November 2008 - tdwg-tag - lists.tdwg.org

[tdwg-tapir] Abundance data
by bar tomas 30 Nov '08

30 Nov '08

Sorry if this question is misplaced in this discussion list, but I haven't been able to find a mailing list on the conceptual aspects of Darwin Core. I am interested to know if there are any recommendations on how to represent abundance in Darwin Core. I have seen some datasets using IndividualCount and SampleSize. For instance, for a fishing survey, would you use IndividualCount for the number of species in a catch, and SampleSize for the distance towed? Thank you very much

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[tdwg-tapir] How to find list of Tapir providers
by bar tomas 28 Nov '08

28 Nov '08

Hi, Is there any list or data portal of Tapir providers? I mean, for instance the gbif data portal (www.*gbif*.org<http://www.gbif.org/>) uses a different protocol; the providers on the gbif portal wouldn't know how to deal with a Tapir request, or am I wrong? Same applies to the OBIS network (www.i*obis*.org <http://www.iobis.org/>). Thanks.

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[tdwg-tapir] Requesting available darwin core elements from data provider
by bar tomas 28 Nov '08

28 Nov '08

Hi, Is there a way to request from a tapir data provider which optional elements of the darwin core schema are actually implemented by the provider in question. I mean, if I understood correctly only a small subset of the Darwin Core are required (GlobalUniqueIdentifier,DateLastModified,BasisOfRecord,InstitutionCode,CollectionCode,CatalogNumber,ScientificName). It would be nice to know what optional elments a given provider implements before formulating a search request to that provider (for instance, whether information defined in the IslandGroup element is available). The metadata response does not provide this information, I think. Thanks a lot. Tomas bar

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Elsevier Grand Challenge Demo
by Roderic Page 27 Nov '08

27 Nov '08

Dear All, Some of you might be interested in my entry for the Elsevier Life Sciences Grand Challenge. The site is http://iphylo.org/~rpage/challenge/www/ , which also has some links to the Challenge web site. Basically, using Molecular Phylogenetics and Evolution as a starting point, I've constructed pages for journal articles, GenBank records, specimens, taxa, etc., and provided links between them (e.g., paper x cites sequence y, which in turn has specimen z as a voucher). It's all a bit rushed (deadline for the contest is this weekend), but I hope it gives some sense of what can happen when we start to link things together (i.e., make things digitally available, give them stable identifiers, and share those identifiers). Some useful starting links The specimen CAS 199007, which is a voucher for one sequences, which has been cited twice http://iphylo.org/~rpage/challenge/www/uri/5042b74dea91280d85a16f9271826cc3 A paper on Gammarus, which shares data with six other studies http://iphylo.org/~rpage/challenge/www/uri/9b5f73ba1142519b57117afb80605f5b A paper on birds, which mistakenly lists a fish sequence http://iphylo.org/~rpage/challenge/www/uri/9b5f73ba1142519b57117afb80605f5b One outcome of this is that I image we could derive citation metrics for things other than scientific papers, such as specimens, sequences, etc. That is, we could quantify the "value" of these data. Comments/brickbats welcome. Regards Rod --------------------------------------------------------- Roderic Page Professor of Taxonomy DEEB, FBLS Graham Kerr Building University of Glasgow Glasgow G12 8QQ, UK Email: r.page(a)bio.gla.ac.uk Tel: +44 141 330 4778 Fax: +44 141 330 2792 AIM: rodpage1962(a)aim.com Facebook: http://www.facebook.com/profile.php?id=1112517192 Twitter: http://twitter.com/rdmpage Blog: http://iphylo.blogspot.com Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html --------------------------------------------------------- Roderic Page Professor of Taxonomy DEEB, FBLS Graham Kerr Building University of Glasgow Glasgow G12 8QQ, UK Email: r.page(a)bio.gla.ac.uk Tel: +44 141 330 4778 Fax: +44 141 330 2792 AIM: rodpage1962(a)aim.com Facebook: http://www.facebook.com/profile.php?id=1112517192 Twitter: http://twitter.com/rdmpage Blog: http://iphylo.blogspot.com Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html

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[tdwg-tapir] Wsdl file for Tapir
by bar tomas 26 Nov '08

26 Nov '08

Hi, Does the tapir protocol have a wsdl file describing the services included in the protocol? I've tried to look for one on the website, but haven't found one. Thanks very much. Tomas Bar

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Are DOIs expensive?
by Gregor Hagedorn 26 Nov '08

26 Nov '08

I previously concurred with arguments against DOI on the basis of cost. However, is this correct? http://www.tib-hannover.de/en/the-tib/doi-registration-agency/ states a yearly fee of 250 EUR for the publisher, not a per-object fee. That is considerably less than the Total Cost of Ownership of running custom-designed LSID software. DOI is well established and many people already know that it can be looked up on the web ... Gregor -- --------------------------------- Gregor Hagedorn Heinrich-Seidel-Str. 2 12167 Berlin skype: g.hagedorn This message is sent on a personal basis and does not constitute an activity of the German Federal Government or its research institutions. Together with any attachments, this message is intended for the addressee(s) only and may not be redistributed without permission.

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Re: [tdwg-tag] Are DOIs expensive?
by Donald.Hobern＠csiro.au 25 Nov '08

25 Nov '08

During the two GUID workshops there were really two reasons why DOIs seemed unworkable on a per-record basis. One was the cost. The other was the requirement for the central DOI administrator to have knowledge of every single DOI so it could be handled separately. (This seemed a ridiculous overhead for the expected use case of assigning identifiers to records as they are added to a database.) If the prefix-based model is indeed available, it could provide most of the expected benefits we hope to achieve through LSIDs. However I suspect that we would end up having to do almost everything to support these DOIs that we have to do for LSIDs. We would still need local resolvers to return the record corresponding to the post-prefix identifier, and we would still need to wrap the DOIs with an HTTP resolver to use them appropriately in the semantic web. The big gain could be a central registry to handle relocating of services. Donald Donald Hobern, Director, Atlas of Living Australia CSIRO Entomology, GPO Box 1700, Canberra, ACT 2601 Phone: (02) 62464352 Mobile: 0437990208 Email: Donald.Hobern(a)csiro.au -----Original Message----- Date: Tue, 25 Nov 2008 11:59:06 +0100 From: "Markus D?ring (GBIF)" <mdoering(a)gbif.org> Subject: Re: [tdwg-tag] Are DOIs expensive? To: "Gregor Hagedorn" <g.m.hagedorn(a)gmail.com> Cc: Technical Architecture Group mailing list <tdwg-tag(a)lists.tdwg.org> Message-ID: <F245595E-8FF9-4277-AE01-88AD4B3F9708(a)gbif.org> Content-Type: text/plain; charset="windows-1252" That is very interesting, Gregor. Apparently it is up to the registration agency on how much they charge (and not the central DOI). There are currently 8 agencies for different areas with the German TIB issuing DOI prefixes for "registration of scientific primary and secondary data" at the cost of 250? per prefix (which allows you to create as many DOIs as you like). http://www.doi.org/handbook_2000/registration_agencies.html#8.2 http://www.doi.org/registration_agencies.html It would also be possible to setup a new registration agency for biodiversity data if we feel this is more suited to our needs. There are several costs associated with this though, an annual membership fee ($35.000), a "franchise fee" for each newly registered name ($0.04/ doi) and a maintenance fee ($0.005/doi). So this is clearly much more expensive and would be around 9 million dollars each year for 200 million occurrence records in GBIF. http://www.doi.org/handbook_2000/registration_agencies.html#8.8 So I guess this is what was investigated before and which is far too expensive. But it should be worth consulting the TIB registry, 250? per publisher doesnt sound bad at all. Markus PS: I am expressing my personal thoughts in this conversation and not GBIFs official policy.

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Blog: UUIDs may be Dangerous
by Roger Hyam 25 Nov '08

25 Nov '08

Hi All, I took a couple of days off but couldn't help thinking about GUIDs and UUIDs especially after the various discussion that were had in Fremantle. I have written these up in a blog here: http://www.hyam.net/blog/archives/90 in case you are interested, Your thoughts are always welcome. Roger ------------------------------------------------------------- Roger Hyam Roger(a)BiodiversityCollectionsIndex.org http://www.BiodiversityCollectionsIndex.org ------------------------------------------------------------- Royal Botanic Garden Edinburgh 20A Inverleith Row, Edinburgh, EH3 5LR, UK Tel: +44 131 552 7171 ext 3015 Fax: +44 131 248 2901 http://www.rbge.org.uk/ -------------------------------------------------------------

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Re: [tdwg-tag] Blog: UUIDs may be Dangerous
by Donald.Hobern＠csiro.au 21 Nov '08

21 Nov '08

I have much sympathy for the concerns about LSIDs but continue to feel that it would prove a mistake for our community to adopt the kinds of URLs that are being suggested in this thread. Kevin is quite correct that much of the reason for promoting LSIDs is a social issue that we want data providers to think hard before issuing LSIDs. I worry however that, even if we deprecate URLs like http://www.my.org/entomology/tomcat/display.jsp?catno=12345 in favour of something more like http://my.org/stable-id/entomologycollection/12345, we are left with the following problems: 1. my.org still needs to step up to the long-term responsibility to handle URL rewriting for these ids. 2. my.org still needs to return data in a standard agreed form (e.g. RDF or OWL) when requested from these URLs. 3. Most important of all, our domain has a long history and information on specimens has value perhaps for centuries - why would we adopt a syntax for persistent long-term identifiers which is so strongly tied to the web and the web technologies of the very early 21st century? Donald Donald Hobern, Director, Atlas of Living Australia CSIRO Entomology, GPO Box 1700, Canberra, ACT 2601 Phone: (02) 62464352 Mobile: 0437990208 Email: Donald.Hobern(a)csiro.au

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SpeciesIndex written up
by Roger Hyam 05 Nov '08

05 Nov '08

Hi All, People made friendly noises after my talk on SpeciesIndexes at TDWG 2008 the other day so I thought I would flesh out the ideas on the TAG wiki. You can see them here: http://wiki.tdwg.org/twiki/bin/view/TAG/SpeciesPages and here http://wiki.tdwg.org/twiki/bin/view/TAG/SpeciesPagesMetaTags If you are looking for displacement activity or a revolution I'd be really grateful for your thoughts - either on the list or on the wiki pages. Some of this seems a little heretical to me as it is so simple. Many thanks, Roger ------------------------------------------------------------- Roger Hyam Roger(a)BiodiversityCollectionsIndex.org http://www.BiodiversityCollectionsIndex.org ------------------------------------------------------------- Royal Botanic Garden Edinburgh 20A Inverleith Row, Edinburgh, EH3 5LR, UK Tel: +44 131 552 7171 ext 3015 Fax: +44 131 248 2901 http://www.rbge.org.uk/ -------------------------------------------------------------

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