October 2004 - tdwg-content

Re: Globally Unique Identifier
by Richard Pyle 31 Oct '04

31 Oct '04

> Richard Pyle writes: > > > "a central question, which Donald included in his > > PowerPoint file, is whether the GUID is assigned to the physical > > object, or to the electronic representation (data record). Most of my > > comments have been from the standpoint that the GUID applies to the > > physical specimen. If it is the electronic records that we wish to > > uniquely identify, then it seems to me that the <objectID> component > > of an LSID should apply to the physical specimen, and multiple > > database records should be uniquely identified using the <version> > > component." > > I think this is not practical. Do you mean those GLOPP organism- > interaction-data that have specimen voucher information can not be > published/referenced in GBIF until I figure out whether a collection > has digitized them (most have never digitized elsewhere!)? Not necessarily. I don't think the issue is whether or not the collection has been digitized, but rather whether GUIDs have already been assigned to the vouchers you want to document in the GLOPP dataset. So, if your question is more along the lines of "do I need to check to see if GUIDs have already been issued to voucher specimens that I cite, before I issue new GUIDs", then my answer -- in the long run, at least -- would be, "well....yes!" That's sort of the fundamental point of the GUIDs, isn't it? But I don't see this as being necessarily burdensome. For example, if your GLOPP dataset included unambiguous pointers to specific voucher specimens (e.g., via InstitutionCode+CollectionCode+CatalogNumber), then it *should* be a relatively quick and straightforward process to find out if GUIDs have already been assigned (if it's not quick & easy, then the GUID service would be horribly inadequate!) If, on the other hand, the GLOPP dataset does not provide unambiguous pointers to specific voucher specimens, then the "vouchered" aspect of those specimen citations seems unsupported, in which case your GUIDs would need to be assigned to virtual/unvouchered "specimens" (analogous to observation records), and hence non-duplicate. > Or if I > find they have not been, when the collection starts to digitize them, > they would have to create for those that have already been published > in GLOPP use a new version of the GLOPP LSID? I would hope that if you assigned GUIDs to GLOPP-relevant voucher specimens that belong to a collection that is not-yet digitized, you would do the courtesy of providing the manager of that collection with a listing of the GUIDs you created for the specific relevant specimens. I would further hope that, when that collection is eventually digitized, the manager would have the wherewithal to assign new GUIDs only to those specimens that did not yet have them. But, as someone who has worked in a natural history collection for nearly two decades (and who bore witness to the transition of the collection from non-digitized to digitized), I certainly do understand the "realities" of this, and fully recognize that my optimistic perspective is likely to be overly idealistic. This is why I feel that duplicate assignment of GUIDs is inevitable (that is, two different numbers for one object; not duplicate GUIDs), and MUST be accommodated in any GUID system that is developed. My main point is that such "redundant" GUID issuance should be minimized (i.e., never done intentionally), and quickly/easily identified as such whenever it is discovered. So....if/when the situation does come up that (for example) GLOPP assigns GUIDs to vouchers on behalf of a non-digitized collection, and that collection later (inadvertently) re-assigns redundant GUIDs to the same set of specimens; that eventual discovery of this duplication should be accommodated by a mechanism for "retiring" one of the IDs into "objective synonomy" of the other ID, and automated systems should be implemented in the resolver service that "auto-forward" the retired ID to the active ID. If your question is more about whether the collection, when it later becomes digitized, should use the same <objectID> ID as was assigned for the GLOPP dataset, but qualify that same Object ID with a unique version number -- then my answer is, "I don't know". That is sort of the question I was trying to ask ('though I didn't ask it very effectively). Basically, I was suggesting that/asking whether it would make sense to pin the <ObjectID> portion of a GUID to the physical object, and using the <version> feature as a unique identifier to electronic representations thereof? > The same applies to taxonomic data - most revisions contain voucher > data. Same solution, I think. For the most part, though -- I see these as "growing pains" of a GUID system during its first years of existence. I would predict that two decades from now, if one were to do an analysis of redundant GUIDs, one would find the bulk of those having been issued relatively early on. Aloha, Rich

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MultilingualDesignPattern
by Gregor Hagedorn 26 Oct '04

26 Oct '04

I try to finish the changes on SDD and UBIF. A major issue in my eyes is to get a final vote on the question how to go along with the MultilingualDesignPattern i.e. use Label/Representation or skip the outer collection container in this case? I apologize for reopening a question that was already debated a long time ago, but in the context of finding common ground with other biodiversity schemata (in UBIF) it seems to be one of the issues people tend to take up as a case of being to complicated. Can you comment and vote on: http://efgblade.cs.umb.edu/twiki/bin/view/UBIF/MultilingualDesignPatte rn Those not wanting to use the WIKI can send email back to me and I will collate their opinion on the WIKI. Many thanks! Gregor ---------------------------------------------------------- Gregor Hagedorn (G.Hagedorn(a)bba.de) Institute for Plant Virology, Microbiology, and Biosafety Federal Research Center for Agriculture and Forestry (BBA) Königin-Luise-Str. 19 Tel: +49-30-8304-2220 14195 Berlin, Germany Fax: +49-30-8304-2203

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Re: Taxonomic Search Engine - Now with GenBank
by Roderic D. M. Page 26 Oct '04

26 Oct '04

This is next on the to do list. The site already makes extensive use of SOAP to talk to two of the source databases, I just need to tidy up the code a bit in preparation for making it a SOAP server. There are also performance issues to address, for which caching might help. Regards Rod >Nice. > >It would be great if you exposed this as a Web Service. There seem to be >several frameworks for doing this with PHP applications. > >Bob Morris > > >Roderic D. M. Page wrote: > >>The Taxonomic Search Engine I recently developed >>(http://darwin.zoology.gla.ac.uk/~rpage/portal/ ) now queries the >>GenBank taxonomy, in addition to ITIS, Index Fungorum, uBio, and >>IPNI. Although GenBank is not an authoritative source of taxonomic >>names, they do have many names not in these other databases. >> >>Regards >> >>Rod >> >>-- >>-------------------------------------------------------- >>Professor Roderic D. M. Page >>Editor Elect, Systematic Biology >>DEEB, IBLS >>Graham Kerr Building >>University of Glasgow >>Glasgow G12 8QP >>United Kingdom >> >> >>Phone: +44 141 330 4778 >>Fax: +44 141 330 2792 >>email: r.page(a)bio.gla.ac.uk >>web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html >>reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html >> >>Subscribe to Systematic Biology through the Society of Systematic >>Biologists Website: http://systematicbiology.org > > >-- >Robert A. Morris >Professor of Computer Science >UMASS-Boston >ram(a)cs.umb.edu >http://www.cs.umb.edu/efg >http://www.cs.umb.edu/~ram >phone (+1)617 287 6466 -- -------------------------------------------------------- Professor Roderic D. M. Page Editor Elect, Systematic Biology DEEB, IBLS Graham Kerr Building University of Glasgow Glasgow G12 8QP United Kingdom Phone: +44 141 330 4778 Fax: +44 141 330 2792 email: r.page(a)bio.gla.ac.uk web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html Subscribe to Systematic Biology through the Society of Systematic Biologists Website: http://systematicbiology.org

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Taxonomic Search Engine - Now with GenBank
by Roderic D. M. Page 26 Oct '04

26 Oct '04

The Taxonomic Search Engine I recently developed (http://darwin.zoology.gla.ac.uk/~rpage/portal/ ) now queries the GenBank taxonomy, in addition to ITIS, Index Fungorum, uBio, and IPNI. Although GenBank is not an authoritative source of taxonomic names, they do have many names not in these other databases. Regards Rod -- -------------------------------------------------------- Professor Roderic D. M. Page Editor Elect, Systematic Biology DEEB, IBLS Graham Kerr Building University of Glasgow Glasgow G12 8QP United Kingdom Phone: +44 141 330 4778 Fax: +44 141 330 2792 email: r.page(a)bio.gla.ac.uk web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html Subscribe to Systematic Biology through the Society of Systematic Biologists Website: http://systematicbiology.org

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Re: Taxonomic Search Engine - Now with GenBank
by Bob Morris 26 Oct '04

26 Oct '04

Nice. It would be great if you exposed this as a Web Service. There seem to be several frameworks for doing this with PHP applications. Bob Morris Roderic D. M. Page wrote: > The Taxonomic Search Engine I recently developed > (http://darwin.zoology.gla.ac.uk/~rpage/portal/ ) now queries the > GenBank taxonomy, in addition to ITIS, Index Fungorum, uBio, and > IPNI. Although GenBank is not an authoritative source of taxonomic > names, they do have many names not in these other databases. > > Regards > > Rod > > -- > -------------------------------------------------------- > Professor Roderic D. M. Page > Editor Elect, Systematic Biology > DEEB, IBLS > Graham Kerr Building > University of Glasgow > Glasgow G12 8QP > United Kingdom > > > Phone: +44 141 330 4778 > Fax: +44 141 330 2792 > email: r.page(a)bio.gla.ac.uk > web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html > reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html > > Subscribe to Systematic Biology through the Society of Systematic > Biologists Website: http://systematicbiology.org -- Robert A. Morris Professor of Computer Science UMASS-Boston ram(a)cs.umb.edu http://www.cs.umb.edu/efg http://www.cs.umb.edu/~ram phone (+1)617 287 6466

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Re: Taxonomic Search Engine - web services and LSIDs
by Joseph Poupin 12 Oct '04

12 Oct '04

Dear Roderic D. M. Page, Congratulation for your 'Taxonomic Search Engine' portal. I maintain a database on tropical crustacea on the Internet (link in my signature) and I am interested to know if your project could include (or point to) that particular database? For example, when I hit 'Calcinus' in your portal I am redirected to ITIS data. Is it possible also to get the list of species that is obtained when 'Calcinus' is entered in the field genus of request form at: http://decapoda.free.fr/search_data.php ? Sincerely. Roderic D. M. Page a écrit: > As a test of various tools for querying multiple taxonomic name > databases I've created a "Taxonomic Search Engine" > (http://darwin.zoology.gla.ac.uk/~rpage/portal/ ) that may be of > interest. > > The site will search external databases (currently ITIS, Index > Fungorum, IPNI, and uBio) for a name. If it finds the name, you can > click on the name to get more details, including a link to the > original web site that provided the name. > > Some examples to try are "Morus", "Physeter macrocephalus", and "Apus > apus". > > Behind the scenes the application talks to each database in turn and > outputs the result in a consistent format (or, as consistent as the > very different database outputs will allow). > > The search engine also outputs Life Science Identifiers (LSIDs) for > each name. Followers of recent discussions on "GUIDs" (Globally > Unique Identifiers) for taxonomic names will know that LSIDs are one > candidate for assigning a GUID to a name. The search engine provides > one way to explore the utility of LSIDs (including links to tools for > viewing them). > > I'd welcome comments/feedback. Future plans include adding more > databases and improving search performance using caching. > > Regards > > Rod Page > > -- > -------------------------------------------------------- > Professor Roderic D. M. Page > Editor Elect, Systematic Biology > DEEB, IBLS > Graham Kerr Building > University of Glasgow > Glasgow G12 8QP > United Kingdom > > > Phone: +44 141 330 4778 > Fax: +44 141 330 2792 > email: r.page(a)bio.gla.ac.uk > web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html > reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html > > Subscribe to Systematic Biology through the Society of Systematic > Biologists Website: http://systematicbiology.org > > > -- ____________________________________________________ POUPIN Joseph - Systèmes d'Information Géographiques Institut de Recherche de l'Ecole Navale Ecole Navale et GEP, LANVEOC - POULMIC BP 600, F29240 BREST ARMEES FRANCE 02 98 23 37 57 - Fax (33) 02 98 23 38 57 - poupin(a)ecole-navale.fr Polynesian Decapoda at: http://decapoda.free.fr/

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Taxonomic Search Engine - web services and LSIDs
by Roderic D. M. Page 11 Oct '04

11 Oct '04

As a test of various tools for querying multiple taxonomic name databases I've created a "Taxonomic Search Engine" (http://darwin.zoology.gla.ac.uk/~rpage/portal/ ) that may be of interest. The site will search external databases (currently ITIS, Index Fungorum, IPNI, and uBio) for a name. If it finds the name, you can click on the name to get more details, including a link to the original web site that provided the name. Some examples to try are "Morus", "Physeter macrocephalus", and "Apus apus". Behind the scenes the application talks to each database in turn and outputs the result in a consistent format (or, as consistent as the very different database outputs will allow). The search engine also outputs Life Science Identifiers (LSIDs) for each name. Followers of recent discussions on "GUIDs" (Globally Unique Identifiers) for taxonomic names will know that LSIDs are one candidate for assigning a GUID to a name. The search engine provides one way to explore the utility of LSIDs (including links to tools for viewing them). I'd welcome comments/feedback. Future plans include adding more databases and improving search performance using caching. Regards Rod Page -- -------------------------------------------------------- Professor Roderic D. M. Page Editor Elect, Systematic Biology DEEB, IBLS Graham Kerr Building University of Glasgow Glasgow G12 8QP United Kingdom Phone: +44 141 330 4778 Fax: +44 141 330 2792 email: r.page(a)bio.gla.ac.uk web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html Subscribe to Systematic Biology through the Society of Systematic Biologists Website: http://systematicbiology.org

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Re: Globally Unique Identifier
by Richard Pyle 05 Oct '04

05 Oct '04

Not enough time to respond in full, but one comment: > I am more reserved about demands to provide a central registry for > taxon concepts (or "derived/secondary" taxon concepts, if the > nomenclatural act of creating a name itself is considered a taxon > concept as well): My solution to this, which I will describe in more detail in my presentation at TDWG, is to assign the GUID to every "Name+Reference" instance ("Reference" here defined broadly; not restricted to publications). A susbset of these instances will be "name-bearing" instances (i.e., "original taxonomic descriptions"), recursively serving as the "Name" part of the Name+Reference instances. Another (overlapping) susbset of these would be "concept-bearing" instances. Still others may simply be specimen determination labels. They all represent a documented use of a taxonomic name by a human (or set of humans). The idea is that taxonomic names do not exist outside of a usage context, and that the usage context is usually objectively discernable and "reusable" (and as such, well-suited for shared universal GUID assigment). Keeping it broad and simple like this allows the same GUID pool to be used for a variety of applications (handles to names and concepts, for the purposes of constructing nomenclatural synonymies, mapping concepts, applying names/concepts to specimens, etc.) Must....get....some....sleep..... Aloha, Rich Richard L. Pyle, PhD Natural Sciences Database Coordinator, Bishop Museum 1525 Bernice St., Honolulu, HI 96817 Ph: (808)848-4115, Fax: (808)847-8252 email: deepreef(a)bishopmuseum.org http://www.bishopmuseum.org/bishop/HBS/pylerichard.html

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Meeting Christchurch
by Gregor Hagedorn 05 Oct '04

05 Oct '04

This is just a reminder to those who can make it to the TDWG 2004 meeting in Christchurch, NZ: After the main meeting, on Saturday 16th, Sunday 17th, and Monday 18th there will be SDD workgroup meeting. The official schedule (http://www.tdwg.org/2004meet/TDWG_2004_ScheduleOverview.htm) is a bit confusing in no longer mentioning the Monday that originally present. The main topics will be: 1. A discussion of the new Lucid version and what SDD and Lucid can learn by a detailed comparison 2. A discussion of the CIPRES program and how SDD can serve this large-scale program by the phylogenetic community. The meeting is open to participation for all those interested. Gregor---------------------------------------------------------- Gregor Hagedorn (G.Hagedorn(a)bba.de) Institute for Plant Virology, Microbiology, and Biosafety Federal Research Center for Agriculture and Forestry (BBA) Königin-Luise-Str. 19 Tel: +49-30-8304-2220 14195 Berlin, Germany Fax: +49-30-8304-2203

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Re: Globally Unique Identifier
by Gregor Hagedorn 05 Oct '04

05 Oct '04

> Regarding assignment of GUIDs to electronic records rather than > physical specimens -- do you feel the same way about taxonomic names? > I'd hate to have 5-10 ID numbers for every taxon name (e.g., one > generated by GBIF, one generated by ITIS, one generated by > Species2000, etc.) My understanding of the whole point of BioGUIDs > was to get away from this sort of duplication. Yes and no. I think the question collapses in the case of nomenclatural records. I believe the codes should move and endorse nomenclatural databases to be authoritative for providing authoritative name records. Since these are data objects, a GUID is natural to them, and real world (which is abstract in the case of names anyways) and data world are congruent. I am more reserved about demands to provide a central registry for taxon concepts (or "derived/secondary" taxon concepts, if the nomenclatural act of creating a name itself is considered a taxon concept as well): If somebody publishes a description of a taxon in Germany, printed or digital, perhaps providing a GUID of the nomenclatural data record the description assigns itself to, perhaps providing a DOI for its publication - I see no reason to go to a separate database, create a taxon concept record there, and then cite it back in your own digital publication. Jessie Kennedy and I differ on this point. Gregor---------------------------------------------------------- Gregor Hagedorn (G.Hagedorn(a)bba.de) Institute for Plant Virology, Microbiology, and Biosafety Federal Research Center for Agriculture and Forestry (BBA) Königin-Luise-Str. 19 Tel: +49-30-8304-2220 14195 Berlin, Germany Fax: +49-30-8304-2203

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