[IPT] Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
John Wieczorek
tuco at berkeley.edu
Wed Oct 24 15:25:06 CEST 2012
On Wed, Oct 24, 2012 at 9:48 AM, John Deck <jdeck at berkeley.edu> wrote:
>
> On Wed, Oct 24, 2012 at 4:30 PM, "Markus Döring (GBIF)" <mdoering at 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:
>> >
>> > 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 at 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 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/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 at gbif.org]
>> > > Sent: Monday, October 22, 2012 11:31 PM
>> > > To: tuco at berkeley.edu
>> > > Cc: Barker, Katharine; ipt at lists.gbif.org; John Deck; Paul Flemons (
>> Paul.Flemons at austmus.gov.au); Dröge, Gabriele; 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> 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-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>>
>> > > 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.e
>> > > du<mailto:tuco at berkeley.edu>>>
>> > > Reply-To:
>> > > "tuco at berkeley.edu<mailto:tuco at berkeley.edu><mailto:tuco at berkeley.e
>> > > du<mailto:tuco at berkeley.edu>>"
>> > > <tuco at berkeley.edu<mailto:tuco at berkeley.edu><mailto:tuco at berkeley.e
>> > > du<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><mail
>> > > to: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><mail
>> > > to:barkerk at si.edu<mailto:barkerk at si.edu>>>>, 'John Deck'
>> > > <jdeck at berkeley.edu<mailto:jdeck at berkeley.edu><mailto:jdeck at berkele
>> > > y.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><ma
>> > > ilto: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.g
>> > > ov.au><mailto:Paul.Flemons at austmus.gov.au<mailto:Paul.Flemons at austm
>> > > us.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 gb
>> > > if.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@
>> > > 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:rjr
>> > > 8222 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.c
>> > > om<mailto:rjr8222 at gmail.com>><mailto:rjr8222 at gmail.com<mailto:rjr82
>> > > 22 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
>> > > @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.gue
>> > > ntsch at bgbm.org>>>'"
>> > > <a.guentsch at bgbm.org<mailto:a.guentsch at bgbm.org><mailto:a.guentsch@
>> > > bgbm.org<mailto:a.guentsch at bgbm.org>><mailto:a.guentsch at bgbm.org<ma
>> > > ilto:a.guentsch at bgbm.org><mailto:a.guentsch at bgbm.org<mailto:a.guent
>> > > sch 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@
>> > > gmail.com<mailto:gtuco.btuco at gmail.com><mailto:gtuco.btuco at gmail.co
>> > > m<mailto:gtuco.btuco at gmail.com>>>'"
>> > > <gtuco.btuco at gmail.com<mailto:gtuco.btuco at gmail.com><mailto:gtuco.b
>> > > tuco at gmail.com<mailto:gtuco.btuco at gmail.com>><mailto:gtuco.btuco at gm
>> > > ail.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:tuc
>> > > o 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.e
>> > > du<mailto:tuco at berkeley.edu>><mailto:tuco at berkeley.edu<mailto:tuco@
>> > > 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:morris
>> > > on 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.u
>> > > k<mailto:morrison at cs.man.ac.uk>>>'"
>> > > <morrison at cs.man.ac.uk<mailto:morrison at cs.man.ac.uk><mailto:morriso
>> > > n at cs.man.ac.uk<mailto:morrison at cs.man.ac.uk>><mailto:morrison at cs.ma
>> > > n.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
>> > > @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<m
>> > > ailto:eotuama at gbif.org>><mailto:eotuama at gbif.org<mailto:eotuama at gbi
>> > > f.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.co
>> > > m<mailto:rjr8222 at gmail.com>><mailto:rjr8222 at gmail.com<mailto:rjr822
>> > > 2 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 b
>> > > gbm.org<mailto:a.guentsch at bgbm.org>><mailto:a.guentsch at bgbm.org<mai
>> > > lto:a.guentsch at bgbm.org><mailto:a.guentsch at bgbm.org<mailto:a.guents
>> > > ch at bgbm.org>>>;
>> > > gtuco.btuco at gmail.com<mailto:gtuco.btuco at gmail.com><mailto:gtuco.bt
>> > > uco 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<m
>> > > ailto:gtuco.btuco at gmail.com>>>;
>> > > 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 b
>> > > erkeley.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:jde
>> > > ck88 at gmail.com<mailto:jdeck88 at gmail.com><mailto:jdeck88 at gmail.com<m
>> > > ailto:jdeck88 at gmail.com>>>
>> > > [mailto:jdeck88 at gmail.com<mailto:jdeck88 at gmail.com><mailto:jdeck88@
>> > > 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<m
>> > > ailto:eotuama at gbif.org>><mailto:eotuama at gbif.org<mailto:eotuama at gbi
>> > > f.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.co
>> > > m<mailto:rjr8222 at gmail.com>><mailto:rjr8222 at gmail.com<mailto:rjr822
>> > > 2 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 b
>> > > gbm.org<mailto:a.guentsch at bgbm.org>><mailto:a.guentsch at bgbm.org<mai
>> > > lto:a.guentsch at bgbm.org><mailto:a.guentsch at bgbm.org<mailto:a.guents
>> > > ch at bgbm.org>>>;
>> > > gtuco.btuco at gmail.com<mailto:gtuco.btuco at gmail.com><mailto:gtuco.bt
>> > > uco 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<m
>> > > ailto:gtuco.btuco at gmail.com>>>;
>> > > 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 b
>> > > erkeley.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&
>> > > 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>>>';
>> 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<m
>> > > ailto:tuco at berkley.edu>><mailto:tuco at berkley.edu<mailto:tuco at berkle
>> > > y.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 b
>> > > gbm.org<mailto:a.guentsch at bgbm.org>><mailto:a.guentsch at bgbm.org<mai
>> > > lto:a.guentsch at bgbm.org><mailto:a.guentsch at bgbm.org<mailto:a.guents
>> > > ch at bgbm.org>>>;
>> > > j.holetschek at bgbm.org<mailto:j.holetschek at bgbm.org><mailto:j.holets
>> > > chek 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<m
>> > > ailto: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:j
>> > > deck 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.O
>> > > RG<mailto:g.droege at BGBM.ORG>><mailto:g.droege at BGBM.ORG<mailto:g.dro
>> > > ege 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 01CDAD34.39
>> > > 1DC790><mailto:image001.png at 01CDAD34.391DC790<mailto:image001.png at 0
>> > > 1CDAD34.391DC790>>] Inspiring the exploration of nature and
>> > > cultures
>> > >
>> > > [cid:image002.jpg at 01CDAD34.391DC790<mailto:image002.jpg at 01CDAD34.39
>> > > 1DC790><mailto:image002.jpg at 01CDAD34.391DC790<mailto:image002.jpg at 0
>> > > 1CDAD34.391DC790>>]
>> > >
>> > >
>> > >
>> > > 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 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.
>> > >
>> > > 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
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > > _______________________________________________
>> > > IPT mailing list
>> > > IPT at lists.gbif.org
>> > > http://lists.gbif.org/mailman/listinfo/ipt
>> >
>> >
>> >
>> >
>> > --
>> > John Deck
>> > (541) 321-0689
>> >
>>
>>
>
>
> --
> John Deck
> (541) 321-0689
>
>
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