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

John Wieczorek tuco at berkeley.edu
Tue Oct 23 02:03:06 CEST 2012


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 at 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 at 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 at 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 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> 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-9vCJonvqcK1pLOaq6H8GSnns/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>>
>>> > >> Reply-To: "tuco at berkeley.edu<mailto:tuco at berkeley.edu>" <
>>> 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>>
>>> > >> Cc: Katharine Barker <barkerk at si.edu<mailto:barkerk at si.edu>>, Paul
>>> Flemons <Paul.Flemons at austmus.gov.au<mailto:Paul.Flemons at austmus.gov.au>>,
>>> John Deck <jdeck at berkeley.edu<mailto:jdeck at berkeley.edu>>, Robert
>>> Hanner <bob.hanner at gmail.com<mailto:bob.hanner at gmail.com>>, Éamonn
>>> Tuama <eotuama at gbif.org<mailto:eotuama at gbif.org>>, Robert Robbins <
>>> rjr8222 at gmail.com<mailto:rjr8222 at gmail.com>>, "Guentsch, Anton" <
>>> 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>> 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>> 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>> 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>]
>>> > >> 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>>>
>>> > >> 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 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>>>
>>> > >> 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>>>
>>> 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:barkerk at si.edu><mailto:barkerk at si.edu<mailto:
>>> barkerk at si.edu>>>>
>>> > >> Date: Thursday, October 18, 2012 1:34 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:
>>> barkerk at si.edu><mailto:barkerk at si.edu<mailto:barkerk at si.edu>>>>, 'John
>>> Deck' <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>>>>, 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>><mailto: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>>>>, "'\"Dröge", Éamonn Tuama <
>>> 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" <WHITACREJ at si.edu<mailto:WHITACREJ at si.edu><mailto:
>>> WHITACREJ at si.edu<mailto:WHITACREJ at si.edu>><mailto:WHITACREJ at si.edu
>>> <mailto:WHITACREJ at si.edu><mailto:WHITACREJ at si.edu<mailto:
>>> WHITACREJ at si.edu>>>>, "'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>>>'" <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>>>>, "'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>>>'" <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>>>'" <
>>> 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>>>'"
>>> <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>>>>
>>> > >> Cc: "'morrison at cs.man.ac.uk<mailto:morrison at cs.man.ac.uk><mailto:
>>> morrison at cs.man.ac.uk<mailto:morrison at cs.man.ac.uk>><mailto:'
>>> morrison at cs.man.ac.uk<mailto:morrison at cs.man.ac.uk><mailto:
>>> morrison at cs.man.ac.uk<mailto:morrison at cs.man.ac.uk>>>'" <
>>> morrison at cs.man.ac.uk<mailto:morrison at cs.man.ac.uk><mailto:
>>> morrison at cs.man.ac.uk<mailto:morrison at cs.man.ac.uk>><mailto:
>>> morrison at cs.man.ac.uk<mailto:morrison at cs.man.ac.uk><mailto:
>>> morrison at cs.man.ac.uk<mailto:morrison at cs.man.ac.uk>>>>, "Parr, Cynthia"
>>> <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 at si.edu><mailto:
>>> parrc at si.edu<mailto:parrc at 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 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
>>> <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>>>;
>>> 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>>>; 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: 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%3Ajdeck88 at gmail.com><mailto:
>>> From%3Ajdeck88 at gmail.com<mailto:From%253Ajdeck88 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 at gmail.com<mailto:
>>> jdeck88 at 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<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.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 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>>>; 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: 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>>>> 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>>>; 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.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>>>;
>>> '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>>>'; '
>>> 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.au><mailto:Paul.Flemons at austmus.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
>>> <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 bgbm.org<mailto:a.guentsch at bgbm.org><mailto:
>>> a.guentsch 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.holetschek at bgbm.org<mailto:
>>> j.holetschek at bgbm.org><mailto: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>>>
>>> > >> 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.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>
>>> > >> 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/>
>>> > >> Like: http://www.facebook.com/australianmuseum
>>> > >> Follow: http://www.twitter.com/austmus
>>> > >> Watch: http://www.youtube.com/austmus
>>> > >> [cid:image001.png at 01CDAD34.391DC790<mailto:
>>> image001.png at 01CDAD34.391DC790><mailto:image001.png at 01CDAD34.391DC790
>>> <mailto:image001.png at 01CDAD34.391DC790>>]
>>> > >> Inspiring the exploration of nature and cultures
>>> > >>
>>> > >> [cid:image002.jpg at 01CDAD34.391DC790<mailto:
>>> image002.jpg at 01CDAD34.391DC790><mailto:image002.jpg at 01CDAD34.391DC790
>>> <mailto:image002.jpg at 01CDAD34.391DC790>>]
>>> > >>
>>> > >>
>>> > >>
>>> > >> The Australian Museum.
>>> > >>
>>> > >> 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
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>>> > >>
>>> > >> Please consider the environment before printing this email.
>>> > >>
>>> > >> This e-mail message has been scanned for Viruses and Content and
>>> cleared by MailMarshal.
>>> > >>
>>> > >>
>>> > >>
>>> > >> --
>>> > >> John Deck
>>> > >> (541) 321-0689<tel:%28541%29%20321-0689><tel:%28541%29%20321-0689>
>>> > >>
>>> > >>
>>> > >>
>>> > >>
>>> > >>
>>> <DNATissueExtensionNotes2-TDWG2012.docx>_______________________________________________
>>> > >> IPT mailing list
>>> > >> IPT at lists.gbif.org
>>> > >> http://lists.gbif.org/mailman/listinfo/ipt
>>> > >
>>> > >
>>> >
>>> >
>>>
>>>
>>
>
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