March 2009 - tdwg-content - lists.tdwg.org

[tdwg-phylo] Reminder: Student application deadline for Summer of Code 2009
by Hilmar Lapp 29 Mar '09

29 Mar '09

*** Please disseminate widely to students at your institution. *** *** Note: Phylogenetics standards are among the project ideas *** *** and members of this Interest Group are among the mentors. *** PHYLOINFORMATICS SUMMER OF CODE 2009 - STUDENT APPLICATION DEADLINE IS APRIL 3 http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2009 The Phyloinformatics Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for evolutionary informatics under the mentorship of experienced developers from around the world. The program is the participation of the US National Evolutionary Synthesis Center (NESCent) as a mentoring organization in the Google Summer of Code(tm) (http://code.google.com/soc/ ). Students in the program will receive a stipend from Google (and a T- shirt solely available to successful participants), and may work from their home, or home institution, for the duration of the 3 month program. Each student will have at least one dedicated mentor to show them the ropes and help them complete their project. NESCent is particularly targeting students interested in both evolutionary biology and software development. Project ideas are listed on the website and range from hardware acceleration for phylogenetic inference, to support for phyloinformatics standards within the BioPerl and BioRuby toolkits, to alignment of next-gen sequencing data, to ontology term markup for biocuration, to semantic interoperability of web-services, to 3D-printing of phylogenies. All project ideas are flexible and many can be adjusted in scope to match the skills of the student. We also welcome novel project ideas that dovetail with student interests. TO APPLY: Instructions are at the website (see "When you apply"). You can find GSoC program rules and eligibility requirements at http://socghop.appspot.com . ***The 12-day application period for students ends on Friday, April 3rd, 2009, at 19:00 UTC (3pm EDT, 12pm PDT).*** INQUIRIES: phylosoc {at} nescent {dot} org. We strongly encourage all interested students to get in touch with us with their ideas as early as possible. 2009 NESCent Phyloinformatics Summer of Code: http://hackathon.nescent.net/Phyloinformatics_Summer_of_Code_2009 Google Summer of Code FAQ: http://socghop.appspot.com/document/show/program/google/gsoc2009/faqs Cyberinfrastructure Traineeships (managed separately from GSoC; postdocs also eligible): http://hackathon.nescent.org/Cyberinfrastructure_Summer_Traineeships_2009 To sign up for quarterly NESCent newsletters: http://www.nescent.org/about/contact.php --------- Todd Vision and Hilmar Lapp National Evolutionary Synthesis Center http://nescent.org

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[tdwg-phylo] Summer of Code 2009
by Hilmar Lapp 19 Mar '09

19 Mar '09

*** Please disseminate widely at your local institutions *** *** so that we reach as many students as possible. *** PHYLOINFORMATICS SUMMER OF CODE 2009 http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2009 The Phyloinformatics Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for evolutionary informatics under the mentorship of experienced developers from around the world. The program is the participation of the US National Evolutionary Synthesis Center (NESCent) as a mentoring organization in the Google Summer of Code(tm) (http:// code.google.com/soc/). Students in the program will receive a stipend from Google (and possibly more importantly, a T-shirt solely available to successful participants), and may work from their home, or home institution, for the duration of the 3 month program. Each student will have at least one dedicated mentor to show them the ropes and help them complete their project. NESCent is particularly targeting students interested in both evolutionary biology and software development. Initial project ideas are listed on the website. These range from hardware accerelation for phylogenetic inference, to tree visualization within a wiki, to alignment of next-gen sequencing data, to development of a reusable ontology term markup module for biocuration. All project ideas are flexible and many can be adjusted in scope to match the skills of the student. We also welcome novel project ideas that dovetail with student interests. TO APPLY: Apply online at the Google Summer of Code website (http:// socghop.appspot.com/), where you will also find GSoC program rules and eligibility requirements. The 12-day application period for students opens on Monday March 23rd and runs through Friday, April 3rd, 2009. INQUIRIES: phylosoc {at} nescent {dot} org. We strongly encourage all interested students to get in touch with us with their ideas as early on as possible. 2009 NESCent Phyloinformatics Summer of Code: http://hackathon.nescent.net/Phyloinformatics_Summer_of_Code_2009 Google Summer of Code FAQ: http://socghop.appspot.com/document/show/program/google/gsoc2009/faqs Cyberinfrastructure Traineeships (managed separately from GSoC; postdocs also eligible): http://hackathon.nescent.org/ Cyberinfrastructure_Summer_Traineeships_2009 To sign up for quarterly NESCent newsletters: http://www.nescent.org/ about/contact.php --------- Todd Vision and Hilmar Lapp National Evolutionary Synthesis Center http://nescent.org

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DarwinCore 1.4 & 'lots'
by Kehan Harman 09 Mar '09

09 Mar '09

Dear All, Markus has asked me to pass this on to this shiny new mailing list as it's the list that's designed for this kind of query. I'm working as part of the Scratchpads project (http://scratchpads.eu) and we're wanting to update our specimen module which is currently based on DarwinCore 1.2.1. We'd like to be able to support the concept of 'lots' within this module and were wondering whether DarwinCore and/or the curatorial extensions for it (or ABCD for that matter) support this. A 'lot' is for example a jar of specimens of n number of species, and this is often the lowest level to which specimens get curated. I'm pretty sure this is taken into account by DarwinCore but just wanted to find out if you know the mapping for this. Markus indicated that with DwC it would only support one name per record. I know that people on this list will have had to deal with this at the application level so maybe you could share how you've done it within your institutions. thanks Kehan Harman ---------- Forwarded message ---------- From: "Markus Döring (GBIF)" <mdoering_at_gbif.org> Date: Tue, Mar 3, 2009 at 5:00 PM Subject: Re: DarwinCore 1.4 & 'lots' To: Kehan Harman <kehanharman_at_gmail.com> Kehan, its not dwc specific really, the problem is known since ages also in ABCD. As far as I remember a "unit" in ABCD is anything the museum curator decides to be a unit. Basically what gets a catalog number. So a single dwc record could represent multiple specimen in case they are "hidden" behind a single catalog number. Thats what I think at least, John Wiezoreck might disagree, better ask him in person. Best would be to use the new tdwg-conten meiling list which is exactly for this. Problem with a single dwc record is of course that only one scientific name applies. Please post this problem to the list, its good for all of us to share the same idea of what a "lot" becomes. markus On Mar 3, 2009, at 17:35, Kehan Harman wrote: > Hi Markus, > Not sure how familiar you are with entomological collections, but > Simon and Vince are looking at the scratchpads specimen module > (currently based on DarwinCore 1.3) and one thing that they'd like to > know about DarwinCore (& the proposed version) is whether it supports > the concept of 'lots' out of the box. A lot is for example a jar of > specimens of n number of species, and this is often the lowest level > to which specimens get curated. I'm pretty sure this is taken into > account by DarwinCore but just wanted to find out if you know the > mapping for this (or who I should talk to to find this out)? The > reason I'm emailing you is you're one of the contributors on > http://rs.tdwg.org/dwc/index.htm. > > Cheers, > Kehan > > > -- -- kehanharman(a)gmail.com http://kehan.wordpress.com skype: kehanharman msn: kehanharman(a)gmail.com Bill Vaughan - "Suburbia is where the developer bulldozes out the trees, then names the streets after them."

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Darwin Core review
by Peter Desmet 06 Mar '09

06 Mar '09

Hi all, I had a look at the Darwin Core terms (http://rs.tdwg.org/dwc/terms/index.htm) and I have some questions and remarks. 1. The "Replaces"-links for terms in the "Complete historical record" (http://rs.tdwg.org/dwc/terms/history/index.htm) always link to themselves. See for example: HigherGeography (http://rs.tdwg.org/dwc/terms/history/index.htm#HigherGeography-2009-01-21). The "Replaces"-link links to same 2009-01-21 instead of 2007-04-17 (http://rs.tdwg.org/dwc/terms/history/index.htm#HigherGeography-2007-04-17). And this 2007-04-17 also links to 2007-04-17 instead of the older 2003-06-17. A link for "Is Replaced By" instead of text would also be useful. 2. As a result, I had some difficulties mapping the terms from DwC 1.4 (http://wiki.tdwg.org/twiki/bin/view/DarwinCore/DarwinCoreDraftStandard) with the new ones. Update: Until I found the Darwin Core Versions document (http://rs.tdwg.org/dwc/terms/history/versions/index.htm). 3. Are the terms StartDayOfYear, EndDayOfYear, StartTimeOfDay, EndTimeOfDay, YearSampled, MonthOfYear, DayOfMonth necessary if you can provide this information in EarliestDateCollected, LatestDateCollected? Or is this to provide e.g. the time at which something was collected if you don't know the date (I don't know if you can express this in EarliestDateCollected)? If so, YearSampled can always be expressed in EarliestDateCollected/LatestDateCollected. 4. Is it possible to provide a different example for SampleRemarks and SamplingEventRemarks for a clearer difference between the two? Now both have "found dead on road". 5. Why is ValidDistributionFlag removed? This looked like an interesting field for all our botanical garden specimens. We now have to express this in SamplingProtocol, which will need a controlled vocabulary for sorting these out. 6. Is Behavior an attribute of a SamplingEvent or Sample? 7. I'm happy with addition of the term "PreviousIdentifications". Is it possible to provide the previous identificators and dates there as well? 8. Can you add multiple "ResourceRelationship", "SampleAttribute", "EventAttribute" to one sample? If yes, how does this work in a flat schema like DwC? 9. The name "SamplingAttributeID" (http://rs.tdwg.org/dwc/terms/index.htm#SamplingAttributeID) should probably be changed to "SampleAttributeID". 10. What terms are mandatory? Best regards, Peter -- Peter Desmet Biodiversity Informatics Manager / Directeur de l'informatique de la biodiversité Montréal Biodiversity Centre / Centre sur la biodiversité de Montréal Canadensys - www.canadensys.net Institut de recherche en biologie végétale Université de Montréal 4101, rue Sherbrooke est Montréal, Québec, H1X 2B2 Canada Télé / Phone: 514-872-5249 Télécopie / Fax: 514-872-9406 Email: peter.desmet.cubc(a)gmail.com

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