[IPT] Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
John Deck
jdeck at berkeley.edu
Wed Oct 24 00:35:25 CEST 2012
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/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
> > 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,
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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
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> >
> >
> >
> > --
> > 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
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>
>
--
John Deck
(541) 321-0689
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