[IPT] Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder

Tue Oct 23 11:19:46 CEST 2012

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 at gmail.com] On Behalf Of Nicolas Noé
Sent: Tuesday, October 23, 2012 11:09 AM
To: Dröge, Gabriele
Cc: "\"Markus Döring (GBIF)\""; tuco at berkeley.edu; snomelf at gmail.com; Paul Flemons (Paul.Flemons at austmus.gov.au); ipt at 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 at gbif.org]

Sent: Monday, October 22, 2012 11:31 PM

To: tuco at berkeley.edu<mailto:tuco at berkeley.edu>

Cc: Barker, Katharine; ipt at lists.gbif.org<mailto:ipt at lists.gbif.org>; John Deck; Paul Flemons (Paul.Flemons at austmus.gov.au<mailto:Paul.Flemons at austmus.gov.au>); Dröge, Gabriele; snomelf at gmail.com<mailto:snomelf at 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 at gbif.org><mailto:mdoering at 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 at gbif.org><mailto:mdoering at 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 at berkeley.edu<mailto:tuco at berkeley.edu><mailto:tuco at berkeley.edu><mailto:tuco at berkeley.edu>>

Reply-To: "tuco at berkeley.edu<mailto:tuco at berkeley.edu><mailto:tuco at berkeley.edu><mailto:tuco at berkeley.edu>"

<tuco at berkeley.edu<mailto:tuco at berkeley.edu><mailto:tuco at berkeley.edu><mailto:tuco at berkeley.edu>>

Date: Sunday, October 21, 2012 10:52 PM

To: Gabriele Droege <g.droege at bgbm.org<mailto:g.droege at bgbm.org><mailto:g.droege at bgbm.org><mailto:g.droege at bgbm.org>>

Cc: Katharine Barker <barkerk at si.edu<mailto:barkerk at si.edu><mailto:barkerk at si.edu><mailto:barkerk at si.edu>>, Paul

Flemons

<Paul.Flemons at austmus.gov.au<mailto:Paul.Flemons at austmus.gov.au><mailto:Paul.Flemons at austmus.gov.au><mailto:Paul.Flemons at austmus.gov.au>>,

John Deck <jdeck at berkeley.edu<mailto:jdeck at berkeley.edu><mailto:jdeck at berkeley.edu><mailto:jdeck at berkeley.edu>>, Robert

Hanner <bob.hanner at gmail.com<mailto:bob.hanner at gmail.com><mailto:bob.hanner at gmail.com><mailto:bob.hanner at gmail.com>>, Éamonn

Tuama <eotuama at gbif.org<mailto:eotuama at gbif.org><mailto:eotuama at gbif.org><mailto:eotuama at gbif.org>>, Robert Robbins

<rjr8222 at gmail.com<mailto:rjr8222 at gmail.com><mailto:rjr8222 at gmail.com><mailto:rjr8222 at gmail.com>>, "Guentsch, Anton"

<a.guentsch at bgbm.org<mailto:a.guentsch at bgbm.org><mailto:a.guentsch at bgbm.org><mailto:a.guentsch at 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 at berkeley.edu<mailto:tuco at berkeley.edu><mailto:tuco at berkeley.edu><mailto:tuco at 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 at berkeley.edu<mailto:tuco at berkeley.edu><mailto:tuco at berkeley.edu><mailto:tuco at 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 at bgbm.org<mailto:g.droege at bgbm.org><mailto:g.droege at bgbm.org><mailto:g.droege at 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 at si.edu<mailto:BarkerK at si.edu><mailto:BarkerK at 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 at berkeley.edu<mailto:tuco at berkeley.edu><mailto:tuco at berkeley.edu><mailto:tuco at berkeley.edu><mailto:tuco at berkeley.e

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Reply-To:

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Date: Sunday, October 21, 2012 12:03 PM

To: Katharine Barker

<barkerk at si.edu<mailto:barkerk at si.edu><mailto:barkerk at si.edu><mailto:barkerk at si.edu><mailto:barkerk at si.edu<mailto<mailto:barkerk at si.edu>

:barkerk at si.edu><mailto:barkerk at 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 at si.edu<mailto:BarkerK at si.edu><mailto:BarkerK at si.edu><mailto:BarkerK at si.edu><mailto:BarkerK at si.edu<mailto:BarkerK at si.edu><mailto:BarkerK at 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 at si.edu<mailto:barkerk at si.edu><mailto:barkerk at si.edu><mailto:barkerk at si.edu><mailto:barkerk at si.edu<mailto<mailto:barkerk at si.edu>

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Date: Thursday, October 18, 2012 1:34 PM

To: Katharine Barker

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.edu><mailto:jdeck at berkeley.edu>>>>, Paul Flemons

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us.gov.au><mailto:Paul.Flemons at austmus.gov.au>>>>, "'\"Dröge", Éamonn Tuama

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"Whitacre, Jamie"

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<parrc at si.edu<mailto:parrc at si.edu><mailto:parrc at si.edu><mailto:parrc at si.edu><mailto:parrc at si.edu<mailto:parrc<mailto:parrc at si.edu>

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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 at gbif.org<mailto:eotuama at gbif.org><mailto:eotuama at gbif.org><mailto:eotuama at gbif.org><mailto:eotuama at gbif.org<m<mailto:eotuama at gbif.org>

ailto:eotuama at gbif.org><mailto:eotuama at gbif.org>><mailto:eotuama at gbif.org<mailto:eotuama at gbi<mailto:eotuama at gbif.org>

f.org><mailto:eotuama at gbif.org><mailto:eotuama at gbif.org<mailto:eotuama at gbif.org><mailto:eotuama at gbif.org>>>;

Whitacre, Jamie;

rjr8222 at gmail.com<mailto:rjr8222 at gmail.com><mailto:rjr8222 at gmail.com><mailto:rjr8222 at gmail.com><mailto:rjr8222 at gmail.co

m<mailto:rjr8222 at gmail.com><mailto:rjr8222 at gmail.com>><mailto:rjr8222 at gmail.com<mailto:rjr822<mailto:rjr8222 at gmail.com>

2 at gmail.com><mailto:rjr8222 at gmail.com><mailto:rjr8222 at gmail.com<mailto:rjr8222 at gmail.com><mailto:rjr8222 at gmail.com>>>;

a.guentsch at bgbm.org<mailto:a.guentsch at bgbm.org><mailto:a.guentsch at bgbm.org><mailto:a.guentsch at bgbm.org><mailto:a.guentsch at b

gbm.org<mailto:a.guentsch at bgbm.org><mailto:a.guentsch at bgbm.org>><mailto:a.guentsch at bgbm.org<mai<mailto:a.guentsch at bgbm.org>

lto:a.guentsch at bgbm.org><mailto:a.guentsch at bgbm.org><mailto:a.guentsch at bgbm.org<mailto:a.guents<mailto:a.guentsch at bgbm.org>

ch at bgbm.org><mailto:a.guentsch at bgbm.org>>>;

gtuco.btuco at gmail.com<mailto:gtuco.btuco at gmail.com><mailto:gtuco.btuco at gmail.com><mailto:gtuco.btuco at gmail.com><mailto:gtuco.bt

uco at gmail.com<mailto:uco at gmail.com><mailto:gtuco.btuco at gmail.com><mailto:gtuco.btuco at gmail.com>><mailto:gtuco.btuco at gma

il.com<mailto:gtuco.btuco at gmail.com><mailto:gtuco.btuco at gmail.com><mailto:gtuco.btuco at gmail.com<m<mailto:gtuco.btuco at gmail.com>

ailto:gtuco.btuco at gmail.com><mailto:gtuco.btuco at gmail.com>>>;

tuco at berkeley.edu<mailto:tuco at berkeley.edu><mailto:tuco at berkeley.edu><mailto:tuco at berkeley.edu><mailto:tuco at berkeley.ed

u<mailto:tuco at berkeley.edu><mailto:tuco at berkeley.edu>><mailto:tuco at berkeley.edu<mailto:tuco at b<mailto:tuco at berkeley.edu>

erkeley.edu><mailto:tuco at berkeley.edu><mailto:tuco at berkeley.edu<mailto:tuco at berkeley.edu><mailto:tuco at 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 at gmail.com<mailto:From:jdeck88 at gmail.com><mailto:From%3Ajdeck88 at gmail.com><mailto:From%3Ajdeck88 at gmail.com><mailto:From

%3Ajdeck88 at gmail.com<mailto:From%253Ajdeck88 at gmail.com><mailto:From%253Ajdeck88 at gmail.com>><mailto:jde

ck88 at gmail.com<mailto:ck88 at gmail.com><mailto:jdeck88 at gmail.com><mailto:jdeck88 at gmail.com><mailto:jdeck88 at gmail.com<m<mailto:jdeck88 at gmail.com>

ailto:jdeck88 at gmail.com><mailto:jdeck88 at gmail.com>>>

[mailto:jdeck88 at gmail.com<mailto:jdeck88 at gmail.com><mailto:jdeck88 at gmail.com><mailto:jdeck88@

gmail.com<mailto:jdeck88 at gmail.com><mailto:jdeck88 at gmail.com>>] On Behalf Of John Deck

Sent: Tuesday, September 25, 2012 4:04 PM

To: Barker, Katharine

Cc: Paul Flemons; "Dröge, Gabriele";

eotuama at gbif.org<mailto:eotuama at gbif.org><mailto:eotuama at gbif.org><mailto:eotuama at gbif.org><mailto:eotuama at gbif.org<m<mailto:eotuama at gbif.org>

ailto:eotuama at gbif.org><mailto:eotuama at gbif.org>><mailto:eotuama at gbif.org<mailto:eotuama at gbi<mailto:eotuama at gbif.org>

f.org><mailto:eotuama at gbif.org><mailto:eotuama at gbif.org<mailto:eotuama at gbif.org><mailto:eotuama at gbif.org>>>;

Whitacre, Jamie;

rjr8222 at gmail.com<mailto:rjr8222 at gmail.com><mailto:rjr8222 at gmail.com><mailto:rjr8222 at gmail.com><mailto:rjr8222 at gmail.co

m<mailto:rjr8222 at gmail.com><mailto:rjr8222 at gmail.com>><mailto:rjr8222 at gmail.com<mailto:rjr822<mailto:rjr8222 at gmail.com>

2 at gmail.com><mailto:rjr8222 at gmail.com><mailto:rjr8222 at gmail.com<mailto:rjr8222 at gmail.com><mailto:rjr8222 at gmail.com>>>;

a.guentsch at bgbm.org<mailto:a.guentsch at bgbm.org><mailto:a.guentsch at bgbm.org><mailto:a.guentsch at bgbm.org><mailto:a.guentsch at b

gbm.org<mailto:a.guentsch at bgbm.org><mailto:a.guentsch at bgbm.org>><mailto:a.guentsch at bgbm.org<mai<mailto:a.guentsch at bgbm.org>

lto:a.guentsch at bgbm.org><mailto:a.guentsch at bgbm.org><mailto:a.guentsch at bgbm.org<mailto:a.guents<mailto:a.guentsch at bgbm.org>

ch at bgbm.org><mailto:a.guentsch at bgbm.org>>>;

gtuco.btuco at gmail.com<mailto:gtuco.btuco at gmail.com><mailto:gtuco.btuco at gmail.com><mailto:gtuco.btuco at gmail.com><mailto:gtuco.bt

uco at gmail.com<mailto:uco at gmail.com><mailto:gtuco.btuco at gmail.com><mailto:gtuco.btuco at gmail.com>><mailto:gtuco.btuco at gma

il.com<mailto:gtuco.btuco at gmail.com><mailto:gtuco.btuco at gmail.com><mailto:gtuco.btuco at gmail.com<m<mailto:gtuco.btuco at gmail.com>

ailto:gtuco.btuco at gmail.com><mailto:gtuco.btuco at gmail.com>>>;

tuco at berkeley.edu<mailto:tuco at berkeley.edu><mailto:tuco at berkeley.edu><mailto:tuco at berkeley.edu><mailto:tuco at berkeley.ed

u<mailto:tuco at berkeley.edu><mailto:tuco at berkeley.edu>><mailto:tuco at berkeley.edu<mailto:tuco at b<mailto:tuco at berkeley.edu>

erkeley.edu><mailto:tuco at berkeley.edu><mailto:tuco at berkeley.edu<mailto:tuco at berkeley.edu><mailto:tuco at 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 at si.edu<mailto:BarkerK at si.edu><mailto:BarkerK at si.edu><mailto:BarkerK at si.edu><mailto:BarkerK at si.edu<mailto:BarkerK at si.edu><mailto:BarkerK at si.edu>><mailto:BarkerK at si.edu<mailto:BarkerK at si.edu><mailto:BarkerK at si.edu><mailto:BarkerK at si.edu<mailto:BarkerK at si.edu><mailto:BarkerK at 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 at gbif.org<mailto:eotuama at gbif.org><mailto:eotuama at gbif.org><mailto:eotuama at gbif.org><mailto:eotuama at gbif.org<mailto:eotuama at gbif.org><mailto:eotuama at gbif.org>><mailto:eotuama at gbif.org<mailto:eotuama at gbif.org><mailto:eotuama at gbif.org><mailto:eotuama at gbif.org<mailto:eotuama at gbif.org><mailto:eotuama at gbif.org>>>; Whitacre, Jamie; 'rjr8222 at gmail.com<mailto:rjr8222 at gmail.com>&<mailto:rjr8222 at gmail.com>

lt;mailto:rjr8222 at gmail.com><mailto:rjr8222 at gmail.com><mailto:rjr8222 at gmail.com<mailto:rjr8222 at gmail.com><mailto:rjr8222 at gmail.com>><mailto:rjr8222 at gmail.com<mailto:rjr8222 at gmail.com><mailto:rjr8222 at gmail.com><mailto:rjr8222 at gmail.com<mailto:rjr8222 at gmail.com><mailto:rjr8222 at gmail.com>>>'; jdeck at berkeley.edu<mailto:jdeck at berkeley.edu><mailto:jdeck at berkeley.edu><mailto:jdeck at berkeley.edu><mailto:jdeck at berkeley.edu<mailto:jdeck at berkeley.edu><mailto:jdeck at berkeley.edu>><mailto:jdeck at berkeley.edu<mailto:jdeck at berkeley.edu><mailto:jdeck at berkeley.edu><mailto:jdeck at berkeley.edu<mailto:jdeck at berkeley.edu><mailto:jdeck at berkeley.edu>>>; 'a.guentsch at bgbm.org<mailto:a.guentsch at bgbm.org><mailto:a.guentsch at bgbm.org><mailto:a.guentsch at bgbm.org><mailto:a.guentsch at bgbm.org<mailto:a.guentsch at bgbm.org><mailto:a.guentsch at bgbm.org>><mailto:a.guentsch at bgbm.org<mailto:a.guentsch at bgbm.org><mailto:a.guentsch at bgbm.org><mailto:a.guentsch at bgbm.org<mailto:a.guentsch at bgbm.org><mailto:a.guentsch at bgbm.org>>>'; 'gtuco.btuco at gmail.com<mailto:gtuco.btuco at gmail.com><mailto:gtuco.btuco at gmail.com><mailto:gtuco.btuco at gmail.com><mailto:gtuco.btuco at gmail.com<mailto:gtuco.btuco at gmail.com><mailto:gtuco.btuco at gmail.com>><mailto:gtuco.btuco at gmail.com<mailto:gtuco.btuco at gmail.com><mailto:gtuco.btuco at gmail.com><mailto:gtuco.btuco at gmail.com<mailto:gtuco.btuco at gmail.com><mailto:gtuco.btuco at gmail.com>>>'; 'tuco at berkeley.edu<mailto:tuco at berkeley.edu><mailto:tuco at berkeley.edu><mailto:tuco at berkeley.edu><mailto:tuco at berkeley.edu<mailto:tuco at berkeley.edu><mailto:tuco at berkeley.edu>><mailto:tuco at berkeley.edu<mailto:tuco at berkeley.edu><mailto:tuco at berkeley.edu><mailto:tuco at berkeley.edu<mailto:tuco at berkeley.edu><mailto:tuco at 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 at austmus.gov.au<mailto:Paul.Flemons at austmus.gov<mailto:Paul.Flemons at austmus.gov.au>

.au><mailto:Paul.Flemons at austmus.gov.au><mailto:Paul.Flemons at austmus.gov.au<mailto:Paul.Flemons at austmus<mailto:Paul.Flemons at austmus.gov.au>

.gov.au><mailto:Paul.Flemons at austmus.gov.au>>]

Sent: Tuesday, August 07, 2012 2:50 AM

To:

tuco at berkley.edu<mailto:tuco at berkley.edu><mailto:tuco at berkley.edu><mailto:tuco at berkley.edu><mailto:tuco at berkley.edu<m<mailto:tuco at berkley.edu>

ailto:tuco at berkley.edu><mailto:tuco at berkley.edu>><mailto:tuco at berkley.edu<mailto:tuco at berkle<mailto:tuco at berkley.edu>

y.edu><mailto:tuco at berkley.edu><mailto:tuco at berkley.edu<mailto:tuco at berkley.edu><mailto:tuco at berkley.edu>>>;

a.guentsch at bgbm.org<mailto:a.guentsch at bgbm.org><mailto:a.guentsch at bgbm.org><mailto:a.guentsch at bgbm.org><mailto:a.guentsch at b

gbm.org<mailto:a.guentsch at bgbm.org><mailto:a.guentsch at bgbm.org>><mailto:a.guentsch at bgbm.org<mai<mailto:a.guentsch at bgbm.org>

lto:a.guentsch at bgbm.org><mailto:a.guentsch at bgbm.org><mailto:a.guentsch at bgbm.org<mailto:a.guents<mailto:a.guentsch at bgbm.org>

ch at bgbm.org><mailto:a.guentsch at bgbm.org>>>;

j.holetschek at bgbm.org<mailto:j.holetschek at bgbm.org><mailto:j.holetschek at bgbm.org><mailto:j.holetschek at bgbm.org><mailto:j.holets

chek at bgbm.org<mailto:chek at bgbm.org><mailto:j.holetschek at bgbm.org><mailto:j.holetschek at bgbm.org>><mailto:j.holetschek at bg

bm.org<mailto:j.holetschek at bgbm.org><mailto:j.holetschek at bgbm.org><mailto:j.holetschek at bgbm.org<m<mailto:j.holetschek at bgbm.org>

ailto:j.holetschek at bgbm.org><mailto:j.holetschek at bgbm.org>>>;

jdeck at berkeley.edu<mailto:jdeck at berkeley.edu><mailto:jdeck at berkeley.edu><mailto:jdeck at berkeley.edu><mailto:jdeck at berkeley

.edu<mailto:jdeck at berkeley.edu><mailto:jdeck at berkeley.edu>><mailto:jdeck at berkeley.edu<mailto:j<mailto:jdeck at berkeley.edu>

deck at berkeley.edu><mailto:jdeck at berkeley.edu><mailto:jdeck at berkeley.edu<mailto:jdeck at berkeley.<mailto:jdeck at berkeley.edu>

edu><mailto:jdeck at berkeley.edu>>>

Cc: Barker, Katharine; Éamonn Ó Tuama [GBIF]; "Dröge, Gabriele"

(g.droege at BGBM.ORG<mailto:g.droege at BGBM.ORG><mailto:g.droege at BGBM.ORG><mailto:g.droege at BGBM.ORG><mailto:g.droege at BGBM.O

RG<mailto:g.droege at BGBM.ORG><mailto:g.droege at BGBM.ORG>><mailto:g.droege at BGBM.ORG<mailto:g.dro<mailto:g.droege at BGBM.ORG>

ege at BGBM.ORG><mailto:g.droege at BGBM.ORG><mailto:g.droege at BGBM.ORG<mailto:g.droege at BGBM.ORG><mailto:g.droege at 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><http://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

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