for DwC-A working with IPT? Are any
changes in the IPT required?
· Review and finalize draft DarwinCore-A DNA/tissue extension
for posting to GBIF site.
Thank you again to everyone who is involved in this project. I look
forward to seeing all of you in Beijing.
Kind Regards,
Katie
From: Barker, Katharine Sent: Friday, September 28, 2012 9:53 AM To: 'John Deck'; Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.org
mailto:eotuama@gbif.org<mailto:eotuama@gbif.org<mailto:eotuama@gbif.org
<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:
eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto: rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org mailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto: a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>; tuco@berkeley.edu mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto: tuco@berkeley.edu><mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu
<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>
Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for
Darwin Core//Telecon next week
Dear all,
We will be meeting this Tuesday at 1pm U.S. Eastern time over Skype in
order to discuss the actions required to develop the draft proposal for the Darwin Core tissue/DNA extension. A proposal for designing, testing, and implementing the GGBN data portal is attached for your reference. Please review the timeline and action items leading up to the TDWG 2012 Conference.
My Skype name is Katharine.Barker1. If possible, please forward me
your skype account names prior to our meeting.
Kind Regards,
Katie
From:jdeck88@gmail.commailto:From%3Ajdeck88@gmail.com<mailto:
From%3Ajdeck88@gmail.commailto:From%253Ajdeck88@gmail.com><mailto: jdeck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@gmail.com mailto:jdeck88@gmail.com>> [mailto:jdeck88@gmail.commailto: jdeck88@gmail.com<mailto:jdeck88@gmail.commailto:jdeck88@gmail.com>] On Behalf Of John Deck
Sent: Tuesday, September 25, 2012 4:04 PM To: Barker, Katharine Cc: Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.org<mailto:
eotuama@gbif.org><mailto:eotuama@gbif.org<mailto:eotuama@gbif.org
<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:
eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto: rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org mailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto: a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>; tuco@berkeley.edu mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto: tuco@berkeley.edu><mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu
<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>
Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for
Darwin Core//Telecon next week
Here is the wrapup of the bioCollections Ontology workshop from last
week at GSC14:
http://biocodecommons.org/workshops/bioCollections/index.html
This is relevant to these discussions since we focussed on what
constitutes a "sample" and also, probably more importantly, processes that work with samples.
We briefly discussed the DwC Tissue Extension and came up with a
proposal for a quick-fix and a more substantial fix. The quick-fix is to create two new BasisOfRecord terms: TissueSubSample, DNAExtract (or some terms like that -- Tuco could provide more clarification on this too). Thus, theoretically we could override the dwc:Occurrence class to mean, for example, TissueSubSample the same way we do for Specimens and Observations. The bigger fix is to more fundamentally re-orient DwC around the notion of "Sample", involving adding/changing some properties although we didn't get into any specifics.
P.s. I can do the 12/1/2 timeslots for that monday or tuesday but not
the 11.
John On Mon, Sep 24, 2012 at 12:39 PM, Barker, Katharine <BarkerK@si.edu
mailto:BarkerK@si.edu<mailto:BarkerK@si.edu<mailto:BarkerK@si.edu
<mailto:BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edu
mailto:BarkerK@si.edu>>> wrote:
Dear all,
We will have a telecon meeting early next week in order to discuss a
draft proposal for the Darwin Core tissue/DNA extension. Gabi, Paul, and I will put together a first draft for discussion to be distributed prior to the telecon. As you know, the goal is to have a working draft ready for our working group to review at the TDWG meeting in Beijing this October.
These are our options for meeting next week: Monday 11am, 12pm, 1pm, 2pm US EDT Tuesday 11am, 12pm, 1pm, 2pm US EDT
Please let me know if you cannot make one of these times.
Thanks again to those of you who provided input last week at the GSC 14
meeting.
Kind Regards,
Katie
From: Barker, Katharine Sent: Wednesday, September 12, 2012 10:51 AM To: 'Paul Flemons'; "Dröge, Gabriele"; eotuama@gbif.org<mailto:
eotuama@gbif.org><mailto:eotuama@gbif.org<mailto:eotuama@gbif.org
<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:
eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; ' rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto: rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>'; jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edu mailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto: jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>>; 'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org mailto:a.guentsch@bgbm.org>>'; 'gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com>>'; 'tuco@berkeley.edu<mailto:tuco@berkeley.edu
<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:
tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu mailto:tuco@berkeley.edu>>'
Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for
Darwin Core
Importance: High
Dear all,
My name is Katie Barker and I am the Global Genome Biodiversity Network
Coordinator. As you know from Paul Flemons, members of the GGBN Data Standards and Data Access Task Force are trying to pull together a task group, which you are all part of, for the upcoming TDWG meeting in Beijing this October in order to address a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members. I am contacting you to schedule a meeting in late September/early October to develop a draft proposal for this extension to be completed at the upcoming TDWG meeting.
Please let me know your availability for the last two weeks of
September and first two weeks of October. There will be some scheduling issues, as there are task group members on the west and east coasts of the U.S., Europe and Australia.
Paul Flemons (in Australia) will be in the U.S. the first week of
October, so maybe we can meet in the afternoon of the 1st, anytime on the second 2nd, or in the morning of the 3rd of October over teleconference (US Eastern Daylight Time). Please let me know if any of these time slots work for you.
Gabi, I believe that you and John Deck will be at the GSC 14 meeting
next week. Is there any chance that you can start drawing up an outline for the proposed extension? We could review the outline during our group telecon and start drafting a proposal for review at the TDWG meeting in October.
Kind Regards,
Katie
Task Group Members:
John Weiczorek - Berkeley Éamonn O'Tuama - GBIF Jamie Whitacre - SI John Deck - Berkeley Robert Robbins - University of California, San Diego Anton Guentsch -
BGBM Gabi Droege- BGBM Paul Flemons- AM
From: Paul Flemons [mailto:Paul.Flemons@austmus.gov.au<mailto:
Paul.Flemons@austmus.gov.au><mailto:Paul.Flemons@austmus.gov.aumailto: Paul.Flemons@austmus.gov.au>]
Sent: Tuesday, August 07, 2012 2:50 AM To: tuco@berkley.edumailto:tuco@berkley.edu<mailto:tuco@berkley.edu
mailto:tuco@berkley.edu><mailto:tuco@berkley.edu<mailto:tuco@berkley.edu
<mailto:tuco@berkley.edumailto:tuco@berkley.edu>>; a.guentsch@bgbm.org
mailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto: a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto: a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org<mailto: j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org><mailto: j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org<mailto: j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org>>; jdeck@berkeley.edu mailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto: jdeck@berkeley.edu><mailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edu
<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>>
Cc: Barker, Katharine; Éamonn Ó Tuama [GBIF]; "Dröge, Gabriele" (
g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG<mailto:g.droege@BGBM.ORG mailto:g.droege@BGBM.ORG><mailto:g.droege@BGBM.ORGmailto: g.droege@BGBM.ORG<mailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG>>)
Subject: Meeting at TDWG 2012 to define a tissue/DNA extension for
Darwin Core
Hi all, I am on the Data Standards and Access Task Force for the Global Genome
Biodiversity Network (http://ggbn.org/) which is in need of a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members.
To this end I am writing to you to ask if you would be interested in
participating in a small working group at TDWG in Beijing this year.
At this stage my plan would be to identify relevant fields for
inclusion in the extension, using ABCDDNA as a reference. If sufficient progress is made then we would submit the extension for ratification by TDWG (is that how its done John?) The GGBN will use whatever comes out of the group to move towards having a suitable DwC based schema for data sharing.
So please let me know if you are willing to participate in the task
group and/or if there is anyone else you feel would be beneficial to have involved.
How much time do you think we will need? I have been thinking that a
day will be needed, so we could make that consist of either one full day or two half days. Im also thinking that during the week will be the best time for this.
Thanks for your time
Best Regards Paul
Paul K J Flemons Manager, Collection Informatics Team Lead, Atlas of Living Australia Biodiversity Volunteer Portal<
http://volunteer.ala.org.au%3E
Biodiversity Information Standards (TDWG) Representative for Oceania
Australian Museum 6 College Street Sydney NSW 2010 Australia t 61 2 9320 6343 m 0413458649 f 61 2 9320 6021
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<DNATissueExtensionNotes2-TDWG2012.docx>_______________________________________________
IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt
Well, let's investigate one thing about your diagram first. Shouldn't there be a one-to-many relationship between Occurrence (specimen) and Sample rather than a many-to-one?
Specimen from the field = Occurrence + Event + Location + Identification + Taxon Sample from the specimen's liver = Sample Sample from the specimen's heart = Sample Sample from the specimen's gut = Sample
yes, thats true. Ididnt think about samples that way when I drafted the diagram.
The scenario I had in my mind was the environmental sample, a vegetation plot survey or just a rock with various lichen species on it. Usually with rich data about the location, habitat and abiotic measurements (lends itself nicely to an extension for samples). In such a sample you then find various species which would be the basis for an occurrence. In the case of metagenomic samples the list of taxa is actually derived information from the amplifications and can vary according to the method used (basically the entire occurrence extension can be derived from the amplifications in this case).
Actually when you take a gut sample from an animal you often are interested in the fauna of that gut, so the occurrences would not be the host, but the bacteria occurring within it.
Markus
And all of the Samples could have multiple Amplifications.
If we want to model this with a Sample Core, then Occurrences may be repeated in the Occurrence extension in your diagram, but every sample would have no more than one Occurrence in the extension file and the sampleID relationship would be one-to-one. If so, then it is also possible to have a Sample Core (Sample rowType) with sampleID as the core record identifier, with "Sample" as basisOfRecord, and with all of the attributes of Sample and of the existing Occurrence Core. This would avoid having a distinct Occurrence extension for Samples, which could get confusing for those who are accustomed to mapping Occurrences already. This combined Sample/Occurrence Core could still have a one-to-many relationship to the Amplifications.
On Mon, Oct 22, 2012 at 1:33 PM, "Markus Döring (GBIF)" mdoering@gbif.org wrote: Adding a new core type to the IPT could be done in less than a day - more work for GBIF would be to support such a format in our indexing code. But if we think its a better solution to go with a new sample core type, I think its worth the extra cost of coding for it.
On 22.10.2012, at 17:53, John Wieczorek wrote:
I like the approach of having a Sample Core, but the approach taken thus far was with the view of being pragmatic to put into practice by January 2013. What do you think could be the possibility of adding a new Core type to the IPT on that time scale? The Darwin Core archive specification can certainly handle it, but the proof is in the implementation.
On Mon, Oct 22, 2012 at 8:11 AM, "Markus Döring (GBIF)" mdoering@gbif.org wrote: Hi all, I only quickly looked through the proposal, but it looks good, pragmatic and definitely to be working for the case when a DNASample equals a single taxon Occurrence.
Im not so sure how well it would work with environmental samples - would we have the sample flattened out and repeated to represent the individual taxa, sexes, ages, etc found in there? I was therefore wondering if anyone had thought about the attached setup before. Sample is at its core and occurrence & dna amplification as extensions with the amplifications (optionally?) refering to the occurrence they belong to.
Another quick observation is that we try to reuse existing terms in extensions as much as possible. Following that rule for example dwc:institutionCode should rather be used instead of dNACollectionCode and probably dc:source for the referenceCitation
until tomorrow, regards, Markus
<sample core.png>
On 22.10.2012, at 12:21, Barker, Katharine wrote:
Dear John,
Please see our working revisions/comments/questions on the DNA/tissue extension for Darwin Core (highlighted in blue). We were able to work through the draft up through "class sample properties": https://docs.google.com/document/d/1RCgIPfu9gAPubjjbog-9vCJonvqcK1pLOaq6H8GS...
The document is also attached for your reference (just incase any of you are unable to access the document).
Please try to respond to our questions and comments prior to our meeting tomorrow (be sure to make these changes using a different color for tracking purposes).
Tomorrow we will like to 1) briefly recap our revisions on the extension so far (addressing questions and comments), 2) complete our review of the extension and 3) identify any remaining issues with DwC working with IPT (and identify if any changes in the IPT are required).
Thank you for your help on this!
Kind Regards,
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu" <tuco@berkeley.edumailto:tuco@berkeley.edu> Date: Sunday, October 21, 2012 10:52 PM To: Gabriele Droege <g.droege@bgbm.orgmailto:g.droege@bgbm.org> Cc: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au>, John Deck <jdeck@berkeley.edumailto:jdeck@berkeley.edu>, Robert Hanner <bob.hanner@gmail.commailto:bob.hanner@gmail.com>, Éamonn Tuama <eotuama@gbif.orgmailto:eotuama@gbif.org>, Robert Robbins <rjr8222@gmail.commailto:rjr8222@gmail.com>, "Guentsch, Anton" <a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org> Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Dear all,
I finished working on the Google Doc "DNA Tissue Extension Notes - TDWG 2012". Feel free to let this be a working document where comments and questions can be added. I've attached a Word Doc version for archival purposes.
I added the two template extension files (DNATissueExtension.txt and DNAAmplificationExtension.txt) to the shared TDWG GGBN working group folder linked below. They are in the form they need to be submitted to GBIF to be added to their extension registry. They would both need to be updated with the term descriptions, examples, and constraints.
https://drive.google.com/#folders/0BxEyFKwB7zY4WEs0WkdtUU5oVnM
Cheers,
John
On Sun, Oct 21, 2012 at 10:38 PM, John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> wrote: Ooops
...at http://goo.gl/kGHmb. Adding touches based on the files Gabi sent. Will tell you all when finished with that and will send it as a Word doc at that time in case there are any issues with Google docs. Should be soon. Let me know if I should share to any different addresses.
Cheers,
John
On Sun, Oct 21, 2012 at 10:34 PM, John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> wrote: That helps a lot, as it clears up some of my own misconceptions. I have shared a document where I have captured the thinking behind a couple of different ways forward with one or two extensions and an example of how the two-extension might look in the context of a Darwin Core Archive. The DNA Tissue Extension Notes Google doc can be found at
On Sun, Oct 21, 2012 at 9:23 PM, "Dröge, Gabriele" <g.droege@bgbm.orgmailto:g.droege@bgbm.org> wrote: Yes we do... Hi John,
Thanks for getting back to us. Attached are two csv files, one with some main DNA facts and the other with associated GenBank entries und publications (2 examples with 2 GenBank entries per DNA sample). I included only UnitID/CollCode/InstCode for the related voucher specimen and I excluded the tissue facts since they are quite similar to the DNA facts and should be mapped independently.
Best, Gabi
-----Original Message----- From: Barker, Katharine [mailto:BarkerK@si.edumailto:BarkerK@si.edu] Sent: Sunday, October 21, 2012 11:41 PM To: Paul Flemons; Dröge, Gabriele Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Paul and Gabi,
Do we have any sample data that John can use as a test case? I think he would like it today, if possible.
Thanks for your help (and the team work).
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>" <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Date: Sunday, October 21, 2012 12:03 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu>> Subject: Re: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Hi Katie,
Messages received. Will have the extension stuff ready within a few hours and hope to be able to attend remotely. One thing in the meantime. Do you have any example data that could be used as a test case to populate a core with this extension? Would like to try that with some realy data to test my assumptions.
Sorry for the delay.
Thanks,
John
On Sun, Oct 21, 2012 at 10:08 AM, Barker, Katharine <BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu>> wrote: Dear John,
I'm sorry that you were unable to attain a visa for China. I was really looking forward to working with you in person with the group. Paul mentioned that he had e-mailed you earlier this evening. Can you please send us the draft for the DarwinCore DNA/tissue extension as soon as possible for review during our working sessions? We have one tomorrow at 1:30 (Beijing time) and another on Tuesday at the same time. It would be really great if you could Skype into either both or one of the sessions.
Thanks for your help on this.
Kind Regards,
Katie
From: <Barker>, Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu><mailto:barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu>>> Date: Thursday, October 18, 2012 1:34 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu><mailto:barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu>>>, 'John Deck' <jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>>>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au><mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au>>>, "'"Dröge", Éamonn Tuama <eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org><mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>>, "Whitacre, Jamie" <WHITACREJ@si.edumailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edumailto:WHITACREJ@si.edu><mailto:WHITACREJ@si.edumailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edumailto:WHITACREJ@si.edu>>>, "'rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:'rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>'" <rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>>, "'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>'" <a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>>, "'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>'" <gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>>, "'tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:'tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>'" <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>> Cc: "'morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:'morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk>>'" <morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk>>>, "Parr, Cynthia" <parrc@si.edumailto:parrc@si.edu<mailto:parrc@si.edumailto:parrc@si.edu><mailto:parrc@si.edumailto:parrc@si.edu<mailto:parrc@si.edumailto:parrc@si.edu>>> Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Dear all,
This is a friendly reminder that we will be meeting next Tuesday afternoon at the TDWG 2012 Conference in order to finalize the draft DarwinCore-A DNA/tissue extension for GGBN. As you know, the immediate need for GGBN members is to publish information on tissues. This will happen through extensions to both ABCDDNA and DarwinCore-A. Here we are focused on developing the DarwinCore-A DNA/tissue extension.
An update on the timeline for developing the draft DarwinCore-A DNA/tissue extension is listed below.
Review content requirements for DarwinCore-A DNA/tissue extension (completed, see attached required DNA and tissue elements)John Weiczorek will develop the draft DarwinCore-A DNA/tissue extension (to be completed for group review prior to our break out session on Tuesday afternoon, October 23).Tuesday October 23, working meeting· Questions to answer before final review of DNA/tissue extension
o How do we include repeatable elements of ABCDDNA into DwC-A-DNA (References to more than one sequence record/publication are mandatory)?
o How do we extend the "Basis of Record" in ABCD and DwC-A and how do we include an element similar to ABCD-"Kind of Unit" to DwC-A?
o What are the remaining issues for DwC-A working with IPT? Are any changes in the IPT required?
· Review and finalize draft DarwinCore-A DNA/tissue extension for posting to GBIF site.
Thank you again to everyone who is involved in this project. I look forward to seeing all of you in Beijing.
Kind Regards,
Katie
From: Barker, Katharine Sent: Friday, September 28, 2012 9:53 AM To: 'John Deck'; Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org><mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>; tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Dear all,
We will be meeting this Tuesday at 1pm U.S. Eastern time over Skype in order to discuss the actions required to develop the draft proposal for the Darwin Core tissue/DNA extension. A proposal for designing, testing, and implementing the GGBN data portal is attached for your reference. Please review the timeline and action items leading up to the TDWG 2012 Conference.
My Skype name is Katharine.Barker1. If possible, please forward me your skype account names prior to our meeting.
Kind Regards,
Katie
From:jdeck88@gmail.commailto:From%3Ajdeck88@gmail.com<mailto:From%3Ajdeck88@gmail.commailto:From%253Ajdeck88@gmail.com><mailto:jdeck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@gmail.commailto:jdeck88@gmail.com>> [mailto:jdeck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@gmail.commailto:jdeck88@gmail.com>] On Behalf Of John Deck Sent: Tuesday, September 25, 2012 4:04 PM To: Barker, Katharine Cc: Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org><mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>; tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Here is the wrapup of the bioCollections Ontology workshop from last week at GSC14:
http://biocodecommons.org/workshops/bioCollections/index.html
This is relevant to these discussions since we focussed on what constitutes a "sample" and also, probably more importantly, processes that work with samples.
We briefly discussed the DwC Tissue Extension and came up with a proposal for a quick-fix and a more substantial fix. The quick-fix is to create two new BasisOfRecord terms: TissueSubSample, DNAExtract (or some terms like that -- Tuco could provide more clarification on this too). Thus, theoretically we could override the dwc:Occurrence class to mean, for example, TissueSubSample the same way we do for Specimens and Observations. The bigger fix is to more fundamentally re-orient DwC around the notion of "Sample", involving adding/changing some properties although we didn't get into any specifics.
P.s. I can do the 12/1/2 timeslots for that monday or tuesday but not the 11.
John On Mon, Sep 24, 2012 at 12:39 PM, Barker, Katharine <BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu><mailto:BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu>>> wrote: Dear all,
We will have a telecon meeting early next week in order to discuss a draft proposal for the Darwin Core tissue/DNA extension. Gabi, Paul, and I will put together a first draft for discussion to be distributed prior to the telecon. As you know, the goal is to have a working draft ready for our working group to review at the TDWG meeting in Beijing this October.
These are our options for meeting next week: Monday 11am, 12pm, 1pm, 2pm US EDT Tuesday 11am, 12pm, 1pm, 2pm US EDT
Please let me know if you cannot make one of these times.
Thanks again to those of you who provided input last week at the GSC 14 meeting.
Kind Regards,
Katie
From: Barker, Katharine Sent: Wednesday, September 12, 2012 10:51 AM To: 'Paul Flemons'; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org><mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; 'rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>'; jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>>; 'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>'; 'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>'; 'tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>' Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core Importance: High
Dear all,
My name is Katie Barker and I am the Global Genome Biodiversity Network Coordinator. As you know from Paul Flemons, members of the GGBN Data Standards and Data Access Task Force are trying to pull together a task group, which you are all part of, for the upcoming TDWG meeting in Beijing this October in order to address a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members. I am contacting you to schedule a meeting in late September/early October to develop a draft proposal for this extension to be completed at the upcoming TDWG meeting.
Please let me know your availability for the last two weeks of September and first two weeks of October. There will be some scheduling issues, as there are task group members on the west and east coasts of the U.S., Europe and Australia.
Paul Flemons (in Australia) will be in the U.S. the first week of October, so maybe we can meet in the afternoon of the 1st, anytime on the second 2nd, or in the morning of the 3rd of October over teleconference (US Eastern Daylight Time). Please let me know if any of these time slots work for you.
Gabi, I believe that you and John Deck will be at the GSC 14 meeting next week. Is there any chance that you can start drawing up an outline for the proposed extension? We could review the outline during our group telecon and start drafting a proposal for review at the TDWG meeting in October.
Kind Regards,
Katie
Task Group Members:
John Weiczorek - Berkeley Éamonn O'Tuama - GBIF Jamie Whitacre - SI John Deck - Berkeley Robert Robbins - University of California, San Diego Anton Guentsch - BGBM Gabi Droege- BGBM Paul Flemons- AM
From: Paul Flemons [mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au>] Sent: Tuesday, August 07, 2012 2:50 AM To: tuco@berkley.edumailto:tuco@berkley.edu<mailto:tuco@berkley.edumailto:tuco@berkley.edu><mailto:tuco@berkley.edumailto:tuco@berkley.edu<mailto:tuco@berkley.edumailto:tuco@berkley.edu>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org<mailto:j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org><mailto:j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org<mailto:j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org>>; jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>> Cc: Barker, Katharine; Éamonn Ó Tuama [GBIF]; "Dröge, Gabriele" (g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG<mailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG><mailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG<mailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG>>) Subject: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core
Hi all, I am on the Data Standards and Access Task Force for the Global Genome Biodiversity Network (http://ggbn.org/) which is in need of a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members.
To this end I am writing to you to ask if you would be interested in participating in a small working group at TDWG in Beijing this year.
At this stage my plan would be to identify relevant fields for inclusion in the extension, using ABCDDNA as a reference. If sufficient progress is made then we would submit the extension for ratification by TDWG (is that how its done John?) The GGBN will use whatever comes out of the group to move towards having a suitable DwC based schema for data sharing.
So please let me know if you are willing to participate in the task group and/or if there is anyone else you feel would be beneficial to have involved.
How much time do you think we will need? I have been thinking that a day will be needed, so we could make that consist of either one full day or two half days. Im also thinking that during the week will be the best time for this.
Thanks for your time
Best Regards Paul
Paul K J Flemons Manager, Collection Informatics Team Lead, Atlas of Living Australia Biodiversity Volunteer Portalhttp://volunteer.ala.org.au Biodiversity Information Standards (TDWG) Representative for Oceania Australian Museum 6 College Street Sydney NSW 2010 Australia t 61 2 9320 6343 m 0413458649 f 61 2 9320 6021 Visit: http://www.australianmuseum.net.auhttp://www.australianmuseum.net.au/ Like: http://www.facebook.com/australianmuseum Follow: http://www.twitter.com/austmus Watch: http://www.youtube.com/austmus [cid:image001.png@01CDAD34.391DC790mailto:image001.png@01CDAD34.391DC790<mailto:image001.png@01CDAD34.391DC790mailto:image001.png@01CDAD34.391DC790>] Inspiring the exploration of nature and cultures
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<DNATissueExtensionNotes2-TDWG2012.docx>_______________________________________________ IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt
I don't think I would mix the concept of Occurrence in that way. It should remain where and when and what was taken "from the wild" by what method. After that is sampling. It may be that a Sample core should not have all of the attributes of an Occurrence, or that the Occurrence core itself is poorly modeled by assuming that the Organisms will be identified. Couldn't we view real-world collecting in a way such that specimens are samples until someone applies some method to better identify them?
On Mon, Oct 22, 2012 at 2:31 PM, "Markus Döring (GBIF)" mdoering@gbif.orgwrote:
Well, let's investigate one thing about your diagram first. Shouldn't
there be a one-to-many relationship between Occurrence (specimen) and Sample rather than a many-to-one?
Specimen from the field = Occurrence + Event + Location + Identification
- Taxon
Sample from the specimen's liver = Sample Sample from the specimen's heart = Sample Sample from the specimen's gut = Sample
yes, thats true. Ididnt think about samples that way when I drafted the diagram.
The scenario I had in my mind was the environmental sample, a vegetation plot survey or just a rock with various lichen species on it. Usually with rich data about the location, habitat and abiotic measurements (lends itself nicely to an extension for samples). In such a sample you then find various species which would be the basis for an occurrence. In the case of metagenomic samples the list of taxa is actually derived information from the amplifications and can vary according to the method used (basically the entire occurrence extension can be derived from the amplifications in this case).
Actually when you take a gut sample from an animal you often are interested in the fauna of that gut, so the occurrences would not be the host, but the bacteria occurring within it.
Markus
And all of the Samples could have multiple Amplifications.
If we want to model this with a Sample Core, then Occurrences may be
repeated in the Occurrence extension in your diagram, but every sample would have no more than one Occurrence in the extension file and the sampleID relationship would be one-to-one. If so, then it is also possible to have a Sample Core (Sample rowType) with sampleID as the core record identifier, with "Sample" as basisOfRecord, and with all of the attributes of Sample and of the existing Occurrence Core. This would avoid having a distinct Occurrence extension for Samples, which could get confusing for those who are accustomed to mapping Occurrences already. This combined Sample/Occurrence Core could still have a one-to-many relationship to the Amplifications.
On Mon, Oct 22, 2012 at 1:33 PM, "Markus Döring (GBIF)" <
mdoering@gbif.org> wrote:
Adding a new core type to the IPT could be done in less than a day -
more work for GBIF would be to support such a format in our indexing code.
But if we think its a better solution to go with a new sample core type,
I think its worth the extra cost of coding for it.
On 22.10.2012, at 17:53, John Wieczorek wrote:
I like the approach of having a Sample Core, but the approach taken
thus far was with the view of being pragmatic to put into practice by January 2013. What do you think could be the possibility of adding a new Core type to the IPT on that time scale? The Darwin Core archive specification can certainly handle it, but the proof is in the implementation.
On Mon, Oct 22, 2012 at 8:11 AM, "Markus Döring (GBIF)" <
mdoering@gbif.org> wrote:
Hi all, I only quickly looked through the proposal, but it looks good,
pragmatic and definitely to be working for the case when a DNASample equals a single taxon Occurrence.
Im not so sure how well it would work with environmental samples -
would we have the sample flattened out and repeated to represent the individual taxa, sexes, ages, etc found in there?
I was therefore wondering if anyone had thought about the attached
setup before. Sample is at its core and occurrence & dna amplification as extensions with the amplifications (optionally?) refering to the occurrence they belong to.
Another quick observation is that we try to reuse existing terms in
extensions as much as possible. Following that rule for example dwc:institutionCode should rather be used instead of dNACollectionCode and probably dc:source for the referenceCitation
until tomorrow, regards, Markus
<sample core.png>
On 22.10.2012, at 12:21, Barker, Katharine wrote:
Dear John,
Please see our working revisions/comments/questions on the DNA/tissue
extension for Darwin Core (highlighted in blue). We were able to work through the draft up through "class sample properties":
https://docs.google.com/document/d/1RCgIPfu9gAPubjjbog-9vCJonvqcK1pLOaq6H8GS...
The document is also attached for your reference (just incase any of
you are unable to access the document).
Please try to respond to our questions and comments prior to our
meeting tomorrow (be sure to make these changes using a different color for tracking purposes).
Tomorrow we will like to 1) briefly recap our revisions on the
extension so far (addressing questions and comments), 2) complete our review of the extension and 3) identify any remaining issues with DwC working with IPT (and identify if any changes in the IPT are required).
Thank you for your help on this!
Kind Regards,
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu" <
tuco@berkeley.edumailto:tuco@berkeley.edu>
Date: Sunday, October 21, 2012 10:52 PM To: Gabriele Droege <g.droege@bgbm.orgmailto:g.droege@bgbm.org> Cc: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu>, Paul
Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au>, John Deck <jdeck@berkeley.edumailto:jdeck@berkeley.edu>, Robert Hanner < bob.hanner@gmail.commailto:bob.hanner@gmail.com>, Éamonn Tuama < eotuama@gbif.orgmailto:eotuama@gbif.org>, Robert Robbins < rjr8222@gmail.commailto:rjr8222@gmail.com>, "Guentsch, Anton" < a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>
Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension
for Darwin Core-draft reminder
Dear all,
I finished working on the Google Doc "DNA Tissue Extension Notes -
TDWG 2012". Feel free to let this be a working document where comments and questions can be added. I've attached a Word Doc version for archival purposes.
I added the two template extension files (DNATissueExtension.txt and
DNAAmplificationExtension.txt) to the shared TDWG GGBN working group folder linked below. They are in the form they need to be submitted to GBIF to be added to their extension registry. They would both need to be updated with the term descriptions, examples, and constraints.
https://drive.google.com/#folders/0BxEyFKwB7zY4WEs0WkdtUU5oVnM
Cheers,
John
On Sun, Oct 21, 2012 at 10:38 PM, John Wieczorek <tuco@berkeley.edu
mailto:tuco@berkeley.edu> wrote:
Ooops
...at http://goo.gl/kGHmb. Adding touches based on the files Gabi
sent. Will tell you all when finished with that and will send it as a Word doc at that time in case there are any issues with Google docs. Should be soon. Let me know if I should share to any different addresses.
Cheers,
John
On Sun, Oct 21, 2012 at 10:34 PM, John Wieczorek <tuco@berkeley.edu
mailto:tuco@berkeley.edu> wrote:
That helps a lot, as it clears up some of my own misconceptions. I
have shared a document where I have captured the thinking behind a couple of different ways forward with one or two extensions and an example of how the two-extension might look in the context of a Darwin Core Archive. The DNA Tissue Extension Notes Google doc can be found at
On Sun, Oct 21, 2012 at 9:23 PM, "Dröge, Gabriele" <g.droege@bgbm.org
mailto:g.droege@bgbm.org> wrote:
Yes we do... Hi John,
Thanks for getting back to us. Attached are two csv files, one with
some main DNA facts and the other with associated GenBank entries und publications (2 examples with 2 GenBank entries per DNA sample).
I included only UnitID/CollCode/InstCode for the related voucher
specimen and I excluded the tissue facts since they are quite similar to the DNA facts and should be mapped independently.
Best, Gabi
-----Original Message----- From: Barker, Katharine [mailto:BarkerK@si.edu<mailto:BarkerK@si.edu
]
Sent: Sunday, October 21, 2012 11:41 PM To: Paul Flemons; Dröge, Gabriele Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension
for Darwin Core-draft reminder
Paul and Gabi,
Do we have any sample data that John can use as a test case? I think
he would like it today, if possible.
Thanks for your help (and the team work).
Katie
From: John Wieczorek <tuco@berkeley.edu<mailto:tuco@berkeley.edu
<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>
Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:
tuco@berkeley.edumailto:tuco@berkeley.edu>" <tuco@berkeley.edumailto: tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>
Date: Sunday, October 21, 2012 12:03 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:
barkerk@si.edumailto:barkerk@si.edu>>
Subject: Re: FW: Meeting at TDWG 2012 to define a tissue/DNA
extension for Darwin Core-draft reminder
Hi Katie,
Messages received. Will have the extension stuff ready within a few
hours and hope to be able to attend remotely. One thing in the meantime. Do you have any example data that could be used as a test case to populate a core with this extension? Would like to try that with some realy data to test my assumptions.
Sorry for the delay.
Thanks,
John
On Sun, Oct 21, 2012 at 10:08 AM, Barker, Katharine <BarkerK@si.edu
mailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu>> wrote:
Dear John,
I'm sorry that you were unable to attain a visa for China. I was
really looking forward to working with you in person with the group. Paul mentioned that he had e-mailed you earlier this evening. Can you please send us the draft for the DarwinCore DNA/tissue extension as soon as possible for review during our working sessions? We have one tomorrow at 1:30 (Beijing time) and another on Tuesday at the same time. It would be really great if you could Skype into either both or one of the sessions.
Thanks for your help on this.
Kind Regards,
Katie
From: <Barker>, Katharine Barker <barkerk@si.edu<mailto:
barkerk@si.edu><mailto:barkerk@si.edumailto:barkerk@si.edu><mailto: barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edumailto: barkerk@si.edu>>>
Date: Thursday, October 18, 2012 1:34 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:
barkerk@si.edumailto:barkerk@si.edu><mailto:barkerk@si.edumailto: barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu>>>, 'John Deck' <jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto: jdeck@berkeley.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edu mailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto: jdeck@berkeley.edu>>>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto: Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.aumailto: Paul.Flemons@austmus.gov.au><mailto:Paul.Flemons@austmus.gov.aumailto: Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.aumailto: Paul.Flemons@austmus.gov.au>>>, "'"Dröge", Éamonn Tuama < eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto: eotuama@gbif.org><mailto:eotuama@gbif.org<mailto:eotuama@gbif.org
<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>>, "Whitacre, Jamie" <
WHITACREJ@si.edumailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edumailto: WHITACREJ@si.edu><mailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edu
<mailto:WHITACREJ@si.edumailto:WHITACREJ@si.edu>>>, "'rjr8222@gmail.com
mailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto: rjr8222@gmail.com><mailto:'rjr8222@gmail.com<mailto:rjr8222@gmail.com
<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>'" <
rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto: rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>>, "'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:' a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org mailto:a.guentsch@bgbm.org>>'" <a.guentsch@bgbm.orgmailto: a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org
<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:
a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>>, "' gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:' gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>'" < gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>>, "' tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu mailto:tuco@berkeley.edu><mailto:'tuco@berkeley.edumailto: tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>'" <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu mailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto: tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>>
Cc: "'morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:
morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:' morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto: morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk>>'" < morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto: morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto: morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto: morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk>>>, "Parr, Cynthia" < parrc@si.edumailto:parrc@si.edu<mailto:parrc@si.edu<mailto:parrc@si.edu
<mailto:parrc@si.edumailto:parrc@si.edu<mailto:parrc@si.edu<mailto:
parrc@si.edu>>>>
Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension
for Darwin Core//Telecon next week
Dear all,
This is a friendly reminder that we will be meeting next Tuesday
afternoon at the TDWG 2012 Conference in order to finalize the draft DarwinCore-A DNA/tissue extension for GGBN. As you know, the immediate need for GGBN members is to publish information on tissues. This will happen through extensions to both ABCDDNA and DarwinCore-A. Here we are focused on developing the DarwinCore-A DNA/tissue extension.
An update on the timeline for developing the draft DarwinCore-A
DNA/tissue extension is listed below.
Review content requirements for DarwinCore-A DNA/tissueextension (completed, see attached required DNA and tissue elements)
John Weiczorek will develop the draft DarwinCore-A DNA/tissueextension (to be completed for group review prior to our break out session on Tuesday afternoon, October 23).
Tuesday October 23, working meeting· Questions to answer before final review of DNA/tissue
extension
o How do we include repeatable elements of ABCDDNA into DwC-A-DNA
(References to more than one sequence record/publication are mandatory)?
o How do we extend the "Basis of Record" in ABCD and DwC-A and how
do we include an element similar to ABCD-"Kind of Unit" to DwC-A?
o What are the remaining issues for DwC-A working with IPT? Are
any changes in the IPT required?
· Review and finalize draft DarwinCore-A DNA/tissue extension
for posting to GBIF site.
Thank you again to everyone who is involved in this project. I look
forward to seeing all of you in Beijing.
Kind Regards,
Katie
From: Barker, Katharine Sent: Friday, September 28, 2012 9:53 AM To: 'John Deck'; Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.org
mailto:eotuama@gbif.org<mailto:eotuama@gbif.org<mailto:eotuama@gbif.org
<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:
eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto: rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org mailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto: a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>; tuco@berkeley.edu mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto: tuco@berkeley.edu><mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu
<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>
Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension
for Darwin Core//Telecon next week
Dear all,
We will be meeting this Tuesday at 1pm U.S. Eastern time over Skype
in order to discuss the actions required to develop the draft proposal for the Darwin Core tissue/DNA extension. A proposal for designing, testing, and implementing the GGBN data portal is attached for your reference. Please review the timeline and action items leading up to the TDWG 2012 Conference.
My Skype name is Katharine.Barker1. If possible, please forward me
your skype account names prior to our meeting.
Kind Regards,
Katie
From:jdeck88@gmail.commailto:From%3Ajdeck88@gmail.com<mailto:
From%3Ajdeck88@gmail.commailto:From%253Ajdeck88@gmail.com><mailto: jdeck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@gmail.com mailto:jdeck88@gmail.com>> [mailto:jdeck88@gmail.commailto: jdeck88@gmail.com<mailto:jdeck88@gmail.commailto:jdeck88@gmail.com>] On Behalf Of John Deck
Sent: Tuesday, September 25, 2012 4:04 PM To: Barker, Katharine Cc: Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.org<mailto:
eotuama@gbif.org><mailto:eotuama@gbif.org<mailto:eotuama@gbif.org
<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:
eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto: rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org mailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto: a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>; tuco@berkeley.edu mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto: tuco@berkeley.edu><mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu
<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>
Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension
for Darwin Core//Telecon next week
Here is the wrapup of the bioCollections Ontology workshop from last
week at GSC14:
http://biocodecommons.org/workshops/bioCollections/index.html
This is relevant to these discussions since we focussed on what
constitutes a "sample" and also, probably more importantly, processes that work with samples.
We briefly discussed the DwC Tissue Extension and came up with a
proposal for a quick-fix and a more substantial fix. The quick-fix is to create two new BasisOfRecord terms: TissueSubSample, DNAExtract (or some terms like that -- Tuco could provide more clarification on this too). Thus, theoretically we could override the dwc:Occurrence class to mean, for example, TissueSubSample the same way we do for Specimens and Observations. The bigger fix is to more fundamentally re-orient DwC around the notion of "Sample", involving adding/changing some properties although we didn't get into any specifics.
P.s. I can do the 12/1/2 timeslots for that monday or tuesday but
not the 11.
John On Mon, Sep 24, 2012 at 12:39 PM, Barker, Katharine <BarkerK@si.edu
mailto:BarkerK@si.edu<mailto:BarkerK@si.edu<mailto:BarkerK@si.edu
<mailto:BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edu
mailto:BarkerK@si.edu>>> wrote:
Dear all,
We will have a telecon meeting early next week in order to discuss a
draft proposal for the Darwin Core tissue/DNA extension. Gabi, Paul, and I will put together a first draft for discussion to be distributed prior to the telecon. As you know, the goal is to have a working draft ready for our working group to review at the TDWG meeting in Beijing this October.
These are our options for meeting next week: Monday 11am, 12pm, 1pm, 2pm US EDT Tuesday 11am, 12pm, 1pm, 2pm US EDT
Please let me know if you cannot make one of these times.
Thanks again to those of you who provided input last week at the GSC
14 meeting.
Kind Regards,
Katie
From: Barker, Katharine Sent: Wednesday, September 12, 2012 10:51 AM To: 'Paul Flemons'; "Dröge, Gabriele"; eotuama@gbif.org<mailto:
eotuama@gbif.org><mailto:eotuama@gbif.org<mailto:eotuama@gbif.org
<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:
eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; ' rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto: rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>'; jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edu mailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto: jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>>; 'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org mailto:a.guentsch@bgbm.org>>'; 'gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com>>'; 'tuco@berkeley.edu<mailto:tuco@berkeley.edu
<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:
tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu mailto:tuco@berkeley.edu>>'
Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension
for Darwin Core
Importance: High
Dear all,
My name is Katie Barker and I am the Global Genome Biodiversity
Network Coordinator. As you know from Paul Flemons, members of the GGBN Data Standards and Data Access Task Force are trying to pull together a task group, which you are all part of, for the upcoming TDWG meeting in Beijing this October in order to address a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members. I am contacting you to schedule a meeting in late September/early October to develop a draft proposal for this extension to be completed at the upcoming TDWG meeting.
Please let me know your availability for the last two weeks of
September and first two weeks of October. There will be some scheduling issues, as there are task group members on the west and east coasts of the U.S., Europe and Australia.
Paul Flemons (in Australia) will be in the U.S. the first week of
October, so maybe we can meet in the afternoon of the 1st, anytime on the second 2nd, or in the morning of the 3rd of October over teleconference (US Eastern Daylight Time). Please let me know if any of these time slots work for you.
Gabi, I believe that you and John Deck will be at the GSC 14 meeting
next week. Is there any chance that you can start drawing up an outline for the proposed extension? We could review the outline during our group telecon and start drafting a proposal for review at the TDWG meeting in October.
Kind Regards,
Katie
Task Group Members:
John Weiczorek - Berkeley Éamonn O'Tuama - GBIF Jamie Whitacre - SI John Deck - Berkeley Robert Robbins - University of California, San Diego Anton Guentsch -
BGBM Gabi Droege- BGBM Paul Flemons- AM
From: Paul Flemons [mailto:Paul.Flemons@austmus.gov.au<mailto:
Paul.Flemons@austmus.gov.au><mailto:Paul.Flemons@austmus.gov.aumailto: Paul.Flemons@austmus.gov.au>]
Sent: Tuesday, August 07, 2012 2:50 AM To: tuco@berkley.edumailto:tuco@berkley.edu<mailto:tuco@berkley.edu
mailto:tuco@berkley.edu><mailto:tuco@berkley.edu<mailto:tuco@berkley.edu
<mailto:tuco@berkley.edumailto:tuco@berkley.edu>>; a.guentsch@bgbm.org
mailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto: a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto: a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org<mailto: j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org><mailto: j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org<mailto: j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org>>; jdeck@berkeley.edu mailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto: jdeck@berkeley.edu><mailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edu
<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>>
Cc: Barker, Katharine; Éamonn Ó Tuama [GBIF]; "Dröge, Gabriele" (
g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG<mailto:g.droege@BGBM.ORG mailto:g.droege@BGBM.ORG><mailto:g.droege@BGBM.ORGmailto: g.droege@BGBM.ORG<mailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG>>)
Subject: Meeting at TDWG 2012 to define a tissue/DNA extension for
Darwin Core
Hi all, I am on the Data Standards and Access Task Force for the Global
Genome Biodiversity Network (http://ggbn.org/) which is in need of a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members.
To this end I am writing to you to ask if you would be interested in
participating in a small working group at TDWG in Beijing this year.
At this stage my plan would be to identify relevant fields for
inclusion in the extension, using ABCDDNA as a reference. If sufficient progress is made then we would submit the extension for ratification by TDWG (is that how its done John?) The GGBN will use whatever comes out of the group to move towards having a suitable DwC based schema for data sharing.
So please let me know if you are willing to participate in the task
group and/or if there is anyone else you feel would be beneficial to have involved.
How much time do you think we will need? I have been thinking that a
day will be needed, so we could make that consist of either one full day or two half days. Im also thinking that during the week will be the best time for this.
Thanks for your time
Best Regards Paul
Paul K J Flemons Manager, Collection Informatics Team Lead, Atlas of Living Australia Biodiversity Volunteer Portal<
http://volunteer.ala.org.au%3E
Biodiversity Information Standards (TDWG) Representative for Oceania
Australian Museum 6 College Street Sydney NSW 2010 Australia t 61 2 9320 6343 m 0413458649 f 61 2 9320 6021
http://www.australianmuseum.net.au/%3E
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image001.png@01CDAD34.391DC790><mailto:image001.png@01CDAD34.391DC790 mailto:image001.png@01CDAD34.391DC790>]
Inspiring the exploration of nature and cultures
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-- John Deck (541) 321-0689tel:%28541%29%20321-0689tel:%28541%29%20321-0689
<DNATissueExtensionNotes2-TDWG2012.docx>_______________________________________________
IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt
Hi guys, Im with John that an environmental sample - is just a sample that in my eyes you wouldnt identify individual species from in the original record of that sample. If you identify individual species from an environmental sample you would then create new records referencing the original sample by association or something like that. Does that make sense? Paul
On 23 October 2012 10:41, John Wieczorek tuco@berkeley.edu wrote:
I don't think I would mix the concept of Occurrence in that way. It should remain where and when and what was taken "from the wild" by what method. After that is sampling. It may be that a Sample core should not have all of the attributes of an Occurrence, or that the Occurrence core itself is poorly modeled by assuming that the Organisms will be identified. Couldn't we view real-world collecting in a way such that specimens are samples until someone applies some method to better identify them?
On Mon, Oct 22, 2012 at 2:31 PM, "Markus Döring (GBIF)" <mdoering@gbif.org
wrote:
Well, let's investigate one thing about your diagram first. Shouldn't
there be a one-to-many relationship between Occurrence (specimen) and Sample rather than a many-to-one?
Specimen from the field = Occurrence + Event + Location +
Identification + Taxon
Sample from the specimen's liver = Sample Sample from the specimen's heart = Sample Sample from the specimen's gut = Sample
yes, thats true. Ididnt think about samples that way when I drafted the diagram.
The scenario I had in my mind was the environmental sample, a vegetation plot survey or just a rock with various lichen species on it. Usually with rich data about the location, habitat and abiotic measurements (lends itself nicely to an extension for samples). In such a sample you then find various species which would be the basis for an occurrence. In the case of metagenomic samples the list of taxa is actually derived information from the amplifications and can vary according to the method used (basically the entire occurrence extension can be derived from the amplifications in this case).
Actually when you take a gut sample from an animal you often are interested in the fauna of that gut, so the occurrences would not be the host, but the bacteria occurring within it.
Markus
And all of the Samples could have multiple Amplifications.
If we want to model this with a Sample Core, then Occurrences may be
repeated in the Occurrence extension in your diagram, but every sample would have no more than one Occurrence in the extension file and the sampleID relationship would be one-to-one. If so, then it is also possible to have a Sample Core (Sample rowType) with sampleID as the core record identifier, with "Sample" as basisOfRecord, and with all of the attributes of Sample and of the existing Occurrence Core. This would avoid having a distinct Occurrence extension for Samples, which could get confusing for those who are accustomed to mapping Occurrences already. This combined Sample/Occurrence Core could still have a one-to-many relationship to the Amplifications.
On Mon, Oct 22, 2012 at 1:33 PM, "Markus Döring (GBIF)" <
mdoering@gbif.org> wrote:
Adding a new core type to the IPT could be done in less than a day -
more work for GBIF would be to support such a format in our indexing code.
But if we think its a better solution to go with a new sample core
type, I think its worth the extra cost of coding for it.
On 22.10.2012, at 17:53, John Wieczorek wrote:
I like the approach of having a Sample Core, but the approach taken
thus far was with the view of being pragmatic to put into practice by January 2013. What do you think could be the possibility of adding a new Core type to the IPT on that time scale? The Darwin Core archive specification can certainly handle it, but the proof is in the implementation.
On Mon, Oct 22, 2012 at 8:11 AM, "Markus Döring (GBIF)" <
mdoering@gbif.org> wrote:
Hi all, I only quickly looked through the proposal, but it looks good,
pragmatic and definitely to be working for the case when a DNASample equals a single taxon Occurrence.
Im not so sure how well it would work with environmental samples -
would we have the sample flattened out and repeated to represent the individual taxa, sexes, ages, etc found in there?
I was therefore wondering if anyone had thought about the attached
setup before. Sample is at its core and occurrence & dna amplification as extensions with the amplifications (optionally?) refering to the occurrence they belong to.
Another quick observation is that we try to reuse existing terms in
extensions as much as possible. Following that rule for example dwc:institutionCode should rather be used instead of dNACollectionCode and probably dc:source for the referenceCitation
until tomorrow, regards, Markus
<sample core.png>
On 22.10.2012, at 12:21, Barker, Katharine wrote:
Dear John,
Please see our working revisions/comments/questions on the
DNA/tissue extension for Darwin Core (highlighted in blue). We were able to work through the draft up through "class sample properties":
https://docs.google.com/document/d/1RCgIPfu9gAPubjjbog-9vCJonvqcK1pLOaq6H8GS...
The document is also attached for your reference (just incase any of
you are unable to access the document).
Please try to respond to our questions and comments prior to our
meeting tomorrow (be sure to make these changes using a different color for tracking purposes).
Tomorrow we will like to 1) briefly recap our revisions on the
extension so far (addressing questions and comments), 2) complete our review of the extension and 3) identify any remaining issues with DwC working with IPT (and identify if any changes in the IPT are required).
Thank you for your help on this!
Kind Regards,
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu" <
tuco@berkeley.edumailto:tuco@berkeley.edu>
Date: Sunday, October 21, 2012 10:52 PM To: Gabriele Droege <g.droege@bgbm.orgmailto:g.droege@bgbm.org> Cc: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu>, Paul
Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au>, John Deck <jdeck@berkeley.edumailto:jdeck@berkeley.edu>, Robert Hanner <bob.hanner@gmail.commailto:bob.hanner@gmail.com>, Éamonn Tuama < eotuama@gbif.orgmailto:eotuama@gbif.org>, Robert Robbins < rjr8222@gmail.commailto:rjr8222@gmail.com>, "Guentsch, Anton" < a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>
Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension
for Darwin Core-draft reminder
Dear all,
I finished working on the Google Doc "DNA Tissue Extension Notes -
TDWG 2012". Feel free to let this be a working document where comments and questions can be added. I've attached a Word Doc version for archival purposes.
I added the two template extension files (DNATissueExtension.txt and
DNAAmplificationExtension.txt) to the shared TDWG GGBN working group folder linked below. They are in the form they need to be submitted to GBIF to be added to their extension registry. They would both need to be updated with the term descriptions, examples, and constraints.
https://drive.google.com/#folders/0BxEyFKwB7zY4WEs0WkdtUU5oVnM
Cheers,
John
On Sun, Oct 21, 2012 at 10:38 PM, John Wieczorek <tuco@berkeley.edu
mailto:tuco@berkeley.edu> wrote:
Ooops
...at http://goo.gl/kGHmb. Adding touches based on the files Gabi
sent. Will tell you all when finished with that and will send it as a Word doc at that time in case there are any issues with Google docs. Should be soon. Let me know if I should share to any different addresses.
Cheers,
John
On Sun, Oct 21, 2012 at 10:34 PM, John Wieczorek <tuco@berkeley.edu
mailto:tuco@berkeley.edu> wrote:
That helps a lot, as it clears up some of my own misconceptions. I
have shared a document where I have captured the thinking behind a couple of different ways forward with one or two extensions and an example of how the two-extension might look in the context of a Darwin Core Archive. The DNA Tissue Extension Notes Google doc can be found at
On Sun, Oct 21, 2012 at 9:23 PM, "Dröge, Gabriele" <
g.droege@bgbm.orgmailto:g.droege@bgbm.org> wrote:
Yes we do... Hi John,
Thanks for getting back to us. Attached are two csv files, one with
some main DNA facts and the other with associated GenBank entries und publications (2 examples with 2 GenBank entries per DNA sample).
I included only UnitID/CollCode/InstCode for the related voucher
specimen and I excluded the tissue facts since they are quite similar to the DNA facts and should be mapped independently.
Best, Gabi
-----Original Message----- From: Barker, Katharine [mailto:BarkerK@si.edu<mailto:BarkerK@si.edu
]
Sent: Sunday, October 21, 2012 11:41 PM To: Paul Flemons; Dröge, Gabriele Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension
for Darwin Core-draft reminder
Paul and Gabi,
Do we have any sample data that John can use as a test case? I
think he would like it today, if possible.
Thanks for your help (and the team work).
Katie
From: John Wieczorek <tuco@berkeley.edu<mailto:tuco@berkeley.edu
<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>
Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:
tuco@berkeley.edumailto:tuco@berkeley.edu>" <tuco@berkeley.edumailto: tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>
Date: Sunday, October 21, 2012 12:03 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:
barkerk@si.edumailto:barkerk@si.edu>>
Subject: Re: FW: Meeting at TDWG 2012 to define a tissue/DNA
extension for Darwin Core-draft reminder
Hi Katie,
Messages received. Will have the extension stuff ready within a few
hours and hope to be able to attend remotely. One thing in the meantime. Do you have any example data that could be used as a test case to populate a core with this extension? Would like to try that with some realy data to test my assumptions.
Sorry for the delay.
Thanks,
John
On Sun, Oct 21, 2012 at 10:08 AM, Barker, Katharine <BarkerK@si.edu
mailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu>> wrote:
Dear John,
I'm sorry that you were unable to attain a visa for China. I was
really looking forward to working with you in person with the group. Paul mentioned that he had e-mailed you earlier this evening. Can you please send us the draft for the DarwinCore DNA/tissue extension as soon as possible for review during our working sessions? We have one tomorrow at 1:30 (Beijing time) and another on Tuesday at the same time. It would be really great if you could Skype into either both or one of the sessions.
Thanks for your help on this.
Kind Regards,
Katie
From: <Barker>, Katharine Barker <barkerk@si.edu<mailto:
barkerk@si.edu><mailto:barkerk@si.edumailto:barkerk@si.edu><mailto: barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edumailto: barkerk@si.edu>>>
Date: Thursday, October 18, 2012 1:34 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:
barkerk@si.edumailto:barkerk@si.edu><mailto:barkerk@si.edumailto: barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu>>>, 'John Deck' <jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto: jdeck@berkeley.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edu mailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto: jdeck@berkeley.edu>>>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto: Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.aumailto: Paul.Flemons@austmus.gov.au><mailto:Paul.Flemons@austmus.gov.aumailto: Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.aumailto: Paul.Flemons@austmus.gov.au>>>, "'"Dröge", Éamonn Tuama < eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto: eotuama@gbif.org><mailto:eotuama@gbif.org<mailto:eotuama@gbif.org
<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>>, "Whitacre, Jamie"
<WHITACREJ@si.edumailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edu mailto:WHITACREJ@si.edu><mailto:WHITACREJ@si.edumailto: WHITACREJ@si.edu<mailto:WHITACREJ@si.edumailto:WHITACREJ@si.edu>>>, "' rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com mailto:rjr8222@gmail.com><mailto:'rjr8222@gmail.commailto: rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>'" <rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto: rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>>, "'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:' a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>'" <a.guentsch@bgbm.org mailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto: a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto: a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto: a.guentsch@bgbm.org>>>, "'gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com><mailto:'gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com>>'" <gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com>>>, "'tuco@berkeley.edu<mailto:tuco@berkeley.edu
<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:'
tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu mailto:tuco@berkeley.edu>>'" <tuco@berkeley.edumailto: tuco@berkeley.edu<mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu
<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:
tuco@berkeley.edumailto:tuco@berkeley.edu>>>
Cc: "'morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:
morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:' morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto: morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk>>'" < morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto: morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto: morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto: morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk>>>, "Parr, Cynthia" < parrc@si.edumailto:parrc@si.edu<mailto:parrc@si.edu<mailto:parrc@si.edu
<mailto:parrc@si.edumailto:parrc@si.edu<mailto:parrc@si.edu<mailto:
parrc@si.edu>>>>
Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension
for Darwin Core//Telecon next week
Dear all,
This is a friendly reminder that we will be meeting next Tuesday
afternoon at the TDWG 2012 Conference in order to finalize the draft DarwinCore-A DNA/tissue extension for GGBN. As you know, the immediate need for GGBN members is to publish information on tissues. This will happen through extensions to both ABCDDNA and DarwinCore-A. Here we are focused on developing the DarwinCore-A DNA/tissue extension.
An update on the timeline for developing the draft DarwinCore-A
DNA/tissue extension is listed below.
Review content requirements for DarwinCore-A DNA/tissueextension (completed, see attached required DNA and tissue elements)
John Weiczorek will develop the draft DarwinCore-ADNA/tissue extension (to be completed for group review prior to our break out session on Tuesday afternoon, October 23).
Tuesday October 23, working meeting· Questions to answer before final review of DNA/tissue
extension
o How do we include repeatable elements of ABCDDNA into DwC-A-DNA
(References to more than one sequence record/publication are mandatory)?
o How do we extend the "Basis of Record" in ABCD and DwC-A and how
do we include an element similar to ABCD-"Kind of Unit" to DwC-A?
o What are the remaining issues for DwC-A working with IPT? Are
any changes in the IPT required?
· Review and finalize draft DarwinCore-A DNA/tissue
extension for posting to GBIF site.
Thank you again to everyone who is involved in this project. I look
forward to seeing all of you in Beijing.
Kind Regards,
Katie
From: Barker, Katharine Sent: Friday, September 28, 2012 9:53 AM To: 'John Deck'; Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.org
mailto:eotuama@gbif.org<mailto:eotuama@gbif.org<mailto:eotuama@gbif.org
<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:
eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto: rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; gtuco.btuco@gmail.com mailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com>>; tuco@berkeley.edu<mailto:tuco@berkeley.edu
<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:
tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu mailto:tuco@berkeley.edu>>
Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension
for Darwin Core//Telecon next week
Dear all,
We will be meeting this Tuesday at 1pm U.S. Eastern time over Skype
in order to discuss the actions required to develop the draft proposal for the Darwin Core tissue/DNA extension. A proposal for designing, testing, and implementing the GGBN data portal is attached for your reference. Please review the timeline and action items leading up to the TDWG 2012 Conference.
My Skype name is Katharine.Barker1. If possible, please forward me
your skype account names prior to our meeting.
Kind Regards,
Katie
From:jdeck88@gmail.commailto:From%3Ajdeck88@gmail.com<mailto:
From%3Ajdeck88@gmail.commailto:From%253Ajdeck88@gmail.com><mailto: jdeck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@gmail.com mailto:jdeck88@gmail.com>> [mailto:jdeck88@gmail.commailto: jdeck88@gmail.com<mailto:jdeck88@gmail.commailto:jdeck88@gmail.com>] On Behalf Of John Deck
Sent: Tuesday, September 25, 2012 4:04 PM To: Barker, Katharine Cc: Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.org<mailto:
eotuama@gbif.org><mailto:eotuama@gbif.org<mailto:eotuama@gbif.org
<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:
eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto: rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; gtuco.btuco@gmail.com mailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com>>; tuco@berkeley.edu<mailto:tuco@berkeley.edu
<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:
tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu mailto:tuco@berkeley.edu>>
Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension
for Darwin Core//Telecon next week
Here is the wrapup of the bioCollections Ontology workshop from last
week at GSC14:
http://biocodecommons.org/workshops/bioCollections/index.html
This is relevant to these discussions since we focussed on what
constitutes a "sample" and also, probably more importantly, processes that work with samples.
We briefly discussed the DwC Tissue Extension and came up with a
proposal for a quick-fix and a more substantial fix. The quick-fix is to create two new BasisOfRecord terms: TissueSubSample, DNAExtract (or some terms like that -- Tuco could provide more clarification on this too). Thus, theoretically we could override the dwc:Occurrence class to mean, for example, TissueSubSample the same way we do for Specimens and Observations. The bigger fix is to more fundamentally re-orient DwC around the notion of "Sample", involving adding/changing some properties although we didn't get into any specifics.
P.s. I can do the 12/1/2 timeslots for that monday or tuesday but
not the 11.
John On Mon, Sep 24, 2012 at 12:39 PM, Barker, Katharine <BarkerK@si.edu
mailto:BarkerK@si.edu<mailto:BarkerK@si.edu<mailto:BarkerK@si.edu
<mailto:BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edu
mailto:BarkerK@si.edu>>> wrote:
Dear all,
We will have a telecon meeting early next week in order to discuss a
draft proposal for the Darwin Core tissue/DNA extension. Gabi, Paul, and I will put together a first draft for discussion to be distributed prior to the telecon. As you know, the goal is to have a working draft ready for our working group to review at the TDWG meeting in Beijing this October.
These are our options for meeting next week: Monday 11am, 12pm, 1pm, 2pm US EDT Tuesday 11am, 12pm, 1pm, 2pm US EDT
Please let me know if you cannot make one of these times.
Thanks again to those of you who provided input last week at the GSC
14 meeting.
Kind Regards,
Katie
From: Barker, Katharine Sent: Wednesday, September 12, 2012 10:51 AM To: 'Paul Flemons'; "Dröge, Gabriele"; eotuama@gbif.org<mailto:
eotuama@gbif.org><mailto:eotuama@gbif.org<mailto:eotuama@gbif.org
<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:
eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; ' rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto: rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>'; jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edu mailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto: jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>>; 'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>'; ' gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>'; ' tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu mailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto: tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>'
Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension
for Darwin Core
Importance: High
Dear all,
My name is Katie Barker and I am the Global Genome Biodiversity
Network Coordinator. As you know from Paul Flemons, members of the GGBN Data Standards and Data Access Task Force are trying to pull together a task group, which you are all part of, for the upcoming TDWG meeting in Beijing this October in order to address a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members. I am contacting you to schedule a meeting in late September/early October to develop a draft proposal for this extension to be completed at the upcoming TDWG meeting.
Please let me know your availability for the last two weeks of
September and first two weeks of October. There will be some scheduling issues, as there are task group members on the west and east coasts of the U.S., Europe and Australia.
Paul Flemons (in Australia) will be in the U.S. the first week of
October, so maybe we can meet in the afternoon of the 1st, anytime on the second 2nd, or in the morning of the 3rd of October over teleconference (US Eastern Daylight Time). Please let me know if any of these time slots work for you.
Gabi, I believe that you and John Deck will be at the GSC 14 meeting
next week. Is there any chance that you can start drawing up an outline for the proposed extension? We could review the outline during our group telecon and start drafting a proposal for review at the TDWG meeting in October.
Kind Regards,
Katie
Task Group Members:
John Weiczorek - Berkeley Éamonn O'Tuama - GBIF Jamie Whitacre - SI John Deck - Berkeley Robert Robbins - University of California, San Diego Anton Guentsch
- BGBM Gabi Droege- BGBM Paul Flemons- AM
From: Paul Flemons [mailto:Paul.Flemons@austmus.gov.au<mailto:
Paul.Flemons@austmus.gov.au><mailto:Paul.Flemons@austmus.gov.aumailto: Paul.Flemons@austmus.gov.au>]
Sent: Tuesday, August 07, 2012 2:50 AM To: tuco@berkley.edumailto:tuco@berkley.edu<mailto:
tuco@berkley.edumailto:tuco@berkley.edu><mailto:tuco@berkley.edu mailto:tuco@berkley.edu<mailto:tuco@berkley.edumailto:tuco@berkley.edu>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; j.holetschek@bgbm.org mailto:j.holetschek@bgbm.org<mailto:j.holetschek@bgbm.orgmailto: j.holetschek@bgbm.org><mailto:j.holetschek@bgbm.orgmailto: j.holetschek@bgbm.org<mailto:j.holetschek@bgbm.orgmailto: j.holetschek@bgbm.org>>; jdeck@berkeley.edu<mailto:jdeck@berkeley.edu
<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu><mailto:
jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edu mailto:jdeck@berkeley.edu>>
Cc: Barker, Katharine; Éamonn Ó Tuama [GBIF]; "Dröge, Gabriele" (
g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG<mailto:g.droege@BGBM.ORG mailto:g.droege@BGBM.ORG><mailto:g.droege@BGBM.ORGmailto: g.droege@BGBM.ORG<mailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG>>)
Subject: Meeting at TDWG 2012 to define a tissue/DNA extension for
Darwin Core
Hi all, I am on the Data Standards and Access Task Force for the Global
Genome Biodiversity Network (http://ggbn.org/) which is in need of a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members.
To this end I am writing to you to ask if you would be interested in
participating in a small working group at TDWG in Beijing this year.
At this stage my plan would be to identify relevant fields for
inclusion in the extension, using ABCDDNA as a reference. If sufficient progress is made then we would submit the extension for ratification by TDWG (is that how its done John?) The GGBN will use whatever comes out of the group to move towards having a suitable DwC based schema for data sharing.
So please let me know if you are willing to participate in the task
group and/or if there is anyone else you feel would be beneficial to have involved.
How much time do you think we will need? I have been thinking that
a day will be needed, so we could make that consist of either one full day or two half days. Im also thinking that during the week will be the best time for this.
Thanks for your time
Best Regards Paul
Paul K J Flemons Manager, Collection Informatics Team Lead, Atlas of Living Australia Biodiversity Volunteer Portal<
http://volunteer.ala.org.au%3E
Biodiversity Information Standards (TDWG) Representative for Oceania
Australian Museum 6 College Street Sydney NSW 2010 Australia t 61 2 9320 6343 m 0413458649 f 61 2 9320 6021
http://www.australianmuseum.net.au/%3E
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The views in this email are those of the user and do not necessarily
reflect the views of the Australian Museum. The information contained in this email message and any accompanying files is or may be confidential and is for the intended recipient only. If you are not the intended recipient, any use, dissemination, reliance, forwarding, printing or copying of this email or any attached files is unauthorised. If you are not the intended recipient, please delete it and notify the sender. The Australian Museum does not guarantee the accuracy of any information contained in this e-mail or attached files. As Internet communications are not secure, the Australian Museum does not accept legal responsibility for the contents of this message or attached files.
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-- John Deck (541) 321-0689tel:%28541%29%20321-0689tel:%28541%29%20321-0689
<DNATissueExtensionNotes2-TDWG2012.docx>_______________________________________________
IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt
Somewhat similar to breaking up a fossil into its component individuals, or splitting a lot?
On Mon, Oct 22, 2012 at 8:51 PM, Paul Flemons snomelf@gmail.com wrote:
Hi guys, Im with John that an environmental sample - is just a sample that in my eyes you wouldnt identify individual species from in the original record of that sample. If you identify individual species from an environmental sample you would then create new records referencing the original sample by association or something like that. Does that make sense? Paul
On 23 October 2012 10:41, John Wieczorek tuco@berkeley.edu wrote:
I don't think I would mix the concept of Occurrence in that way. It should remain where and when and what was taken "from the wild" by what method. After that is sampling. It may be that a Sample core should not have all of the attributes of an Occurrence, or that the Occurrence core itself is poorly modeled by assuming that the Organisms will be identified. Couldn't we view real-world collecting in a way such that specimens are samples until someone applies some method to better identify them?
On Mon, Oct 22, 2012 at 2:31 PM, "Markus Döring (GBIF)" < mdoering@gbif.org> wrote:
Well, let's investigate one thing about your diagram first. Shouldn't
there be a one-to-many relationship between Occurrence (specimen) and Sample rather than a many-to-one?
Specimen from the field = Occurrence + Event + Location +
Identification + Taxon
Sample from the specimen's liver = Sample Sample from the specimen's heart = Sample Sample from the specimen's gut = Sample
yes, thats true. Ididnt think about samples that way when I drafted the diagram.
The scenario I had in my mind was the environmental sample, a vegetation plot survey or just a rock with various lichen species on it. Usually with rich data about the location, habitat and abiotic measurements (lends itself nicely to an extension for samples). In such a sample you then find various species which would be the basis for an occurrence. In the case of metagenomic samples the list of taxa is actually derived information from the amplifications and can vary according to the method used (basically the entire occurrence extension can be derived from the amplifications in this case).
Actually when you take a gut sample from an animal you often are interested in the fauna of that gut, so the occurrences would not be the host, but the bacteria occurring within it.
Markus
And all of the Samples could have multiple Amplifications.
If we want to model this with a Sample Core, then Occurrences may be
repeated in the Occurrence extension in your diagram, but every sample would have no more than one Occurrence in the extension file and the sampleID relationship would be one-to-one. If so, then it is also possible to have a Sample Core (Sample rowType) with sampleID as the core record identifier, with "Sample" as basisOfRecord, and with all of the attributes of Sample and of the existing Occurrence Core. This would avoid having a distinct Occurrence extension for Samples, which could get confusing for those who are accustomed to mapping Occurrences already. This combined Sample/Occurrence Core could still have a one-to-many relationship to the Amplifications.
On Mon, Oct 22, 2012 at 1:33 PM, "Markus Döring (GBIF)" <
mdoering@gbif.org> wrote:
Adding a new core type to the IPT could be done in less than a day -
more work for GBIF would be to support such a format in our indexing code.
But if we think its a better solution to go with a new sample core
type, I think its worth the extra cost of coding for it.
On 22.10.2012, at 17:53, John Wieczorek wrote:
I like the approach of having a Sample Core, but the approach taken
thus far was with the view of being pragmatic to put into practice by January 2013. What do you think could be the possibility of adding a new Core type to the IPT on that time scale? The Darwin Core archive specification can certainly handle it, but the proof is in the implementation.
On Mon, Oct 22, 2012 at 8:11 AM, "Markus Döring (GBIF)" <
mdoering@gbif.org> wrote:
Hi all, I only quickly looked through the proposal, but it looks good,
pragmatic and definitely to be working for the case when a DNASample equals a single taxon Occurrence.
Im not so sure how well it would work with environmental samples -
would we have the sample flattened out and repeated to represent the individual taxa, sexes, ages, etc found in there?
I was therefore wondering if anyone had thought about the attached
setup before. Sample is at its core and occurrence & dna amplification as extensions with the amplifications (optionally?) refering to the occurrence they belong to.
Another quick observation is that we try to reuse existing terms in
extensions as much as possible. Following that rule for example dwc:institutionCode should rather be used instead of dNACollectionCode and probably dc:source for the referenceCitation
until tomorrow, regards, Markus
<sample core.png>
On 22.10.2012, at 12:21, Barker, Katharine wrote:
Dear John,
Please see our working revisions/comments/questions on the
DNA/tissue extension for Darwin Core (highlighted in blue). We were able to work through the draft up through "class sample properties":
https://docs.google.com/document/d/1RCgIPfu9gAPubjjbog-9vCJonvqcK1pLOaq6H8GS...
The document is also attached for your reference (just incase any
of you are unable to access the document).
Please try to respond to our questions and comments prior to our
meeting tomorrow (be sure to make these changes using a different color for tracking purposes).
Tomorrow we will like to 1) briefly recap our revisions on the
extension so far (addressing questions and comments), 2) complete our review of the extension and 3) identify any remaining issues with DwC working with IPT (and identify if any changes in the IPT are required).
Thank you for your help on this!
Kind Regards,
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu" <
tuco@berkeley.edumailto:tuco@berkeley.edu>
Date: Sunday, October 21, 2012 10:52 PM To: Gabriele Droege <g.droege@bgbm.orgmailto:g.droege@bgbm.org> Cc: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu>, Paul
Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au>, John Deck <jdeck@berkeley.edumailto:jdeck@berkeley.edu>, Robert Hanner <bob.hanner@gmail.commailto:bob.hanner@gmail.com>, Éamonn Tuama <eotuama@gbif.orgmailto:eotuama@gbif.org>, Robert Robbins < rjr8222@gmail.commailto:rjr8222@gmail.com>, "Guentsch, Anton" < a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>
Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension
for Darwin Core-draft reminder
Dear all,
I finished working on the Google Doc "DNA Tissue Extension Notes -
TDWG 2012". Feel free to let this be a working document where comments and questions can be added. I've attached a Word Doc version for archival purposes.
I added the two template extension files (DNATissueExtension.txt
and DNAAmplificationExtension.txt) to the shared TDWG GGBN working group folder linked below. They are in the form they need to be submitted to GBIF to be added to their extension registry. They would both need to be updated with the term descriptions, examples, and constraints.
https://drive.google.com/#folders/0BxEyFKwB7zY4WEs0WkdtUU5oVnM
Cheers,
John
On Sun, Oct 21, 2012 at 10:38 PM, John Wieczorek <tuco@berkeley.edu
mailto:tuco@berkeley.edu> wrote:
Ooops
...at http://goo.gl/kGHmb. Adding touches based on the files Gabi
sent. Will tell you all when finished with that and will send it as a Word doc at that time in case there are any issues with Google docs. Should be soon. Let me know if I should share to any different addresses.
Cheers,
John
On Sun, Oct 21, 2012 at 10:34 PM, John Wieczorek <tuco@berkeley.edu
mailto:tuco@berkeley.edu> wrote:
That helps a lot, as it clears up some of my own misconceptions. I
have shared a document where I have captured the thinking behind a couple of different ways forward with one or two extensions and an example of how the two-extension might look in the context of a Darwin Core Archive. The DNA Tissue Extension Notes Google doc can be found at
On Sun, Oct 21, 2012 at 9:23 PM, "Dröge, Gabriele" <
g.droege@bgbm.orgmailto:g.droege@bgbm.org> wrote:
Yes we do... Hi John,
Thanks for getting back to us. Attached are two csv files, one with
some main DNA facts and the other with associated GenBank entries und publications (2 examples with 2 GenBank entries per DNA sample).
I included only UnitID/CollCode/InstCode for the related voucher
specimen and I excluded the tissue facts since they are quite similar to the DNA facts and should be mapped independently.
Best, Gabi
-----Original Message----- From: Barker, Katharine [mailto:BarkerK@si.edu<mailto:
BarkerK@si.edu>]
Sent: Sunday, October 21, 2012 11:41 PM To: Paul Flemons; Dröge, Gabriele Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension
for Darwin Core-draft reminder
Paul and Gabi,
Do we have any sample data that John can use as a test case? I
think he would like it today, if possible.
Thanks for your help (and the team work).
Katie
From: John Wieczorek <tuco@berkeley.edu<mailto:tuco@berkeley.edu
<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>
Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:
tuco@berkeley.edumailto:tuco@berkeley.edu>" <tuco@berkeley.edumailto: tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>
Date: Sunday, October 21, 2012 12:03 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:
barkerk@si.edumailto:barkerk@si.edu>>
Subject: Re: FW: Meeting at TDWG 2012 to define a tissue/DNA
extension for Darwin Core-draft reminder
Hi Katie,
Messages received. Will have the extension stuff ready within a few
hours and hope to be able to attend remotely. One thing in the meantime. Do you have any example data that could be used as a test case to populate a core with this extension? Would like to try that with some realy data to test my assumptions.
Sorry for the delay.
Thanks,
John
On Sun, Oct 21, 2012 at 10:08 AM, Barker, Katharine <BarkerK@si.edu
mailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu>> wrote:
Dear John,
I'm sorry that you were unable to attain a visa for China. I was
really looking forward to working with you in person with the group. Paul mentioned that he had e-mailed you earlier this evening. Can you please send us the draft for the DarwinCore DNA/tissue extension as soon as possible for review during our working sessions? We have one tomorrow at 1:30 (Beijing time) and another on Tuesday at the same time. It would be really great if you could Skype into either both or one of the sessions.
Thanks for your help on this.
Kind Regards,
Katie
From: <Barker>, Katharine Barker <barkerk@si.edu<mailto:
barkerk@si.edu><mailto:barkerk@si.edumailto:barkerk@si.edu><mailto: barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edumailto: barkerk@si.edu>>>
Date: Thursday, October 18, 2012 1:34 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:
barkerk@si.edumailto:barkerk@si.edu><mailto:barkerk@si.edumailto: barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu>>>, 'John Deck' <jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto: jdeck@berkeley.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edu mailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto: jdeck@berkeley.edu>>>, Paul Flemons <Paul.Flemons@austmus.gov.au mailto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.au mailto:Paul.Flemons@austmus.gov.au><mailto:Paul.Flemons@austmus.gov.au mailto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.au mailto:Paul.Flemons@austmus.gov.au>>>, "'"Dröge", Éamonn Tuama < eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.org mailto:eotuama@gbif.org><mailto:eotuama@gbif.orgmailto: eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>>, "Whitacre, Jamie" <WHITACREJ@si.edumailto:WHITACREJ@si.edu<mailto: WHITACREJ@si.edumailto:WHITACREJ@si.edu><mailto:WHITACREJ@si.edu mailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edumailto: WHITACREJ@si.edu>>>, "'rjr8222@gmail.com<mailto:rjr8222@gmail.com
<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:'
rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com mailto:rjr8222@gmail.com>>'" <rjr8222@gmail.commailto: rjr8222@gmail.com<mailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com
<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:
rjr8222@gmail.commailto:rjr8222@gmail.com>>>, "'a.guentsch@bgbm.org mailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto: a.guentsch@bgbm.org><mailto:'a.guentsch@bgbm.orgmailto: a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto: a.guentsch@bgbm.org>>'" <a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org
<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:
a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>>, "' gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:' gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>'" < gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>>, "' tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu mailto:tuco@berkeley.edu><mailto:'tuco@berkeley.edumailto: tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>'" <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu mailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto: tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>>
Cc: "'morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:
morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:' morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto: morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk>>'" < morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto: morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto: morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto: morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk>>>, "Parr, Cynthia" <parrc@si.edumailto:parrc@si.edu<mailto:parrc@si.edumailto: parrc@si.edu><mailto:parrc@si.edumailto:parrc@si.edu<mailto: parrc@si.edumailto:parrc@si.edu>>>
Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension
for Darwin Core//Telecon next week
Dear all,
This is a friendly reminder that we will be meeting next Tuesday
afternoon at the TDWG 2012 Conference in order to finalize the draft DarwinCore-A DNA/tissue extension for GGBN. As you know, the immediate need for GGBN members is to publish information on tissues. This will happen through extensions to both ABCDDNA and DarwinCore-A. Here we are focused on developing the DarwinCore-A DNA/tissue extension.
An update on the timeline for developing the draft DarwinCore-A
DNA/tissue extension is listed below.
Review content requirements for DarwinCore-A DNA/tissueextension (completed, see attached required DNA and tissue elements)
John Weiczorek will develop the draft DarwinCore-ADNA/tissue extension (to be completed for group review prior to our break out session on Tuesday afternoon, October 23).
Tuesday October 23, working meeting· Questions to answer before final review of DNA/tissue
extension
o How do we include repeatable elements of ABCDDNA into DwC-A-DNA
(References to more than one sequence record/publication are mandatory)?
o How do we extend the "Basis of Record" in ABCD and DwC-A and
how do we include an element similar to ABCD-"Kind of Unit" to DwC-A?
o What are the remaining issues for DwC-A working with IPT? Are
any changes in the IPT required?
· Review and finalize draft DarwinCore-A DNA/tissue
extension for posting to GBIF site.
Thank you again to everyone who is involved in this project. I
look forward to seeing all of you in Beijing.
Kind Regards,
Katie
From: Barker, Katharine Sent: Friday, September 28, 2012 9:53 AM To: 'John Deck'; Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.org
mailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto: eotuama@gbif.org><mailto:eotuama@gbif.org<mailto:eotuama@gbif.org
<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie;
rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto: rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; gtuco.btuco@gmail.com mailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com>>; tuco@berkeley.edu<mailto:tuco@berkeley.edu
<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:
tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu mailto:tuco@berkeley.edu>>
Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension
for Darwin Core//Telecon next week
Dear all,
We will be meeting this Tuesday at 1pm U.S. Eastern time over Skype
in order to discuss the actions required to develop the draft proposal for the Darwin Core tissue/DNA extension. A proposal for designing, testing, and implementing the GGBN data portal is attached for your reference. Please review the timeline and action items leading up to the TDWG 2012 Conference.
My Skype name is Katharine.Barker1. If possible, please forward me
your skype account names prior to our meeting.
Kind Regards,
Katie
From:jdeck88@gmail.commailto:From%3Ajdeck88@gmail.com<mailto:
From%3Ajdeck88@gmail.commailto:From%253Ajdeck88@gmail.com><mailto: jdeck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@gmail.com mailto:jdeck88@gmail.com>> [mailto:jdeck88@gmail.commailto: jdeck88@gmail.com<mailto:jdeck88@gmail.commailto:jdeck88@gmail.com>] On Behalf Of John Deck
Sent: Tuesday, September 25, 2012 4:04 PM To: Barker, Katharine Cc: Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.org<mailto:
eotuama@gbif.org><mailto:eotuama@gbif.org<mailto:eotuama@gbif.org
<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:
eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto: rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; gtuco.btuco@gmail.com mailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com>>; tuco@berkeley.edu<mailto:tuco@berkeley.edu
<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:
tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu mailto:tuco@berkeley.edu>>
Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension
for Darwin Core//Telecon next week
Here is the wrapup of the bioCollections Ontology workshop from
last week at GSC14:
http://biocodecommons.org/workshops/bioCollections/index.html
This is relevant to these discussions since we focussed on what
constitutes a "sample" and also, probably more importantly, processes that work with samples.
We briefly discussed the DwC Tissue Extension and came up with a
proposal for a quick-fix and a more substantial fix. The quick-fix is to create two new BasisOfRecord terms: TissueSubSample, DNAExtract (or some terms like that -- Tuco could provide more clarification on this too). Thus, theoretically we could override the dwc:Occurrence class to mean, for example, TissueSubSample the same way we do for Specimens and Observations. The bigger fix is to more fundamentally re-orient DwC around the notion of "Sample", involving adding/changing some properties although we didn't get into any specifics.
P.s. I can do the 12/1/2 timeslots for that monday or tuesday but
not the 11.
John On Mon, Sep 24, 2012 at 12:39 PM, Barker, Katharine <BarkerK@si.edu
mailto:BarkerK@si.edu<mailto:BarkerK@si.edu<mailto:BarkerK@si.edu
<mailto:BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edu
mailto:BarkerK@si.edu>>> wrote:
Dear all,
We will have a telecon meeting early next week in order to discuss
a draft proposal for the Darwin Core tissue/DNA extension. Gabi, Paul, and I will put together a first draft for discussion to be distributed prior to the telecon. As you know, the goal is to have a working draft ready for our working group to review at the TDWG meeting in Beijing this October.
These are our options for meeting next week: Monday 11am, 12pm, 1pm, 2pm US EDT Tuesday 11am, 12pm, 1pm, 2pm US EDT
Please let me know if you cannot make one of these times.
Thanks again to those of you who provided input last week at the
GSC 14 meeting.
Kind Regards,
Katie
From: Barker, Katharine Sent: Wednesday, September 12, 2012 10:51 AM To: 'Paul Flemons'; "Dröge, Gabriele"; eotuama@gbif.org<mailto:
eotuama@gbif.org><mailto:eotuama@gbif.org<mailto:eotuama@gbif.org
<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:
eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; ' rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto: rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>'; jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edu mailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto: jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>>; 'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>'; ' gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>'; ' tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu mailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto: tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>'
Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension
for Darwin Core
Importance: High
Dear all,
My name is Katie Barker and I am the Global Genome Biodiversity
Network Coordinator. As you know from Paul Flemons, members of the GGBN Data Standards and Data Access Task Force are trying to pull together a task group, which you are all part of, for the upcoming TDWG meeting in Beijing this October in order to address a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members. I am contacting you to schedule a meeting in late September/early October to develop a draft proposal for this extension to be completed at the upcoming TDWG meeting.
Please let me know your availability for the last two weeks of
September and first two weeks of October. There will be some scheduling issues, as there are task group members on the west and east coasts of the U.S., Europe and Australia.
Paul Flemons (in Australia) will be in the U.S. the first week of
October, so maybe we can meet in the afternoon of the 1st, anytime on the second 2nd, or in the morning of the 3rd of October over teleconference (US Eastern Daylight Time). Please let me know if any of these time slots work for you.
Gabi, I believe that you and John Deck will be at the GSC 14
meeting next week. Is there any chance that you can start drawing up an outline for the proposed extension? We could review the outline during our group telecon and start drafting a proposal for review at the TDWG meeting in October.
Kind Regards,
Katie
Task Group Members:
John Weiczorek - Berkeley Éamonn O'Tuama - GBIF Jamie Whitacre - SI John Deck - Berkeley Robert Robbins - University of California, San Diego Anton Guentsch
- BGBM Gabi Droege- BGBM Paul Flemons- AM
From: Paul Flemons [mailto:Paul.Flemons@austmus.gov.au<mailto:
Paul.Flemons@austmus.gov.au><mailto:Paul.Flemons@austmus.gov.aumailto: Paul.Flemons@austmus.gov.au>]
Sent: Tuesday, August 07, 2012 2:50 AM To: tuco@berkley.edumailto:tuco@berkley.edu<mailto:
tuco@berkley.edumailto:tuco@berkley.edu><mailto:tuco@berkley.edu mailto:tuco@berkley.edu<mailto:tuco@berkley.edumailto: tuco@berkley.edu>>; a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org
<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:
a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; j.holetschek@bgbm.org mailto:j.holetschek@bgbm.org<mailto:j.holetschek@bgbm.orgmailto: j.holetschek@bgbm.org><mailto:j.holetschek@bgbm.orgmailto: j.holetschek@bgbm.org<mailto:j.holetschek@bgbm.orgmailto: j.holetschek@bgbm.org>>; jdeck@berkeley.edu<mailto:jdeck@berkeley.edu
<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu><mailto:
jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edu mailto:jdeck@berkeley.edu>>
Cc: Barker, Katharine; Éamonn Ó Tuama [GBIF]; "Dröge, Gabriele" (
g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG<mailto:g.droege@BGBM.ORG mailto:g.droege@BGBM.ORG><mailto:g.droege@BGBM.ORGmailto: g.droege@BGBM.ORG<mailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG>>)
Subject: Meeting at TDWG 2012 to define a tissue/DNA extension for
Darwin Core
Hi all, I am on the Data Standards and Access Task Force for the Global
Genome Biodiversity Network (http://ggbn.org/) which is in need of a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members.
To this end I am writing to you to ask if you would be interested
in participating in a small working group at TDWG in Beijing this year.
At this stage my plan would be to identify relevant fields for
inclusion in the extension, using ABCDDNA as a reference. If sufficient progress is made then we would submit the extension for ratification by TDWG (is that how its done John?) The GGBN will use whatever comes out of the group to move towards having a suitable DwC based schema for data sharing.
So please let me know if you are willing to participate in the task
group and/or if there is anyone else you feel would be beneficial to have involved.
How much time do you think we will need? I have been thinking that
a day will be needed, so we could make that consist of either one full day or two half days. Im also thinking that during the week will be the best time for this.
Thanks for your time
Best Regards Paul
Paul K J Flemons Manager, Collection Informatics Team Lead, Atlas of Living Australia Biodiversity Volunteer Portal<
http://volunteer.ala.org.au%3E
Biodiversity Information Standards (TDWG) Representative for
Oceania Australian Museum 6 College Street Sydney NSW 2010 Australia t 61 2 9320 6343 m 0413458649 f 61 2 9320 6021
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<DNATissueExtensionNotes2-TDWG2012.docx>_______________________________________________
IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt
Yes I think so
Paul Flemons Collection Informatics Manager Australian Museum
On 23/10/2012, at 8:03 AM, John Wieczorek tuco@berkeley.edu wrote:
Somewhat similar to breaking up a fossil into its component individuals, or splitting a lot?
On Mon, Oct 22, 2012 at 8:51 PM, Paul Flemons snomelf@gmail.com wrote: Hi guys, Im with John that an environmental sample - is just a sample that in my eyes you wouldnt identify individual species from in the original record of that sample. If you identify individual species from an environmental sample you would then create new records referencing the original sample by association or something like that. Does that make sense? Paul
On 23 October 2012 10:41, John Wieczorek tuco@berkeley.edu wrote: I don't think I would mix the concept of Occurrence in that way. It should remain where and when and what was taken "from the wild" by what method. After that is sampling. It may be that a Sample core should not have all of the attributes of an Occurrence, or that the Occurrence core itself is poorly modeled by assuming that the Organisms will be identified. Couldn't we view real-world collecting in a way such that specimens are samples until someone applies some method to better identify them?
On Mon, Oct 22, 2012 at 2:31 PM, "Markus Döring (GBIF)" mdoering@gbif.org wrote:
Well, let's investigate one thing about your diagram first. Shouldn't there be a one-to-many relationship between Occurrence (specimen) and Sample rather than a many-to-one?
Specimen from the field = Occurrence + Event + Location + Identification + Taxon Sample from the specimen's liver = Sample Sample from the specimen's heart = Sample Sample from the specimen's gut = Sample
yes, thats true. Ididnt think about samples that way when I drafted the diagram.
The scenario I had in my mind was the environmental sample, a vegetation plot survey or just a rock with various lichen species on it. Usually with rich data about the location, habitat and abiotic measurements (lends itself nicely to an extension for samples). In such a sample you then find various species which would be the basis for an occurrence. In the case of metagenomic samples the list of taxa is actually derived information from the amplifications and can vary according to the method used (basically the entire occurrence extension can be derived from the amplifications in this case).
Actually when you take a gut sample from an animal you often are interested in the fauna of that gut, so the occurrences would not be the host, but the bacteria occurring within it.
Markus
And all of the Samples could have multiple Amplifications.
If we want to model this with a Sample Core, then Occurrences may be repeated in the Occurrence extension in your diagram, but every sample would have no more than one Occurrence in the extension file and the sampleID relationship would be one-to-one. If so, then it is also possible to have a Sample Core (Sample rowType) with sampleID as the core record identifier, with "Sample" as basisOfRecord, and with all of the attributes of Sample and of the existing Occurrence Core. This would avoid having a distinct Occurrence extension for Samples, which could get confusing for those who are accustomed to mapping Occurrences already. This combined Sample/Occurrence Core could still have a one-to-many relationship to the Amplifications.
On Mon, Oct 22, 2012 at 1:33 PM, "Markus Döring (GBIF)" mdoering@gbif.org wrote: Adding a new core type to the IPT could be done in less than a day - more work for GBIF would be to support such a format in our indexing code. But if we think its a better solution to go with a new sample core type, I think its worth the extra cost of coding for it.
On 22.10.2012, at 17:53, John Wieczorek wrote:
I like the approach of having a Sample Core, but the approach taken thus far was with the view of being pragmatic to put into practice by January 2013. What do you think could be the possibility of adding a new Core type to the IPT on that time scale? The Darwin Core archive specification can certainly handle it, but the proof is in the implementation.
On Mon, Oct 22, 2012 at 8:11 AM, "Markus Döring (GBIF)" mdoering@gbif.org wrote: Hi all, I only quickly looked through the proposal, but it looks good, pragmatic and definitely to be working for the case when a DNASample equals a single taxon Occurrence.
Im not so sure how well it would work with environmental samples - would we have the sample flattened out and repeated to represent the individual taxa, sexes, ages, etc found in there? I was therefore wondering if anyone had thought about the attached setup before. Sample is at its core and occurrence & dna amplification as extensions with the amplifications (optionally?) refering to the occurrence they belong to.
Another quick observation is that we try to reuse existing terms in extensions as much as possible. Following that rule for example dwc:institutionCode should rather be used instead of dNACollectionCode and probably dc:source for the referenceCitation
until tomorrow, regards, Markus
<sample core.png>
On 22.10.2012, at 12:21, Barker, Katharine wrote:
Dear John,
Please see our working revisions/comments/questions on the DNA/tissue extension for Darwin Core (highlighted in blue). We were able to work through the draft up through "class sample properties": https://docs.google.com/document/d/1RCgIPfu9gAPubjjbog-9vCJonvqcK1pLOaq6H8GS...
The document is also attached for your reference (just incase any of you are unable to access the document).
Please try to respond to our questions and comments prior to our meeting tomorrow (be sure to make these changes using a different color for tracking purposes).
Tomorrow we will like to 1) briefly recap our revisions on the extension so far (addressing questions and comments), 2) complete our review of the extension and 3) identify any remaining issues with DwC working with IPT (and identify if any changes in the IPT are required).
Thank you for your help on this!
Kind Regards,
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu" <tuco@berkeley.edumailto:tuco@berkeley.edu> Date: Sunday, October 21, 2012 10:52 PM To: Gabriele Droege <g.droege@bgbm.orgmailto:g.droege@bgbm.org> Cc: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au>, John Deck <jdeck@berkeley.edumailto:jdeck@berkeley.edu>, Robert Hanner <bob.hanner@gmail.commailto:bob.hanner@gmail.com>, Éamonn Tuama <eotuama@gbif.orgmailto:eotuama@gbif.org>, Robert Robbins <rjr8222@gmail.commailto:rjr8222@gmail.com>, "Guentsch, Anton" <a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org> Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Dear all,
I finished working on the Google Doc "DNA Tissue Extension Notes - TDWG 2012". Feel free to let this be a working document where comments and questions can be added. I've attached a Word Doc version for archival purposes.
I added the two template extension files (DNATissueExtension.txt and DNAAmplificationExtension.txt) to the shared TDWG GGBN working group folder linked below. They are in the form they need to be submitted to GBIF to be added to their extension registry. They would both need to be updated with the term descriptions, examples, and constraints.
https://drive.google.com/#folders/0BxEyFKwB7zY4WEs0WkdtUU5oVnM
Cheers,
John
On Sun, Oct 21, 2012 at 10:38 PM, John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> wrote: Ooops
...at http://goo.gl/kGHmb. Adding touches based on the files Gabi sent. Will tell you all when finished with that and will send it as a Word doc at that time in case there are any issues with Google docs. Should be soon. Let me know if I should share to any different addresses.
Cheers,
John
On Sun, Oct 21, 2012 at 10:34 PM, John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> wrote: That helps a lot, as it clears up some of my own misconceptions. I have shared a document where I have captured the thinking behind a couple of different ways forward with one or two extensions and an example of how the two-extension might look in the context of a Darwin Core Archive. The DNA Tissue Extension Notes Google doc can be found at
On Sun, Oct 21, 2012 at 9:23 PM, "Dröge, Gabriele" <g.droege@bgbm.orgmailto:g.droege@bgbm.org> wrote: Yes we do... Hi John,
Thanks for getting back to us. Attached are two csv files, one with some main DNA facts and the other with associated GenBank entries und publications (2 examples with 2 GenBank entries per DNA sample). I included only UnitID/CollCode/InstCode for the related voucher specimen and I excluded the tissue facts since they are quite similar to the DNA facts and should be mapped independently.
Best, Gabi
-----Original Message----- From: Barker, Katharine [mailto:BarkerK@si.edumailto:BarkerK@si.edu] Sent: Sunday, October 21, 2012 11:41 PM To: Paul Flemons; Dröge, Gabriele Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Paul and Gabi,
Do we have any sample data that John can use as a test case? I think he would like it today, if possible.
Thanks for your help (and the team work).
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>" <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Date: Sunday, October 21, 2012 12:03 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu>> Subject: Re: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Hi Katie,
Messages received. Will have the extension stuff ready within a few hours and hope to be able to attend remotely. One thing in the meantime. Do you have any example data that could be used as a test case to populate a core with this extension? Would like to try that with some realy data to test my assumptions.
Sorry for the delay.
Thanks,
John
On Sun, Oct 21, 2012 at 10:08 AM, Barker, Katharine <BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu>> wrote: Dear John,
I'm sorry that you were unable to attain a visa for China. I was really looking forward to working with you in person with the group. Paul mentioned that he had e-mailed you earlier this evening. Can you please send us the draft for the DarwinCore DNA/tissue extension as soon as possible for review during our working sessions? We have one tomorrow at 1:30 (Beijing time) and another on Tuesday at the same time. It would be really great if you could Skype into either both or one of the sessions.
Thanks for your help on this.
Kind Regards,
Katie
From: <Barker>, Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu><mailto:barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu>>> Date: Thursday, October 18, 2012 1:34 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu><mailto:barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edumailto:barkerk@si.edu>>>, 'John Deck' <jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>>>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au><mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au>>>, "'"Dröge", Éamonn Tuama <eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org><mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>>, "Whitacre, Jamie" <WHITACREJ@si.edumailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edumailto:WHITACREJ@si.edu><mailto:WHITACREJ@si.edumailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edumailto:WHITACREJ@si.edu>>>, "'rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:'rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>'" <rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>>, "'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>'" <a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>>, "'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>'" <gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>>, "'tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:'tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>'" <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>> Cc: "'morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:'morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk>>'" <morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk>>>, "Parr, Cynthia" <parrc@si.edumailto:parrc@si.edu<mailto:parrc@si.edumailto:parrc@si.edu><mailto:parrc@si.edumailto:parrc@si.edu<mailto:parrc@si.edumailto:parrc@si.edu>>> Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Dear all,
This is a friendly reminder that we will be meeting next Tuesday afternoon at the TDWG 2012 Conference in order to finalize the draft DarwinCore-A DNA/tissue extension for GGBN. As you know, the immediate need for GGBN members is to publish information on tissues. This will happen through extensions to both ABCDDNA and DarwinCore-A. Here we are focused on developing the DarwinCore-A DNA/tissue extension.
An update on the timeline for developing the draft DarwinCore-A DNA/tissue extension is listed below.
Review content requirements for DarwinCore-A DNA/tissue extension (completed, see attached required DNA and tissue elements)John Weiczorek will develop the draft DarwinCore-A DNA/tissue extension (to be completed for group review prior to our break out session on Tuesday afternoon, October 23).Tuesday October 23, working meeting· Questions to answer before final review of DNA/tissue extension
o How do we include repeatable elements of ABCDDNA into DwC-A-DNA (References to more than one sequence record/publication are mandatory)?
o How do we extend the "Basis of Record" in ABCD and DwC-A and how do we include an element similar to ABCD-"Kind of Unit" to DwC-A?
o What are the remaining issues for DwC-A working with IPT? Are any changes in the IPT required?
· Review and finalize draft DarwinCore-A DNA/tissue extension for posting to GBIF site.
Thank you again to everyone who is involved in this project. I look forward to seeing all of you in Beijing.
Kind Regards,
Katie
From: Barker, Katharine Sent: Friday, September 28, 2012 9:53 AM To: 'John Deck'; Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org><mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>; tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Dear all,
We will be meeting this Tuesday at 1pm U.S. Eastern time over Skype in order to discuss the actions required to develop the draft proposal for the Darwin Core tissue/DNA extension. A proposal for designing, testing, and implementing the GGBN data portal is attached for your reference. Please review the timeline and action items leading up to the TDWG 2012 Conference.
My Skype name is Katharine.Barker1. If possible, please forward me your skype account names prior to our meeting.
Kind Regards,
Katie
From:jdeck88@gmail.commailto:From%3Ajdeck88@gmail.com<mailto:From%3Ajdeck88@gmail.commailto:From%253Ajdeck88@gmail.com><mailto:jdeck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@gmail.commailto:jdeck88@gmail.com>> [mailto:jdeck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@gmail.commailto:jdeck88@gmail.com>] On Behalf Of John Deck Sent: Tuesday, September 25, 2012 4:04 PM To: Barker, Katharine Cc: Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org><mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>; tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Here is the wrapup of the bioCollections Ontology workshop from last week at GSC14:
http://biocodecommons.org/workshops/bioCollections/index.html
This is relevant to these discussions since we focussed on what constitutes a "sample" and also, probably more importantly, processes that work with samples.
We briefly discussed the DwC Tissue Extension and came up with a proposal for a quick-fix and a more substantial fix. The quick-fix is to create two new BasisOfRecord terms: TissueSubSample, DNAExtract (or some terms like that -- Tuco could provide more clarification on this too). Thus, theoretically we could override the dwc:Occurrence class to mean, for example, TissueSubSample the same way we do for Specimens and Observations. The bigger fix is to more fundamentally re-orient DwC around the notion of "Sample", involving adding/changing some properties although we didn't get into any specifics.
P.s. I can do the 12/1/2 timeslots for that monday or tuesday but not the 11.
John On Mon, Sep 24, 2012 at 12:39 PM, Barker, Katharine <BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu><mailto:BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu>>> wrote: Dear all,
We will have a telecon meeting early next week in order to discuss a draft proposal for the Darwin Core tissue/DNA extension. Gabi, Paul, and I will put together a first draft for discussion to be distributed prior to the telecon. As you know, the goal is to have a working draft ready for our working group to review at the TDWG meeting in Beijing this October.
These are our options for meeting next week: Monday 11am, 12pm, 1pm, 2pm US EDT Tuesday 11am, 12pm, 1pm, 2pm US EDT
Please let me know if you cannot make one of these times.
Thanks again to those of you who provided input last week at the GSC 14 meeting.
Kind Regards,
Katie
From: Barker, Katharine Sent: Wednesday, September 12, 2012 10:51 AM To: 'Paul Flemons'; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org><mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; 'rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>'; jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>>; 'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>'; 'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>'; 'tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>' Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core Importance: High
Dear all,
My name is Katie Barker and I am the Global Genome Biodiversity Network Coordinator. As you know from Paul Flemons, members of the GGBN Data Standards and Data Access Task Force are trying to pull together a task group, which you are all part of, for the upcoming TDWG meeting in Beijing this October in order to address a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members. I am contacting you to schedule a meeting in late September/early October to develop a draft proposal for this extension to be completed at the upcoming TDWG meeting.
Please let me know your availability for the last two weeks of September and first two weeks of October. There will be some scheduling issues, as there are task group members on the west and east coasts of the U.S., Europe and Australia.
Paul Flemons (in Australia) will be in the U.S. the first week of October, so maybe we can meet in the afternoon of the 1st, anytime on the second 2nd, or in the morning of the 3rd of October over teleconference (US Eastern Daylight Time). Please let me know if any of these time slots work for you.
Gabi, I believe that you and John Deck will be at the GSC 14 meeting next week. Is there any chance that you can start drawing up an outline for the proposed extension? We could review the outline during our group telecon and start drafting a proposal for review at the TDWG meeting in October.
Kind Regards,
Katie
Task Group Members:
John Weiczorek - Berkeley Éamonn O'Tuama - GBIF Jamie Whitacre - SI John Deck - Berkeley Robert Robbins - University of California, San Diego Anton Guentsch - BGBM Gabi Droege- BGBM Paul Flemons- AM
From: Paul Flemons [mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au>] Sent: Tuesday, August 07, 2012 2:50 AM To: tuco@berkley.edumailto:tuco@berkley.edu<mailto:tuco@berkley.edumailto:tuco@berkley.edu><mailto:tuco@berkley.edumailto:tuco@berkley.edu<mailto:tuco@berkley.edumailto:tuco@berkley.edu>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>; j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org<mailto:j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org><mailto:j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org<mailto:j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org>>; jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>> Cc: Barker, Katharine; Éamonn Ó Tuama [GBIF]; "Dröge, Gabriele" (g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG<mailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG><mailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG<mailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG>>) Subject: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core
Hi all, I am on the Data Standards and Access Task Force for the Global Genome Biodiversity Network (http://ggbn.org/) which is in need of a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members.
To this end I am writing to you to ask if you would be interested in participating in a small working group at TDWG in Beijing this year.
At this stage my plan would be to identify relevant fields for inclusion in the extension, using ABCDDNA as a reference. If sufficient progress is made then we would submit the extension for ratification by TDWG (is that how its done John?) The GGBN will use whatever comes out of the group to move towards having a suitable DwC based schema for data sharing.
So please let me know if you are willing to participate in the task group and/or if there is anyone else you feel would be beneficial to have involved.
How much time do you think we will need? I have been thinking that a day will be needed, so we could make that consist of either one full day or two half days. Im also thinking that during the week will be the best time for this.
Thanks for your time
Best Regards Paul
Paul K J Flemons Manager, Collection Informatics Team Lead, Atlas of Living Australia Biodiversity Volunteer Portalhttp://volunteer.ala.org.au Biodiversity Information Standards (TDWG) Representative for Oceania Australian Museum 6 College Street Sydney NSW 2010 Australia t 61 2 9320 6343 m 0413458649 f 61 2 9320 6021 Visit: http://www.australianmuseum.net.auhttp://www.australianmuseum.net.au/ Like: http://www.facebook.com/australianmuseum Follow: http://www.twitter.com/austmus Watch: http://www.youtube.com/austmus [cid:image001.png@01CDAD34.391DC790mailto:image001.png@01CDAD34.391DC790<mailto:image001.png@01CDAD34.391DC790mailto:image001.png@01CDAD34.391DC790>] Inspiring the exploration of nature and cultures
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<DNATissueExtensionNotes2-TDWG2012.docx>_______________________________________________ IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt
Thanks to all of you for your feedback. I don't understand the figure you created (Markus?). I had a look at http://code.google.com/p/gbif-ecat/wiki/DwCArchive and I think we will keep the core schema in the middle as it is now (Basis of Resource, Taxon or Occurrence).
All what we need to refer to associated objects (samples (tissues, DNA, RNA,...) or other specimens) is an association extension with the identifiers of the referenced records, similar to the UnitAssociation container in ABCD. This extension should have a one to many relation to the core. The DNAAmplification extension is only required if the sample record is a DNA sample, since in this extension so far only DNA specific facts are included (GenBankAccessionNo etc.). The SampleFacts-Extension is quite similar to the main DNA extension of ABCD.
Find attached my figure based on the one from the DwCArchive website. This is how I think it could work and how I understand the star schema, but maybe I am wrong :-). Environmental samples are more complicate maybe we can discuss this topic later (next year)?
Best, Gabi
-----Original Message----- From: "Markus Döring (GBIF)" [mailto:mdoering@gbif.org] Sent: Monday, October 22, 2012 11:31 PM To: tuco@berkeley.edu Cc: Barker, Katharine; ipt@lists.gbif.org; John Deck; Paul Flemons (Paul.Flemons@austmus.gov.au); Dröge, Gabriele; snomelf@gmail.com; Robert Hanner; Guentsch, Anton; Robert Robbins Subject: Re: [IPT] Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Well, let's investigate one thing about your diagram first. Shouldn't there be a one-to-many relationship between Occurrence (specimen) and Sample rather than a many-to-one?
Specimen from the field = Occurrence + Event + Location + Identification + Taxon Sample from the specimen's liver = Sample Sample from the specimen's heart = Sample Sample from the specimen's gut = Sample
yes, thats true. Ididnt think about samples that way when I drafted the diagram.
The scenario I had in my mind was the environmental sample, a vegetation plot survey or just a rock with various lichen species on it. Usually with rich data about the location, habitat and abiotic measurements (lends itself nicely to an extension for samples). In such a sample you then find various species which would be the basis for an occurrence. In the case of metagenomic samples the list of taxa is actually derived information from the amplifications and can vary according to the method used (basically the entire occurrence extension can be derived from the amplifications in this case).
Actually when you take a gut sample from an animal you often are interested in the fauna of that gut, so the occurrences would not be the host, but the bacteria occurring within it.
Markus
And all of the Samples could have multiple Amplifications.
If we want to model this with a Sample Core, then Occurrences may be repeated in the Occurrence extension in your diagram, but every sample would have no more than one Occurrence in the extension file and the sampleID relationship would be one-to-one. If so, then it is also possible to have a Sample Core (Sample rowType) with sampleID as the core record identifier, with "Sample" as basisOfRecord, and with all of the attributes of Sample and of the existing Occurrence Core. This would avoid having a distinct Occurrence extension for Samples, which could get confusing for those who are accustomed to mapping Occurrences already. This combined Sample/Occurrence Core could still have a one-to-many relationship to the Amplifications.
On Mon, Oct 22, 2012 at 1:33 PM, "Markus Döring (GBIF)" mdoering@gbif.org wrote: Adding a new core type to the IPT could be done in less than a day - more work for GBIF would be to support such a format in our indexing code. But if we think its a better solution to go with a new sample core type, I think its worth the extra cost of coding for it.
On 22.10.2012, at 17:53, John Wieczorek wrote:
I like the approach of having a Sample Core, but the approach taken thus far was with the view of being pragmatic to put into practice by January 2013. What do you think could be the possibility of adding a new Core type to the IPT on that time scale? The Darwin Core archive specification can certainly handle it, but the proof is in the implementation.
On Mon, Oct 22, 2012 at 8:11 AM, "Markus Döring (GBIF)" mdoering@gbif.org wrote: Hi all, I only quickly looked through the proposal, but it looks good, pragmatic and definitely to be working for the case when a DNASample equals a single taxon Occurrence.
Im not so sure how well it would work with environmental samples - would we have the sample flattened out and repeated to represent the individual taxa, sexes, ages, etc found in there? I was therefore wondering if anyone had thought about the attached setup before. Sample is at its core and occurrence & dna amplification as extensions with the amplifications (optionally?) refering to the occurrence they belong to.
Another quick observation is that we try to reuse existing terms in extensions as much as possible. Following that rule for example dwc:institutionCode should rather be used instead of dNACollectionCode and probably dc:source for the referenceCitation
until tomorrow, regards, Markus
<sample core.png>
On 22.10.2012, at 12:21, Barker, Katharine wrote:
Dear John,
Please see our working revisions/comments/questions on the DNA/tissue extension for Darwin Core (highlighted in blue). We were able to work through the draft up through "class sample properties": https://docs.google.com/document/d/1RCgIPfu9gAPubjjbog-9vCJonvqcK1p LOaq6H8GSnns/edit
The document is also attached for your reference (just incase any of you are unable to access the document).
Please try to respond to our questions and comments prior to our meeting tomorrow (be sure to make these changes using a different color for tracking purposes).
Tomorrow we will like to 1) briefly recap our revisions on the extension so far (addressing questions and comments), 2) complete our review of the extension and 3) identify any remaining issues with DwC working with IPT (and identify if any changes in the IPT are required).
Thank you for your help on this!
Kind Regards,
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu" <tuco@berkeley.edumailto:tuco@berkeley.edu> Date: Sunday, October 21, 2012 10:52 PM To: Gabriele Droege <g.droege@bgbm.orgmailto:g.droege@bgbm.org> Cc: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au>, John Deck <jdeck@berkeley.edumailto:jdeck@berkeley.edu>, Robert Hanner <bob.hanner@gmail.commailto:bob.hanner@gmail.com>, Éamonn Tuama <eotuama@gbif.orgmailto:eotuama@gbif.org>, Robert Robbins <rjr8222@gmail.commailto:rjr8222@gmail.com>, "Guentsch, Anton" <a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org> Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Dear all,
I finished working on the Google Doc "DNA Tissue Extension Notes - TDWG 2012". Feel free to let this be a working document where comments and questions can be added. I've attached a Word Doc version for archival purposes.
I added the two template extension files (DNATissueExtension.txt and DNAAmplificationExtension.txt) to the shared TDWG GGBN working group folder linked below. They are in the form they need to be submitted to GBIF to be added to their extension registry. They would both need to be updated with the term descriptions, examples, and constraints.
https://drive.google.com/#folders/0BxEyFKwB7zY4WEs0WkdtUU5oVnM
Cheers,
John
On Sun, Oct 21, 2012 at 10:38 PM, John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> wrote: Ooops
...at http://goo.gl/kGHmb. Adding touches based on the files Gabi sent. Will tell you all when finished with that and will send it as a Word doc at that time in case there are any issues with Google docs. Should be soon. Let me know if I should share to any different addresses.
Cheers,
John
On Sun, Oct 21, 2012 at 10:34 PM, John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> wrote: That helps a lot, as it clears up some of my own misconceptions. I have shared a document where I have captured the thinking behind a couple of different ways forward with one or two extensions and an example of how the two-extension might look in the context of a Darwin Core Archive. The DNA Tissue Extension Notes Google doc can be found at
On Sun, Oct 21, 2012 at 9:23 PM, "Dröge, Gabriele" <g.droege@bgbm.orgmailto:g.droege@bgbm.org> wrote: Yes we do... Hi John,
Thanks for getting back to us. Attached are two csv files, one with some main DNA facts and the other with associated GenBank entries und publications (2 examples with 2 GenBank entries per DNA sample). I included only UnitID/CollCode/InstCode for the related voucher specimen and I excluded the tissue facts since they are quite similar to the DNA facts and should be mapped independently.
Best, Gabi
-----Original Message----- From: Barker, Katharine [mailto:BarkerK@si.edumailto:BarkerK@si.edu] Sent: Sunday, October 21, 2012 11:41 PM To: Paul Flemons; Dröge, Gabriele Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Paul and Gabi,
Do we have any sample data that John can use as a test case? I think he would like it today, if possible.
Thanks for your help (and the team work).
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu>> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu>" <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu>> Date: Sunday, October 21, 2012 12:03 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edu<mailto :barkerk@si.edu>>> Subject: Re: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Hi Katie,
Messages received. Will have the extension stuff ready within a few hours and hope to be able to attend remotely. One thing in the meantime. Do you have any example data that could be used as a test case to populate a core with this extension? Would like to try that with some realy data to test my assumptions.
Sorry for the delay.
Thanks,
John
On Sun, Oct 21, 2012 at 10:08 AM, Barker, Katharine <BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu>> wrote: Dear John,
I'm sorry that you were unable to attain a visa for China. I was really looking forward to working with you in person with the group. Paul mentioned that he had e-mailed you earlier this evening. Can you please send us the draft for the DarwinCore DNA/tissue extension as soon as possible for review during our working sessions? We have one tomorrow at 1:30 (Beijing time) and another on Tuesday at the same time. It would be really great if you could Skype into either both or one of the sessions.
Thanks for your help on this.
Kind Regards,
Katie
From: <Barker>, Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edu<mailto :barkerk@si.edu>><mailto:barkerk@si.edumailto:barkerk@si.edu<mail to:barkerk@si.edumailto:barkerk@si.edu>>> Date: Thursday, October 18, 2012 1:34 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edu<mailto :barkerk@si.edu>><mailto:barkerk@si.edumailto:barkerk@si.edu<mail to:barkerk@si.edumailto:barkerk@si.edu>>>, 'John Deck' <jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkele y.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto: jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley .edu>>>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au<ma ilto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.au
<mailto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.g
ov.au><mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austm us.gov.au>>>, "'"Dröge", Éamonn Tuama <eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.org< mailto:eotuama@gbif.org>><mailto:eotuama@gbif.orgmailto:eotuama@gb if.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>>, "Whitacre, Jamie" <WHITACREJ@si.edumailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edu< mailto:WHITACREJ@si.edu>><mailto:WHITACREJ@si.edumailto:WHITACREJ@ si.edu<mailto:WHITACREJ@si.edumailto:WHITACREJ@si.edu>>>, "'rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail. commailto:rjr8222@gmail.com><mailto:'rjr8222@gmail.commailto:rjr 8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>
'"
<rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.c ommailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr82 22@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>> , "'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch @bgbm.orgmailto:a.guentsch@bgbm.org><mailto:'a.guentsch@bgbm.org< mailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.gue ntsch@bgbm.org>>'" <a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@ bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<ma ilto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guent sch@bgbm.org>>>, "'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco. btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:'gtuco.btuco@ gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.co mmailto:gtuco.btuco@gmail.com>>'" <gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.b tuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gm ail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com< mailto:gtuco.btuco@gmail.com>>>>, "'tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley. edumailto:tuco@berkeley.edu><mailto:'tuco@berkeley.edumailto:tuc o@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>
'"
<tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@ berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>> Cc: "'morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morris on@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:'morrison@cs. man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.u kmailto:morrison@cs.man.ac.uk>>'" <morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morriso n@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:morrison@cs.ma n.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.uk< mailto:morrison@cs.man.ac.uk>>>>, "Parr, Cynthia" <parrc@si.edumailto:parrc@si.edu<mailto:parrc@si.edumailto:parrc @si.edu><mailto:parrc@si.edumailto:parrc@si.edu<mailto:parrc@si. edumailto:parrc@si.edu>>> Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Dear all,
This is a friendly reminder that we will be meeting next Tuesday afternoon at the TDWG 2012 Conference in order to finalize the draft DarwinCore-A DNA/tissue extension for GGBN. As you know, the immediate need for GGBN members is to publish information on tissues. This will happen through extensions to both ABCDDNA and DarwinCore-A. Here we are focused on developing the DarwinCore-A DNA/tissue extension.
An update on the timeline for developing the draft DarwinCore-A DNA/tissue extension is listed below.
Review content requirements for DarwinCore-A DNA/tissue extension (completed, see attached required DNA and tissue elements)John Weiczorek will develop the draft DarwinCore-A DNA/tissue extension (to be completed for group review prior to our break out session on Tuesday afternoon, October 23).Tuesday October 23, working meeting· Questions to answer before final review of DNA/tissue extension
o How do we include repeatable elements of ABCDDNA into DwC-A-DNA (References to more than one sequence record/publication are mandatory)?
o How do we extend the "Basis of Record" in ABCD and DwC-A and how do we include an element similar to ABCD-"Kind of Unit" to DwC-A?
o What are the remaining issues for DwC-A working with IPT? Are any changes in the IPT required?
· Review and finalize draft DarwinCore-A DNA/tissue extension for posting to GBIF site.
Thank you again to everyone who is involved in this project. I look forward to seeing all of you in Beijing.
Kind Regards,
Katie
From: Barker, Katharine Sent: Friday, September 28, 2012 9:53 AM To: 'John Deck'; Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.org<m ailto:eotuama@gbif.org>><mailto:eotuama@gbif.orgmailto:eotuama@gbi f.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.co mmailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr822 2@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@b gbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mai lto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guents ch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.bt uco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gma il.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com<m ailto:gtuco.btuco@gmail.com>>>; tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.ed umailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@b erkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Dear all,
We will be meeting this Tuesday at 1pm U.S. Eastern time over Skype in order to discuss the actions required to develop the draft proposal for the Darwin Core tissue/DNA extension. A proposal for designing, testing, and implementing the GGBN data portal is attached for your reference. Please review the timeline and action items leading up to the TDWG 2012 Conference.
My Skype name is Katharine.Barker1. If possible, please forward me your skype account names prior to our meeting.
Kind Regards,
Katie
From:jdeck88@gmail.commailto:From%3Ajdeck88@gmail.com<mailto:From %3Ajdeck88@gmail.commailto:From%253Ajdeck88@gmail.com><mailto:jde ck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@gmail.com<m ailto:jdeck88@gmail.com>>> [mailto:jdeck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@ gmail.commailto:jdeck88@gmail.com>] On Behalf Of John Deck Sent: Tuesday, September 25, 2012 4:04 PM To: Barker, Katharine Cc: Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.org<m ailto:eotuama@gbif.org>><mailto:eotuama@gbif.orgmailto:eotuama@gbi f.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.co mmailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr822 2@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@b gbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mai lto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guents ch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.bt uco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gma il.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com<m ailto:gtuco.btuco@gmail.com>>>; tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.ed umailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@b erkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Here is the wrapup of the bioCollections Ontology workshop from last week at GSC14:
http://biocodecommons.org/workshops/bioCollections/index.html
This is relevant to these discussions since we focussed on what constitutes a "sample" and also, probably more importantly, processes that work with samples.
We briefly discussed the DwC Tissue Extension and came up with a proposal for a quick-fix and a more substantial fix. The quick-fix is to create two new BasisOfRecord terms: TissueSubSample, DNAExtract (or some terms like that -- Tuco could provide more clarification on this too). Thus, theoretically we could override the dwc:Occurrence class to mean, for example, TissueSubSample the same way we do for Specimens and Observations. The bigger fix is to more fundamentally re-orient DwC around the notion of "Sample", involving adding/changing some properties although we didn't get into any specifics.
P.s. I can do the 12/1/2 timeslots for that monday or tuesday but not the 11.
John On Mon, Sep 24, 2012 at 12:39 PM, Barker, Katharine <BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu><mailto:BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu>>> wrote: Dear all,
We will have a telecon meeting early next week in order to discuss a draft proposal for the Darwin Core tissue/DNA extension. Gabi, Paul, and I will put together a first draft for discussion to be distributed prior to the telecon. As you know, the goal is to have a working draft ready for our working group to review at the TDWG meeting in Beijing this October.
These are our options for meeting next week: Monday 11am, 12pm, 1pm, 2pm US EDT Tuesday 11am, 12pm, 1pm, 2pm US EDT
Please let me know if you cannot make one of these times.
Thanks again to those of you who provided input last week at the GSC 14 meeting.
Kind Regards,
Katie
From: Barker, Katharine Sent: Wednesday, September 12, 2012 10:51 AM To: 'Paul Flemons'; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org><mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; 'rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>'; jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>>; 'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>'; 'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>'; 'tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>' Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core Importance: High
Dear all,
My name is Katie Barker and I am the Global Genome Biodiversity Network Coordinator. As you know from Paul Flemons, members of the GGBN Data Standards and Data Access Task Force are trying to pull together a task group, which you are all part of, for the upcoming TDWG meeting in Beijing this October in order to address a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members. I am contacting you to schedule a meeting in late September/early October to develop a draft proposal for this extension to be completed at the upcoming TDWG meeting.
Please let me know your availability for the last two weeks of September and first two weeks of October. There will be some scheduling issues, as there are task group members on the west and east coasts of the U.S., Europe and Australia.
Paul Flemons (in Australia) will be in the U.S. the first week of October, so maybe we can meet in the afternoon of the 1st, anytime on the second 2nd, or in the morning of the 3rd of October over teleconference (US Eastern Daylight Time). Please let me know if any of these time slots work for you.
Gabi, I believe that you and John Deck will be at the GSC 14 meeting next week. Is there any chance that you can start drawing up an outline for the proposed extension? We could review the outline during our group telecon and start drafting a proposal for review at the TDWG meeting in October.
Kind Regards,
Katie
Task Group Members:
John Weiczorek - Berkeley Éamonn O'Tuama - GBIF Jamie Whitacre - SI John Deck - Berkeley Robert Robbins - University of California, San Diego Anton Guentsch
- BGBM Gabi Droege- BGBM Paul Flemons- AM
From: Paul Flemons [mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov .au<mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus .gov.au>] Sent: Tuesday, August 07, 2012 2:50 AM To: tuco@berkley.edumailto:tuco@berkley.edu<mailto:tuco@berkley.edu<m ailto:tuco@berkley.edu>><mailto:tuco@berkley.edumailto:tuco@berkle y.edu<mailto:tuco@berkley.edumailto:tuco@berkley.edu>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@b gbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mai lto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guents ch@bgbm.org>>; j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org<mailto:j.holets chek@bgbm.orgmailto:j.holetschek@bgbm.org><mailto:j.holetschek@bg bm.orgmailto:j.holetschek@bgbm.org<mailto:j.holetschek@bgbm.org<m ailto:j.holetschek@bgbm.org>>>; jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley .edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto:j deck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley. edu>> Cc: Barker, Katharine; Éamonn Ó Tuama [GBIF]; "Dröge, Gabriele" (g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG<mailto:g.droege@BGBM.O RGmailto:g.droege@BGBM.ORG><mailto:g.droege@BGBM.ORGmailto:g.dro ege@BGBM.ORG<mailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG>>) Subject: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core
Hi all, I am on the Data Standards and Access Task Force for the Global Genome Biodiversity Network (http://ggbn.org/) which is in need of a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members.
To this end I am writing to you to ask if you would be interested in participating in a small working group at TDWG in Beijing this year.
At this stage my plan would be to identify relevant fields for inclusion in the extension, using ABCDDNA as a reference. If sufficient progress is made then we would submit the extension for ratification by TDWG (is that how its done John?) The GGBN will use whatever comes out of the group to move towards having a suitable DwC based schema for data sharing.
So please let me know if you are willing to participate in the task group and/or if there is anyone else you feel would be beneficial to have involved.
How much time do you think we will need? I have been thinking that a day will be needed, so we could make that consist of either one full day or two half days. Im also thinking that during the week will be the best time for this.
Thanks for your time
Best Regards Paul
Paul K J Flemons Manager, Collection Informatics Team Lead, Atlas of Living Australia Biodiversity Volunteer Portalhttp://volunteer.ala.org.au Biodiversity Information Standards (TDWG) Representative for Oceania Australian Museum 6 College Street Sydney NSW 2010 Australia t 61 2 9320 6343 m 0413458649 f 61 2 9320 6021 Visit: http://www.australianmuseum.net.auhttp://www.australianmuseum.net. au/ Like: http://www.facebook.com/australianmuseum Follow: http://www.twitter.com/austmus Watch: http://www.youtube.com/austmus [cid:image001.png@01CDAD34.391DC790mailto:image001.png@01CDAD34.39 1DC790<mailto:image001.png@01CDAD34.391DC790mailto:image001.png@0 1CDAD34.391DC790>] Inspiring the exploration of nature and cultures
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<DNATissueExtensionNotes2-TDWG2012.docx>___________________________ ____________________ IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt
Now with attachment...
Thanks to all of you for your feedback. I don't understand the figure you created (Markus?). I had a look at http://code.google.com/p/gbif-ecat/wiki/DwCArchive and I think we will keep the core schema in the middle as it is now (Basis of Resource, Taxon or Occurrence).
All what we need to refer to associated objects (samples (tissues, DNA, RNA,...) or other specimens) is an association extension with the identifiers of the referenced records, similar to the UnitAssociation container in ABCD. This extension should have a one to many relation to the core. The DNAAmplification extension is only required if the sample record is a DNA sample, since in this extension so far only DNA specific facts are included (GenBankAccessionNo etc.). The SampleFacts-Extension is quite similar to the main DNA extension of ABCD.
Find attached my figure based on the one from the DwCArchive website. This is how I think it could work and how I understand the star schema, but maybe I am wrong :-). Environmental samples are more complicate maybe we can discuss this topic later (next year)?
Best, Gabi
-----Original Message----- From: "Markus Döring (GBIF)" [mailto:mdoering@gbif.org] Sent: Monday, October 22, 2012 11:31 PM To: tuco@berkeley.edu Cc: Barker, Katharine; ipt@lists.gbif.org; John Deck; Paul Flemons (Paul.Flemons@austmus.gov.au); Dröge, Gabriele; snomelf@gmail.com; Robert Hanner; Guentsch, Anton; Robert Robbins Subject: Re: [IPT] Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Well, let's investigate one thing about your diagram first. Shouldn't there be a one-to-many relationship between Occurrence (specimen) and Sample rather than a many-to-one?
Specimen from the field = Occurrence + Event + Location + Identification + Taxon Sample from the specimen's liver = Sample Sample from the specimen's heart = Sample Sample from the specimen's gut = Sample
yes, thats true. Ididnt think about samples that way when I drafted the diagram.
The scenario I had in my mind was the environmental sample, a vegetation plot survey or just a rock with various lichen species on it. Usually with rich data about the location, habitat and abiotic measurements (lends itself nicely to an extension for samples). In such a sample you then find various species which would be the basis for an occurrence. In the case of metagenomic samples the list of taxa is actually derived information from the amplifications and can vary according to the method used (basically the entire occurrence extension can be derived from the amplifications in this case).
Actually when you take a gut sample from an animal you often are interested in the fauna of that gut, so the occurrences would not be the host, but the bacteria occurring within it.
Markus
And all of the Samples could have multiple Amplifications.
If we want to model this with a Sample Core, then Occurrences may be repeated in the Occurrence extension in your diagram, but every sample would have no more than one Occurrence in the extension file and the sampleID relationship would be one-to-one. If so, then it is also possible to have a Sample Core (Sample rowType) with sampleID as the core record identifier, with "Sample" as basisOfRecord, and with all of the attributes of Sample and of the existing Occurrence Core. This would avoid having a distinct Occurrence extension for Samples, which could get confusing for those who are accustomed to mapping Occurrences already. This combined Sample/Occurrence Core could still have a one-to-many relationship to the Amplifications.
On Mon, Oct 22, 2012 at 1:33 PM, "Markus Döring (GBIF)" mdoering@gbif.org wrote: Adding a new core type to the IPT could be done in less than a day - more work for GBIF would be to support such a format in our indexing code. But if we think its a better solution to go with a new sample core type, I think its worth the extra cost of coding for it.
On 22.10.2012, at 17:53, John Wieczorek wrote:
I like the approach of having a Sample Core, but the approach taken thus far was with the view of being pragmatic to put into practice by January 2013. What do you think could be the possibility of adding a new Core type to the IPT on that time scale? The Darwin Core archive specification can certainly handle it, but the proof is in the implementation.
On Mon, Oct 22, 2012 at 8:11 AM, "Markus Döring (GBIF)" mdoering@gbif.org wrote: Hi all, I only quickly looked through the proposal, but it looks good, pragmatic and definitely to be working for the case when a DNASample equals a single taxon Occurrence.
Im not so sure how well it would work with environmental samples - would we have the sample flattened out and repeated to represent the individual taxa, sexes, ages, etc found in there? I was therefore wondering if anyone had thought about the attached setup before. Sample is at its core and occurrence & dna amplification as extensions with the amplifications (optionally?) refering to the occurrence they belong to.
Another quick observation is that we try to reuse existing terms in extensions as much as possible. Following that rule for example dwc:institutionCode should rather be used instead of dNACollectionCode and probably dc:source for the referenceCitation
until tomorrow, regards, Markus
<sample core.png>
On 22.10.2012, at 12:21, Barker, Katharine wrote:
Dear John,
Please see our working revisions/comments/questions on the DNA/tissue extension for Darwin Core (highlighted in blue). We were able to work through the draft up through "class sample properties": https://docs.google.com/document/d/1RCgIPfu9gAPubjjbog-9vCJonvqcK1p LOaq6H8GSnns/edit
The document is also attached for your reference (just incase any of you are unable to access the document).
Please try to respond to our questions and comments prior to our meeting tomorrow (be sure to make these changes using a different color for tracking purposes).
Tomorrow we will like to 1) briefly recap our revisions on the extension so far (addressing questions and comments), 2) complete our review of the extension and 3) identify any remaining issues with DwC working with IPT (and identify if any changes in the IPT are required).
Thank you for your help on this!
Kind Regards,
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu" <tuco@berkeley.edumailto:tuco@berkeley.edu> Date: Sunday, October 21, 2012 10:52 PM To: Gabriele Droege <g.droege@bgbm.orgmailto:g.droege@bgbm.org> Cc: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au>, John Deck <jdeck@berkeley.edumailto:jdeck@berkeley.edu>, Robert Hanner <bob.hanner@gmail.commailto:bob.hanner@gmail.com>, Éamonn Tuama <eotuama@gbif.orgmailto:eotuama@gbif.org>, Robert Robbins <rjr8222@gmail.commailto:rjr8222@gmail.com>, "Guentsch, Anton" <a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org> Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Dear all,
I finished working on the Google Doc "DNA Tissue Extension Notes - TDWG 2012". Feel free to let this be a working document where comments and questions can be added. I've attached a Word Doc version for archival purposes.
I added the two template extension files (DNATissueExtension.txt and DNAAmplificationExtension.txt) to the shared TDWG GGBN working group folder linked below. They are in the form they need to be submitted to GBIF to be added to their extension registry. They would both need to be updated with the term descriptions, examples, and constraints.
https://drive.google.com/#folders/0BxEyFKwB7zY4WEs0WkdtUU5oVnM
Cheers,
John
On Sun, Oct 21, 2012 at 10:38 PM, John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> wrote: Ooops
...at http://goo.gl/kGHmb. Adding touches based on the files Gabi sent. Will tell you all when finished with that and will send it as a Word doc at that time in case there are any issues with Google docs. Should be soon. Let me know if I should share to any different addresses.
Cheers,
John
On Sun, Oct 21, 2012 at 10:34 PM, John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> wrote: That helps a lot, as it clears up some of my own misconceptions. I have shared a document where I have captured the thinking behind a couple of different ways forward with one or two extensions and an example of how the two-extension might look in the context of a Darwin Core Archive. The DNA Tissue Extension Notes Google doc can be found at
On Sun, Oct 21, 2012 at 9:23 PM, "Dröge, Gabriele" <g.droege@bgbm.orgmailto:g.droege@bgbm.org> wrote: Yes we do... Hi John,
Thanks for getting back to us. Attached are two csv files, one with some main DNA facts and the other with associated GenBank entries und publications (2 examples with 2 GenBank entries per DNA sample). I included only UnitID/CollCode/InstCode for the related voucher specimen and I excluded the tissue facts since they are quite similar to the DNA facts and should be mapped independently.
Best, Gabi
-----Original Message----- From: Barker, Katharine [mailto:BarkerK@si.edumailto:BarkerK@si.edu] Sent: Sunday, October 21, 2012 11:41 PM To: Paul Flemons; Dröge, Gabriele Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Paul and Gabi,
Do we have any sample data that John can use as a test case? I think he would like it today, if possible.
Thanks for your help (and the team work).
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu>> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu>" <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu>> Date: Sunday, October 21, 2012 12:03 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edu<mailto :barkerk@si.edu>>> Subject: Re: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Hi Katie,
Messages received. Will have the extension stuff ready within a few hours and hope to be able to attend remotely. One thing in the meantime. Do you have any example data that could be used as a test case to populate a core with this extension? Would like to try that with some realy data to test my assumptions.
Sorry for the delay.
Thanks,
John
On Sun, Oct 21, 2012 at 10:08 AM, Barker, Katharine <BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu>> wrote: Dear John,
I'm sorry that you were unable to attain a visa for China. I was really looking forward to working with you in person with the group. Paul mentioned that he had e-mailed you earlier this evening. Can you please send us the draft for the DarwinCore DNA/tissue extension as soon as possible for review during our working sessions? We have one tomorrow at 1:30 (Beijing time) and another on Tuesday at the same time. It would be really great if you could Skype into either both or one of the sessions.
Thanks for your help on this.
Kind Regards,
Katie
From: <Barker>, Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edu<mailto :barkerk@si.edu>><mailto:barkerk@si.edumailto:barkerk@si.edu<mail to:barkerk@si.edumailto:barkerk@si.edu>>> Date: Thursday, October 18, 2012 1:34 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edu<mailto :barkerk@si.edu>><mailto:barkerk@si.edumailto:barkerk@si.edu<mail to:barkerk@si.edumailto:barkerk@si.edu>>>, 'John Deck' <jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkele y.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto: jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley .edu>>>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au<ma ilto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.au
<mailto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.g
ov.au><mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austm us.gov.au>>>, "'"Dröge", Éamonn Tuama <eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.org< mailto:eotuama@gbif.org>><mailto:eotuama@gbif.orgmailto:eotuama@gb if.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>>, "Whitacre, Jamie" <WHITACREJ@si.edumailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edu< mailto:WHITACREJ@si.edu>><mailto:WHITACREJ@si.edumailto:WHITACREJ@ si.edu<mailto:WHITACREJ@si.edumailto:WHITACREJ@si.edu>>>, "'rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail. commailto:rjr8222@gmail.com><mailto:'rjr8222@gmail.commailto:rjr 8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>
'"
<rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.c ommailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr82 22@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>> , "'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch @bgbm.orgmailto:a.guentsch@bgbm.org><mailto:'a.guentsch@bgbm.org< mailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.gue ntsch@bgbm.org>>'" <a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@ bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<ma ilto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guent sch@bgbm.org>>>, "'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco. btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:'gtuco.btuco@ gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.co mmailto:gtuco.btuco@gmail.com>>'" <gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.b tuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gm ail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com< mailto:gtuco.btuco@gmail.com>>>>, "'tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley. edumailto:tuco@berkeley.edu><mailto:'tuco@berkeley.edumailto:tuc o@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>
'"
<tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@ berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>> Cc: "'morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morris on@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:'morrison@cs. man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.u kmailto:morrison@cs.man.ac.uk>>'" <morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morriso n@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:morrison@cs.ma n.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.uk< mailto:morrison@cs.man.ac.uk>>>>, "Parr, Cynthia" <parrc@si.edumailto:parrc@si.edu<mailto:parrc@si.edumailto:parrc @si.edu><mailto:parrc@si.edumailto:parrc@si.edu<mailto:parrc@si. edumailto:parrc@si.edu>>> Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Dear all,
This is a friendly reminder that we will be meeting next Tuesday afternoon at the TDWG 2012 Conference in order to finalize the draft DarwinCore-A DNA/tissue extension for GGBN. As you know, the immediate need for GGBN members is to publish information on tissues. This will happen through extensions to both ABCDDNA and DarwinCore-A. Here we are focused on developing the DarwinCore-A DNA/tissue extension.
An update on the timeline for developing the draft DarwinCore-A DNA/tissue extension is listed below.
Review content requirements for DarwinCore-A DNA/tissue extension (completed, see attached required DNA and tissue elements)John Weiczorek will develop the draft DarwinCore-A DNA/tissue extension (to be completed for group review prior to our break out session on Tuesday afternoon, October 23).Tuesday October 23, working meeting· Questions to answer before final review of DNA/tissue extension
o How do we include repeatable elements of ABCDDNA into DwC-A-DNA (References to more than one sequence record/publication are mandatory)?
o How do we extend the "Basis of Record" in ABCD and DwC-A and how do we include an element similar to ABCD-"Kind of Unit" to DwC-A?
o What are the remaining issues for DwC-A working with IPT? Are any changes in the IPT required?
· Review and finalize draft DarwinCore-A DNA/tissue extension for posting to GBIF site.
Thank you again to everyone who is involved in this project. I look forward to seeing all of you in Beijing.
Kind Regards,
Katie
From: Barker, Katharine Sent: Friday, September 28, 2012 9:53 AM To: 'John Deck'; Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.org<m ailto:eotuama@gbif.org>><mailto:eotuama@gbif.orgmailto:eotuama@gbi f.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.co mmailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr822 2@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@b gbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mai lto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guents ch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.bt uco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gma il.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com<m ailto:gtuco.btuco@gmail.com>>>; tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.ed umailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@b erkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Dear all,
We will be meeting this Tuesday at 1pm U.S. Eastern time over Skype in order to discuss the actions required to develop the draft proposal for the Darwin Core tissue/DNA extension. A proposal for designing, testing, and implementing the GGBN data portal is attached for your reference. Please review the timeline and action items leading up to the TDWG 2012 Conference.
My Skype name is Katharine.Barker1. If possible, please forward me your skype account names prior to our meeting.
Kind Regards,
Katie
From:jdeck88@gmail.commailto:From%3Ajdeck88@gmail.com<mailto:From %3Ajdeck88@gmail.commailto:From%253Ajdeck88@gmail.com><mailto:jde ck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@gmail.com<m ailto:jdeck88@gmail.com>>> [mailto:jdeck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@ gmail.commailto:jdeck88@gmail.com>] On Behalf Of John Deck Sent: Tuesday, September 25, 2012 4:04 PM To: Barker, Katharine Cc: Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.org<m ailto:eotuama@gbif.org>><mailto:eotuama@gbif.orgmailto:eotuama@gbi f.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.co mmailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr822 2@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@b gbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mai lto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guents ch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.bt uco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gma il.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com<m ailto:gtuco.btuco@gmail.com>>>; tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.ed umailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@b erkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Here is the wrapup of the bioCollections Ontology workshop from last week at GSC14:
http://biocodecommons.org/workshops/bioCollections/index.html
This is relevant to these discussions since we focussed on what constitutes a "sample" and also, probably more importantly, processes that work with samples.
We briefly discussed the DwC Tissue Extension and came up with a proposal for a quick-fix and a more substantial fix. The quick-fix is to create two new BasisOfRecord terms: TissueSubSample, DNAExtract (or some terms like that -- Tuco could provide more clarification on this too). Thus, theoretically we could override the dwc:Occurrence class to mean, for example, TissueSubSample the same way we do for Specimens and Observations. The bigger fix is to more fundamentally re-orient DwC around the notion of "Sample", involving adding/changing some properties although we didn't get into any specifics.
P.s. I can do the 12/1/2 timeslots for that monday or tuesday but not the 11.
John On Mon, Sep 24, 2012 at 12:39 PM, Barker, Katharine <BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu><mailto:BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu>>> wrote: Dear all,
We will have a telecon meeting early next week in order to discuss a draft proposal for the Darwin Core tissue/DNA extension. Gabi, Paul, and I will put together a first draft for discussion to be distributed prior to the telecon. As you know, the goal is to have a working draft ready for our working group to review at the TDWG meeting in Beijing this October.
These are our options for meeting next week: Monday 11am, 12pm, 1pm, 2pm US EDT Tuesday 11am, 12pm, 1pm, 2pm US EDT
Please let me know if you cannot make one of these times.
Thanks again to those of you who provided input last week at the GSC 14 meeting.
Kind Regards,
Katie
From: Barker, Katharine Sent: Wednesday, September 12, 2012 10:51 AM To: 'Paul Flemons'; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org><mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; 'rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>'; jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>>; 'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>'; 'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>'; 'tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>' Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core Importance: High
Dear all,
My name is Katie Barker and I am the Global Genome Biodiversity Network Coordinator. As you know from Paul Flemons, members of the GGBN Data Standards and Data Access Task Force are trying to pull together a task group, which you are all part of, for the upcoming TDWG meeting in Beijing this October in order to address a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members. I am contacting you to schedule a meeting in late September/early October to develop a draft proposal for this extension to be completed at the upcoming TDWG meeting.
Please let me know your availability for the last two weeks of September and first two weeks of October. There will be some scheduling issues, as there are task group members on the west and east coasts of the U.S., Europe and Australia.
Paul Flemons (in Australia) will be in the U.S. the first week of October, so maybe we can meet in the afternoon of the 1st, anytime on the second 2nd, or in the morning of the 3rd of October over teleconference (US Eastern Daylight Time). Please let me know if any of these time slots work for you.
Gabi, I believe that you and John Deck will be at the GSC 14 meeting next week. Is there any chance that you can start drawing up an outline for the proposed extension? We could review the outline during our group telecon and start drafting a proposal for review at the TDWG meeting in October.
Kind Regards,
Katie
Task Group Members:
John Weiczorek - Berkeley Éamonn O'Tuama - GBIF Jamie Whitacre - SI John Deck - Berkeley Robert Robbins - University of California, San Diego Anton Guentsch
- BGBM Gabi Droege- BGBM Paul Flemons- AM
From: Paul Flemons [mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov .au<mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus .gov.au>] Sent: Tuesday, August 07, 2012 2:50 AM To: tuco@berkley.edumailto:tuco@berkley.edu<mailto:tuco@berkley.edu<m ailto:tuco@berkley.edu>><mailto:tuco@berkley.edumailto:tuco@berkle y.edu<mailto:tuco@berkley.edumailto:tuco@berkley.edu>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@b gbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mai lto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guents ch@bgbm.org>>; j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org<mailto:j.holets chek@bgbm.orgmailto:j.holetschek@bgbm.org><mailto:j.holetschek@bg bm.orgmailto:j.holetschek@bgbm.org<mailto:j.holetschek@bgbm.org<m ailto:j.holetschek@bgbm.org>>>; jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley .edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto:j deck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley. edu>> Cc: Barker, Katharine; Éamonn Ó Tuama [GBIF]; "Dröge, Gabriele" (g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG<mailto:g.droege@BGBM.O RGmailto:g.droege@BGBM.ORG><mailto:g.droege@BGBM.ORGmailto:g.dro ege@BGBM.ORG<mailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG>>) Subject: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core
Hi all, I am on the Data Standards and Access Task Force for the Global Genome Biodiversity Network (http://ggbn.org/) which is in need of a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members.
To this end I am writing to you to ask if you would be interested in participating in a small working group at TDWG in Beijing this year.
At this stage my plan would be to identify relevant fields for inclusion in the extension, using ABCDDNA as a reference. If sufficient progress is made then we would submit the extension for ratification by TDWG (is that how its done John?) The GGBN will use whatever comes out of the group to move towards having a suitable DwC based schema for data sharing.
So please let me know if you are willing to participate in the task group and/or if there is anyone else you feel would be beneficial to have involved.
How much time do you think we will need? I have been thinking that a day will be needed, so we could make that consist of either one full day or two half days. Im also thinking that during the week will be the best time for this.
Thanks for your time
Best Regards Paul
Paul K J Flemons Manager, Collection Informatics Team Lead, Atlas of Living Australia Biodiversity Volunteer Portalhttp://volunteer.ala.org.au Biodiversity Information Standards (TDWG) Representative for Oceania Australian Museum 6 College Street Sydney NSW 2010 Australia t 61 2 9320 6343 m 0413458649 f 61 2 9320 6021 Visit: http://www.australianmuseum.net.auhttp://www.australianmuseum.net. au/ Like: http://www.facebook.com/australianmuseum Follow: http://www.twitter.com/austmus Watch: http://www.youtube.com/austmus [cid:image001.png@01CDAD34.391DC790mailto:image001.png@01CDAD34.39 1DC790<mailto:image001.png@01CDAD34.391DC790mailto:image001.png@0 1CDAD34.391DC790>] Inspiring the exploration of nature and cultures
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<DNATissueExtensionNotes2-TDWG2012.docx>___________________________ ____________________ IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt
Dear all,
I'm joining this conversation quite late, feel free to correct me if I say something stupid.
From what I just read, it appears we have two totally different use-cases here:
* Environmental samples, where the central piece of data is the sample * Tissue samples, that are just new low-level data about a specimen
To me, we probably won't be able to merge these two things to find a single clean, pragmatic & simple solution. The former will need the sample at the core, the latter is probably better with a goold old Occurrence at the core.
If we agree we have two distinct problems to solve, maybe it is wise to assess which one is priority #1, solve it now, implement it in IPT and gather real-world feedback before solving issue #2 ?
I feel I'm not really bringing something new on the table, but the point I'd like to make is that maybe we should be care about the "let's-find-a-perfect-solution-that-fits-it-all" syndrom, with all his well-known consequences (complex implementation + risk of losing users).
thanks,
Nicolas
On 10/23/12 03:54, "Dröge, Gabriele" wrote:
Now with attachment...
Thanks to all of you for your feedback. I don't understand the figure you created (Markus?). I had a look at http://code.google.com/p/gbif-ecat/wiki/DwCArchive and I think we will keep the core schema in the middle as it is now (Basis of Resource, Taxon or Occurrence).
All what we need to refer to associated objects (samples (tissues, DNA, RNA,...) or other specimens) is an association extension with the identifiers of the referenced records, similar to the UnitAssociation container in ABCD. This extension should have a one to many relation to the core. The DNAAmplification extension is only required if the sample record is a DNA sample, since in this extension so far only DNA specific facts are included (GenBankAccessionNo etc.). The SampleFacts-Extension is quite similar to the main DNA extension of ABCD.
Find attached my figure based on the one from the DwCArchive website. This is how I think it could work and how I understand the star schema, but maybe I am wrong :-). Environmental samples are more complicate maybe we can discuss this topic later (next year)?
Best, Gabi
-----Original Message----- From: "Markus Döring (GBIF)" [mailto:mdoering@gbif.org] Sent: Monday, October 22, 2012 11:31 PM To: tuco@berkeley.edu Cc: Barker, Katharine; ipt@lists.gbif.org; John Deck; Paul Flemons (Paul.Flemons@austmus.gov.au); Dröge, Gabriele; snomelf@gmail.com; Robert Hanner; Guentsch, Anton; Robert Robbins Subject: Re: [IPT] Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Well, let's investigate one thing about your diagram first. Shouldn't there be a one-to-many relationship between Occurrence (specimen) and Sample rather than a many-to-one?
Specimen from the field = Occurrence + Event + Location + Identification + Taxon Sample from the specimen's liver = Sample Sample from the specimen's heart = Sample Sample from the specimen's gut = Sample
yes, thats true. Ididnt think about samples that way when I drafted the diagram.
The scenario I had in my mind was the environmental sample, a vegetation plot survey or just a rock with various lichen species on it. Usually with rich data about the location, habitat and abiotic measurements (lends itself nicely to an extension for samples). In such a sample you then find various species which would be the basis for an occurrence. In the case of metagenomic samples the list of taxa is actually derived information from the amplifications and can vary according to the method used (basically the entire occurrence extension can be derived from the amplifications in this case).
Actually when you take a gut sample from an animal you often are interested in the fauna of that gut, so the occurrences would not be the host, but the bacteria occurring within it.
Markus
And all of the Samples could have multiple Amplifications.
If we want to model this with a Sample Core, then Occurrences may be repeated in the Occurrence extension in your diagram, but every sample would have no more than one Occurrence in the extension file and the sampleID relationship would be one-to-one. If so, then it is also possible to have a Sample Core (Sample rowType) with sampleID as the core record identifier, with "Sample" as basisOfRecord, and with all of the attributes of Sample and of the existing Occurrence Core. This would avoid having a distinct Occurrence extension for Samples, which could get confusing for those who are accustomed to mapping Occurrences already. This combined Sample/Occurrence Core could still have a one-to-many relationship to the Amplifications.
On Mon, Oct 22, 2012 at 1:33 PM, "Markus Döring (GBIF)" mdoering@gbif.org wrote: Adding a new core type to the IPT could be done in less than a day - more work for GBIF would be to support such a format in our indexing code. But if we think its a better solution to go with a new sample core type, I think its worth the extra cost of coding for it.
On 22.10.2012, at 17:53, John Wieczorek wrote:
I like the approach of having a Sample Core, but the approach taken thus far was with the view of being pragmatic to put into practice by January 2013. What do you think could be the possibility of adding a new Core type to the IPT on that time scale? The Darwin Core archive specification can certainly handle it, but the proof is in the implementation.
On Mon, Oct 22, 2012 at 8:11 AM, "Markus Döring (GBIF)" mdoering@gbif.org wrote: Hi all, I only quickly looked through the proposal, but it looks good, pragmatic and definitely to be working for the case when a DNASample equals a single taxon Occurrence.
Im not so sure how well it would work with environmental samples - would we have the sample flattened out and repeated to represent the individual taxa, sexes, ages, etc found in there? I was therefore wondering if anyone had thought about the attached setup before. Sample is at its core and occurrence & dna amplification as extensions with the amplifications (optionally?) refering to the occurrence they belong to.
Another quick observation is that we try to reuse existing terms in extensions as much as possible. Following that rule for example dwc:institutionCode should rather be used instead of dNACollectionCode and probably dc:source for the referenceCitation
until tomorrow, regards, Markus
<sample core.png>
On 22.10.2012, at 12:21, Barker, Katharine wrote:
Dear John,
Please see our working revisions/comments/questions on the DNA/tissue extension for Darwin Core (highlighted in blue). We were able to work through the draft up through "class sample properties": https://docs.google.com/document/d/1RCgIPfu9gAPubjjbog-9vCJonvqcK1p LOaq6H8GSnns/edit
The document is also attached for your reference (just incase any of you are unable to access the document).
Please try to respond to our questions and comments prior to our meeting tomorrow (be sure to make these changes using a different color for tracking purposes).
Tomorrow we will like to 1) briefly recap our revisions on the extension so far (addressing questions and comments), 2) complete our review of the extension and 3) identify any remaining issues with DwC working with IPT (and identify if any changes in the IPT are required).
Thank you for your help on this!
Kind Regards,
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu" <tuco@berkeley.edumailto:tuco@berkeley.edu> Date: Sunday, October 21, 2012 10:52 PM To: Gabriele Droege <g.droege@bgbm.orgmailto:g.droege@bgbm.org> Cc: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au>, John Deck <jdeck@berkeley.edumailto:jdeck@berkeley.edu>, Robert Hanner <bob.hanner@gmail.commailto:bob.hanner@gmail.com>, Éamonn Tuama <eotuama@gbif.orgmailto:eotuama@gbif.org>, Robert Robbins <rjr8222@gmail.commailto:rjr8222@gmail.com>, "Guentsch, Anton" <a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org> Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Dear all,
I finished working on the Google Doc "DNA Tissue Extension Notes - TDWG 2012". Feel free to let this be a working document where comments and questions can be added. I've attached a Word Doc version for archival purposes.
I added the two template extension files (DNATissueExtension.txt and DNAAmplificationExtension.txt) to the shared TDWG GGBN working group folder linked below. They are in the form they need to be submitted to GBIF to be added to their extension registry. They would both need to be updated with the term descriptions, examples, and constraints.
https://drive.google.com/#folders/0BxEyFKwB7zY4WEs0WkdtUU5oVnM
Cheers,
John
On Sun, Oct 21, 2012 at 10:38 PM, John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> wrote: Ooops
...at http://goo.gl/kGHmb. Adding touches based on the files Gabi sent. Will tell you all when finished with that and will send it as a Word doc at that time in case there are any issues with Google docs. Should be soon. Let me know if I should share to any different addresses.
Cheers,
John
On Sun, Oct 21, 2012 at 10:34 PM, John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> wrote: That helps a lot, as it clears up some of my own misconceptions. I have shared a document where I have captured the thinking behind a couple of different ways forward with one or two extensions and an example of how the two-extension might look in the context of a Darwin Core Archive. The DNA Tissue Extension Notes Google doc can be found at
On Sun, Oct 21, 2012 at 9:23 PM, "Dröge, Gabriele" <g.droege@bgbm.orgmailto:g.droege@bgbm.org> wrote: Yes we do... Hi John,
Thanks for getting back to us. Attached are two csv files, one with some main DNA facts and the other with associated GenBank entries und publications (2 examples with 2 GenBank entries per DNA sample). I included only UnitID/CollCode/InstCode for the related voucher specimen and I excluded the tissue facts since they are quite similar to the DNA facts and should be mapped independently.
Best, Gabi
-----Original Message----- From: Barker, Katharine [mailto:BarkerK@si.edumailto:BarkerK@si.edu] Sent: Sunday, October 21, 2012 11:41 PM To: Paul Flemons; Dröge, Gabriele Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Paul and Gabi,
Do we have any sample data that John can use as a test case? I think he would like it today, if possible.
Thanks for your help (and the team work).
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu>> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu>" <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu>> Date: Sunday, October 21, 2012 12:03 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edu<mailto :barkerk@si.edu>>> Subject: Re: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Hi Katie,
Messages received. Will have the extension stuff ready within a few hours and hope to be able to attend remotely. One thing in the meantime. Do you have any example data that could be used as a test case to populate a core with this extension? Would like to try that with some realy data to test my assumptions.
Sorry for the delay.
Thanks,
John
On Sun, Oct 21, 2012 at 10:08 AM, Barker, Katharine <BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu>> wrote: Dear John,
I'm sorry that you were unable to attain a visa for China. I was really looking forward to working with you in person with the group. Paul mentioned that he had e-mailed you earlier this evening. Can you please send us the draft for the DarwinCore DNA/tissue extension as soon as possible for review during our working sessions? We have one tomorrow at 1:30 (Beijing time) and another on Tuesday at the same time. It would be really great if you could Skype into either both or one of the sessions.
Thanks for your help on this.
Kind Regards,
Katie
From: <Barker>, Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edu<mailto :barkerk@si.edu>><mailto:barkerk@si.edumailto:barkerk@si.edu<mail to:barkerk@si.edumailto:barkerk@si.edu>>> Date: Thursday, October 18, 2012 1:34 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edu<mailto :barkerk@si.edu>><mailto:barkerk@si.edumailto:barkerk@si.edu<mail to:barkerk@si.edumailto:barkerk@si.edu>>>, 'John Deck' <jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkele y.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto: jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley .edu>>>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au<ma ilto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.au
<mailto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.g
ov.au><mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austm us.gov.au>>>, "'"Dröge", Éamonn Tuama <eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.org< mailto:eotuama@gbif.org>><mailto:eotuama@gbif.orgmailto:eotuama@gb if.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>>, "Whitacre, Jamie" <WHITACREJ@si.edumailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edu< mailto:WHITACREJ@si.edu>><mailto:WHITACREJ@si.edumailto:WHITACREJ@ si.edu<mailto:WHITACREJ@si.edumailto:WHITACREJ@si.edu>>>, "'rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail. commailto:rjr8222@gmail.com><mailto:'rjr8222@gmail.commailto:rjr 8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>
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<rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.c ommailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr82 22@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>> , "'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch @bgbm.orgmailto:a.guentsch@bgbm.org><mailto:'a.guentsch@bgbm.org< mailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.gue ntsch@bgbm.org>>'" <a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@ bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<ma ilto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guent sch@bgbm.org>>>, "'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco. btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:'gtuco.btuco@ gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.co mmailto:gtuco.btuco@gmail.com>>'" <gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.b tuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gm ail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com< mailto:gtuco.btuco@gmail.com>>>>, "'tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley. edumailto:tuco@berkeley.edu><mailto:'tuco@berkeley.edumailto:tuc o@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>
'"
<tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@ berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>> Cc: "'morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morris on@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:'morrison@cs. man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.u kmailto:morrison@cs.man.ac.uk>>'" <morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morriso n@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:morrison@cs.ma n.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.uk< mailto:morrison@cs.man.ac.uk>>>>, "Parr, Cynthia" <parrc@si.edumailto:parrc@si.edu<mailto:parrc@si.edumailto:parrc @si.edu><mailto:parrc@si.edumailto:parrc@si.edu<mailto:parrc@si. edumailto:parrc@si.edu>>> Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Dear all,
This is a friendly reminder that we will be meeting next Tuesday afternoon at the TDWG 2012 Conference in order to finalize the draft DarwinCore-A DNA/tissue extension for GGBN. As you know, the immediate need for GGBN members is to publish information on tissues. This will happen through extensions to both ABCDDNA and DarwinCore-A. Here we are focused on developing the DarwinCore-A DNA/tissue extension.
An update on the timeline for developing the draft DarwinCore-A DNA/tissue extension is listed below.
Review content requirements for DarwinCore-A DNA/tissue extension (completed, see attached required DNA and tissue elements)John Weiczorek will develop the draft DarwinCore-A DNA/tissue extension (to be completed for group review prior to our break out session on Tuesday afternoon, October 23).Tuesday October 23, working meeting· Questions to answer before final review of DNA/tissue extension
o How do we include repeatable elements of ABCDDNA into DwC-A-DNA (References to more than one sequence record/publication are mandatory)?
o How do we extend the "Basis of Record" in ABCD and DwC-A and how do we include an element similar to ABCD-"Kind of Unit" to DwC-A?
o What are the remaining issues for DwC-A working with IPT? Are any changes in the IPT required?
· Review and finalize draft DarwinCore-A DNA/tissue extension for posting to GBIF site.
Thank you again to everyone who is involved in this project. I look forward to seeing all of you in Beijing.
Kind Regards,
Katie
From: Barker, Katharine Sent: Friday, September 28, 2012 9:53 AM To: 'John Deck'; Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.org<m ailto:eotuama@gbif.org>><mailto:eotuama@gbif.orgmailto:eotuama@gbi f.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.co mmailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr822 2@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@b gbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mai lto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guents ch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.bt uco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gma il.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com<m ailto:gtuco.btuco@gmail.com>>>; tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.ed umailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@b erkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Dear all,
We will be meeting this Tuesday at 1pm U.S. Eastern time over Skype in order to discuss the actions required to develop the draft proposal for the Darwin Core tissue/DNA extension. A proposal for designing, testing, and implementing the GGBN data portal is attached for your reference. Please review the timeline and action items leading up to the TDWG 2012 Conference.
My Skype name is Katharine.Barker1. If possible, please forward me your skype account names prior to our meeting.
Kind Regards,
Katie
From:jdeck88@gmail.commailto:From%3Ajdeck88@gmail.com<mailto:From %3Ajdeck88@gmail.commailto:From%253Ajdeck88@gmail.com><mailto:jde ck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@gmail.com<m ailto:jdeck88@gmail.com>>> [mailto:jdeck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@ gmail.commailto:jdeck88@gmail.com>] On Behalf Of John Deck Sent: Tuesday, September 25, 2012 4:04 PM To: Barker, Katharine Cc: Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.org<m ailto:eotuama@gbif.org>><mailto:eotuama@gbif.orgmailto:eotuama@gbi f.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.co mmailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr822 2@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@b gbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mai lto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guents ch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.bt uco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gma il.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com<m ailto:gtuco.btuco@gmail.com>>>; tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.ed umailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@b erkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Here is the wrapup of the bioCollections Ontology workshop from last week at GSC14:
http://biocodecommons.org/workshops/bioCollections/index.html
This is relevant to these discussions since we focussed on what constitutes a "sample" and also, probably more importantly, processes that work with samples.
We briefly discussed the DwC Tissue Extension and came up with a proposal for a quick-fix and a more substantial fix. The quick-fix is to create two new BasisOfRecord terms: TissueSubSample, DNAExtract (or some terms like that -- Tuco could provide more clarification on this too). Thus, theoretically we could override the dwc:Occurrence class to mean, for example, TissueSubSample the same way we do for Specimens and Observations. The bigger fix is to more fundamentally re-orient DwC around the notion of "Sample", involving adding/changing some properties although we didn't get into any specifics.
P.s. I can do the 12/1/2 timeslots for that monday or tuesday but not the 11.
John On Mon, Sep 24, 2012 at 12:39 PM, Barker, Katharine <BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu><mailto:BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu>>> wrote: Dear all,
We will have a telecon meeting early next week in order to discuss a draft proposal for the Darwin Core tissue/DNA extension. Gabi, Paul, and I will put together a first draft for discussion to be distributed prior to the telecon. As you know, the goal is to have a working draft ready for our working group to review at the TDWG meeting in Beijing this October.
These are our options for meeting next week: Monday 11am, 12pm, 1pm, 2pm US EDT Tuesday 11am, 12pm, 1pm, 2pm US EDT
Please let me know if you cannot make one of these times.
Thanks again to those of you who provided input last week at the GSC 14 meeting.
Kind Regards,
Katie
From: Barker, Katharine Sent: Wednesday, September 12, 2012 10:51 AM To: 'Paul Flemons'; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org><mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; 'rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>'; jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>>; 'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>'; 'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>'; 'tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>' Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core Importance: High
Dear all,
My name is Katie Barker and I am the Global Genome Biodiversity Network Coordinator. As you know from Paul Flemons, members of the GGBN Data Standards and Data Access Task Force are trying to pull together a task group, which you are all part of, for the upcoming TDWG meeting in Beijing this October in order to address a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members. I am contacting you to schedule a meeting in late September/early October to develop a draft proposal for this extension to be completed at the upcoming TDWG meeting.
Please let me know your availability for the last two weeks of September and first two weeks of October. There will be some scheduling issues, as there are task group members on the west and east coasts of the U.S., Europe and Australia.
Paul Flemons (in Australia) will be in the U.S. the first week of October, so maybe we can meet in the afternoon of the 1st, anytime on the second 2nd, or in the morning of the 3rd of October over teleconference (US Eastern Daylight Time). Please let me know if any of these time slots work for you.
Gabi, I believe that you and John Deck will be at the GSC 14 meeting next week. Is there any chance that you can start drawing up an outline for the proposed extension? We could review the outline during our group telecon and start drafting a proposal for review at the TDWG meeting in October.
Kind Regards,
Katie
Task Group Members:
John Weiczorek - Berkeley Éamonn O'Tuama - GBIF Jamie Whitacre - SI John Deck - Berkeley Robert Robbins - University of California, San Diego Anton Guentsch
- BGBM Gabi Droege- BGBM Paul Flemons- AM
From: Paul Flemons [mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov .au<mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus .gov.au>] Sent: Tuesday, August 07, 2012 2:50 AM To: tuco@berkley.edumailto:tuco@berkley.edu<mailto:tuco@berkley.edu<m ailto:tuco@berkley.edu>><mailto:tuco@berkley.edumailto:tuco@berkle y.edu<mailto:tuco@berkley.edumailto:tuco@berkley.edu>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@b gbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mai lto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guents ch@bgbm.org>>; j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org<mailto:j.holets chek@bgbm.orgmailto:j.holetschek@bgbm.org><mailto:j.holetschek@bg bm.orgmailto:j.holetschek@bgbm.org<mailto:j.holetschek@bgbm.org<m ailto:j.holetschek@bgbm.org>>>; jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley .edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto:j deck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley. edu>> Cc: Barker, Katharine; Éamonn Ó Tuama [GBIF]; "Dröge, Gabriele" (g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG<mailto:g.droege@BGBM.O RGmailto:g.droege@BGBM.ORG><mailto:g.droege@BGBM.ORGmailto:g.dro ege@BGBM.ORG<mailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG>>) Subject: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core
Hi all, I am on the Data Standards and Access Task Force for the Global Genome Biodiversity Network (http://ggbn.org/) which is in need of a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members.
To this end I am writing to you to ask if you would be interested in participating in a small working group at TDWG in Beijing this year.
At this stage my plan would be to identify relevant fields for inclusion in the extension, using ABCDDNA as a reference. If sufficient progress is made then we would submit the extension for ratification by TDWG (is that how its done John?) The GGBN will use whatever comes out of the group to move towards having a suitable DwC based schema for data sharing.
So please let me know if you are willing to participate in the task group and/or if there is anyone else you feel would be beneficial to have involved.
How much time do you think we will need? I have been thinking that a day will be needed, so we could make that consist of either one full day or two half days. Im also thinking that during the week will be the best time for this.
Thanks for your time
Best Regards Paul
Paul K J Flemons Manager, Collection Informatics Team Lead, Atlas of Living Australia Biodiversity Volunteer Portalhttp://volunteer.ala.org.au Biodiversity Information Standards (TDWG) Representative for Oceania Australian Museum 6 College Street Sydney NSW 2010 Australia t 61 2 9320 6343 m 0413458649 f 61 2 9320 6021 Visit: http://www.australianmuseum.net.auhttp://www.australianmuseum.net. au/ Like: http://www.facebook.com/australianmuseum Follow: http://www.twitter.com/austmus Watch: http://www.youtube.com/austmus [cid:image001.png@01CDAD34.391DC790mailto:image001.png@01CDAD34.39 1DC790<mailto:image001.png@01CDAD34.391DC790mailto:image001.png@0 1CDAD34.391DC790>] Inspiring the exploration of nature and cultures
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<DNATissueExtensionNotes2-TDWG2012.docx>___________________________ ____________________ IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt
IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt
Dear Nicolas,
you are right. Tissue samples are priority 1, that should be solved until end of January 2013. Environmental samples are quite different, we should discuss this topic later. We are on a good way and hope to finish the draft for the new classes today.
Best, Gabi
From: Nicolas Noé [mailto:niconoebiodiversity@gmail.com] On Behalf Of Nicolas Noé Sent: Tuesday, October 23, 2012 11:09 AM To: Dröge, Gabriele Cc: ""Markus Döring (GBIF)""; tuco@berkeley.edu; snomelf@gmail.com; Paul Flemons (Paul.Flemons@austmus.gov.au); ipt@lists.gbif.org; Robert Robbins; John Deck; Robert Hanner; Guentsch, Anton; Barker, Katharine Subject: Re: [IPT] Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Dear all,
I'm joining this conversation quite late, feel free to correct me if I say something stupid.
From what I just read, it appears we have two totally different use-cases here:
* Environmental samples, where the central piece of data is the sample * Tissue samples, that are just new low-level data about a specimen
To me, we probably won't be able to merge these two things to find a single clean, pragmatic & simple solution. The former will need the sample at the core, the latter is probably better with a goold old Occurrence at the core.
If we agree we have two distinct problems to solve, maybe it is wise to assess which one is priority #1, solve it now, implement it in IPT and gather real-world feedback before solving issue #2 ?
I feel I'm not really bringing something new on the table, but the point I'd like to make is that maybe we should be care about the "let's-find-a-perfect-solution-that-fits-it-all" syndrom, with all his well-known consequences (complex implementation + risk of losing users).
thanks,
Nicolas On 10/23/12 03:54, "Dröge, Gabriele" wrote:
Now with attachment...
Thanks to all of you for your feedback. I don't understand the figure you created (Markus?).
I had a look at http://code.google.com/p/gbif-ecat/wiki/DwCArchive and I think we will keep the core schema in the middle as it is now (Basis of Resource, Taxon or Occurrence).
All what we need to refer to associated objects (samples (tissues, DNA, RNA,...) or other specimens) is an association extension with the identifiers of the referenced records, similar to the UnitAssociation container in ABCD. This extension should have a one to many relation to the core.
The DNAAmplification extension is only required if the sample record is a DNA sample, since in this extension so far only DNA specific facts are included (GenBankAccessionNo etc.). The SampleFacts-Extension is quite similar to the main DNA extension of ABCD.
Find attached my figure based on the one from the DwCArchive website. This is how I think it could work and how I understand the star schema, but maybe I am wrong :-). Environmental samples are more complicate maybe we can discuss this topic later (next year)?
Best,
Gabi
-----Original Message-----
From: "Markus Döring (GBIF)" [mailto:mdoering@gbif.org]
Sent: Monday, October 22, 2012 11:31 PM
To: tuco@berkeley.edumailto:tuco@berkeley.edu
Cc: Barker, Katharine; ipt@lists.gbif.orgmailto:ipt@lists.gbif.org; John Deck; Paul Flemons (Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au); Dröge, Gabriele; snomelf@gmail.commailto:snomelf@gmail.com; Robert Hanner; Guentsch, Anton; Robert Robbins
Subject: Re: [IPT] Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Well, let's investigate one thing about your diagram first. Shouldn't there be a one-to-many relationship between Occurrence (specimen) and Sample rather than a many-to-one?
Specimen from the field = Occurrence + Event + Location +
Identification + Taxon Sample from the specimen's liver = Sample
Sample from the specimen's heart = Sample Sample from the specimen's
gut = Sample
yes, thats true. Ididnt think about samples that way when I drafted the diagram.
The scenario I had in my mind was the environmental sample, a vegetation plot survey or just a rock with various lichen species on it. Usually with rich data about the location, habitat and abiotic measurements (lends itself nicely to an extension for samples). In such a sample you then find various species which would be the basis for an occurrence. In the case of metagenomic samples the list of taxa is actually derived information from the amplifications and can vary according to the method used (basically the entire occurrence extension can be derived from the amplifications in this case).
Actually when you take a gut sample from an animal you often are interested in the fauna of that gut, so the occurrences would not be the host, but the bacteria occurring within it.
Markus
And all of the Samples could have multiple Amplifications.
If we want to model this with a Sample Core, then Occurrences may be repeated in the Occurrence extension in your diagram, but every sample would have no more than one Occurrence in the extension file and the sampleID relationship would be one-to-one. If so, then it is also possible to have a Sample Core (Sample rowType) with sampleID as the core record identifier, with "Sample" as basisOfRecord, and with all of the attributes of Sample and of the existing Occurrence Core. This would avoid having a distinct Occurrence extension for Samples, which could get confusing for those who are accustomed to mapping Occurrences already. This combined Sample/Occurrence Core could still have a one-to-many relationship to the Amplifications.
On Mon, Oct 22, 2012 at 1:33 PM, "Markus Döring (GBIF)" mdoering@gbif.orgmailto:mdoering@gbif.org wrote:
Adding a new core type to the IPT could be done in less than a day - more work for GBIF would be to support such a format in our indexing code.
But if we think its a better solution to go with a new sample core type, I think its worth the extra cost of coding for it.
On 22.10.2012, at 17:53, John Wieczorek wrote:
I like the approach of having a Sample Core, but the approach taken thus far was with the view of being pragmatic to put into practice by January 2013. What do you think could be the possibility of adding a new Core type to the IPT on that time scale? The Darwin Core archive specification can certainly handle it, but the proof is in the implementation.
On Mon, Oct 22, 2012 at 8:11 AM, "Markus Döring (GBIF)" mdoering@gbif.orgmailto:mdoering@gbif.org wrote:
Hi all,
I only quickly looked through the proposal, but it looks good, pragmatic and definitely to be working for the case when a DNASample equals a single taxon Occurrence.
Im not so sure how well it would work with environmental samples - would we have the sample flattened out and repeated to represent the individual taxa, sexes, ages, etc found in there?
I was therefore wondering if anyone had thought about the attached setup before. Sample is at its core and occurrence & dna amplification as extensions with the amplifications (optionally?) refering to the occurrence they belong to.
Another quick observation is that we try to reuse existing terms in
extensions as much as possible. Following that rule for example
dwc:institutionCode should rather be used instead of
dNACollectionCode and probably dc:source for the referenceCitation
until tomorrow, regards,
Markus
<sample core.png>
On 22.10.2012, at 12:21, Barker, Katharine wrote:
Dear John,
Please see our working revisions/comments/questions on the DNA/tissue extension for Darwin Core (highlighted in blue). We were able to work through the draft up through "class sample properties":
https://docs.google.com/document/d/1RCgIPfu9gAPubjjbog-9vCJonvqcK1p
LOaq6H8GSnns/edit
The document is also attached for your reference (just incase any of you are unable to access the document).
Please try to respond to our questions and comments prior to our meeting tomorrow (be sure to make these changes using a different color for tracking purposes).
Tomorrow we will like to 1) briefly recap our revisions on the extension so far (addressing questions and comments), 2) complete our review of the extension and 3) identify any remaining issues with DwC working with IPT (and identify if any changes in the IPT are required).
Thank you for your help on this!
Kind Regards,
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edu>
Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edu"
<tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edu>
Date: Sunday, October 21, 2012 10:52 PM
To: Gabriele Droege <g.droege@bgbm.orgmailto:g.droege@bgbm.orgmailto:g.droege@bgbm.orgmailto:g.droege@bgbm.org>
Cc: Katharine Barker <barkerk@si.edumailto:barkerk@si.edumailto:barkerk@si.edumailto:barkerk@si.edu>, Paul
Flemons
<Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au>,
John Deck <jdeck@berkeley.edumailto:jdeck@berkeley.edumailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>, Robert
Hanner <bob.hanner@gmail.commailto:bob.hanner@gmail.commailto:bob.hanner@gmail.commailto:bob.hanner@gmail.com>, Éamonn
Tuama <eotuama@gbif.orgmailto:eotuama@gbif.orgmailto:eotuama@gbif.orgmailto:eotuama@gbif.org>, Robert Robbins
<rjr8222@gmail.commailto:rjr8222@gmail.commailto:rjr8222@gmail.commailto:rjr8222@gmail.com>, "Guentsch, Anton"
<a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>
Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension
for Darwin Core-draft reminder
Dear all,
I finished working on the Google Doc "DNA Tissue Extension Notes - TDWG 2012". Feel free to let this be a working document where comments and questions can be added. I've attached a Word Doc version for archival purposes.
I added the two template extension files (DNATissueExtension.txt and DNAAmplificationExtension.txt) to the shared TDWG GGBN working group folder linked below. They are in the form they need to be submitted to GBIF to be added to their extension registry. They would both need to be updated with the term descriptions, examples, and constraints.
https://drive.google.com/#folders/0BxEyFKwB7zY4WEs0WkdtUU5oVnM
Cheers,
John
On Sun, Oct 21, 2012 at 10:38 PM, John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edu> wrote:
Ooops
...at http://goo.gl/kGHmb. Adding touches based on the files Gabi sent. Will tell you all when finished with that and will send it as a Word doc at that time in case there are any issues with Google docs. Should be soon. Let me know if I should share to any different addresses.
Cheers,
John
On Sun, Oct 21, 2012 at 10:34 PM, John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edu> wrote:
That helps a lot, as it clears up some of my own misconceptions. I
have shared a document where I have captured the thinking behind a
couple of different ways forward with one or two extensions and an
example of how the two-extension might look in the context of a
Darwin Core Archive. The DNA Tissue Extension Notes Google doc can
be found at
On Sun, Oct 21, 2012 at 9:23 PM, "Dröge, Gabriele" <g.droege@bgbm.orgmailto:g.droege@bgbm.orgmailto:g.droege@bgbm.orgmailto:g.droege@bgbm.org> wrote:
Yes we do...
Hi John,
Thanks for getting back to us. Attached are two csv files, one with some main DNA facts and the other with associated GenBank entries und publications (2 examples with 2 GenBank entries per DNA sample).
I included only UnitID/CollCode/InstCode for the related voucher specimen and I excluded the tissue facts since they are quite similar to the DNA facts and should be mapped independently.
Best,
Gabi
-----Original Message-----
From: Barker, Katharine
[mailto:BarkerK@si.edumailto:BarkerK@si.edumailto:BarkerK@si.edu]
Sent: Sunday, October 21, 2012 11:41 PM
To: Paul Flemons; Dröge, Gabriele
Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension
for Darwin Core-draft reminder
Paul and Gabi,
Do we have any sample data that John can use as a test case? I think he would like it today, if possible.
Thanks for your help (and the team work).
Katie
From: John Wieczorek
<tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e
dumailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>
Reply-To:
"tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e
dumailto:tuco@berkeley.edumailto:tuco@berkeley.edu>"
<tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e
dumailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>
Date: Sunday, October 21, 2012 12:03 PM
To: Katharine Barker
<barkerk@si.edumailto:barkerk@si.edumailto:barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edu<mailtomailto:barkerk@si.edu
:barkerk@si.edu>mailto:barkerk@si.edu>>
Subject: Re: FW: Meeting at TDWG 2012 to define a tissue/DNA
extension for Darwin Core-draft reminder
Hi Katie,
Messages received. Will have the extension stuff ready within a few hours and hope to be able to attend remotely. One thing in the meantime. Do you have any example data that could be used as a test case to populate a core with this extension? Would like to try that with some realy data to test my assumptions.
Sorry for the delay.
Thanks,
John
On Sun, Oct 21, 2012 at 10:08 AM, Barker, Katharine <BarkerK@si.edumailto:BarkerK@si.edumailto:BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edumailto:BarkerK@si.edu>> wrote:
Dear John,
I'm sorry that you were unable to attain a visa for China. I was really looking forward to working with you in person with the group. Paul mentioned that he had e-mailed you earlier this evening. Can you please send us the draft for the DarwinCore DNA/tissue extension as soon as possible for review during our working sessions? We have one tomorrow at 1:30 (Beijing time) and another on Tuesday at the same time. It would be really great if you could Skype into either both or one of the sessions.
Thanks for your help on this.
Kind Regards,
Katie
From: <Barker>, Katharine Barker
<barkerk@si.edumailto:barkerk@si.edumailto:barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edu<mailtomailto:barkerk@si.edu
:barkerk@si.edu>mailto:barkerk@si.edu><mailto:barkerk@si.edumailto:barkerk@si.edumailto:barkerk@si.edu<mail
to:barkerk@si.edumailto:to:barkerk@si.edumailto:barkerk@si.edumailto:barkerk@si.edu>>>
Date: Thursday, October 18, 2012 1:34 PM
To: Katharine Barker
<barkerk@si.edumailto:barkerk@si.edumailto:barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edu<mailtomailto:barkerk@si.edu
:barkerk@si.edu>mailto:barkerk@si.edu><mailto:barkerk@si.edumailto:barkerk@si.edumailto:barkerk@si.edu<mail
to:barkerk@si.edumailto:to:barkerk@si.edumailto:barkerk@si.edumailto:barkerk@si.edu>>>, 'John Deck'
<jdeck@berkeley.edumailto:jdeck@berkeley.edumailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkele
y.edumailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edu<mailto:mailto:jdeck@berkeley.edu
jdeck@berkeley.edu>mailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edu<mailto:jdeck@berkeleymailto:jdeck@berkeley.edu
.edu>mailto:jdeck@berkeley.edu>>>, Paul Flemons
<Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au<ma
ilto:Paul.Flemons@austmus.gov.aumailto:ilto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.au
<mailto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.g
ov.au><mailto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmmailto:Paul.Flemons@austmus.gov.au
us.gov.au>mailto:Paul.Flemons@austmus.gov.au>>>, "'"Dröge", Éamonn Tuama
<eotuama@gbif.orgmailto:eotuama@gbif.orgmailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.org<mailto:eotuama@gbif.org
mailto:eotuama@gbif.org>mailto:eotuama@gbif.org><mailto:eotuama@gbif.org<mailto:eotuama@gbmailto:eotuama@gbif.org
if.org>mailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>>,
"Whitacre, Jamie"
<WHITACREJ@si.edumailto:WHITACREJ@si.edumailto:WHITACREJ@si.edumailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edu
mailto:WHITACREJ@si.edu>mailto:WHITACREJ@si.edu><mailto:WHITACREJ@si.edu<mailto:WHITACREJ@mailto:WHITACREJ@si.edu
si.edu>mailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edumailto:WHITACREJ@si.edumailto:WHITACREJ@si.edu>>>,
"'rjr8222@gmail.commailto:rjr8222@gmail.commailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.
commailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:'rjr8222@gmail.com<mailto:rjrmailto:rjr8222@gmail.com
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'"
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ommailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:rjr8222@gmail.com<mailto:rjr82mailto:rjr8222@gmail.com
22@gmail.com>mailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>>
,
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bgbm.orgmailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mamailto:a.guentsch@bgbm.org
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sch@bgbm.org>mailto:a.guentsch@bgbm.org>>>,
"'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.
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ail.commailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com
mailto:gtuco.btuco@gmail.com>mailto:gtuco.btuco@gmail.com>>>,
"'tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.
edumailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:'tuco@berkeley.edu<mailto:tucmailto:tuco@berkeley.edu
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'"
<tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e
dumailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edu<mailto:tuco@mailto:tuco@berkeley.edu
berkeley.edu>mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>>
Cc:
"'morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morris
on@cs.man.ac.ukmailto:on@cs.man.ac.ukmailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:'morrison@cs.
man.ac.ukmailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.u
kmailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk>>'"
<morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morriso
n@cs.man.ac.ukmailto:n@cs.man.ac.ukmailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:morrison@cs.ma
n.ac.ukmailto:morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.uk
mailto:morrison@cs.man.ac.uk>mailto:morrison@cs.man.ac.uk>>>, "Parr, Cynthia"
<parrc@si.edumailto:parrc@si.edumailto:parrc@si.edumailto:parrc@si.edu<mailto:parrc@si.edu<mailto:parrcmailto:parrc@si.edu
@si.edu>mailto:parrc@si.edu><mailto:parrc@si.edumailto:parrc@si.edumailto:parrc@si.edu<mailto:parrc@si.
edumailto:parrc@si.edumailto:parrc@si.edu>>>
Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension
for Darwin Core//Telecon next week
Dear all,
This is a friendly reminder that we will be meeting next Tuesday afternoon at the TDWG 2012 Conference in order to finalize the draft DarwinCore-A DNA/tissue extension for GGBN. As you know, the immediate need for GGBN members is to publish information on tissues. This will happen through extensions to both ABCDDNA and DarwinCore-A. Here we are focused on developing the DarwinCore-A DNA/tissue extension.
An update on the timeline for developing the draft DarwinCore-A DNA/tissue extension is listed below.
1) Review content requirements for DarwinCore-A DNA/tissue extension (completed, see attached required DNA and tissue elements)
2) John Weiczorek will develop the draft DarwinCore-A DNA/tissue extension (to be completed for group review prior to our break out session on Tuesday afternoon, October 23).
3) Tuesday October 23, working meeting
· Questions to answer before final review of DNA/tissue extension
o How do we include repeatable elements of ABCDDNA into DwC-A-DNA (References to more than one sequence record/publication are mandatory)?
o How do we extend the "Basis of Record" in ABCD and DwC-A and how do we include an element similar to ABCD-"Kind of Unit" to DwC-A?
o What are the remaining issues for DwC-A working with IPT? Are any changes in the IPT required?
· Review and finalize draft DarwinCore-A DNA/tissue extension for posting to GBIF site.
Thank you again to everyone who is involved in this project. I look forward to seeing all of you in Beijing.
Kind Regards,
Katie
From: Barker, Katharine
Sent: Friday, September 28, 2012 9:53 AM
To: 'John Deck'; Paul Flemons; "Dröge, Gabriele";
eotuama@gbif.orgmailto:eotuama@gbif.orgmailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.org<mmailto:eotuama@gbif.org
ailto:eotuama@gbif.org>mailto:eotuama@gbif.org><mailto:eotuama@gbif.org<mailto:eotuama@gbimailto:eotuama@gbif.org
f.org>mailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>;
Whitacre, Jamie;
rjr8222@gmail.commailto:rjr8222@gmail.commailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.co
mmailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:rjr8222@gmail.com<mailto:rjr822mailto:rjr8222@gmail.com
2@gmail.com>mailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>;
a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@b
gbm.orgmailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<maimailto:a.guentsch@bgbm.org
lto:a.guentsch@bgbm.org>mailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org<mailto:a.guentsmailto:a.guentsch@bgbm.org
ch@bgbm.org>mailto:a.guentsch@bgbm.org>>;
gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.bt
uco@gmail.commailto:uco@gmail.commailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gma
il.commailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com<mmailto:gtuco.btuco@gmail.com
ailto:gtuco.btuco@gmail.com>mailto:gtuco.btuco@gmail.com>>;
tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.ed
umailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edu<mailto:tuco@bmailto:tuco@berkeley.edu
erkeley.edu>mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>
Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension
for Darwin Core//Telecon next week
Dear all,
We will be meeting this Tuesday at 1pm U.S. Eastern time over Skype in order to discuss the actions required to develop the draft proposal for the Darwin Core tissue/DNA extension. A proposal for designing, testing, and implementing the GGBN data portal is attached for your reference. Please review the timeline and action items leading up to the TDWG 2012 Conference.
My Skype name is Katharine.Barker1. If possible, please forward me your skype account names prior to our meeting.
Kind Regards,
Katie
From:jdeck88@gmail.commailto:From:jdeck88@gmail.commailto:From%3Ajdeck88@gmail.commailto:From%3Ajdeck88@gmail.com<mailto:From
%3Ajdeck88@gmail.commailto:From%253Ajdeck88@gmail.commailto:From%253Ajdeck88@gmail.com><mailto:jde
ck88@gmail.commailto:ck88@gmail.commailto:jdeck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@gmail.com<mmailto:jdeck88@gmail.com
ailto:jdeck88@gmail.com>mailto:jdeck88@gmail.com>>
[mailto:jdeck88@gmail.commailto:jdeck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@
gmail.commailto:jdeck88@gmail.commailto:jdeck88@gmail.com>] On Behalf Of John Deck
Sent: Tuesday, September 25, 2012 4:04 PM
To: Barker, Katharine
Cc: Paul Flemons; "Dröge, Gabriele";
eotuama@gbif.orgmailto:eotuama@gbif.orgmailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.org<mmailto:eotuama@gbif.org
ailto:eotuama@gbif.org>mailto:eotuama@gbif.org><mailto:eotuama@gbif.org<mailto:eotuama@gbimailto:eotuama@gbif.org
f.org>mailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>;
Whitacre, Jamie;
rjr8222@gmail.commailto:rjr8222@gmail.commailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.co
mmailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:rjr8222@gmail.com<mailto:rjr822mailto:rjr8222@gmail.com
2@gmail.com>mailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>;
a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@b
gbm.orgmailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<maimailto:a.guentsch@bgbm.org
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ch@bgbm.org>mailto:a.guentsch@bgbm.org>>;
gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.bt
uco@gmail.commailto:uco@gmail.commailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gma
il.commailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com<mmailto:gtuco.btuco@gmail.com
ailto:gtuco.btuco@gmail.com>mailto:gtuco.btuco@gmail.com>>;
tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.ed
umailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edu<mailto:tuco@bmailto:tuco@berkeley.edu
erkeley.edu>mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>
Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension
for Darwin Core//Telecon next week
Here is the wrapup of the bioCollections Ontology workshop from last week at GSC14:
http://biocodecommons.org/workshops/bioCollections/index.html
This is relevant to these discussions since we focussed on what constitutes a "sample" and also, probably more importantly, processes that work with samples.
We briefly discussed the DwC Tissue Extension and came up with a proposal for a quick-fix and a more substantial fix. The quick-fix is to create two new BasisOfRecord terms: TissueSubSample, DNAExtract (or some terms like that -- Tuco could provide more clarification on this too). Thus, theoretically we could override the dwc:Occurrence class to mean, for example, TissueSubSample the same way we do for Specimens and Observations. The bigger fix is to more fundamentally re-orient DwC around the notion of "Sample", involving adding/changing some properties although we didn't get into any specifics.
P.s. I can do the 12/1/2 timeslots for that monday or tuesday but not the 11.
John
On Mon, Sep 24, 2012 at 12:39 PM, Barker, Katharine <BarkerK@si.edumailto:BarkerK@si.edumailto:BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edumailto:BarkerK@si.edu><mailto:BarkerK@si.edumailto:BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edumailto:BarkerK@si.edu>>> wrote:
Dear all,
We will have a telecon meeting early next week in order to discuss a draft proposal for the Darwin Core tissue/DNA extension. Gabi, Paul, and I will put together a first draft for discussion to be distributed prior to the telecon. As you know, the goal is to have a working draft ready for our working group to review at the TDWG meeting in Beijing this October.
These are our options for meeting next week:
Monday 11am, 12pm, 1pm, 2pm US EDT
Tuesday 11am, 12pm, 1pm, 2pm US EDT
Please let me know if you cannot make one of these times.
Thanks again to those of you who provided input last week at the GSC 14 meeting.
Kind Regards,
Katie
From: Barker, Katharine
Sent: Wednesday, September 12, 2012 10:51 AM
To: 'Paul Flemons'; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.orgmailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.orgmailto:eotuama@gbif.org><mailto:eotuama@gbif.orgmailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; 'rjr8222@gmail.commailto:rjr8222@gmail.com&mailto:rjr8222@gmail.com
lt;mailto:rjr8222@gmail.com>mailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>'; jdeck@berkeley.edumailto:jdeck@berkeley.edumailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>>; 'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>'; 'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>'; 'tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>'
Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension
for Darwin Core
Importance: High
Dear all,
My name is Katie Barker and I am the Global Genome Biodiversity Network Coordinator. As you know from Paul Flemons, members of the GGBN Data Standards and Data Access Task Force are trying to pull together a task group, which you are all part of, for the upcoming TDWG meeting in Beijing this October in order to address a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members. I am contacting you to schedule a meeting in late September/early October to develop a draft proposal for this extension to be completed at the upcoming TDWG meeting.
Please let me know your availability for the last two weeks of September and first two weeks of October. There will be some scheduling issues, as there are task group members on the west and east coasts of the U.S., Europe and Australia.
Paul Flemons (in Australia) will be in the U.S. the first week of October, so maybe we can meet in the afternoon of the 1st, anytime on the second 2nd, or in the morning of the 3rd of October over teleconference (US Eastern Daylight Time). Please let me know if any of these time slots work for you.
Gabi, I believe that you and John Deck will be at the GSC 14 meeting next week. Is there any chance that you can start drawing up an outline for the proposed extension? We could review the outline during our group telecon and start drafting a proposal for review at the TDWG meeting in October.
Kind Regards,
Katie
Task Group Members:
John Weiczorek - Berkeley
Éamonn O'Tuama - GBIF
Jamie Whitacre - SI
John Deck - Berkeley
Robert Robbins - University of California, San Diego Anton Guentsch
- BGBM Gabi Droege- BGBM Paul Flemons- AM
From: Paul Flemons
[mailto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.govmailto:Paul.Flemons@austmus.gov.au
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.gov.au>mailto:Paul.Flemons@austmus.gov.au>]
Sent: Tuesday, August 07, 2012 2:50 AM
To:
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edu>mailto:jdeck@berkeley.edu>>
Cc: Barker, Katharine; Éamonn Ó Tuama [GBIF]; "Dröge, Gabriele"
(g.droege@BGBM.ORGmailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG<mailto:g.droege@BGBM.O
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Subject: Meeting at TDWG 2012 to define a tissue/DNA extension for
Darwin Core
Hi all,
I am on the Data Standards and Access Task Force for the Global Genome Biodiversity Network (http://ggbn.org/) which is in need of a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members.
To this end I am writing to you to ask if you would be interested in participating in a small working group at TDWG in Beijing this year.
At this stage my plan would be to identify relevant fields for inclusion in the extension, using ABCDDNA as a reference. If sufficient progress is made then we would submit the extension for ratification by TDWG (is that how its done John?) The GGBN will use whatever comes out of the group to move towards having a suitable DwC based schema for data sharing.
So please let me know if you are willing to participate in the task group and/or if there is anyone else you feel would be beneficial to have involved.
How much time do you think we will need? I have been thinking that a day will be needed, so we could make that consist of either one full day or two half days. Im also thinking that during the week will be the best time for this.
Thanks for your time
Best Regards
Paul
Paul K J Flemons
Manager, Collection Informatics
Team Lead, Atlas of Living Australia Biodiversity Volunteer
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Nicolas, Gabi, I very much agree that these are separate issues and if we leave out metagenomics for now things becomes much simpler and cleaner. I will add this note to the google doc, but feel free to remove it again if it serves a different scope.
Markus
On 23.10.2012, at 11:19, Dröge, Gabriele wrote:
Dear Nicolas,
you are right. Tissue samples are priority 1, that should be solved until end of January 2013. Environmental samples are quite different, we should discuss this topic later. We are on a good way and hope to finish the draft for the new classes today.
Best, Gabi
From: Nicolas Noé [mailto:niconoebiodiversity@gmail.com] On Behalf Of Nicolas Noé Sent: Tuesday, October 23, 2012 11:09 AM To: Dröge, Gabriele Cc: ""Markus Döring (GBIF)""; tuco@berkeley.edu; snomelf@gmail.com; Paul Flemons (Paul.Flemons@austmus.gov.au); ipt@lists.gbif.org; Robert Robbins; John Deck; Robert Hanner; Guentsch, Anton; Barker, Katharine Subject: Re: [IPT] Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Dear all,
I'm joining this conversation quite late, feel free to correct me if I say something stupid.
From what I just read, it appears we have two totally different use-cases here: • Environmental samples, where the central piece of data is the sample • Tissue samples, that are just new low-level data about a specimen To me, we probably won't be able to merge these two things to find a single clean, pragmatic & simple solution. The former will need the sample at the core, the latter is probably better with a goold old Occurrence at the core.
If we agree we have two distinct problems to solve, maybe it is wise to assess which one is priority #1, solve it now, implement it in IPT and gather real-world feedback before solving issue #2 ?
I feel I'm not really bringing something new on the table, but the point I'd like to make is that maybe we should be care about the "let's-find-a-perfect-solution-that-fits-it-all" syndrom, with all his well-known consequences (complex implementation + risk of losing users).
thanks,
Nicolas
On 10/23/12 03:54, "Dröge, Gabriele" wrote: Now with attachment...
Thanks to all of you for your feedback. I don't understand the figure you created (Markus?). I had a look at http://code.google.com/p/gbif-ecat/wiki/DwCArchive and I think we will keep the core schema in the middle as it is now (Basis of Resource, Taxon or Occurrence).
All what we need to refer to associated objects (samples (tissues, DNA, RNA,...) or other specimens) is an association extension with the identifiers of the referenced records, similar to the UnitAssociation container in ABCD. This extension should have a one to many relation to the core. The DNAAmplification extension is only required if the sample record is a DNA sample, since in this extension so far only DNA specific facts are included (GenBankAccessionNo etc.). The SampleFacts-Extension is quite similar to the main DNA extension of ABCD.
Find attached my figure based on the one from the DwCArchive website. This is how I think it could work and how I understand the star schema, but maybe I am wrong :-). Environmental samples are more complicate maybe we can discuss this topic later (next year)?
Best, Gabi
-----Original Message----- From: "Markus Döring (GBIF)" [mailto:mdoering@gbif.org] Sent: Monday, October 22, 2012 11:31 PM To: tuco@berkeley.edu Cc: Barker, Katharine; ipt@lists.gbif.org; John Deck; Paul Flemons (Paul.Flemons@austmus.gov.au); Dröge, Gabriele; snomelf@gmail.com; Robert Hanner; Guentsch, Anton; Robert Robbins Subject: Re: [IPT] Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Well, let's investigate one thing about your diagram first. Shouldn't there be a one-to-many relationship between Occurrence (specimen) and Sample rather than a many-to-one?
Specimen from the field = Occurrence + Event + Location + Identification + Taxon Sample from the specimen's liver = Sample Sample from the specimen's heart = Sample Sample from the specimen's gut = Sample
yes, thats true. Ididnt think about samples that way when I drafted the diagram.
The scenario I had in my mind was the environmental sample, a vegetation plot survey or just a rock with various lichen species on it. Usually with rich data about the location, habitat and abiotic measurements (lends itself nicely to an extension for samples). In such a sample you then find various species which would be the basis for an occurrence. In the case of metagenomic samples the list of taxa is actually derived information from the amplifications and can vary according to the method used (basically the entire occurrence extension can be derived from the amplifications in this case).
Actually when you take a gut sample from an animal you often are interested in the fauna of that gut, so the occurrences would not be the host, but the bacteria occurring within it.
Markus
And all of the Samples could have multiple Amplifications.
If we want to model this with a Sample Core, then Occurrences may be repeated in the Occurrence extension in your diagram, but every sample would have no more than one Occurrence in the extension file and the sampleID relationship would be one-to-one. If so, then it is also possible to have a Sample Core (Sample rowType) with sampleID as the core record identifier, with "Sample" as basisOfRecord, and with all of the attributes of Sample and of the existing Occurrence Core. This would avoid having a distinct Occurrence extension for Samples, which could get confusing for those who are accustomed to mapping Occurrences already. This combined Sample/Occurrence Core could still have a one-to-many relationship to the Amplifications.
On Mon, Oct 22, 2012 at 1:33 PM, "Markus Döring (GBIF)" mdoering@gbif.org wrote: Adding a new core type to the IPT could be done in less than a day - more work for GBIF would be to support such a format in our indexing code. But if we think its a better solution to go with a new sample core type, I think its worth the extra cost of coding for it.
On 22.10.2012, at 17:53, John Wieczorek wrote:
I like the approach of having a Sample Core, but the approach taken thus far was with the view of being pragmatic to put into practice by January 2013. What do you think could be the possibility of adding a new Core type to the IPT on that time scale? The Darwin Core archive specification can certainly handle it, but the proof is in the implementation.
On Mon, Oct 22, 2012 at 8:11 AM, "Markus Döring (GBIF)" mdoering@gbif.org wrote: Hi all, I only quickly looked through the proposal, but it looks good, pragmatic and definitely to be working for the case when a DNASample equals a single taxon Occurrence.
Im not so sure how well it would work with environmental samples - would we have the sample flattened out and repeated to represent the individual taxa, sexes, ages, etc found in there? I was therefore wondering if anyone had thought about the attached setup before. Sample is at its core and occurrence & dna amplification as extensions with the amplifications (optionally?) refering to the occurrence they belong to.
Another quick observation is that we try to reuse existing terms in extensions as much as possible. Following that rule for example dwc:institutionCode should rather be used instead of dNACollectionCode and probably dc:source for the referenceCitation
until tomorrow, regards, Markus
<sample core.png>
On 22.10.2012, at 12:21, Barker, Katharine wrote:
Dear John,
Please see our working revisions/comments/questions on the DNA/tissue extension for Darwin Core (highlighted in blue). We were able to work through the draft up through "class sample properties": https://docs.google.com/document/d/1RCgIPfu9gAPubjjbog-9vCJonvqcK1p LOaq6H8GSnns/edit
The document is also attached for your reference (just incase any of you are unable to access the document).
Please try to respond to our questions and comments prior to our meeting tomorrow (be sure to make these changes using a different color for tracking purposes).
Tomorrow we will like to 1) briefly recap our revisions on the extension so far (addressing questions and comments), 2) complete our review of the extension and 3) identify any remaining issues with DwC working with IPT (and identify if any changes in the IPT are required).
Thank you for your help on this!
Kind Regards,
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu" <tuco@berkeley.edumailto:tuco@berkeley.edu> Date: Sunday, October 21, 2012 10:52 PM To: Gabriele Droege <g.droege@bgbm.orgmailto:g.droege@bgbm.org> Cc: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au>, John Deck <jdeck@berkeley.edumailto:jdeck@berkeley.edu>, Robert Hanner <bob.hanner@gmail.commailto:bob.hanner@gmail.com>, Éamonn Tuama <eotuama@gbif.orgmailto:eotuama@gbif.org>, Robert Robbins <rjr8222@gmail.commailto:rjr8222@gmail.com>, "Guentsch, Anton" <a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org> Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Dear all,
I finished working on the Google Doc "DNA Tissue Extension Notes - TDWG 2012". Feel free to let this be a working document where comments and questions can be added. I've attached a Word Doc version for archival purposes.
I added the two template extension files (DNATissueExtension.txt and DNAAmplificationExtension.txt) to the shared TDWG GGBN working group folder linked below. They are in the form they need to be submitted to GBIF to be added to their extension registry. They would both need to be updated with the term descriptions, examples, and constraints.
https://drive.google.com/#folders/0BxEyFKwB7zY4WEs0WkdtUU5oVnM
Cheers,
John
On Sun, Oct 21, 2012 at 10:38 PM, John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> wrote: Ooops
...at http://goo.gl/kGHmb. Adding touches based on the files Gabi sent. Will tell you all when finished with that and will send it as a Word doc at that time in case there are any issues with Google docs. Should be soon. Let me know if I should share to any different addresses.
Cheers,
John
On Sun, Oct 21, 2012 at 10:34 PM, John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> wrote: That helps a lot, as it clears up some of my own misconceptions. I have shared a document where I have captured the thinking behind a couple of different ways forward with one or two extensions and an example of how the two-extension might look in the context of a Darwin Core Archive. The DNA Tissue Extension Notes Google doc can be found at
On Sun, Oct 21, 2012 at 9:23 PM, "Dröge, Gabriele" <g.droege@bgbm.orgmailto:g.droege@bgbm.org> wrote: Yes we do... Hi John,
Thanks for getting back to us. Attached are two csv files, one with some main DNA facts and the other with associated GenBank entries und publications (2 examples with 2 GenBank entries per DNA sample). I included only UnitID/CollCode/InstCode for the related voucher specimen and I excluded the tissue facts since they are quite similar to the DNA facts and should be mapped independently.
Best, Gabi
-----Original Message----- From: Barker, Katharine [mailto:BarkerK@si.edumailto:BarkerK@si.edu] Sent: Sunday, October 21, 2012 11:41 PM To: Paul Flemons; Dröge, Gabriele Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Paul and Gabi,
Do we have any sample data that John can use as a test case? I think he would like it today, if possible.
Thanks for your help (and the team work).
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu>> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu>" <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu>> Date: Sunday, October 21, 2012 12:03 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edu<mailto :barkerk@si.edu>>> Subject: Re: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Hi Katie,
Messages received. Will have the extension stuff ready within a few hours and hope to be able to attend remotely. One thing in the meantime. Do you have any example data that could be used as a test case to populate a core with this extension? Would like to try that with some realy data to test my assumptions.
Sorry for the delay.
Thanks,
John
On Sun, Oct 21, 2012 at 10:08 AM, Barker, Katharine <BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu>> wrote: Dear John,
I'm sorry that you were unable to attain a visa for China. I was really looking forward to working with you in person with the group. Paul mentioned that he had e-mailed you earlier this evening. Can you please send us the draft for the DarwinCore DNA/tissue extension as soon as possible for review during our working sessions? We have one tomorrow at 1:30 (Beijing time) and another on Tuesday at the same time. It would be really great if you could Skype into either both or one of the sessions.
Thanks for your help on this.
Kind Regards,
Katie
From: <Barker>, Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edu<mailto :barkerk@si.edu>><mailto:barkerk@si.edumailto:barkerk@si.edu<mail to:barkerk@si.edumailto:barkerk@si.edu>>> Date: Thursday, October 18, 2012 1:34 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edu<mailto :barkerk@si.edu>><mailto:barkerk@si.edumailto:barkerk@si.edu<mail to:barkerk@si.edumailto:barkerk@si.edu>>>, 'John Deck' <jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkele y.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto: jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley .edu>>>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au<ma ilto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.au <mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.g ov.au<mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austm us.gov.au>>>, "'"Dröge", Éamonn Tuama <eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.org< mailto:eotuama@gbif.org>><mailto:eotuama@gbif.orgmailto:eotuama@gb if.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>>, "Whitacre, Jamie" <WHITACREJ@si.edumailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edu< mailto:WHITACREJ@si.edu>><mailto:WHITACREJ@si.edumailto:WHITACREJ@ si.edu<mailto:WHITACREJ@si.edumailto:WHITACREJ@si.edu>>>, "'rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail. commailto:rjr8222@gmail.com><mailto:'rjr8222@gmail.commailto:rjr 8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com> '" <rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.c ommailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr82 22@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>> , "'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch @bgbm.orgmailto:a.guentsch@bgbm.org><mailto:'a.guentsch@bgbm.org< mailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.gue ntsch@bgbm.org>>'" <a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@ bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<ma ilto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guent sch@bgbm.org>>>, "'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco. btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:'gtuco.btuco@ gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.co mmailto:gtuco.btuco@gmail.com>>'" <gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.b tuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gm ail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com< mailto:gtuco.btuco@gmail.com>>>>, "'tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley. edumailto:tuco@berkeley.edu><mailto:'tuco@berkeley.edumailto:tuc o@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu> '" <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@ berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>> Cc: "'morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morris on@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:'morrison@cs. man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.u kmailto:morrison@cs.man.ac.uk>>'" <morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morriso n@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:morrison@cs.ma n.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.uk< mailto:morrison@cs.man.ac.uk>>>>, "Parr, Cynthia" <parrc@si.edumailto:parrc@si.edu<mailto:parrc@si.edumailto:parrc @si.edu><mailto:parrc@si.edumailto:parrc@si.edu<mailto:parrc@si. edumailto:parrc@si.edu>>> Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Dear all,
This is a friendly reminder that we will be meeting next Tuesday afternoon at the TDWG 2012 Conference in order to finalize the draft DarwinCore-A DNA/tissue extension for GGBN. As you know, the immediate need for GGBN members is to publish information on tissues. This will happen through extensions to both ABCDDNA and DarwinCore-A. Here we are focused on developing the DarwinCore-A DNA/tissue extension.
An update on the timeline for developing the draft DarwinCore-A DNA/tissue extension is listed below.
Review content requirements for DarwinCore-A DNA/tissue extension (completed, see attached required DNA and tissue elements)John Weiczorek will develop the draft DarwinCore-A DNA/tissue extension (to be completed for group review prior to our break out session on Tuesday afternoon, October 23).Tuesday October 23, working meeting· Questions to answer before final review of DNA/tissue extension
o How do we include repeatable elements of ABCDDNA into DwC-A-DNA (References to more than one sequence record/publication are mandatory)?
o How do we extend the "Basis of Record" in ABCD and DwC-A and how do we include an element similar to ABCD-"Kind of Unit" to DwC-A?
o What are the remaining issues for DwC-A working with IPT? Are any changes in the IPT required?
· Review and finalize draft DarwinCore-A DNA/tissue extension for posting to GBIF site.
Thank you again to everyone who is involved in this project. I look forward to seeing all of you in Beijing.
Kind Regards,
Katie
From: Barker, Katharine Sent: Friday, September 28, 2012 9:53 AM To: 'John Deck'; Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.org<m ailto:eotuama@gbif.org>><mailto:eotuama@gbif.orgmailto:eotuama@gbi f.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.co mmailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr822 2@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@b gbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mai lto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guents ch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.bt uco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gma il.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com<m ailto:gtuco.btuco@gmail.com>>>; tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.ed umailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@b erkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Dear all,
We will be meeting this Tuesday at 1pm U.S. Eastern time over Skype in order to discuss the actions required to develop the draft proposal for the Darwin Core tissue/DNA extension. A proposal for designing, testing, and implementing the GGBN data portal is attached for your reference. Please review the timeline and action items leading up to the TDWG 2012 Conference.
My Skype name is Katharine.Barker1. If possible, please forward me your skype account names prior to our meeting.
Kind Regards,
Katie
From:jdeck88@gmail.commailto:From%3Ajdeck88@gmail.com<mailto:From %3Ajdeck88@gmail.commailto:From%253Ajdeck88@gmail.com><mailto:jde ck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@gmail.com<m ailto:jdeck88@gmail.com>>> [mailto:jdeck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@ gmail.commailto:jdeck88@gmail.com>] On Behalf Of John Deck Sent: Tuesday, September 25, 2012 4:04 PM To: Barker, Katharine Cc: Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.org<m ailto:eotuama@gbif.org>><mailto:eotuama@gbif.orgmailto:eotuama@gbi f.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.co mmailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr822 2@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@b gbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mai lto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guents ch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.bt uco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gma il.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com<m ailto:gtuco.btuco@gmail.com>>>; tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.ed umailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@b erkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Here is the wrapup of the bioCollections Ontology workshop from last week at GSC14:
http://biocodecommons.org/workshops/bioCollections/index.html
This is relevant to these discussions since we focussed on what constitutes a "sample" and also, probably more importantly, processes that work with samples.
We briefly discussed the DwC Tissue Extension and came up with a proposal for a quick-fix and a more substantial fix. The quick-fix is to create two new BasisOfRecord terms: TissueSubSample, DNAExtract (or some terms like that -- Tuco could provide more clarification on this too). Thus, theoretically we could override the dwc:Occurrence class to mean, for example, TissueSubSample the same way we do for Specimens and Observations. The bigger fix is to more fundamentally re-orient DwC around the notion of "Sample", involving adding/changing some properties although we didn't get into any specifics.
P.s. I can do the 12/1/2 timeslots for that monday or tuesday but not the 11.
John On Mon, Sep 24, 2012 at 12:39 PM, Barker, Katharine <BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu><mailto:BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu>>> wrote: Dear all,
We will have a telecon meeting early next week in order to discuss a draft proposal for the Darwin Core tissue/DNA extension. Gabi, Paul, and I will put together a first draft for discussion to be distributed prior to the telecon. As you know, the goal is to have a working draft ready for our working group to review at the TDWG meeting in Beijing this October.
These are our options for meeting next week: Monday 11am, 12pm, 1pm, 2pm US EDT Tuesday 11am, 12pm, 1pm, 2pm US EDT
Please let me know if you cannot make one of these times.
Thanks again to those of you who provided input last week at the GSC 14 meeting.
Kind Regards,
Katie
From: Barker, Katharine Sent: Wednesday, September 12, 2012 10:51 AM To: 'Paul Flemons'; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org><mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; 'rjr8222@gmail.com& lt;mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>'; jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>>; 'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>'; 'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>'; 'tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>' Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core Importance: High
Dear all,
My name is Katie Barker and I am the Global Genome Biodiversity Network Coordinator. As you know from Paul Flemons, members of the GGBN Data Standards and Data Access Task Force are trying to pull together a task group, which you are all part of, for the upcoming TDWG meeting in Beijing this October in order to address a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members. I am contacting you to schedule a meeting in late September/early October to develop a draft proposal for this extension to be completed at the upcoming TDWG meeting.
Please let me know your availability for the last two weeks of September and first two weeks of October. There will be some scheduling issues, as there are task group members on the west and east coasts of the U.S., Europe and Australia.
Paul Flemons (in Australia) will be in the U.S. the first week of October, so maybe we can meet in the afternoon of the 1st, anytime on the second 2nd, or in the morning of the 3rd of October over teleconference (US Eastern Daylight Time). Please let me know if any of these time slots work for you.
Gabi, I believe that you and John Deck will be at the GSC 14 meeting next week. Is there any chance that you can start drawing up an outline for the proposed extension? We could review the outline during our group telecon and start drafting a proposal for review at the TDWG meeting in October.
Kind Regards,
Katie
Task Group Members:
John Weiczorek - Berkeley Éamonn O'Tuama - GBIF Jamie Whitacre - SI John Deck - Berkeley Robert Robbins - University of California, San Diego Anton Guentsch
- BGBM Gabi Droege- BGBM Paul Flemons- AM
From: Paul Flemons [mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov .au<mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus .gov.au>] Sent: Tuesday, August 07, 2012 2:50 AM To: tuco@berkley.edumailto:tuco@berkley.edu<mailto:tuco@berkley.edu<m ailto:tuco@berkley.edu>><mailto:tuco@berkley.edumailto:tuco@berkle y.edu<mailto:tuco@berkley.edumailto:tuco@berkley.edu>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@b gbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mai lto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guents ch@bgbm.org>>; j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org<mailto:j.holets chek@bgbm.orgmailto:j.holetschek@bgbm.org><mailto:j.holetschek@bg bm.orgmailto:j.holetschek@bgbm.org<mailto:j.holetschek@bgbm.org<m ailto:j.holetschek@bgbm.org>>>; jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley .edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto:j deck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley. edu>> Cc: Barker, Katharine; Éamonn Ó Tuama [GBIF]; "Dröge, Gabriele" (g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG<mailto:g.droege@BGBM.O RGmailto:g.droege@BGBM.ORG><mailto:g.droege@BGBM.ORGmailto:g.dro ege@BGBM.ORG<mailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG>>) Subject: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core
Hi all, I am on the Data Standards and Access Task Force for the Global Genome Biodiversity Network (http://ggbn.org/) which is in need of a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members.
To this end I am writing to you to ask if you would be interested in participating in a small working group at TDWG in Beijing this year.
At this stage my plan would be to identify relevant fields for inclusion in the extension, using ABCDDNA as a reference. If sufficient progress is made then we would submit the extension for ratification by TDWG (is that how its done John?) The GGBN will use whatever comes out of the group to move towards having a suitable DwC based schema for data sharing.
So please let me know if you are willing to participate in the task group and/or if there is anyone else you feel would be beneficial to have involved.
How much time do you think we will need? I have been thinking that a day will be needed, so we could make that consist of either one full day or two half days. Im also thinking that during the week will be the best time for this.
Thanks for your time
Best Regards Paul
Paul K J Flemons Manager, Collection Informatics Team Lead, Atlas of Living Australia Biodiversity Volunteer Portalhttp://volunteer.ala.org.au Biodiversity Information Standards (TDWG) Representative for Oceania Australian Museum 6 College Street Sydney NSW 2010 Australia t 61 2 9320 6343 m 0413458649 f 61 2 9320 6021 Visit: http://www.australianmuseum.net.auhttp://www.australianmuseum.net. au/ Like: http://www.facebook.com/australianmuseum Follow: http://www.twitter.com/austmus Watch: http://www.youtube.com/austmus [cid:image001.png@01CDAD34.391DC790mailto:image001.png@01CDAD34.39 1DC790<mailto:image001.png@01CDAD34.391DC790mailto:image001.png@0 1CDAD34.391DC790>] Inspiring the exploration of nature and cultures
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<DNATissueExtensionNotes2-TDWG2012.docx>___________________________ ____________________ IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt
IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt
Hi folks...
I see alot of use cases now, and projecting into the next several years, that indicate we may need to extend our thinking of the "individual as single organism" view of the world. This is especially true when we're talking about preserving things for eventual sequencing. Here are some examples:
1. There are alot of new sequencing approaches... not just metagenomic sequencing, where one can identify hundreds/thousands of things from a single sample, but also metatranscriptomics, metaproteomics, and the like where we care more about what is being coded for in a particular environment vs. what the name of the individual is. Is this biodiversity? I say so, yes, just that what we care about ultimately is happening on a very low level.
2. Lichens are composed of multiple different organisms and ascribing a single name to the lichen is rather misleading as (i'm told) that the fungus/photosynthetic partners do not always hold true within single "species".
3. Assigning a common taxonomic aggregate name for a "lot" of insects may be OK, but in many environmental samples these would have to be categorized merely as "life".
4. Finally, as Robbins has been pointing out this week, even things we consider as individual organisms human, mouse, not to mention the examples of termite, cow (rumen bacteria) operate only in the context of their interaction with their microorganisms. Granted, the vast majority of current work in museums and data in GBIF are not recording these interactions explicitly but the growth in this line of study is on a trajectory that we can't ignore.
So, back to the decision on whether to make "sample" the core or to add terms to basisOfRecord in conjunction with "Occurrence" at the core. Both ways have advantages/disadvantages and i've personally made arguments on both sides of this debate :) However, the more that i think about this and consider what I'm hearing both at GSC and TDWG, i'm more convinced now that having "sample" at the core is a better approach, especially if it can be implemented in less than a day within IPT. Also, my feeling here is that it will ultimately lead to more productive interactions between the growing number of cases where we care both about "genomics" and "biodiversity".
We're heading off on a field trip today... back tonight, and then we have a Genomic Biodiversity Working/Interest Group meeting tomorrow Thursday afternoon (Beijing time)
John
On Tue, Oct 23, 2012 at 5:30 PM, "Markus Döring (GBIF)" mdoering@gbif.orgwrote:
Nicolas, Gabi, I very much agree that these are separate issues and if we leave out metagenomics for now things becomes much simpler and cleaner. I will add this note to the google doc, but feel free to remove it again if it serves a different scope.
Markus
On 23.10.2012, at 11:19, Dröge, Gabriele wrote:
Dear Nicolas,
you are right. Tissue samples are priority 1, that should be solved
until end of January 2013. Environmental samples are quite different, we should discuss this topic later.
We are on a good way and hope to finish the draft for the new classes
today.
Best, Gabi
From: Nicolas Noé [mailto:niconoebiodiversity@gmail.com] On Behalf Of
Nicolas Noé
Sent: Tuesday, October 23, 2012 11:09 AM To: Dröge, Gabriele Cc: ""Markus Döring (GBIF)""; tuco@berkeley.edu; snomelf@gmail.com;
Paul Flemons (Paul.Flemons@austmus.gov.au); ipt@lists.gbif.org; Robert Robbins; John Deck; Robert Hanner; Guentsch, Anton; Barker, Katharine
Subject: Re: [IPT] Meeting at TDWG 2012 to define a tissue/DNA extension
for Darwin Core-draft reminder
Dear all,
I'm joining this conversation quite late, feel free to correct me if I
say something stupid.
From what I just read, it appears we have two totally different
use-cases here:
• Environmental samples, where the central piece of data is thesample
• Tissue samples, that are just new low-level data about a specimenTo me, we probably won't be able to merge these two things to find a
single clean, pragmatic & simple solution. The former will need the sample at the core, the latter is probably better with a goold old Occurrence at the core.
If we agree we have two distinct problems to solve, maybe it is wise to
assess which one is priority #1, solve it now, implement it in IPT and gather real-world feedback before solving issue #2 ?
I feel I'm not really bringing something new on the table, but the point
I'd like to make is that maybe we should be care about the "let's-find-a-perfect-solution-that-fits-it-all" syndrom, with all his well-known consequences (complex implementation + risk of losing users).
thanks,
Nicolas
On 10/23/12 03:54, "Dröge, Gabriele" wrote: Now with attachment...
Thanks to all of you for your feedback. I don't understand the figure
you created (Markus?).
I had a look at http://code.google.com/p/gbif-ecat/wiki/DwCArchive and
I think we will keep the core schema in the middle as it is now (Basis of Resource, Taxon or Occurrence).
All what we need to refer to associated objects (samples (tissues, DNA,
RNA,...) or other specimens) is an association extension with the identifiers of the referenced records, similar to the UnitAssociation container in ABCD. This extension should have a one to many relation to the core.
The DNAAmplification extension is only required if the sample record is
a DNA sample, since in this extension so far only DNA specific facts are included (GenBankAccessionNo etc.). The SampleFacts-Extension is quite similar to the main DNA extension of ABCD.
Find attached my figure based on the one from the DwCArchive website.
This is how I think it could work and how I understand the star schema, but maybe I am wrong :-). Environmental samples are more complicate maybe we can discuss this topic later (next year)?
Best, Gabi
-----Original Message----- From: "Markus Döring (GBIF)" [mailto:mdoering@gbif.org] Sent: Monday, October 22, 2012 11:31 PM To: tuco@berkeley.edu Cc: Barker, Katharine; ipt@lists.gbif.org; John Deck; Paul Flemons (
Paul.Flemons@austmus.gov.au); Dröge, Gabriele; snomelf@gmail.com; Robert Hanner; Guentsch, Anton; Robert Robbins
Subject: Re: [IPT] Meeting at TDWG 2012 to define a tissue/DNA extension
for Darwin Core-draft reminder
Well, let's investigate one thing about your diagram first. Shouldn't
there be a one-to-many relationship between Occurrence (specimen) and Sample rather than a many-to-one?
Specimen from the field = Occurrence + Event + Location + Identification + Taxon Sample from the specimen's liver = Sample Sample from the specimen's heart = Sample Sample from the specimen's gut = Sample
yes, thats true. Ididnt think about samples that way when I drafted the
diagram.
The scenario I had in my mind was the environmental sample, a vegetation
plot survey or just a rock with various lichen species on it. Usually with rich data about the location, habitat and abiotic measurements (lends itself nicely to an extension for samples). In such a sample you then find various species which would be the basis for an occurrence. In the case of metagenomic samples the list of taxa is actually derived information from the amplifications and can vary according to the method used (basically the entire occurrence extension can be derived from the amplifications in this case).
Actually when you take a gut sample from an animal you often are
interested in the fauna of that gut, so the occurrences would not be the host, but the bacteria occurring within it.
Markus
And all of the Samples could have multiple Amplifications.
If we want to model this with a Sample Core, then Occurrences may be
repeated in the Occurrence extension in your diagram, but every sample would have no more than one Occurrence in the extension file and the sampleID relationship would be one-to-one. If so, then it is also possible to have a Sample Core (Sample rowType) with sampleID as the core record identifier, with "Sample" as basisOfRecord, and with all of the attributes of Sample and of the existing Occurrence Core. This would avoid having a distinct Occurrence extension for Samples, which could get confusing for those who are accustomed to mapping Occurrences already. This combined Sample/Occurrence Core could still have a one-to-many relationship to the Amplifications.
On Mon, Oct 22, 2012 at 1:33 PM, "Markus Döring (GBIF)" <
mdoering@gbif.org> wrote:
Adding a new core type to the IPT could be done in less than a day -
more work for GBIF would be to support such a format in our indexing code.
But if we think its a better solution to go with a new sample core type,
I think its worth the extra cost of coding for it.
On 22.10.2012, at 17:53, John Wieczorek wrote:
I like the approach of having a Sample Core, but the approach taken thus
far was with the view of being pragmatic to put into practice by January 2013. What do you think could be the possibility of adding a new Core type to the IPT on that time scale? The Darwin Core archive specification can certainly handle it, but the proof is in the implementation.
On Mon, Oct 22, 2012 at 8:11 AM, "Markus Döring (GBIF)" <
mdoering@gbif.org> wrote:
Hi all, I only quickly looked through the proposal, but it looks good, pragmatic
and definitely to be working for the case when a DNASample equals a single taxon Occurrence.
Im not so sure how well it would work with environmental samples - would
we have the sample flattened out and repeated to represent the individual taxa, sexes, ages, etc found in there?
I was therefore wondering if anyone had thought about the attached setup
before. Sample is at its core and occurrence & dna amplification as extensions with the amplifications (optionally?) refering to the occurrence they belong to.
Another quick observation is that we try to reuse existing terms in extensions as much as possible. Following that rule for example dwc:institutionCode should rather be used instead of dNACollectionCode and probably dc:source for the referenceCitation
until tomorrow, regards, Markus
<sample core.png>
On 22.10.2012, at 12:21, Barker, Katharine wrote:
Dear John,
Please see our working revisions/comments/questions on the DNA/tissue
extension for Darwin Core (highlighted in blue). We were able to work through the draft up through "class sample properties":
https://docs.google.com/document/d/1RCgIPfu9gAPubjjbog-9vCJonvqcK1p LOaq6H8GSnns/edit
The document is also attached for your reference (just incase any of you
are unable to access the document).
Please try to respond to our questions and comments prior to our meeting
tomorrow (be sure to make these changes using a different color for tracking purposes).
Tomorrow we will like to 1) briefly recap our revisions on the extension
so far (addressing questions and comments), 2) complete our review of the extension and 3) identify any remaining issues with DwC working with IPT (and identify if any changes in the IPT are required).
Thank you for your help on this!
Kind Regards,
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu" <tuco@berkeley.edumailto:tuco@berkeley.edu> Date: Sunday, October 21, 2012 10:52 PM To: Gabriele Droege <g.droege@bgbm.orgmailto:g.droege@bgbm.org> Cc: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au>, John Deck <jdeck@berkeley.edumailto:jdeck@berkeley.edu>, Robert Hanner <bob.hanner@gmail.commailto:bob.hanner@gmail.com>, Éamonn Tuama <eotuama@gbif.orgmailto:eotuama@gbif.org>, Robert Robbins <rjr8222@gmail.commailto:rjr8222@gmail.com>, "Guentsch, Anton" <a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org> Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Dear all,
I finished working on the Google Doc "DNA Tissue Extension Notes - TDWG
2012". Feel free to let this be a working document where comments and questions can be added. I've attached a Word Doc version for archival purposes.
I added the two template extension files (DNATissueExtension.txt and
DNAAmplificationExtension.txt) to the shared TDWG GGBN working group folder linked below. They are in the form they need to be submitted to GBIF to be added to their extension registry. They would both need to be updated with the term descriptions, examples, and constraints.
https://drive.google.com/#folders/0BxEyFKwB7zY4WEs0WkdtUU5oVnM
Cheers,
John
On Sun, Oct 21, 2012 at 10:38 PM, John Wieczorek <tuco@berkeley.edu
mailto:tuco@berkeley.edu> wrote:
Ooops
...at http://goo.gl/kGHmb. Adding touches based on the files Gabi
sent. Will tell you all when finished with that and will send it as a Word doc at that time in case there are any issues with Google docs. Should be soon. Let me know if I should share to any different addresses.
Cheers,
John
On Sun, Oct 21, 2012 at 10:34 PM, John Wieczorek <tuco@berkeley.edu
mailto:tuco@berkeley.edu> wrote:
That helps a lot, as it clears up some of my own misconceptions. I have shared a document where I have captured the thinking behind a couple of different ways forward with one or two extensions and an example of how the two-extension might look in the context of a Darwin Core Archive. The DNA Tissue Extension Notes Google doc can be found at
On Sun, Oct 21, 2012 at 9:23 PM, "Dröge, Gabriele" <g.droege@bgbm.org
mailto:g.droege@bgbm.org> wrote:
Yes we do... Hi John,
Thanks for getting back to us. Attached are two csv files, one with some
main DNA facts and the other with associated GenBank entries und publications (2 examples with 2 GenBank entries per DNA sample).
I included only UnitID/CollCode/InstCode for the related voucher
specimen and I excluded the tissue facts since they are quite similar to the DNA facts and should be mapped independently.
Best, Gabi
-----Original Message----- From: Barker, Katharine [mailto:BarkerK@si.edumailto:BarkerK@si.edu] Sent: Sunday, October 21, 2012 11:41 PM To: Paul Flemons; Dröge, Gabriele Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Paul and Gabi,
Do we have any sample data that John can use as a test case? I think he
would like it today, if possible.
Thanks for your help (and the team work).
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu>> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu>" <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu>> Date: Sunday, October 21, 2012 12:03 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edu<mailto :barkerk@si.edu>>> Subject: Re: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Hi Katie,
Messages received. Will have the extension stuff ready within a few
hours and hope to be able to attend remotely. One thing in the meantime. Do you have any example data that could be used as a test case to populate a core with this extension? Would like to try that with some realy data to test my assumptions.
Sorry for the delay.
Thanks,
John
On Sun, Oct 21, 2012 at 10:08 AM, Barker, Katharine <BarkerK@si.edu
mailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu>> wrote:
Dear John,
I'm sorry that you were unable to attain a visa for China. I was really
looking forward to working with you in person with the group. Paul mentioned that he had e-mailed you earlier this evening. Can you please send us the draft for the DarwinCore DNA/tissue extension as soon as possible for review during our working sessions? We have one tomorrow at 1:30 (Beijing time) and another on Tuesday at the same time. It would be really great if you could Skype into either both or one of the sessions.
Thanks for your help on this.
Kind Regards,
Katie
From: <Barker>, Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edu<mailto :barkerk@si.edu>><mailto:barkerk@si.edumailto:barkerk@si.edu<mail to:barkerk@si.edumailto:barkerk@si.edu>>> Date: Thursday, October 18, 2012 1:34 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edu<mailto :barkerk@si.edu>><mailto:barkerk@si.edumailto:barkerk@si.edu<mail to:barkerk@si.edumailto:barkerk@si.edu>>>, 'John Deck' <jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkele y.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto: jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley .edu>>>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au<ma ilto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.au <mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.g ov.au<mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austm us.gov.au>>>, "'"Dröge", Éamonn Tuama <eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.org< mailto:eotuama@gbif.org>><mailto:eotuama@gbif.orgmailto:eotuama@gb if.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>>, "Whitacre, Jamie" <WHITACREJ@si.edumailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edu< mailto:WHITACREJ@si.edu>><mailto:WHITACREJ@si.edumailto:WHITACREJ@ si.edu<mailto:WHITACREJ@si.edumailto:WHITACREJ@si.edu>>>, "'rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail. commailto:rjr8222@gmail.com><mailto:'rjr8222@gmail.commailto:rjr 8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com> '" <rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.c ommailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr82 22@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>> , "'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch @bgbm.orgmailto:a.guentsch@bgbm.org><mailto:'a.guentsch@bgbm.org< mailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.gue ntsch@bgbm.org>>'" <a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@ bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<ma ilto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guent sch@bgbm.org>>>, "'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco. btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:'gtuco.btuco@ gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.co mmailto:gtuco.btuco@gmail.com>>'" <gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.b tuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gm ail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com< mailto:gtuco.btuco@gmail.com>>>>, "'tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley. edumailto:tuco@berkeley.edu><mailto:'tuco@berkeley.edumailto:tuc o@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu> '" <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@ berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>> Cc: "'morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morris on@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:'morrison@cs. man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.u kmailto:morrison@cs.man.ac.uk>>'" <morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morriso n@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:morrison@cs.ma n.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.uk< mailto:morrison@cs.man.ac.uk>>>>, "Parr, Cynthia" <parrc@si.edumailto:parrc@si.edu<mailto:parrc@si.edumailto:parrc @si.edu><mailto:parrc@si.edumailto:parrc@si.edu<mailto:parrc@si. edumailto:parrc@si.edu>>> Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Dear all,
This is a friendly reminder that we will be meeting next Tuesday
afternoon at the TDWG 2012 Conference in order to finalize the draft DarwinCore-A DNA/tissue extension for GGBN. As you know, the immediate need for GGBN members is to publish information on tissues. This will happen through extensions to both ABCDDNA and DarwinCore-A. Here we are focused on developing the DarwinCore-A DNA/tissue extension.
An update on the timeline for developing the draft DarwinCore-A
DNA/tissue extension is listed below.
Review content requirements for DarwinCore-A DNA/tissueextension (completed, see attached required DNA and tissue elements)
John Weiczorek will develop the draft DarwinCore-A DNA/tissueextension (to be completed for group review prior to our break out session on Tuesday afternoon, October 23).
Tuesday October 23, working meeting· Questions to answer before final review of DNA/tissue
extension
o How do we include repeatable elements of ABCDDNA into DwC-A-DNA
(References to more than one sequence record/publication are mandatory)?
o How do we extend the "Basis of Record" in ABCD and DwC-A and how do
we include an element similar to ABCD-"Kind of Unit" to DwC-A?
o What are the remaining issues for DwC-A working with IPT? Are any
changes in the IPT required?
· Review and finalize draft DarwinCore-A DNA/tissue extension
for posting to GBIF site.
Thank you again to everyone who is involved in this project. I look
forward to seeing all of you in Beijing.
Kind Regards,
Katie
From: Barker, Katharine Sent: Friday, September 28, 2012 9:53 AM To: 'John Deck'; Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.org<m ailto:eotuama@gbif.org>><mailto:eotuama@gbif.orgmailto:eotuama@gbi f.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.co mmailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr822 2@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@b gbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mai lto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guents ch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.bt uco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gma il.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com<m ailto:gtuco.btuco@gmail.com>>>; tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.ed umailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@b erkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Dear all,
We will be meeting this Tuesday at 1pm U.S. Eastern time over Skype in
order to discuss the actions required to develop the draft proposal for the Darwin Core tissue/DNA extension. A proposal for designing, testing, and implementing the GGBN data portal is attached for your reference. Please review the timeline and action items leading up to the TDWG 2012 Conference.
My Skype name is Katharine.Barker1. If possible, please forward me your
skype account names prior to our meeting.
Kind Regards,
Katie
From:jdeck88@gmail.commailto:From%3Ajdeck88@gmail.com<mailto:From %3Ajdeck88@gmail.commailto:From%253Ajdeck88@gmail.com><mailto:jde ck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@gmail.com<m ailto:jdeck88@gmail.com>>> [mailto:jdeck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@ gmail.commailto:jdeck88@gmail.com>] On Behalf Of John Deck Sent: Tuesday, September 25, 2012 4:04 PM To: Barker, Katharine Cc: Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.org<m ailto:eotuama@gbif.org>><mailto:eotuama@gbif.orgmailto:eotuama@gbi f.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.co mmailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr822 2@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@b gbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mai lto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guents ch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.bt uco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gma il.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com<m ailto:gtuco.btuco@gmail.com>>>; tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.ed umailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@b erkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Here is the wrapup of the bioCollections Ontology workshop from last
week at GSC14:
http://biocodecommons.org/workshops/bioCollections/index.html
This is relevant to these discussions since we focussed on what
constitutes a "sample" and also, probably more importantly, processes that work with samples.
We briefly discussed the DwC Tissue Extension and came up with a
proposal for a quick-fix and a more substantial fix. The quick-fix is to create two new BasisOfRecord terms: TissueSubSample, DNAExtract (or some terms like that -- Tuco could provide more clarification on this too). Thus, theoretically we could override the dwc:Occurrence class to mean, for example, TissueSubSample the same way we do for Specimens and Observations. The bigger fix is to more fundamentally re-orient DwC around the notion of "Sample", involving adding/changing some properties although we didn't get into any specifics.
P.s. I can do the 12/1/2 timeslots for that monday or tuesday but not
the 11.
John On Mon, Sep 24, 2012 at 12:39 PM, Barker, Katharine <BarkerK@si.edu
mailto:BarkerK@si.edu<mailto:BarkerK@si.edu<mailto:BarkerK@si.edu
<mailto:BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edu
mailto:BarkerK@si.edu>>> wrote:
Dear all,
We will have a telecon meeting early next week in order to discuss a
draft proposal for the Darwin Core tissue/DNA extension. Gabi, Paul, and I will put together a first draft for discussion to be distributed prior to the telecon. As you know, the goal is to have a working draft ready for our working group to review at the TDWG meeting in Beijing this October.
These are our options for meeting next week: Monday 11am, 12pm, 1pm, 2pm US EDT Tuesday 11am, 12pm, 1pm, 2pm US EDT
Please let me know if you cannot make one of these times.
Thanks again to those of you who provided input last week at the GSC 14
meeting.
Kind Regards,
Katie
From: Barker, Katharine Sent: Wednesday, September 12, 2012 10:51 AM To: 'Paul Flemons'; "Dröge, Gabriele"; eotuama@gbif.org<mailto:
eotuama@gbif.org><mailto:eotuama@gbif.org<mailto:eotuama@gbif.org
<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:
eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; ' rjr8222@gmail.com&
lt;mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.com<mailto:
rjr8222@gmail.com>><mailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com
<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>';
jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edu mailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto: jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>>; 'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org mailto:a.guentsch@bgbm.org>>'; 'gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com>>'; 'tuco@berkeley.edu<mailto:tuco@berkeley.edu
<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:
tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu mailto:tuco@berkeley.edu>>'
Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core Importance: High
Dear all,
My name is Katie Barker and I am the Global Genome Biodiversity Network
Coordinator. As you know from Paul Flemons, members of the GGBN Data Standards and Data Access Task Force are trying to pull together a task group, which you are all part of, for the upcoming TDWG meeting in Beijing this October in order to address a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members. I am contacting you to schedule a meeting in late September/early October to develop a draft proposal for this extension to be completed at the upcoming TDWG meeting.
Please let me know your availability for the last two weeks of September
and first two weeks of October. There will be some scheduling issues, as there are task group members on the west and east coasts of the U.S., Europe and Australia.
Paul Flemons (in Australia) will be in the U.S. the first week of
October, so maybe we can meet in the afternoon of the 1st, anytime on the second 2nd, or in the morning of the 3rd of October over teleconference (US Eastern Daylight Time). Please let me know if any of these time slots work for you.
Gabi, I believe that you and John Deck will be at the GSC 14 meeting
next week. Is there any chance that you can start drawing up an outline for the proposed extension? We could review the outline during our group telecon and start drafting a proposal for review at the TDWG meeting in October.
Kind Regards,
Katie
Task Group Members:
John Weiczorek - Berkeley Éamonn O'Tuama - GBIF Jamie Whitacre - SI John Deck - Berkeley Robert Robbins - University of California, San Diego Anton Guentsch
- BGBM Gabi Droege- BGBM Paul Flemons- AM
From: Paul Flemons [mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov .au<mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus .gov.au>] Sent: Tuesday, August 07, 2012 2:50 AM To: tuco@berkley.edumailto:tuco@berkley.edu<mailto:tuco@berkley.edu<m ailto:tuco@berkley.edu>><mailto:tuco@berkley.edumailto:tuco@berkle y.edu<mailto:tuco@berkley.edumailto:tuco@berkley.edu>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@b gbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mai lto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guents ch@bgbm.org>>; j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org<mailto:j.holets chek@bgbm.orgmailto:j.holetschek@bgbm.org><mailto:j.holetschek@bg bm.orgmailto:j.holetschek@bgbm.org<mailto:j.holetschek@bgbm.org<m ailto:j.holetschek@bgbm.org>>>; jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley .edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto:j deck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley. edu>> Cc: Barker, Katharine; Éamonn Ó Tuama [GBIF]; "Dröge, Gabriele" (g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG<mailto:g.droege@BGBM.O RGmailto:g.droege@BGBM.ORG><mailto:g.droege@BGBM.ORGmailto:g.dro ege@BGBM.ORG<mailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG>>) Subject: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core
Hi all, I am on the Data Standards and Access Task Force for the Global Genome
Biodiversity Network (http://ggbn.org/) which is in need of a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members.
To this end I am writing to you to ask if you would be interested in
participating in a small working group at TDWG in Beijing this year.
At this stage my plan would be to identify relevant fields for inclusion
in the extension, using ABCDDNA as a reference. If sufficient progress is made then we would submit the extension for ratification by TDWG (is that how its done John?) The GGBN will use whatever comes out of the group to move towards having a suitable DwC based schema for data sharing.
So please let me know if you are willing to participate in the task
group and/or if there is anyone else you feel would be beneficial to have involved.
How much time do you think we will need? I have been thinking that a
day will be needed, so we could make that consist of either one full day or two half days. Im also thinking that during the week will be the best time for this.
Thanks for your time
Best Regards Paul
Paul K J Flemons Manager, Collection Informatics Team Lead, Atlas of Living Australia Biodiversity Volunteer Portalhttp://volunteer.ala.org.au Biodiversity Information Standards (TDWG) Representative for Oceania Australian Museum 6 College Street Sydney NSW 2010 Australia t 61 2 9320 6343 m 0413458649 f 61 2 9320 6021 Visit: http://www.australianmuseum.net.auhttp://www.australianmuseum.net. au/ Like: http://www.facebook.com/australianmuseum Follow: http://www.twitter.com/austmus Watch: http://www.youtube.com/austmus [cid:image001.png@01CDAD34.391DC790mailto:image001.png@01CDAD34.39 1DC790<mailto:image001.png@01CDAD34.391DC790mailto:image001.png@0 1CDAD34.391DC790>] Inspiring the exploration of nature and cultures
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very right John. So far these multi taxon cases have been so rare that we could live with ignoring them. But its a growing field that we need to handle better.
I just wanted to stress that adding a new core type to the IPT *codebase* takes a less than a day, but that we would still have to write documentation and translate that which takes more time. And not least publishing a sample core using the IPT is one thing, consuming/indexing it at GBIF or anywhere else is another story. Sample core data would not immediately be visible in the GBIF network. It would take us some time to adjust our indexing to the new data type.
Another observation I have about treating samples as an extension to Occurrence. What does the core occurrence record and its unique! occurrenceID represent after all - an occurrence based on the derived sample or the original "specimen"? I would think that it had to be the sample based occurrence, as if its the specimen then the occurrenceID would not be unique and it would break the dwca. So if you have a collected fish with occurrenceID=1 and a derived tissue sample with occurrenceID=1.2 the occurrenceID 1 (the fish itself) could only show up in some relationship extension, but not in the core dwca occurrence file.
best, Markus
On 24.10.2012, at 00:35, John Deck wrote:
Hi folks...
I see alot of use cases now, and projecting into the next several years, that indicate we may need to extend our thinking of the "individual as single organism" view of the world. This is especially true when we're talking about preserving things for eventual sequencing. Here are some examples:
There are alot of new sequencing approaches... not just metagenomic sequencing, where one can identify hundreds/thousands of things from a single sample, but also metatranscriptomics, metaproteomics, and the like where we care more about what is being coded for in a particular environment vs. what the name of the individual is. Is this biodiversity? I say so, yes, just that what we care about ultimately is happening on a very low level.
Lichens are composed of multiple different organisms and ascribing a single name to the lichen is rather misleading as (i'm told) that the fungus/photosynthetic partners do not always hold true within single "species".
Assigning a common taxonomic aggregate name for a "lot" of insects may be OK, but in many environmental samples these would have to be categorized merely as "life".
Finally, as Robbins has been pointing out this week, even things we consider as individual organisms human, mouse, not to mention the examples of termite, cow (rumen bacteria) operate only in the context of their interaction with their microorganisms. Granted, the vast majority of current work in museums and data in GBIF are not recording these interactions explicitly but the growth in this line of study is on a trajectory that we can't ignore.
So, back to the decision on whether to make "sample" the core or to add terms to basisOfRecord in conjunction with "Occurrence" at the core. Both ways have advantages/disadvantages and i've personally made arguments on both sides of this debate :) However, the more that i think about this and consider what I'm hearing both at GSC and TDWG, i'm more convinced now that having "sample" at the core is a better approach, especially if it can be implemented in less than a day within IPT. Also, my feeling here is that it will ultimately lead to more productive interactions between the growing number of cases where we care both about "genomics" and "biodiversity".
We're heading off on a field trip today... back tonight, and then we have a Genomic Biodiversity Working/Interest Group meeting tomorrow Thursday afternoon (Beijing time)
John
On Tue, Oct 23, 2012 at 5:30 PM, "Markus Döring (GBIF)" mdoering@gbif.org wrote: Nicolas, Gabi, I very much agree that these are separate issues and if we leave out metagenomics for now things becomes much simpler and cleaner. I will add this note to the google doc, but feel free to remove it again if it serves a different scope.
Markus
On 23.10.2012, at 11:19, Dröge, Gabriele wrote:
Dear Nicolas,
you are right. Tissue samples are priority 1, that should be solved until end of January 2013. Environmental samples are quite different, we should discuss this topic later. We are on a good way and hope to finish the draft for the new classes today.
Best, Gabi
From: Nicolas Noé [mailto:niconoebiodiversity@gmail.com] On Behalf Of Nicolas Noé Sent: Tuesday, October 23, 2012 11:09 AM To: Dröge, Gabriele Cc: ""Markus Döring (GBIF)""; tuco@berkeley.edu; snomelf@gmail.com; Paul Flemons (Paul.Flemons@austmus.gov.au); ipt@lists.gbif.org; Robert Robbins; John Deck; Robert Hanner; Guentsch, Anton; Barker, Katharine Subject: Re: [IPT] Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Dear all,
I'm joining this conversation quite late, feel free to correct me if I say something stupid.
From what I just read, it appears we have two totally different use-cases here: • Environmental samples, where the central piece of data is the sample • Tissue samples, that are just new low-level data about a specimen To me, we probably won't be able to merge these two things to find a single clean, pragmatic & simple solution. The former will need the sample at the core, the latter is probably better with a goold old Occurrence at the core.
If we agree we have two distinct problems to solve, maybe it is wise to assess which one is priority #1, solve it now, implement it in IPT and gather real-world feedback before solving issue #2 ?
I feel I'm not really bringing something new on the table, but the point I'd like to make is that maybe we should be care about the "let's-find-a-perfect-solution-that-fits-it-all" syndrom, with all his well-known consequences (complex implementation + risk of losing users).
thanks,
Nicolas
On 10/23/12 03:54, "Dröge, Gabriele" wrote: Now with attachment...
Thanks to all of you for your feedback. I don't understand the figure you created (Markus?). I had a look at http://code.google.com/p/gbif-ecat/wiki/DwCArchive and I think we will keep the core schema in the middle as it is now (Basis of Resource, Taxon or Occurrence).
All what we need to refer to associated objects (samples (tissues, DNA, RNA,...) or other specimens) is an association extension with the identifiers of the referenced records, similar to the UnitAssociation container in ABCD. This extension should have a one to many relation to the core. The DNAAmplification extension is only required if the sample record is a DNA sample, since in this extension so far only DNA specific facts are included (GenBankAccessionNo etc.). The SampleFacts-Extension is quite similar to the main DNA extension of ABCD.
Find attached my figure based on the one from the DwCArchive website. This is how I think it could work and how I understand the star schema, but maybe I am wrong :-). Environmental samples are more complicate maybe we can discuss this topic later (next year)?
Best, Gabi
-----Original Message----- From: "Markus Döring (GBIF)" [mailto:mdoering@gbif.org] Sent: Monday, October 22, 2012 11:31 PM To: tuco@berkeley.edu Cc: Barker, Katharine; ipt@lists.gbif.org; John Deck; Paul Flemons (Paul.Flemons@austmus.gov.au); Dröge, Gabriele; snomelf@gmail.com; Robert Hanner; Guentsch, Anton; Robert Robbins Subject: Re: [IPT] Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Well, let's investigate one thing about your diagram first. Shouldn't there be a one-to-many relationship between Occurrence (specimen) and Sample rather than a many-to-one?
Specimen from the field = Occurrence + Event + Location + Identification + Taxon Sample from the specimen's liver = Sample Sample from the specimen's heart = Sample Sample from the specimen's gut = Sample
yes, thats true. Ididnt think about samples that way when I drafted the diagram.
The scenario I had in my mind was the environmental sample, a vegetation plot survey or just a rock with various lichen species on it. Usually with rich data about the location, habitat and abiotic measurements (lends itself nicely to an extension for samples). In such a sample you then find various species which would be the basis for an occurrence. In the case of metagenomic samples the list of taxa is actually derived information from the amplifications and can vary according to the method used (basically the entire occurrence extension can be derived from the amplifications in this case).
Actually when you take a gut sample from an animal you often are interested in the fauna of that gut, so the occurrences would not be the host, but the bacteria occurring within it.
Markus
And all of the Samples could have multiple Amplifications.
If we want to model this with a Sample Core, then Occurrences may be repeated in the Occurrence extension in your diagram, but every sample would have no more than one Occurrence in the extension file and the sampleID relationship would be one-to-one. If so, then it is also possible to have a Sample Core (Sample rowType) with sampleID as the core record identifier, with "Sample" as basisOfRecord, and with all of the attributes of Sample and of the existing Occurrence Core. This would avoid having a distinct Occurrence extension for Samples, which could get confusing for those who are accustomed to mapping Occurrences already. This combined Sample/Occurrence Core could still have a one-to-many relationship to the Amplifications.
On Mon, Oct 22, 2012 at 1:33 PM, "Markus Döring (GBIF)" mdoering@gbif.org wrote: Adding a new core type to the IPT could be done in less than a day - more work for GBIF would be to support such a format in our indexing code. But if we think its a better solution to go with a new sample core type, I think its worth the extra cost of coding for it.
On 22.10.2012, at 17:53, John Wieczorek wrote:
I like the approach of having a Sample Core, but the approach taken thus far was with the view of being pragmatic to put into practice by January 2013. What do you think could be the possibility of adding a new Core type to the IPT on that time scale? The Darwin Core archive specification can certainly handle it, but the proof is in the implementation.
On Mon, Oct 22, 2012 at 8:11 AM, "Markus Döring (GBIF)" mdoering@gbif.org wrote: Hi all, I only quickly looked through the proposal, but it looks good, pragmatic and definitely to be working for the case when a DNASample equals a single taxon Occurrence.
Im not so sure how well it would work with environmental samples - would we have the sample flattened out and repeated to represent the individual taxa, sexes, ages, etc found in there? I was therefore wondering if anyone had thought about the attached setup before. Sample is at its core and occurrence & dna amplification as extensions with the amplifications (optionally?) refering to the occurrence they belong to.
Another quick observation is that we try to reuse existing terms in extensions as much as possible. Following that rule for example dwc:institutionCode should rather be used instead of dNACollectionCode and probably dc:source for the referenceCitation
until tomorrow, regards, Markus
<sample core.png>
On 22.10.2012, at 12:21, Barker, Katharine wrote:
Dear John,
Please see our working revisions/comments/questions on the DNA/tissue extension for Darwin Core (highlighted in blue). We were able to work through the draft up through "class sample properties": https://docs.google.com/document/d/1RCgIPfu9gAPubjjbog-9vCJonvqcK1p LOaq6H8GSnns/edit
The document is also attached for your reference (just incase any of you are unable to access the document).
Please try to respond to our questions and comments prior to our meeting tomorrow (be sure to make these changes using a different color for tracking purposes).
Tomorrow we will like to 1) briefly recap our revisions on the extension so far (addressing questions and comments), 2) complete our review of the extension and 3) identify any remaining issues with DwC working with IPT (and identify if any changes in the IPT are required).
Thank you for your help on this!
Kind Regards,
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu" <tuco@berkeley.edumailto:tuco@berkeley.edu> Date: Sunday, October 21, 2012 10:52 PM To: Gabriele Droege <g.droege@bgbm.orgmailto:g.droege@bgbm.org> Cc: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au>, John Deck <jdeck@berkeley.edumailto:jdeck@berkeley.edu>, Robert Hanner <bob.hanner@gmail.commailto:bob.hanner@gmail.com>, Éamonn Tuama <eotuama@gbif.orgmailto:eotuama@gbif.org>, Robert Robbins <rjr8222@gmail.commailto:rjr8222@gmail.com>, "Guentsch, Anton" <a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org> Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Dear all,
I finished working on the Google Doc "DNA Tissue Extension Notes - TDWG 2012". Feel free to let this be a working document where comments and questions can be added. I've attached a Word Doc version for archival purposes.
I added the two template extension files (DNATissueExtension.txt and DNAAmplificationExtension.txt) to the shared TDWG GGBN working group folder linked below. They are in the form they need to be submitted to GBIF to be added to their extension registry. They would both need to be updated with the term descriptions, examples, and constraints.
https://drive.google.com/#folders/0BxEyFKwB7zY4WEs0WkdtUU5oVnM
Cheers,
John
On Sun, Oct 21, 2012 at 10:38 PM, John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> wrote: Ooops
...at http://goo.gl/kGHmb. Adding touches based on the files Gabi sent. Will tell you all when finished with that and will send it as a Word doc at that time in case there are any issues with Google docs. Should be soon. Let me know if I should share to any different addresses.
Cheers,
John
On Sun, Oct 21, 2012 at 10:34 PM, John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> wrote: That helps a lot, as it clears up some of my own misconceptions. I have shared a document where I have captured the thinking behind a couple of different ways forward with one or two extensions and an example of how the two-extension might look in the context of a Darwin Core Archive. The DNA Tissue Extension Notes Google doc can be found at
On Sun, Oct 21, 2012 at 9:23 PM, "Dröge, Gabriele" <g.droege@bgbm.orgmailto:g.droege@bgbm.org> wrote: Yes we do... Hi John,
Thanks for getting back to us. Attached are two csv files, one with some main DNA facts and the other with associated GenBank entries und publications (2 examples with 2 GenBank entries per DNA sample). I included only UnitID/CollCode/InstCode for the related voucher specimen and I excluded the tissue facts since they are quite similar to the DNA facts and should be mapped independently.
Best, Gabi
-----Original Message----- From: Barker, Katharine [mailto:BarkerK@si.edumailto:BarkerK@si.edu] Sent: Sunday, October 21, 2012 11:41 PM To: Paul Flemons; Dröge, Gabriele Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Paul and Gabi,
Do we have any sample data that John can use as a test case? I think he would like it today, if possible.
Thanks for your help (and the team work).
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu>> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu>" <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu>> Date: Sunday, October 21, 2012 12:03 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edu<mailto :barkerk@si.edu>>> Subject: Re: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Hi Katie,
Messages received. Will have the extension stuff ready within a few hours and hope to be able to attend remotely. One thing in the meantime. Do you have any example data that could be used as a test case to populate a core with this extension? Would like to try that with some realy data to test my assumptions.
Sorry for the delay.
Thanks,
John
On Sun, Oct 21, 2012 at 10:08 AM, Barker, Katharine <BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu>> wrote: Dear John,
I'm sorry that you were unable to attain a visa for China. I was really looking forward to working with you in person with the group. Paul mentioned that he had e-mailed you earlier this evening. Can you please send us the draft for the DarwinCore DNA/tissue extension as soon as possible for review during our working sessions? We have one tomorrow at 1:30 (Beijing time) and another on Tuesday at the same time. It would be really great if you could Skype into either both or one of the sessions.
Thanks for your help on this.
Kind Regards,
Katie
From: <Barker>, Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edu<mailto :barkerk@si.edu>><mailto:barkerk@si.edumailto:barkerk@si.edu<mail to:barkerk@si.edumailto:barkerk@si.edu>>> Date: Thursday, October 18, 2012 1:34 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edu<mailto :barkerk@si.edu>><mailto:barkerk@si.edumailto:barkerk@si.edu<mail to:barkerk@si.edumailto:barkerk@si.edu>>>, 'John Deck' <jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkele y.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto: jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley .edu>>>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au<ma ilto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.au <mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.g ov.au<mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austm us.gov.au>>>, "'"Dröge", Éamonn Tuama <eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.org< mailto:eotuama@gbif.org>><mailto:eotuama@gbif.orgmailto:eotuama@gb if.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>>, "Whitacre, Jamie" <WHITACREJ@si.edumailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edu< mailto:WHITACREJ@si.edu>><mailto:WHITACREJ@si.edumailto:WHITACREJ@ si.edu<mailto:WHITACREJ@si.edumailto:WHITACREJ@si.edu>>>, "'rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail. commailto:rjr8222@gmail.com><mailto:'rjr8222@gmail.commailto:rjr 8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com> '" <rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.c ommailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr82 22@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>> , "'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch @bgbm.orgmailto:a.guentsch@bgbm.org><mailto:'a.guentsch@bgbm.org< mailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.gue ntsch@bgbm.org>>'" <a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@ bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<ma ilto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guent sch@bgbm.org>>>, "'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco. btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:'gtuco.btuco@ gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.co mmailto:gtuco.btuco@gmail.com>>'" <gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.b tuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gm ail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com< mailto:gtuco.btuco@gmail.com>>>>, "'tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley. edumailto:tuco@berkeley.edu><mailto:'tuco@berkeley.edumailto:tuc o@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu> '" <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@ berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>> Cc: "'morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morris on@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:'morrison@cs. man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.u kmailto:morrison@cs.man.ac.uk>>'" <morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morriso n@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:morrison@cs.ma n.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.uk< mailto:morrison@cs.man.ac.uk>>>>, "Parr, Cynthia" <parrc@si.edumailto:parrc@si.edu<mailto:parrc@si.edumailto:parrc @si.edu><mailto:parrc@si.edumailto:parrc@si.edu<mailto:parrc@si. edumailto:parrc@si.edu>>> Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Dear all,
This is a friendly reminder that we will be meeting next Tuesday afternoon at the TDWG 2012 Conference in order to finalize the draft DarwinCore-A DNA/tissue extension for GGBN. As you know, the immediate need for GGBN members is to publish information on tissues. This will happen through extensions to both ABCDDNA and DarwinCore-A. Here we are focused on developing the DarwinCore-A DNA/tissue extension.
An update on the timeline for developing the draft DarwinCore-A DNA/tissue extension is listed below.
Review content requirements for DarwinCore-A DNA/tissue extension (completed, see attached required DNA and tissue elements)John Weiczorek will develop the draft DarwinCore-A DNA/tissue extension (to be completed for group review prior to our break out session on Tuesday afternoon, October 23).Tuesday October 23, working meeting· Questions to answer before final review of DNA/tissue extension
o How do we include repeatable elements of ABCDDNA into DwC-A-DNA (References to more than one sequence record/publication are mandatory)?
o How do we extend the "Basis of Record" in ABCD and DwC-A and how do we include an element similar to ABCD-"Kind of Unit" to DwC-A?
o What are the remaining issues for DwC-A working with IPT? Are any changes in the IPT required?
· Review and finalize draft DarwinCore-A DNA/tissue extension for posting to GBIF site.
Thank you again to everyone who is involved in this project. I look forward to seeing all of you in Beijing.
Kind Regards,
Katie
From: Barker, Katharine Sent: Friday, September 28, 2012 9:53 AM To: 'John Deck'; Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.org<m ailto:eotuama@gbif.org>><mailto:eotuama@gbif.orgmailto:eotuama@gbi f.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.co mmailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr822 2@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@b gbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mai lto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guents ch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.bt uco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gma il.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com<m ailto:gtuco.btuco@gmail.com>>>; tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.ed umailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@b erkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Dear all,
We will be meeting this Tuesday at 1pm U.S. Eastern time over Skype in order to discuss the actions required to develop the draft proposal for the Darwin Core tissue/DNA extension. A proposal for designing, testing, and implementing the GGBN data portal is attached for your reference. Please review the timeline and action items leading up to the TDWG 2012 Conference.
My Skype name is Katharine.Barker1. If possible, please forward me your skype account names prior to our meeting.
Kind Regards,
Katie
From:jdeck88@gmail.commailto:From%3Ajdeck88@gmail.com<mailto:From %3Ajdeck88@gmail.commailto:From%253Ajdeck88@gmail.com><mailto:jde ck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@gmail.com<m ailto:jdeck88@gmail.com>>> [mailto:jdeck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@ gmail.commailto:jdeck88@gmail.com>] On Behalf Of John Deck Sent: Tuesday, September 25, 2012 4:04 PM To: Barker, Katharine Cc: Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.org<m ailto:eotuama@gbif.org>><mailto:eotuama@gbif.orgmailto:eotuama@gbi f.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.co mmailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr822 2@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@b gbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mai lto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guents ch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.bt uco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gma il.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com<m ailto:gtuco.btuco@gmail.com>>>; tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.ed umailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@b erkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Here is the wrapup of the bioCollections Ontology workshop from last week at GSC14:
http://biocodecommons.org/workshops/bioCollections/index.html
This is relevant to these discussions since we focussed on what constitutes a "sample" and also, probably more importantly, processes that work with samples.
We briefly discussed the DwC Tissue Extension and came up with a proposal for a quick-fix and a more substantial fix. The quick-fix is to create two new BasisOfRecord terms: TissueSubSample, DNAExtract (or some terms like that -- Tuco could provide more clarification on this too). Thus, theoretically we could override the dwc:Occurrence class to mean, for example, TissueSubSample the same way we do for Specimens and Observations. The bigger fix is to more fundamentally re-orient DwC around the notion of "Sample", involving adding/changing some properties although we didn't get into any specifics.
P.s. I can do the 12/1/2 timeslots for that monday or tuesday but not the 11.
John On Mon, Sep 24, 2012 at 12:39 PM, Barker, Katharine <BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu><mailto:BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu>>> wrote: Dear all,
We will have a telecon meeting early next week in order to discuss a draft proposal for the Darwin Core tissue/DNA extension. Gabi, Paul, and I will put together a first draft for discussion to be distributed prior to the telecon. As you know, the goal is to have a working draft ready for our working group to review at the TDWG meeting in Beijing this October.
These are our options for meeting next week: Monday 11am, 12pm, 1pm, 2pm US EDT Tuesday 11am, 12pm, 1pm, 2pm US EDT
Please let me know if you cannot make one of these times.
Thanks again to those of you who provided input last week at the GSC 14 meeting.
Kind Regards,
Katie
From: Barker, Katharine Sent: Wednesday, September 12, 2012 10:51 AM To: 'Paul Flemons'; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org><mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; 'rjr8222@gmail.com& lt;mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>'; jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>>; 'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>'; 'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>'; 'tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>' Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core Importance: High
Dear all,
My name is Katie Barker and I am the Global Genome Biodiversity Network Coordinator. As you know from Paul Flemons, members of the GGBN Data Standards and Data Access Task Force are trying to pull together a task group, which you are all part of, for the upcoming TDWG meeting in Beijing this October in order to address a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members. I am contacting you to schedule a meeting in late September/early October to develop a draft proposal for this extension to be completed at the upcoming TDWG meeting.
Please let me know your availability for the last two weeks of September and first two weeks of October. There will be some scheduling issues, as there are task group members on the west and east coasts of the U.S., Europe and Australia.
Paul Flemons (in Australia) will be in the U.S. the first week of October, so maybe we can meet in the afternoon of the 1st, anytime on the second 2nd, or in the morning of the 3rd of October over teleconference (US Eastern Daylight Time). Please let me know if any of these time slots work for you.
Gabi, I believe that you and John Deck will be at the GSC 14 meeting next week. Is there any chance that you can start drawing up an outline for the proposed extension? We could review the outline during our group telecon and start drafting a proposal for review at the TDWG meeting in October.
Kind Regards,
Katie
Task Group Members:
John Weiczorek - Berkeley Éamonn O'Tuama - GBIF Jamie Whitacre - SI John Deck - Berkeley Robert Robbins - University of California, San Diego Anton Guentsch
- BGBM Gabi Droege- BGBM Paul Flemons- AM
From: Paul Flemons [mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov .au<mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus .gov.au>] Sent: Tuesday, August 07, 2012 2:50 AM To: tuco@berkley.edumailto:tuco@berkley.edu<mailto:tuco@berkley.edu<m ailto:tuco@berkley.edu>><mailto:tuco@berkley.edumailto:tuco@berkle y.edu<mailto:tuco@berkley.edumailto:tuco@berkley.edu>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@b gbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mai lto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guents ch@bgbm.org>>; j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org<mailto:j.holets chek@bgbm.orgmailto:j.holetschek@bgbm.org><mailto:j.holetschek@bg bm.orgmailto:j.holetschek@bgbm.org<mailto:j.holetschek@bgbm.org<m ailto:j.holetschek@bgbm.org>>>; jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley .edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto:j deck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley. edu>> Cc: Barker, Katharine; Éamonn Ó Tuama [GBIF]; "Dröge, Gabriele" (g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG<mailto:g.droege@BGBM.O RGmailto:g.droege@BGBM.ORG><mailto:g.droege@BGBM.ORGmailto:g.dro ege@BGBM.ORG<mailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG>>) Subject: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core
Hi all, I am on the Data Standards and Access Task Force for the Global Genome Biodiversity Network (http://ggbn.org/) which is in need of a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members.
To this end I am writing to you to ask if you would be interested in participating in a small working group at TDWG in Beijing this year.
At this stage my plan would be to identify relevant fields for inclusion in the extension, using ABCDDNA as a reference. If sufficient progress is made then we would submit the extension for ratification by TDWG (is that how its done John?) The GGBN will use whatever comes out of the group to move towards having a suitable DwC based schema for data sharing.
So please let me know if you are willing to participate in the task group and/or if there is anyone else you feel would be beneficial to have involved.
How much time do you think we will need? I have been thinking that a day will be needed, so we could make that consist of either one full day or two half days. Im also thinking that during the week will be the best time for this.
Thanks for your time
Best Regards Paul
Paul K J Flemons Manager, Collection Informatics Team Lead, Atlas of Living Australia Biodiversity Volunteer Portalhttp://volunteer.ala.org.au Biodiversity Information Standards (TDWG) Representative for Oceania Australian Museum 6 College Street Sydney NSW 2010 Australia t 61 2 9320 6343 m 0413458649 f 61 2 9320 6021 Visit: http://www.australianmuseum.net.auhttp://www.australianmuseum.net. au/ Like: http://www.facebook.com/australianmuseum Follow: http://www.twitter.com/austmus Watch: http://www.youtube.com/austmus [cid:image001.png@01CDAD34.391DC790mailto:image001.png@01CDAD34.39 1DC790<mailto:image001.png@01CDAD34.391DC790mailto:image001.png@0 1CDAD34.391DC790>] Inspiring the exploration of nature and cultures
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<DNATissueExtensionNotes2-TDWG2012.docx>___________________________ ____________________ IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt
IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt
-- John Deck (541) 321-0689
On Wed, Oct 24, 2012 at 4:30 PM, "Markus Döring (GBIF)" mdoering@gbif.orgwrote:
very right John. So far these multi taxon cases have been so rare that we could live with ignoring them. But its a growing field that we need to handle better.
I just wanted to stress that adding a new core type to the IPT *codebase* takes a less than a day, but that we would still have to write documentation and translate that which takes more time. And not least publishing a sample core using the IPT is one thing, consuming/indexing it at GBIF or anywhere else is another story. Sample core data would not immediately be visible in the GBIF network. It would take us some time to adjust our indexing to the new data type.
Ah yes, thanks for clarifying the implementation issues (and they're really easy for me because i'm not the one doing it!). One path is to approve a Beta release of the Extension (& IPT codebase) to allow time for testing the indexing component.
Another observation I have about treating samples as an extension to Occurrence. What does the core occurrence record and its unique! occurrenceID represent after all - an occurrence based on the derived sample or the original "specimen"? I would think that it had to be the sample based occurrence, as if its the specimen then the occurrenceID would not be unique and it would break the dwca. So if you have a collected fish with occurrenceID=1 and a derived tissue sample with occurrenceID=1.2 the occurrenceID 1 (the fish itself) could only show up in some relationship extension, but not in the core dwca occurrence file.
good point
best, Markus
On 24.10.2012, at 00:35, John Deck wrote:
Hi folks...
I see alot of use cases now, and projecting into the next several years,
that indicate we may need to extend our thinking of the "individual as single organism" view of the world. This is especially true when we're talking about preserving things for eventual sequencing. Here are some examples:
- There are alot of new sequencing approaches... not just metagenomic
sequencing, where one can identify hundreds/thousands of things from a single sample, but also metatranscriptomics, metaproteomics, and the like where we care more about what is being coded for in a particular environment vs. what the name of the individual is. Is this biodiversity? I say so, yes, just that what we care about ultimately is happening on a very low level.
- Lichens are composed of multiple different organisms and ascribing a
single name to the lichen is rather misleading as (i'm told) that the fungus/photosynthetic partners do not always hold true within single "species".
- Assigning a common taxonomic aggregate name for a "lot" of insects
may be OK, but in many environmental samples these would have to be categorized merely as "life".
- Finally, as Robbins has been pointing out this week, even things we
consider as individual organisms human, mouse, not to mention the examples of termite, cow (rumen bacteria) operate only in the context of their interaction with their microorganisms. Granted, the vast majority of current work in museums and data in GBIF are not recording these interactions explicitly but the growth in this line of study is on a trajectory that we can't ignore.
So, back to the decision on whether to make "sample" the core or to add
terms to basisOfRecord in conjunction with "Occurrence" at the core. Both ways have advantages/disadvantages and i've personally made arguments on both sides of this debate :) However, the more that i think about this and consider what I'm hearing both at GSC and TDWG, i'm more convinced now that having "sample" at the core is a better approach, especially if it can be implemented in less than a day within IPT. Also, my feeling here is that it will ultimately lead to more productive interactions between the growing number of cases where we care both about "genomics" and "biodiversity".
We're heading off on a field trip today... back tonight, and then we
have a Genomic Biodiversity Working/Interest Group meeting tomorrow Thursday afternoon (Beijing time)
John
On Tue, Oct 23, 2012 at 5:30 PM, "Markus Döring (GBIF)" <
mdoering@gbif.org> wrote:
Nicolas, Gabi, I very much agree that these are separate issues and if we leave out
metagenomics for now things becomes much simpler and cleaner.
I will add this note to the google doc, but feel free to remove it again
if it serves a different scope.
Markus
On 23.10.2012, at 11:19, Dröge, Gabriele wrote:
Dear Nicolas,
you are right. Tissue samples are priority 1, that should be solved
until end of January 2013. Environmental samples are quite different, we should discuss this topic later.
We are on a good way and hope to finish the draft for the new classes
today.
Best, Gabi
From: Nicolas Noé [mailto:niconoebiodiversity@gmail.com] On Behalf Of
Nicolas Noé
Sent: Tuesday, October 23, 2012 11:09 AM To: Dröge, Gabriele Cc: ""Markus Döring (GBIF)""; tuco@berkeley.edu; snomelf@gmail.com;
Paul Flemons (Paul.Flemons@austmus.gov.au); ipt@lists.gbif.org; Robert Robbins; John Deck; Robert Hanner; Guentsch, Anton; Barker, Katharine
Subject: Re: [IPT] Meeting at TDWG 2012 to define a tissue/DNA
extension for Darwin Core-draft reminder
Dear all,
I'm joining this conversation quite late, feel free to correct me if I
say something stupid.
From what I just read, it appears we have two totally different
use-cases here:
• Environmental samples, where the central piece of data is thesample
• Tissue samples, that are just new low-level data about aspecimen
To me, we probably won't be able to merge these two things to find a
single clean, pragmatic & simple solution. The former will need the sample at the core, the latter is probably better with a goold old Occurrence at the core.
If we agree we have two distinct problems to solve, maybe it is wise
to assess which one is priority #1, solve it now, implement it in IPT and gather real-world feedback before solving issue #2 ?
I feel I'm not really bringing something new on the table, but the
point I'd like to make is that maybe we should be care about the "let's-find-a-perfect-solution-that-fits-it-all" syndrom, with all his well-known consequences (complex implementation + risk of losing users).
thanks,
Nicolas
On 10/23/12 03:54, "Dröge, Gabriele" wrote: Now with attachment...
Thanks to all of you for your feedback. I don't understand the figure
you created (Markus?).
I had a look at http://code.google.com/p/gbif-ecat/wiki/DwCArchiveand I think we will keep the core schema in the middle as it is now (Basis
of Resource, Taxon or Occurrence).
All what we need to refer to associated objects (samples (tissues,
DNA, RNA,...) or other specimens) is an association extension with the identifiers of the referenced records, similar to the UnitAssociation container in ABCD. This extension should have a one to many relation to the core.
The DNAAmplification extension is only required if the sample record
is a DNA sample, since in this extension so far only DNA specific facts are included (GenBankAccessionNo etc.). The SampleFacts-Extension is quite similar to the main DNA extension of ABCD.
Find attached my figure based on the one from the DwCArchive website.
This is how I think it could work and how I understand the star schema, but maybe I am wrong :-). Environmental samples are more complicate maybe we can discuss this topic later (next year)?
Best, Gabi
-----Original Message----- From: "Markus Döring (GBIF)" [mailto:mdoering@gbif.org] Sent: Monday, October 22, 2012 11:31 PM To: tuco@berkeley.edu Cc: Barker, Katharine; ipt@lists.gbif.org; John Deck; Paul Flemons (
Paul.Flemons@austmus.gov.au); Dröge, Gabriele; snomelf@gmail.com; Robert Hanner; Guentsch, Anton; Robert Robbins
Subject: Re: [IPT] Meeting at TDWG 2012 to define a tissue/DNA
extension for Darwin Core-draft reminder
Well, let's investigate one thing about your diagram first. Shouldn't
there be a one-to-many relationship between Occurrence (specimen) and Sample rather than a many-to-one?
Specimen from the field = Occurrence + Event + Location + Identification + Taxon Sample from the specimen's liver = Sample Sample from the specimen's heart = Sample Sample from the specimen's gut = Sample
yes, thats true. Ididnt think about samples that way when I drafted
the diagram.
The scenario I had in my mind was the environmental sample, a
vegetation plot survey or just a rock with various lichen species on it. Usually with rich data about the location, habitat and abiotic measurements (lends itself nicely to an extension for samples). In such a sample you then find various species which would be the basis for an occurrence. In the case of metagenomic samples the list of taxa is actually derived information from the amplifications and can vary according to the method used (basically the entire occurrence extension can be derived from the amplifications in this case).
Actually when you take a gut sample from an animal you often are
interested in the fauna of that gut, so the occurrences would not be the host, but the bacteria occurring within it.
Markus
And all of the Samples could have multiple Amplifications.
If we want to model this with a Sample Core, then Occurrences may be
repeated in the Occurrence extension in your diagram, but every sample would have no more than one Occurrence in the extension file and the sampleID relationship would be one-to-one. If so, then it is also possible to have a Sample Core (Sample rowType) with sampleID as the core record identifier, with "Sample" as basisOfRecord, and with all of the attributes of Sample and of the existing Occurrence Core. This would avoid having a distinct Occurrence extension for Samples, which could get confusing for those who are accustomed to mapping Occurrences already. This combined Sample/Occurrence Core could still have a one-to-many relationship to the Amplifications.
On Mon, Oct 22, 2012 at 1:33 PM, "Markus Döring (GBIF)" <
mdoering@gbif.org> wrote:
Adding a new core type to the IPT could be done in less than a day -
more work for GBIF would be to support such a format in our indexing code.
But if we think its a better solution to go with a new sample core
type, I think its worth the extra cost of coding for it.
On 22.10.2012, at 17:53, John Wieczorek wrote:
I like the approach of having a Sample Core, but the approach taken
thus far was with the view of being pragmatic to put into practice by January 2013. What do you think could be the possibility of adding a new Core type to the IPT on that time scale? The Darwin Core archive specification can certainly handle it, but the proof is in the implementation.
On Mon, Oct 22, 2012 at 8:11 AM, "Markus Döring (GBIF)" <
mdoering@gbif.org> wrote:
Hi all, I only quickly looked through the proposal, but it looks good,
pragmatic and definitely to be working for the case when a DNASample equals a single taxon Occurrence.
Im not so sure how well it would work with environmental samples -
would we have the sample flattened out and repeated to represent the individual taxa, sexes, ages, etc found in there?
I was therefore wondering if anyone had thought about the attached
setup before. Sample is at its core and occurrence & dna amplification as extensions with the amplifications (optionally?) refering to the occurrence they belong to.
Another quick observation is that we try to reuse existing terms in extensions as much as possible. Following that rule for example dwc:institutionCode should rather be used instead of dNACollectionCode and probably dc:source for the referenceCitation
until tomorrow, regards, Markus
<sample core.png>
On 22.10.2012, at 12:21, Barker, Katharine wrote:
Dear John,
Please see our working revisions/comments/questions on the DNA/tissue
extension for Darwin Core (highlighted in blue). We were able to work through the draft up through "class sample properties":
https://docs.google.com/document/d/1RCgIPfu9gAPubjjbog-9vCJonvqcK1p LOaq6H8GSnns/edit
The document is also attached for your reference (just incase any of
you are unable to access the document).
Please try to respond to our questions and comments prior to our
meeting tomorrow (be sure to make these changes using a different color for tracking purposes).
Tomorrow we will like to 1) briefly recap our revisions on the
extension so far (addressing questions and comments), 2) complete our review of the extension and 3) identify any remaining issues with DwC working with IPT (and identify if any changes in the IPT are required).
Thank you for your help on this!
Kind Regards,
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu" <tuco@berkeley.edumailto:tuco@berkeley.edu> Date: Sunday, October 21, 2012 10:52 PM To: Gabriele Droege <g.droege@bgbm.orgmailto:g.droege@bgbm.org> Cc: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au>, John Deck <jdeck@berkeley.edumailto:jdeck@berkeley.edu>, Robert Hanner <bob.hanner@gmail.commailto:bob.hanner@gmail.com>, Éamonn Tuama <eotuama@gbif.orgmailto:eotuama@gbif.org>, Robert Robbins <rjr8222@gmail.commailto:rjr8222@gmail.com>, "Guentsch, Anton" <a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org> Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Dear all,
I finished working on the Google Doc "DNA Tissue Extension Notes -
TDWG 2012". Feel free to let this be a working document where comments and questions can be added. I've attached a Word Doc version for archival purposes.
I added the two template extension files (DNATissueExtension.txt and
DNAAmplificationExtension.txt) to the shared TDWG GGBN working group folder linked below. They are in the form they need to be submitted to GBIF to be added to their extension registry. They would both need to be updated with the term descriptions, examples, and constraints.
https://drive.google.com/#folders/0BxEyFKwB7zY4WEs0WkdtUU5oVnM
Cheers,
John
On Sun, Oct 21, 2012 at 10:38 PM, John Wieczorek <tuco@berkeley.edu
mailto:tuco@berkeley.edu> wrote:
Ooops
...at http://goo.gl/kGHmb. Adding touches based on the files Gabi
sent. Will tell you all when finished with that and will send it as a Word doc at that time in case there are any issues with Google docs. Should be soon. Let me know if I should share to any different addresses.
Cheers,
John
On Sun, Oct 21, 2012 at 10:34 PM, John Wieczorek <tuco@berkeley.edu
mailto:tuco@berkeley.edu> wrote:
That helps a lot, as it clears up some of my own misconceptions. I have shared a document where I have captured the thinking behind a couple of different ways forward with one or two extensions and an example of how the two-extension might look in the context of a Darwin Core Archive. The DNA Tissue Extension Notes Google doc can be found at
On Sun, Oct 21, 2012 at 9:23 PM, "Dröge, Gabriele" <g.droege@bgbm.org
mailto:g.droege@bgbm.org> wrote:
Yes we do... Hi John,
Thanks for getting back to us. Attached are two csv files, one with
some main DNA facts and the other with associated GenBank entries und publications (2 examples with 2 GenBank entries per DNA sample).
I included only UnitID/CollCode/InstCode for the related voucher
specimen and I excluded the tissue facts since they are quite similar to the DNA facts and should be mapped independently.
Best, Gabi
-----Original Message----- From: Barker, Katharine [mailto:BarkerK@si.edumailto:BarkerK@si.edu] Sent: Sunday, October 21, 2012 11:41 PM To: Paul Flemons; Dröge, Gabriele Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Paul and Gabi,
Do we have any sample data that John can use as a test case? I think
he would like it today, if possible.
Thanks for your help (and the team work).
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu>> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu>" <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu>> Date: Sunday, October 21, 2012 12:03 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edu<mailto :barkerk@si.edu>>> Subject: Re: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Hi Katie,
Messages received. Will have the extension stuff ready within a few
hours and hope to be able to attend remotely. One thing in the meantime. Do you have any example data that could be used as a test case to populate a core with this extension? Would like to try that with some realy data to test my assumptions.
Sorry for the delay.
Thanks,
John
On Sun, Oct 21, 2012 at 10:08 AM, Barker, Katharine <BarkerK@si.edu
mailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu>> wrote:
Dear John,
I'm sorry that you were unable to attain a visa for China. I was
really looking forward to working with you in person with the group. Paul mentioned that he had e-mailed you earlier this evening. Can you please send us the draft for the DarwinCore DNA/tissue extension as soon as possible for review during our working sessions? We have one tomorrow at 1:30 (Beijing time) and another on Tuesday at the same time. It would be really great if you could Skype into either both or one of the sessions.
Thanks for your help on this.
Kind Regards,
Katie
From: <Barker>, Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edu<mailto :barkerk@si.edu>><mailto:barkerk@si.edumailto:barkerk@si.edu<mail to:barkerk@si.edumailto:barkerk@si.edu>>> Date: Thursday, October 18, 2012 1:34 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edu<mailto :barkerk@si.edu>><mailto:barkerk@si.edumailto:barkerk@si.edu<mail to:barkerk@si.edumailto:barkerk@si.edu>>>, 'John Deck' <jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkele y.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto: jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley .edu>>>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au<ma ilto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.au <mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.g ov.au<mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austm us.gov.au>>>, "'"Dröge", Éamonn Tuama <eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.org< mailto:eotuama@gbif.org>><mailto:eotuama@gbif.orgmailto:eotuama@gb if.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>>, "Whitacre, Jamie" <WHITACREJ@si.edumailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edu< mailto:WHITACREJ@si.edu>><mailto:WHITACREJ@si.edumailto:WHITACREJ@ si.edu<mailto:WHITACREJ@si.edumailto:WHITACREJ@si.edu>>>, "'rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail. commailto:rjr8222@gmail.com><mailto:'rjr8222@gmail.commailto:rjr 8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com> '" <rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.c ommailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr82 22@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>> , "'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch @bgbm.orgmailto:a.guentsch@bgbm.org><mailto:'a.guentsch@bgbm.org< mailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.gue ntsch@bgbm.org>>'" <a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@ bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<ma ilto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guent sch@bgbm.org>>>, "'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco. btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:'gtuco.btuco@ gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.co mmailto:gtuco.btuco@gmail.com>>'" <gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.b tuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gm ail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com< mailto:gtuco.btuco@gmail.com>>>>, "'tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley. edumailto:tuco@berkeley.edu><mailto:'tuco@berkeley.edumailto:tuc o@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu> '" <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@ berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>> Cc: "'morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morris on@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:'morrison@cs. man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.u kmailto:morrison@cs.man.ac.uk>>'" <morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morriso n@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:morrison@cs.ma n.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.uk< mailto:morrison@cs.man.ac.uk>>>>, "Parr, Cynthia" <parrc@si.edumailto:parrc@si.edu<mailto:parrc@si.edumailto:parrc @si.edu><mailto:parrc@si.edumailto:parrc@si.edu<mailto:parrc@si. edumailto:parrc@si.edu>>> Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Dear all,
This is a friendly reminder that we will be meeting next Tuesday
afternoon at the TDWG 2012 Conference in order to finalize the draft DarwinCore-A DNA/tissue extension for GGBN. As you know, the immediate need for GGBN members is to publish information on tissues. This will happen through extensions to both ABCDDNA and DarwinCore-A. Here we are focused on developing the DarwinCore-A DNA/tissue extension.
An update on the timeline for developing the draft DarwinCore-A
DNA/tissue extension is listed below.
Review content requirements for DarwinCore-A DNA/tissueextension (completed, see attached required DNA and tissue elements)
John Weiczorek will develop the draft DarwinCore-A DNA/tissueextension (to be completed for group review prior to our break out session on Tuesday afternoon, October 23).
Tuesday October 23, working meeting· Questions to answer before final review of DNA/tissue
extension
o How do we include repeatable elements of ABCDDNA into DwC-A-DNA
(References to more than one sequence record/publication are mandatory)?
o How do we extend the "Basis of Record" in ABCD and DwC-A and how
do we include an element similar to ABCD-"Kind of Unit" to DwC-A?
o What are the remaining issues for DwC-A working with IPT? Are any
changes in the IPT required?
· Review and finalize draft DarwinCore-A DNA/tissue extension
for posting to GBIF site.
Thank you again to everyone who is involved in this project. I look
forward to seeing all of you in Beijing.
Kind Regards,
Katie
From: Barker, Katharine Sent: Friday, September 28, 2012 9:53 AM To: 'John Deck'; Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.org<m ailto:eotuama@gbif.org>><mailto:eotuama@gbif.orgmailto:eotuama@gbi f.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.co mmailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr822 2@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@b gbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mai lto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guents ch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.bt uco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gma il.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com<m ailto:gtuco.btuco@gmail.com>>>; tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.ed umailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@b erkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Dear all,
We will be meeting this Tuesday at 1pm U.S. Eastern time over Skype in
order to discuss the actions required to develop the draft proposal for the Darwin Core tissue/DNA extension. A proposal for designing, testing, and implementing the GGBN data portal is attached for your reference. Please review the timeline and action items leading up to the TDWG 2012 Conference.
My Skype name is Katharine.Barker1. If possible, please forward me
your skype account names prior to our meeting.
Kind Regards,
Katie
From:jdeck88@gmail.commailto:From%3Ajdeck88@gmail.com<mailto:From %3Ajdeck88@gmail.commailto:From%253Ajdeck88@gmail.com><mailto:jde ck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@gmail.com<m ailto:jdeck88@gmail.com>>> [mailto:jdeck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@ gmail.commailto:jdeck88@gmail.com>] On Behalf Of John Deck Sent: Tuesday, September 25, 2012 4:04 PM To: Barker, Katharine Cc: Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.org<m ailto:eotuama@gbif.org>><mailto:eotuama@gbif.orgmailto:eotuama@gbi f.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.co mmailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr822 2@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@b gbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mai lto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guents ch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.bt uco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gma il.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com<m ailto:gtuco.btuco@gmail.com>>>; tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.ed umailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@b erkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Here is the wrapup of the bioCollections Ontology workshop from last
week at GSC14:
http://biocodecommons.org/workshops/bioCollections/index.html
This is relevant to these discussions since we focussed on what
constitutes a "sample" and also, probably more importantly, processes that work with samples.
We briefly discussed the DwC Tissue Extension and came up with a
proposal for a quick-fix and a more substantial fix. The quick-fix is to create two new BasisOfRecord terms: TissueSubSample, DNAExtract (or some terms like that -- Tuco could provide more clarification on this too). Thus, theoretically we could override the dwc:Occurrence class to mean, for example, TissueSubSample the same way we do for Specimens and Observations. The bigger fix is to more fundamentally re-orient DwC around the notion of "Sample", involving adding/changing some properties although we didn't get into any specifics.
P.s. I can do the 12/1/2 timeslots for that monday or tuesday but not
the 11.
John On Mon, Sep 24, 2012 at 12:39 PM, Barker, Katharine <BarkerK@si.edu
mailto:BarkerK@si.edu<mailto:BarkerK@si.edu<mailto:BarkerK@si.edu
<mailto:BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edu
mailto:BarkerK@si.edu>>> wrote:
Dear all,
We will have a telecon meeting early next week in order to discuss a
draft proposal for the Darwin Core tissue/DNA extension. Gabi, Paul, and I will put together a first draft for discussion to be distributed prior to the telecon. As you know, the goal is to have a working draft ready for our working group to review at the TDWG meeting in Beijing this October.
These are our options for meeting next week: Monday 11am, 12pm, 1pm, 2pm US EDT Tuesday 11am, 12pm, 1pm, 2pm US EDT
Please let me know if you cannot make one of these times.
Thanks again to those of you who provided input last week at the GSC
14 meeting.
Kind Regards,
Katie
From: Barker, Katharine Sent: Wednesday, September 12, 2012 10:51 AM To: 'Paul Flemons'; "Dröge, Gabriele"; eotuama@gbif.org<mailto:
eotuama@gbif.org><mailto:eotuama@gbif.org<mailto:eotuama@gbif.org
<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:
eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; ' rjr8222@gmail.com&
lt;mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.com<mailto:
rjr8222@gmail.com>><mailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com
<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>';
jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edu mailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto: jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>>; 'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org mailto:a.guentsch@bgbm.org>>'; 'gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.commailto: gtuco.btuco@gmail.com>>'; 'tuco@berkeley.edu<mailto:tuco@berkeley.edu
<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu><mailto:
tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu mailto:tuco@berkeley.edu>>'
Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core Importance: High
Dear all,
My name is Katie Barker and I am the Global Genome Biodiversity
Network Coordinator. As you know from Paul Flemons, members of the GGBN Data Standards and Data Access Task Force are trying to pull together a task group, which you are all part of, for the upcoming TDWG meeting in Beijing this October in order to address a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members. I am contacting you to schedule a meeting in late September/early October to develop a draft proposal for this extension to be completed at the upcoming TDWG meeting.
Please let me know your availability for the last two weeks of
September and first two weeks of October. There will be some scheduling issues, as there are task group members on the west and east coasts of the U.S., Europe and Australia.
Paul Flemons (in Australia) will be in the U.S. the first week of
October, so maybe we can meet in the afternoon of the 1st, anytime on the second 2nd, or in the morning of the 3rd of October over teleconference (US Eastern Daylight Time). Please let me know if any of these time slots work for you.
Gabi, I believe that you and John Deck will be at the GSC 14 meeting
next week. Is there any chance that you can start drawing up an outline for the proposed extension? We could review the outline during our group telecon and start drafting a proposal for review at the TDWG meeting in October.
Kind Regards,
Katie
Task Group Members:
John Weiczorek - Berkeley Éamonn O'Tuama - GBIF Jamie Whitacre - SI John Deck - Berkeley Robert Robbins - University of California, San Diego Anton Guentsch
- BGBM Gabi Droege- BGBM Paul Flemons- AM
From: Paul Flemons [mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov .au<mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus .gov.au>] Sent: Tuesday, August 07, 2012 2:50 AM To: tuco@berkley.edumailto:tuco@berkley.edu<mailto:tuco@berkley.edu<m ailto:tuco@berkley.edu>><mailto:tuco@berkley.edumailto:tuco@berkle y.edu<mailto:tuco@berkley.edumailto:tuco@berkley.edu>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@b gbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mai lto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guents ch@bgbm.org>>; j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org<mailto:j.holets chek@bgbm.orgmailto:j.holetschek@bgbm.org><mailto:j.holetschek@bg bm.orgmailto:j.holetschek@bgbm.org<mailto:j.holetschek@bgbm.org<m ailto:j.holetschek@bgbm.org>>>; jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley .edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto:j deck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley. edu>> Cc: Barker, Katharine; Éamonn Ó Tuama [GBIF]; "Dröge, Gabriele" (g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG<mailto:g.droege@BGBM.O RGmailto:g.droege@BGBM.ORG><mailto:g.droege@BGBM.ORGmailto:g.dro ege@BGBM.ORG<mailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG>>) Subject: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core
Hi all, I am on the Data Standards and Access Task Force for the Global Genome
Biodiversity Network (http://ggbn.org/) which is in need of a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members.
To this end I am writing to you to ask if you would be interested in
participating in a small working group at TDWG in Beijing this year.
At this stage my plan would be to identify relevant fields for
inclusion in the extension, using ABCDDNA as a reference. If sufficient progress is made then we would submit the extension for ratification by TDWG (is that how its done John?) The GGBN will use whatever comes out of the group to move towards having a suitable DwC based schema for data sharing.
So please let me know if you are willing to participate in the task
group and/or if there is anyone else you feel would be beneficial to have involved.
How much time do you think we will need? I have been thinking that a
day will be needed, so we could make that consist of either one full day or two half days. Im also thinking that during the week will be the best time for this.
Thanks for your time
Best Regards Paul
Paul K J Flemons Manager, Collection Informatics Team Lead, Atlas of Living Australia Biodiversity Volunteer Portalhttp://volunteer.ala.org.au Biodiversity Information Standards (TDWG) Representative for Oceania Australian Museum 6 College Street Sydney NSW 2010 Australia t 61 2 9320 6343 m 0413458649 f 61 2 9320 6021 Visit: http://www.australianmuseum.net.auhttp://www.australianmuseum.net. au/ Like: http://www.facebook.com/australianmuseum Follow: http://www.twitter.com/austmus Watch: http://www.youtube.com/austmus [cid:image001.png@01CDAD34.391DC790mailto:image001.png@01CDAD34.39 1DC790<mailto:image001.png@01CDAD34.391DC790mailto:image001.png@0 1CDAD34.391DC790>] Inspiring the exploration of nature and cultures
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<DNATissueExtensionNotes2-TDWG2012.docx>___________________________ ____________________ IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt
IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt
-- John Deck (541) 321-0689
On Wed, Oct 24, 2012 at 9:48 AM, John Deck jdeck@berkeley.edu wrote:
On Wed, Oct 24, 2012 at 4:30 PM, "Markus Döring (GBIF)" <mdoering@gbif.org
wrote:
very right John. So far these multi taxon cases have been so rare that we could live with ignoring them. But its a growing field that we need to handle better.
I just wanted to stress that adding a new core type to the IPT *codebase* takes a less than a day, but that we would still have to write documentation and translate that which takes more time. And not least publishing a sample core using the IPT is one thing, consuming/indexing it at GBIF or anywhere else is another story. Sample core data would not immediately be visible in the GBIF network. It would take us some time to adjust our indexing to the new data type.
Ah yes, thanks for clarifying the implementation issues (and they're really easy for me because i'm not the one doing it!). One path is to approve a Beta release of the Extension (& IPT codebase) to allow time for testing the indexing component.
Another observation I have about treating samples as an extension to Occurrence. What does the core occurrence record and its unique! occurrenceID represent after all - an occurrence based on the derived sample or the original "specimen"? I would think that it had to be the sample based occurrence, as if its the specimen then the occurrenceID would not be unique and it would break the dwca. So if you have a collected fish with occurrenceID=1 and a derived tissue sample with occurrenceID=1.2 the occurrenceID 1 (the fish itself) could only show up in some relationship extension, but not in the core dwca occurrence file.
good point
I agree that an Occurrence Core will not work except if there is a one-to-one relationship between the Occurrence and the Sample. That scenario is the one explained in "Darwin Core Archive Example 1 - Occurrence Core" in the Google Doc "DNA Tissue Extension Notes - TDWG 2012" at http://goo.gl/kGHmb. That model seems to limited to be viable.
An alternative is explained in "Darwin Core Archive Example 2 - Sample Core" in that same document. There the sampleID is the unique identifier and the occurrenceID can be repeated either in that Core data type or in a completely separate extension. I would not make Sample into a subtype of Occurrence, especially since Occurrence is already overloaded because it is a simplification of things that happen in the field and the organisms and physical or digital objects resulting from that activity.
best, Markus
On 24.10.2012, at 00:35, John Deck wrote:
Hi folks...
I see alot of use cases now, and projecting into the next several
years, that indicate we may need to extend our thinking of the "individual as single organism" view of the world. This is especially true when we're talking about preserving things for eventual sequencing. Here are some examples:
- There are alot of new sequencing approaches... not just metagenomic
sequencing, where one can identify hundreds/thousands of things from a single sample, but also metatranscriptomics, metaproteomics, and the like where we care more about what is being coded for in a particular environment vs. what the name of the individual is. Is this biodiversity? I say so, yes, just that what we care about ultimately is happening on a very low level.
- Lichens are composed of multiple different organisms and ascribing a
single name to the lichen is rather misleading as (i'm told) that the fungus/photosynthetic partners do not always hold true within single "species".
- Assigning a common taxonomic aggregate name for a "lot" of insects
may be OK, but in many environmental samples these would have to be categorized merely as "life".
- Finally, as Robbins has been pointing out this week, even things we
consider as individual organisms human, mouse, not to mention the examples of termite, cow (rumen bacteria) operate only in the context of their interaction with their microorganisms. Granted, the vast majority of current work in museums and data in GBIF are not recording these interactions explicitly but the growth in this line of study is on a trajectory that we can't ignore.
So, back to the decision on whether to make "sample" the core or to add
terms to basisOfRecord in conjunction with "Occurrence" at the core. Both ways have advantages/disadvantages and i've personally made arguments on both sides of this debate :) However, the more that i think about this and consider what I'm hearing both at GSC and TDWG, i'm more convinced now that having "sample" at the core is a better approach, especially if it can be implemented in less than a day within IPT. Also, my feeling here is that it will ultimately lead to more productive interactions between the growing number of cases where we care both about "genomics" and "biodiversity".
We're heading off on a field trip today... back tonight, and then we
have a Genomic Biodiversity Working/Interest Group meeting tomorrow Thursday afternoon (Beijing time)
John
On Tue, Oct 23, 2012 at 5:30 PM, "Markus Döring (GBIF)" <
mdoering@gbif.org> wrote:
Nicolas, Gabi, I very much agree that these are separate issues and if we leave out
metagenomics for now things becomes much simpler and cleaner.
I will add this note to the google doc, but feel free to remove it
again if it serves a different scope.
Markus
On 23.10.2012, at 11:19, Dröge, Gabriele wrote:
Dear Nicolas,
you are right. Tissue samples are priority 1, that should be solved
until end of January 2013. Environmental samples are quite different, we should discuss this topic later.
We are on a good way and hope to finish the draft for the new classes
today.
Best, Gabi
From: Nicolas Noé [mailto:niconoebiodiversity@gmail.com] On Behalf
Of Nicolas Noé
Sent: Tuesday, October 23, 2012 11:09 AM To: Dröge, Gabriele Cc: ""Markus Döring (GBIF)""; tuco@berkeley.edu; snomelf@gmail.com;
Paul Flemons (Paul.Flemons@austmus.gov.au); ipt@lists.gbif.org; Robert Robbins; John Deck; Robert Hanner; Guentsch, Anton; Barker, Katharine
Subject: Re: [IPT] Meeting at TDWG 2012 to define a tissue/DNA
extension for Darwin Core-draft reminder
Dear all,
I'm joining this conversation quite late, feel free to correct me if
I say something stupid.
From what I just read, it appears we have two totally different
use-cases here:
• Environmental samples, where the central piece of data is thesample
• Tissue samples, that are just new low-level data about aspecimen
To me, we probably won't be able to merge these two things to find a
single clean, pragmatic & simple solution. The former will need the sample at the core, the latter is probably better with a goold old Occurrence at the core.
If we agree we have two distinct problems to solve, maybe it is wise
to assess which one is priority #1, solve it now, implement it in IPT and gather real-world feedback before solving issue #2 ?
I feel I'm not really bringing something new on the table, but the
point I'd like to make is that maybe we should be care about the "let's-find-a-perfect-solution-that-fits-it-all" syndrom, with all his well-known consequences (complex implementation + risk of losing users).
thanks,
Nicolas
On 10/23/12 03:54, "Dröge, Gabriele" wrote: Now with attachment...
Thanks to all of you for your feedback. I don't understand the figure
you created (Markus?).
I had a look at http://code.google.com/p/gbif-ecat/wiki/DwCArchiveand I think we will keep the core schema in the middle as it is now (Basis
of Resource, Taxon or Occurrence).
All what we need to refer to associated objects (samples (tissues,
DNA, RNA,...) or other specimens) is an association extension with the identifiers of the referenced records, similar to the UnitAssociation container in ABCD. This extension should have a one to many relation to the core.
The DNAAmplification extension is only required if the sample record
is a DNA sample, since in this extension so far only DNA specific facts are included (GenBankAccessionNo etc.). The SampleFacts-Extension is quite similar to the main DNA extension of ABCD.
Find attached my figure based on the one from the DwCArchive website.
This is how I think it could work and how I understand the star schema, but maybe I am wrong :-). Environmental samples are more complicate maybe we can discuss this topic later (next year)?
Best, Gabi
-----Original Message----- From: "Markus Döring (GBIF)" [mailto:mdoering@gbif.org] Sent: Monday, October 22, 2012 11:31 PM To: tuco@berkeley.edu Cc: Barker, Katharine; ipt@lists.gbif.org; John Deck; Paul Flemons (
Paul.Flemons@austmus.gov.au); Dröge, Gabriele; snomelf@gmail.com; Robert Hanner; Guentsch, Anton; Robert Robbins
Subject: Re: [IPT] Meeting at TDWG 2012 to define a tissue/DNA
extension for Darwin Core-draft reminder
Well, let's investigate one thing about your diagram first. Shouldn't
there be a one-to-many relationship between Occurrence (specimen) and Sample rather than a many-to-one?
Specimen from the field = Occurrence + Event + Location + Identification + Taxon Sample from the specimen's liver = Sample Sample from the specimen's heart = Sample Sample from the specimen's gut = Sample
yes, thats true. Ididnt think about samples that way when I drafted
the diagram.
The scenario I had in my mind was the environmental sample, a
vegetation plot survey or just a rock with various lichen species on it. Usually with rich data about the location, habitat and abiotic measurements (lends itself nicely to an extension for samples). In such a sample you then find various species which would be the basis for an occurrence. In the case of metagenomic samples the list of taxa is actually derived information from the amplifications and can vary according to the method used (basically the entire occurrence extension can be derived from the amplifications in this case).
Actually when you take a gut sample from an animal you often are
interested in the fauna of that gut, so the occurrences would not be the host, but the bacteria occurring within it.
Markus
And all of the Samples could have multiple Amplifications.
If we want to model this with a Sample Core, then Occurrences may be
repeated in the Occurrence extension in your diagram, but every sample would have no more than one Occurrence in the extension file and the sampleID relationship would be one-to-one. If so, then it is also possible to have a Sample Core (Sample rowType) with sampleID as the core record identifier, with "Sample" as basisOfRecord, and with all of the attributes of Sample and of the existing Occurrence Core. This would avoid having a distinct Occurrence extension for Samples, which could get confusing for those who are accustomed to mapping Occurrences already. This combined Sample/Occurrence Core could still have a one-to-many relationship to the Amplifications.
On Mon, Oct 22, 2012 at 1:33 PM, "Markus Döring (GBIF)" <
mdoering@gbif.org> wrote:
Adding a new core type to the IPT could be done in less than a day -
more work for GBIF would be to support such a format in our indexing code.
But if we think its a better solution to go with a new sample core
type, I think its worth the extra cost of coding for it.
On 22.10.2012, at 17:53, John Wieczorek wrote:
I like the approach of having a Sample Core, but the approach taken
thus far was with the view of being pragmatic to put into practice by January 2013. What do you think could be the possibility of adding a new Core type to the IPT on that time scale? The Darwin Core archive specification can certainly handle it, but the proof is in the implementation.
On Mon, Oct 22, 2012 at 8:11 AM, "Markus Döring (GBIF)" <
mdoering@gbif.org> wrote:
Hi all, I only quickly looked through the proposal, but it looks good,
pragmatic and definitely to be working for the case when a DNASample equals a single taxon Occurrence.
Im not so sure how well it would work with environmental samples -
would we have the sample flattened out and repeated to represent the individual taxa, sexes, ages, etc found in there?
I was therefore wondering if anyone had thought about the attached
setup before. Sample is at its core and occurrence & dna amplification as extensions with the amplifications (optionally?) refering to the occurrence they belong to.
Another quick observation is that we try to reuse existing terms in extensions as much as possible. Following that rule for example dwc:institutionCode should rather be used instead of dNACollectionCode and probably dc:source for the referenceCitation
until tomorrow, regards, Markus
<sample core.png>
On 22.10.2012, at 12:21, Barker, Katharine wrote:
Dear John,
Please see our working revisions/comments/questions on the DNA/tissue
extension for Darwin Core (highlighted in blue). We were able to work through the draft up through "class sample properties":
https://docs.google.com/document/d/1RCgIPfu9gAPubjjbog-9vCJonvqcK1p LOaq6H8GSnns/edit
The document is also attached for your reference (just incase any of
you are unable to access the document).
Please try to respond to our questions and comments prior to our
meeting tomorrow (be sure to make these changes using a different color for tracking purposes).
Tomorrow we will like to 1) briefly recap our revisions on the
extension so far (addressing questions and comments), 2) complete our review of the extension and 3) identify any remaining issues with DwC working with IPT (and identify if any changes in the IPT are required).
Thank you for your help on this!
Kind Regards,
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu" <tuco@berkeley.edumailto:tuco@berkeley.edu> Date: Sunday, October 21, 2012 10:52 PM To: Gabriele Droege <g.droege@bgbm.orgmailto:g.droege@bgbm.org> Cc: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au>, John Deck <jdeck@berkeley.edumailto:jdeck@berkeley.edu>, Robert Hanner <bob.hanner@gmail.commailto:bob.hanner@gmail.com>, Éamonn Tuama <eotuama@gbif.orgmailto:eotuama@gbif.org>, Robert Robbins <rjr8222@gmail.commailto:rjr8222@gmail.com>, "Guentsch, Anton" <a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org> Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Dear all,
I finished working on the Google Doc "DNA Tissue Extension Notes -
TDWG 2012". Feel free to let this be a working document where comments and questions can be added. I've attached a Word Doc version for archival purposes.
I added the two template extension files (DNATissueExtension.txt and
DNAAmplificationExtension.txt) to the shared TDWG GGBN working group folder linked below. They are in the form they need to be submitted to GBIF to be added to their extension registry. They would both need to be updated with the term descriptions, examples, and constraints.
https://drive.google.com/#folders/0BxEyFKwB7zY4WEs0WkdtUU5oVnM
Cheers,
John
On Sun, Oct 21, 2012 at 10:38 PM, John Wieczorek <tuco@berkeley.edu
mailto:tuco@berkeley.edu> wrote:
Ooops
...at http://goo.gl/kGHmb. Adding touches based on the files Gabi
sent. Will tell you all when finished with that and will send it as a Word doc at that time in case there are any issues with Google docs. Should be soon. Let me know if I should share to any different addresses.
Cheers,
John
On Sun, Oct 21, 2012 at 10:34 PM, John Wieczorek <tuco@berkeley.edu
mailto:tuco@berkeley.edu> wrote:
That helps a lot, as it clears up some of my own misconceptions. I have shared a document where I have captured the thinking behind a couple of different ways forward with one or two extensions and an example of how the two-extension might look in the context of a Darwin Core Archive. The DNA Tissue Extension Notes Google doc can be found at
On Sun, Oct 21, 2012 at 9:23 PM, "Dröge, Gabriele" <g.droege@bgbm.org
mailto:g.droege@bgbm.org> wrote:
Yes we do... Hi John,
Thanks for getting back to us. Attached are two csv files, one with
some main DNA facts and the other with associated GenBank entries und publications (2 examples with 2 GenBank entries per DNA sample).
I included only UnitID/CollCode/InstCode for the related voucher
specimen and I excluded the tissue facts since they are quite similar to the DNA facts and should be mapped independently.
Best, Gabi
-----Original Message----- From: Barker, Katharine [mailto:BarkerK@si.edumailto:BarkerK@si.edu] Sent: Sunday, October 21, 2012 11:41 PM To: Paul Flemons; Dröge, Gabriele Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Paul and Gabi,
Do we have any sample data that John can use as a test case? I think
he would like it today, if possible.
Thanks for your help (and the team work).
Katie
From: John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu>> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu>" <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu>> Date: Sunday, October 21, 2012 12:03 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edu<mailto :barkerk@si.edu>>> Subject: Re: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
Hi Katie,
Messages received. Will have the extension stuff ready within a few
hours and hope to be able to attend remotely. One thing in the meantime. Do you have any example data that could be used as a test case to populate a core with this extension? Would like to try that with some realy data to test my assumptions.
Sorry for the delay.
Thanks,
John
On Sun, Oct 21, 2012 at 10:08 AM, Barker, Katharine <BarkerK@si.edu
mailto:BarkerK@si.edu<mailto:BarkerK@si.edumailto:BarkerK@si.edu>> wrote:
Dear John,
I'm sorry that you were unable to attain a visa for China. I was
really looking forward to working with you in person with the group. Paul mentioned that he had e-mailed you earlier this evening. Can you please send us the draft for the DarwinCore DNA/tissue extension as soon as possible for review during our working sessions? We have one tomorrow at 1:30 (Beijing time) and another on Tuesday at the same time. It would be really great if you could Skype into either both or one of the sessions.
Thanks for your help on this.
Kind Regards,
Katie
From: <Barker>, Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edu<mailto :barkerk@si.edu>><mailto:barkerk@si.edumailto:barkerk@si.edu<mail to:barkerk@si.edumailto:barkerk@si.edu>>> Date: Thursday, October 18, 2012 1:34 PM To: Katharine Barker <barkerk@si.edumailto:barkerk@si.edu<mailto:barkerk@si.edu<mailto :barkerk@si.edu>><mailto:barkerk@si.edumailto:barkerk@si.edu<mail to:barkerk@si.edumailto:barkerk@si.edu>>>, 'John Deck' <jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkele y.edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto: jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley .edu>>>, Paul Flemons <Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov.au<ma ilto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.au <mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.g ov.au<mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austm us.gov.au>>>, "'"Dröge", Éamonn Tuama <eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.org< mailto:eotuama@gbif.org>><mailto:eotuama@gbif.orgmailto:eotuama@gb if.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>>, "Whitacre, Jamie" <WHITACREJ@si.edumailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edu< mailto:WHITACREJ@si.edu>><mailto:WHITACREJ@si.edumailto:WHITACREJ@ si.edu<mailto:WHITACREJ@si.edumailto:WHITACREJ@si.edu>>>, "'rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail. commailto:rjr8222@gmail.com><mailto:'rjr8222@gmail.commailto:rjr 8222@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com> '" <rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.c ommailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr82 22@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>> , "'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch @bgbm.orgmailto:a.guentsch@bgbm.org><mailto:'a.guentsch@bgbm.org< mailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.gue ntsch@bgbm.org>>'" <a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@ bgbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<ma ilto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guent sch@bgbm.org>>>, "'gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco. btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:'gtuco.btuco@ gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.co mmailto:gtuco.btuco@gmail.com>>'" <gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.b tuco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gm ail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com< mailto:gtuco.btuco@gmail.com>>>>, "'tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley. edumailto:tuco@berkeley.edu><mailto:'tuco@berkeley.edumailto:tuc o@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu> '" <tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.e dumailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@ berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>> Cc: "'morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morris on@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:'morrison@cs. man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.u kmailto:morrison@cs.man.ac.uk>>'" <morrison@cs.man.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morriso n@cs.man.ac.ukmailto:morrison@cs.man.ac.uk><mailto:morrison@cs.ma n.ac.ukmailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.uk< mailto:morrison@cs.man.ac.uk>>>>, "Parr, Cynthia" <parrc@si.edumailto:parrc@si.edu<mailto:parrc@si.edumailto:parrc @si.edu><mailto:parrc@si.edumailto:parrc@si.edu<mailto:parrc@si. edumailto:parrc@si.edu>>> Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Dear all,
This is a friendly reminder that we will be meeting next Tuesday
afternoon at the TDWG 2012 Conference in order to finalize the draft DarwinCore-A DNA/tissue extension for GGBN. As you know, the immediate need for GGBN members is to publish information on tissues. This will happen through extensions to both ABCDDNA and DarwinCore-A. Here we are focused on developing the DarwinCore-A DNA/tissue extension.
An update on the timeline for developing the draft DarwinCore-A
DNA/tissue extension is listed below.
Review content requirements for DarwinCore-A DNA/tissueextension (completed, see attached required DNA and tissue elements)
John Weiczorek will develop the draft DarwinCore-A DNA/tissueextension (to be completed for group review prior to our break out session on Tuesday afternoon, October 23).
Tuesday October 23, working meeting· Questions to answer before final review of DNA/tissue
extension
o How do we include repeatable elements of ABCDDNA into DwC-A-DNA
(References to more than one sequence record/publication are mandatory)?
o How do we extend the "Basis of Record" in ABCD and DwC-A and how
do we include an element similar to ABCD-"Kind of Unit" to DwC-A?
o What are the remaining issues for DwC-A working with IPT? Are
any changes in the IPT required?
· Review and finalize draft DarwinCore-A DNA/tissue extension
for posting to GBIF site.
Thank you again to everyone who is involved in this project. I look
forward to seeing all of you in Beijing.
Kind Regards,
Katie
From: Barker, Katharine Sent: Friday, September 28, 2012 9:53 AM To: 'John Deck'; Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.org<m ailto:eotuama@gbif.org>><mailto:eotuama@gbif.orgmailto:eotuama@gbi f.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.co mmailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr822 2@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@b gbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mai lto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guents ch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.bt uco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gma il.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com<m ailto:gtuco.btuco@gmail.com>>>; tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.ed umailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@b erkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Dear all,
We will be meeting this Tuesday at 1pm U.S. Eastern time over Skype
in order to discuss the actions required to develop the draft proposal for the Darwin Core tissue/DNA extension. A proposal for designing, testing, and implementing the GGBN data portal is attached for your reference. Please review the timeline and action items leading up to the TDWG 2012 Conference.
My Skype name is Katharine.Barker1. If possible, please forward me
your skype account names prior to our meeting.
Kind Regards,
Katie
From:jdeck88@gmail.commailto:From%3Ajdeck88@gmail.com<mailto:From %3Ajdeck88@gmail.commailto:From%253Ajdeck88@gmail.com><mailto:jde ck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@gmail.com<m ailto:jdeck88@gmail.com>>> [mailto:jdeck88@gmail.commailto:jdeck88@gmail.com<mailto:jdeck88@ gmail.commailto:jdeck88@gmail.com>] On Behalf Of John Deck Sent: Tuesday, September 25, 2012 4:04 PM To: Barker, Katharine Cc: Paul Flemons; "Dröge, Gabriele"; eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:eotuama@gbif.org<m ailto:eotuama@gbif.org>><mailto:eotuama@gbif.orgmailto:eotuama@gbi f.org<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; rjr8222@gmail.commailto:rjr8222@gmail.com<mailto:rjr8222@gmail.co mmailto:rjr8222@gmail.com><mailto:rjr8222@gmail.commailto:rjr822 2@gmail.com<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@b gbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mai lto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guents ch@bgbm.org>>; gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto:gtuco.bt uco@gmail.commailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gma il.commailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com<m ailto:gtuco.btuco@gmail.com>>>; tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.ed umailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto:tuco@b erkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>> Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week
Here is the wrapup of the bioCollections Ontology workshop from last
week at GSC14:
http://biocodecommons.org/workshops/bioCollections/index.html
This is relevant to these discussions since we focussed on what
constitutes a "sample" and also, probably more importantly, processes that work with samples.
We briefly discussed the DwC Tissue Extension and came up with a
proposal for a quick-fix and a more substantial fix. The quick-fix is to create two new BasisOfRecord terms: TissueSubSample, DNAExtract (or some terms like that -- Tuco could provide more clarification on this too). Thus, theoretically we could override the dwc:Occurrence class to mean, for example, TissueSubSample the same way we do for Specimens and Observations. The bigger fix is to more fundamentally re-orient DwC around the notion of "Sample", involving adding/changing some properties although we didn't get into any specifics.
P.s. I can do the 12/1/2 timeslots for that monday or tuesday but
not the 11.
John On Mon, Sep 24, 2012 at 12:39 PM, Barker, Katharine <BarkerK@si.edu
mailto:BarkerK@si.edu<mailto:BarkerK@si.edu<mailto:BarkerK@si.edu
<mailto:BarkerK@si.edumailto:BarkerK@si.edu<mailto:BarkerK@si.edu
mailto:BarkerK@si.edu>>> wrote:
Dear all,
We will have a telecon meeting early next week in order to discuss a
draft proposal for the Darwin Core tissue/DNA extension. Gabi, Paul, and I will put together a first draft for discussion to be distributed prior to the telecon. As you know, the goal is to have a working draft ready for our working group to review at the TDWG meeting in Beijing this October.
These are our options for meeting next week: Monday 11am, 12pm, 1pm, 2pm US EDT Tuesday 11am, 12pm, 1pm, 2pm US EDT
Please let me know if you cannot make one of these times.
Thanks again to those of you who provided input last week at the GSC
14 meeting.
Kind Regards,
Katie
From: Barker, Katharine Sent: Wednesday, September 12, 2012 10:51 AM To: 'Paul Flemons'; "Dröge, Gabriele"; eotuama@gbif.org<mailto:
eotuama@gbif.org><mailto:eotuama@gbif.org<mailto:eotuama@gbif.org
<mailto:eotuama@gbif.orgmailto:eotuama@gbif.org<mailto:
eotuama@gbif.orgmailto:eotuama@gbif.org>>; Whitacre, Jamie; ' rjr8222@gmail.com&
lt;mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.com<mailto:
rjr8222@gmail.com>><mailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com
<mailto:rjr8222@gmail.commailto:rjr8222@gmail.com>>';
jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edu mailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto: jdeck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley.edu>>; 'a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org><mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto: a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org>>'; ' gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com><mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com<mailto: gtuco.btuco@gmail.commailto:gtuco.btuco@gmail.com>>'; ' tuco@berkeley.edumailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu mailto:tuco@berkeley.edu><mailto:tuco@berkeley.edumailto: tuco@berkeley.edu<mailto:tuco@berkeley.edumailto:tuco@berkeley.edu>>'
Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core Importance: High
Dear all,
My name is Katie Barker and I am the Global Genome Biodiversity
Network Coordinator. As you know from Paul Flemons, members of the GGBN Data Standards and Data Access Task Force are trying to pull together a task group, which you are all part of, for the upcoming TDWG meeting in Beijing this October in order to address a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members. I am contacting you to schedule a meeting in late September/early October to develop a draft proposal for this extension to be completed at the upcoming TDWG meeting.
Please let me know your availability for the last two weeks of
September and first two weeks of October. There will be some scheduling issues, as there are task group members on the west and east coasts of the U.S., Europe and Australia.
Paul Flemons (in Australia) will be in the U.S. the first week of
October, so maybe we can meet in the afternoon of the 1st, anytime on the second 2nd, or in the morning of the 3rd of October over teleconference (US Eastern Daylight Time). Please let me know if any of these time slots work for you.
Gabi, I believe that you and John Deck will be at the GSC 14 meeting
next week. Is there any chance that you can start drawing up an outline for the proposed extension? We could review the outline during our group telecon and start drafting a proposal for review at the TDWG meeting in October.
Kind Regards,
Katie
Task Group Members:
John Weiczorek - Berkeley Éamonn O'Tuama - GBIF Jamie Whitacre - SI John Deck - Berkeley Robert Robbins - University of California, San Diego Anton Guentsch
- BGBM Gabi Droege- BGBM Paul Flemons- AM
From: Paul Flemons [mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus.gov .au<mailto:Paul.Flemons@austmus.gov.aumailto:Paul.Flemons@austmus .gov.au>] Sent: Tuesday, August 07, 2012 2:50 AM To: tuco@berkley.edumailto:tuco@berkley.edu<mailto:tuco@berkley.edu<m ailto:tuco@berkley.edu>><mailto:tuco@berkley.edumailto:tuco@berkle y.edu<mailto:tuco@berkley.edumailto:tuco@berkley.edu>>; a.guentsch@bgbm.orgmailto:a.guentsch@bgbm.org<mailto:a.guentsch@b gbm.orgmailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mai lto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.orgmailto:a.guents ch@bgbm.org>>; j.holetschek@bgbm.orgmailto:j.holetschek@bgbm.org<mailto:j.holets chek@bgbm.orgmailto:j.holetschek@bgbm.org><mailto:j.holetschek@bg bm.orgmailto:j.holetschek@bgbm.org<mailto:j.holetschek@bgbm.org<m ailto:j.holetschek@bgbm.org>>>; jdeck@berkeley.edumailto:jdeck@berkeley.edu<mailto:jdeck@berkeley .edumailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edumailto:j deck@berkeley.edu<mailto:jdeck@berkeley.edumailto:jdeck@berkeley. edu>> Cc: Barker, Katharine; Éamonn Ó Tuama [GBIF]; "Dröge, Gabriele" (g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG<mailto:g.droege@BGBM.O RGmailto:g.droege@BGBM.ORG><mailto:g.droege@BGBM.ORGmailto:g.dro ege@BGBM.ORG<mailto:g.droege@BGBM.ORGmailto:g.droege@BGBM.ORG>>) Subject: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core
Hi all, I am on the Data Standards and Access Task Force for the Global
Genome Biodiversity Network (http://ggbn.org/) which is in need of a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members.
To this end I am writing to you to ask if you would be interested in
participating in a small working group at TDWG in Beijing this year.
At this stage my plan would be to identify relevant fields for
inclusion in the extension, using ABCDDNA as a reference. If sufficient progress is made then we would submit the extension for ratification by TDWG (is that how its done John?) The GGBN will use whatever comes out of the group to move towards having a suitable DwC based schema for data sharing.
So please let me know if you are willing to participate in the task
group and/or if there is anyone else you feel would be beneficial to have involved.
How much time do you think we will need? I have been thinking that a
day will be needed, so we could make that consist of either one full day or two half days. Im also thinking that during the week will be the best time for this.
Thanks for your time
Best Regards Paul
Paul K J Flemons Manager, Collection Informatics Team Lead, Atlas of Living Australia Biodiversity Volunteer Portalhttp://volunteer.ala.org.au Biodiversity Information Standards (TDWG) Representative for Oceania Australian Museum 6 College Street Sydney NSW 2010 Australia t 61 2 9320 6343 m 0413458649 f 61 2 9320 6021 Visit: http://www.australianmuseum.net.auhttp://www.australianmuseum.net. au/ Like: http://www.facebook.com/australianmuseum Follow: http://www.twitter.com/austmus Watch: http://www.youtube.com/austmus [cid:image001.png@01CDAD34.391DC790mailto:image001.png@01CDAD34.39 1DC790<mailto:image001.png@01CDAD34.391DC790mailto:image001.png@0 1CDAD34.391DC790>] Inspiring the exploration of nature and cultures
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participants (8)
-
"Dröge, Gabriele" -
"Markus Döring (GBIF)" -
Barker, Katharine -
John Deck -
John Wieczorek -
Nicolas Noé -
Paul Flemons -
Snomelf＠gmail.com