[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 14:48:30 CEST 2012
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
> 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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