May 2006 - tdwg-tag - lists.tdwg.org

Re: [tdwg-tapir] GUID support in TAPIR (or BioCASe)
by "Döring, Markus" 06 Jun '06

06 Jun '06

Ricardo, I agree to Renatos explanations. Just wanted to add that a basic LSID resolving service shouldnt be hard to add to PyWrapper. From what I understand from LSIDs its just an additional WSDL pointing to the http-get based URL resolution eplained by renato below. But providers would have to take care of creating and storing LSID within their existing databases. And conversion of named parameters into positional ones will be added to pywrapper easily and for sure - just because they look nicer. -- Markus > -----Ursprüngliche Nachricht----- > Von: tdwg-tapir-bounces(a)lists.tdwg.org > [mailto:tdwg-tapir-bounces@lists.tdwg.org] Im Auftrag von > Renato De Giovanni > Gesendet: Dienstag, 30. Mai 2006 21:38 > An: tdwg-tapir(a)lists.tdwg.org > Betreff: Re: [tdwg-tapir] GUID support in TAPIR (or BioCASe) > > Hi Ricardo, > > I'll try to answer your questions... > > > 1) Does the protocol or the implementation explicitly > handle any form > > Globally Unique Identifiers? Does it adopt a specific > technology (DOI, > > Handle, POI, LSID), or does it provide support for any GUID > technology. > > If so, what are the requirements for using a new technology? > > No, TAPIR doesn't handle those technologies in terms of > having any sort of implicit resolution mechanisms or any > other specific behaviour. TAPIR can "serve" GUIDs if they are > part of a conceptual schema and if providers store the > corresponding values in their local databases. However, they > will be treated just as simple strings, both in filters and > output models. > > > 2) Are there any required fields/concepts on the > application profiles > > (ABCD for example) that are specifically designed to > accommodate GUIDs? > > As far as I know ABCD has "UnitGUID", "DatasetGUID" and URLs > for MultimediaObjects. The new version of DarwinCore has a > GlobalUniqueIdentifier concept. > > > 3) Does the protocol provide any specific resolution > mechanism (i.e., > > returning a single object based on an ID passed on the request)? > > TAPIR could work very nicely with PURLs just by making use of > standard Web technologies. For instance, ABCD and DarwinCore > providers could define a custom search template that would > require the catalog number as a parameter and would return an > RDF output model for the respective object. In this case, a > request could look > like: > > http://example.net/provider.cgi?op=view&template=someuri&cnum=123 > > Which could be easily wrapped as a PURL: > > http://purl.org/provider/123 > > So the representation of that object could be retrieved from > any browser or from any script using standard HTTP libraries. > > Providers would obviously be free to decide about the output > model for their objects (an RDF representation, or ABCD, or > plain DarwinCore...), and if the template should take an > additional parameter for versioning (or maybe the response > could just include a changelog), and if it would be desirable > to have two different search templates (for data and > metadata) and so on. > > Resolution of any other kind of GUIDs would require > additional software considering only a pure TAPIR > implementation. Unless the implementation decides to offer > additional services as part of the package. > > > 4) Any other aspects of the protocol or implementation > regarding GUIDs. > > Only minor things like recommending GUIDs to identify > "relatedEntities" in TAPIR metadata responses. I guess we > will probably recommend PURLs for templates, output models, > concepts and conceptual schemas. > > Hope this helps... > > Best Regards, > -- > Renato > > _______________________________________________ > tdwg-tapir mailing list > tdwg-tapir(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-tapir_lists.tdwg.org >

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[tdwg-tapir] GUID support in TAPIR (or BioCASe)
by Ricardo Scachetti Pereira 30 May '06

30 May '06

Hi folks, I am preparing an analysis of how existing provider software handle globally unique identifiers. I would like to ask if anyone on the list could give me more details about whether and how TAPIR handles GUIDs. I am also interested in details about how specific implementations of the protocol handle GUIDs (such as the PyWrapper or others). More specifically, I am looking to answers to the following questions: 1) Does the protocol or the implementation explicitly handle any form Globally Unique Identifiers? Does it adopt a specific technology (DOI, Handle, POI, LSID), or does it provide support for any GUID technology. If so, what are the requirements for using a new technology? 2) Are there any required fields/concepts on the application profiles (ABCD for example) that are specifically designed to accommodate GUIDs? 3) Does the protocol provide any specific resolution mechanism (i.e., returning a single object based on an ID passed on the request)? 4) Any other aspects of the protocol or implementation regarding GUIDs. I intend to write a white paper on the topic and also give a talk about it during the Second Workshop on Globally Unique Identifiers (GUID-2) next month in Edinburgh. I will post links to the documents once they are published. Any help is greatly appreciated. Have a great weekend. Regards, Ricardo PS. Note that did not mention DiGIR, DiGIR2 and Darwin Core on my request above because I am a bit more familiar with them (though information about them is appreciated, too).

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Re: [Tdwg-guid] DOIs and persistence -- when DOIs go bad
by Robert Huber 29 May '06

29 May '06

Dear all, I'm very happy about this discussion as it (imho) clarifies a lot what role PublicationBank might play and what difficulties might occur. I agree with Roderic that there could be 2 major compoments: > 1. A central place where anybody who makes a mapping can upload that > mapping (or have it harvested automatically) -> 1) The bibliographic/GUID database > 2. A central place (same as 1 above) where anybody can go to ask > whether there is a mapping for an item of literature (or an > identifier). -> 2) The bibliographic/GUID resolver service > I use "central" loosely, it might be a case of few brokers for the > major taxonomic groups/databases. PublicationBank can surely not be a monolithic thing but rather take use of the existing services/databases and act as a information broker (..at least true for the resolver services) I hope I'll find some time this week to draw a figure.. I have started to collect some information on potential services and players on the WIKI already, if you know more ... any suggestion is welcome. Sorry Roderic for sending this mail to your email address first, I was too quickly pressing the reply button.. best regards, Robert Dr. Robert Huber WDC-MARE / PANGAEA - www.pangaea.de, www.wdc-mare.org Stratigraphy.net - www.stratigraphy.net _____________________________________________ MARUM - Institute for Marine Environmental Sciences (location) University Bremen Leobener Strasse POP 330 440 28359 Bremen Phone ++49 421 218-65593, Fax ++49 421 218-65505 e-mail rhuber@@wdc-mare.org, robert.huber(a)stratigraphy.net

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[Tdwg-guid] DOIs and persistence -- when DOIs go bad
by Roderic Page 26 May '06

26 May '06

I know we've pretty much abandoned DOIs, but I thought the following example might serve as a reminder that persistence is a social problem, not a technical one. DOIs are perhaps the most widespread GUIDs relevant to our area, and have a lot of technical and financial resources behind them. But they can still fail. For example, the DOI 10.1600/0363-6445(2003)028[0387:PORLFR]2.0.CO;2 doesn't exist in CrossRef (try http://dx.doi.org/10.1600/0363-6445(2003)028[0387:PORLFR]2.0.CO;2). The paper with this DOI is here: http://www.bioone.org/perlserv/?request=get- abstract&doi=10.1600%2F0363 -6445%282003%29028%5B0387%3APORLFR%5D2.0.CO%3B2 This problem affects a lot of BioOne-hosted journals (for another example see my comments on using Flickr to store Open Access images - http://iphylo.blogspot.com/2006/05/open-access-taxonomy.html). I've been in touch with both CrossRef and BioOne about this, and it may be a few months before this is resolved (BioOne have installed some new software, and haven't registered their DOIs -- which as far as I can figure out violates CrossRef's rules). The DOI example above is particularly annoying for me, because it relates to IPNI's LSIDs. One of my favourite plant taxa is Poissonia heterantha (lsidres:urn:lsid:ipni.org:names:20012728-1). The IPNI metadata for this name include the following: <tn:publishedIn>Syst. Bot. 28(2): 401 (2003). </tn:publishedIn> Wouldn't it be nice to have something like: <tn:publishedIn rdf:resource="doi:10.1600/0363-6445(2003)028[0387:PORLFR]2.0.CO;2" /> Given a DOI, users can locate the article quickly and, via CrossRef, extract metadata. The more taxonomic literature is associated with GUIDs such as DOIs, Handles, and LSIDs, the better. It's interesting (and disconcerting) that even DOIs can be screwed up. Rod ------------------------------------------------------------------------ ---------------------------------------- Professor Roderic D. M. Page Editor, 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 Search for taxon names: http://darwin.zoology.gla.ac.uk/~rpage/portal/ Find out what we know about a species: http://ispecies.org Rod's rants on phyloinformatics: http://iphylo.blogspot.com

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Re: [Tdwg-guid] DOIs and persistence -- when DOIs go bad
by Roderic Page 26 May '06

26 May '06

Yes, but the question is whether we all have to do this separately or not. Put another way, the Poissonia paper mentioned earlier exists in TreeBASE, and I've been mapping TreeBASE literature to external ids (e.g., Google Scholar, DOIs, etc.). Now, if IPNI does the same this is duplicated effort, plus we might each miss some mappings found by the other. I guess what I'm suggesting is two things: 1. A central place where anybody who makes a mapping can upload that mapping (or have it harvested automatically) 2. A central place (same as 1 above) where anybody can go to ask whether there is a mapping for an item of literature (or an identifier). Of course, this can all be done in RDF, but RDF just gives as a means for expressing the mapping, not the actual mapping itself. I use "central" loosely, it might be a case of few brokers for the major taxonomic groups/databases. Rod On 26 May 2006, at 11:58, Kevin Richards wrote: > Isn't this what RDF metadata for literature gives us? Ie a semantic > web > of literature. > Kevin > >>>> Roderic Page <r.page(a)bio.gla.ac.uk> 05/26/06 9:37 PM >>> > > It would be cool to have a GUID "broker" that, say could take a DOI and > > say "well, IPNI calls this reference xxxxxx, and MOBOT have it as > yyyyyy, and there's a handle hdl:zzzzz for it, etc." It could also > mimic CrossRef by taking bibliographic data and attempting to match > that to an existing GUID. In otherwords, it would be an OpenURL > resolver. > > Regards > > Rod > > > > > > >> >> Sally*** Sally Hinchcliffe >> *** Computer section, Royal Botanic Gardens, Kew >> *** tel: +44 (0)20 8332 5708 >> *** S.Hinchcliffe(a)rbgkew.org.uk >> >> >> > ----------------------------------------------------------------------- > - > > ---------------------------------------- > Professor Roderic D. M. Page > Editor, 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 > Search for taxon names: http://darwin.zoology.gla.ac.uk/~rpage/portal/ > Find out what we know about a species: http://ispecies.org > Rod's rants on phyloinformatics: http://iphylo.blogspot.com > > > Send instant messages to your online friends > http://uk.messenger.yahoo.com > > > _______________________________________________ > TDWG-GUID mailing list > TDWG-GUID(a)mailman.nhm.ku.edu > http://mailman.nhm.ku.edu/mailman/listinfo/tdwg-guid > > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > +++++ > WARNING: This email and any attachments may be confidential and/or > privileged. They are intended for the addressee only and are not to be > read, > used, copied or disseminated by anyone receiving them in error. If > you are > not the intended recipient, please notify the sender by return email > and > delete this message and any attachments. > > The views expressed in this email are those of the sender and do not > necessarily reflect the official views of Landcare Research. > > Landcare Research > http://www.landcareresearch.co.nz > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > +++++ > > > > ------------------------------------------------------------------------ ---------------------------------------- Professor Roderic D. M. Page Editor, 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 Search for taxon names: http://darwin.zoology.gla.ac.uk/~rpage/portal/ Find out what we know about a species: http://ispecies.org Rod's rants on phyloinformatics: http://iphylo.blogspot.com

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Re: [Tdwg-guid] DOIs and persistence -- when DOIs go bad
by Kevin Richards 26 May '06

26 May '06

Isn't this what RDF metadata for literature gives us? Ie a semantic web of literature. Kevin >>> Roderic Page <r.page(a)bio.gla.ac.uk> 05/26/06 9:37 PM >>> It would be cool to have a GUID "broker" that, say could take a DOI and say "well, IPNI calls this reference xxxxxx, and MOBOT have it as yyyyyy, and there's a handle hdl:zzzzz for it, etc." It could also mimic CrossRef by taking bibliographic data and attempting to match that to an existing GUID. In otherwords, it would be an OpenURL resolver. Regards Rod > > Sally*** Sally Hinchcliffe > *** Computer section, Royal Botanic Gardens, Kew > *** tel: +44 (0)20 8332 5708 > *** S.Hinchcliffe(a)rbgkew.org.uk > > > ------------------------------------------------------------------------ ---------------------------------------- Professor Roderic D. M. Page Editor, 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 Search for taxon names: http://darwin.zoology.gla.ac.uk/~rpage/portal/ Find out what we know about a species: http://ispecies.org Rod's rants on phyloinformatics: http://iphylo.blogspot.com Send instant messages to your online friends http://uk.messenger.yahoo.com _______________________________________________ TDWG-GUID mailing list TDWG-GUID(a)mailman.nhm.ku.edu http://mailman.nhm.ku.edu/mailman/listinfo/tdwg-guid ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ WARNING: This email and any attachments may be confidential and/or privileged. They are intended for the addressee only and are not to be read, used, copied or disseminated by anyone receiving them in error. If you are not the intended recipient, please notify the sender by return email and delete this message and any attachments. The views expressed in this email are those of the sender and do not necessarily reflect the official views of Landcare Research. Landcare Research http://www.landcareresearch.co.nz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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Re: [Tdwg-guid] DOIs and persistence -- when DOIs go bad [ Scanned for viruses ]
by Paul Kirk 26 May '06

26 May '06

My guess is that almost all the legacy data, specifically the references and not digital images/xml documents, are already digitized by someone somewhere and the challenge is herding these cats into a collaborative environment (? EDIT). It need either a big pile of cat food (a.k.a. cash) or a project (? BHL) which does it, and if you are not participating and/or collaborating you are left behind. *IF* the TDWG standard(s) for Serial Publications (BPH) and Books/Non-serials (TL2) were available electronically we would already have a 'set of numbers' for these sub-objects which could be spliced into exiting databases - that would be a big step forward i.m.h.o. In CABI 'mycology' we already have ... c. 60000 macroreferences, mostly to the systematic literature c. 180000 microreferences in IF (from the 400000 names - the balance without references), 41000 linked to macroreferences and 8500 linked to the page images of the protologue c. 60000 page images including 30000 for 'the' two major thesauri of the mycology systematic literature (1753 - 1930) - these just waiting to be OCR'd and parsed (anyone interested?? ... or with systems to do this automatically??) We just need some 'structures' to work to and it will all rather rapidly fall together ... ever the optimist. Paul Dr Paul M. Kirk Biosystematist CABI Bioscience Bakeham Lane Egham Surrey TW20 9TY UK tel. (+44) (0)1491 829023, fax (+44) (0)1491 829100, email p.kirk(a)cabi.org www.cabi-bioscience.org; www.indexfungorum.org ________________________________ From: tdwg-guid-bounces(a)mailman.nhm.ku.edu on behalf of Sally Hinchcliffe Sent: Fri 26/05/2006 09:12 To: Roderic Page Cc: neil Thomson; tdwg-guid(a)mailman.nhm.ku.edu Subject: Re: [Tdwg-guid] DOIs and persistence -- when DOIs go bad [ Scanned for viruses ] Rod wrote: ... > The DOI example above is particularly annoying for me, because it > relates to IPNI's LSIDs. One of my favourite plant taxa is Poissonia > heterantha (lsidres:urn:lsid:ipni.org:names:20012728-1). The IPNI > metadata for this name include the following: > > <tn:publishedIn>Syst. Bot. 28(2): 401 (2003). </tn:publishedIn> > > Wouldn't it be nice to have something like: > > <tn:publishedIn > rdf:resource="doi:10.1600/0363-6445(2003)028[0387:PORLFR]2.0.CO;2" /> > > Given a DOI, users can locate the article quickly and, via CrossRef, > extract metadata. The more taxonomic literature is associated with > GUIDs such as DOIs, Handles, and LSIDs, the better. This somewhat relates to a cross conversation (sorry, fell off the mailing list) we've been having with Neil Thomson about his BHL proposal & it points up another social problem, this time with legacy data Even if the DOIs were working as advertised, what would it take to get to the point where we could supplement 'Syst. Bot. 28(2): 401 (2003).' with "doi:10.1600/0363-6445(2003)028[0387:PORLFR]2.0.CO;2" ? This example is actually quite close to being doable programmatically. 'Syst. Bot.' is a standardised publication abbreviation in IPNI, and the collation is in a standard form too, so if we had a source of DOIs tied to articles in Syst. Bot. we could imagine writing a routine to programmatically import the relevant DOI into the IPNI record. We're chugging away with standardisation in IPNI and we're doing updates at the moment that are cleaning up aspects of 10,000, 15,000, up to 50,000 records at a time. But there are 1.5 million records to do and we can still find (just from within Poissonia) citations like 'Adansonia, ix. (1870) 295. ' or 'Bol. Mus. Hist. Nat. Tucuman no. 6: 8. 1925 Hauman, in Kew Bull. 1925: 279. 1925 ' which look much less tractable 60% of publications are not standardised in IPNI, and of the standardised ones many of them predate DOIs (are there any moves among journals to retrofit DOIs to older series?) Plus I've noticed in the IPNI and other editors at Kew a strange reluctance to type in strings that look like '10.1600/0363-6445(2003)028[0387:PORLFR]2.0.CO;2' - I don't know whether barcode reading technology could help here... I think that any solution to standardising citations of literature must inevitably include (if not be confined to) some use of the infrastructure that DOIs represent. But we will also have to come up with a plan that will help us deal with the vast weight of legacy data that databases like IPNI carry Sally*** Sally Hinchcliffe *** Computer section, Royal Botanic Gardens, Kew *** tel: +44 (0)20 8332 5708 *** S.Hinchcliffe(a)rbgkew.org.uk _______________________________________________ TDWG-GUID mailing list TDWG-GUID(a)mailman.nhm.ku.edu http://mailman.nhm.ku.edu/mailman/listinfo/tdwg-guid

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[Tdwg-guid] LSID tester modifications
by Roderic Page 25 May '06

25 May '06

The LSID tester (http://linnaeus.zoology.gla.ac.uk/~rpage/lsid/tester/) can now handle the new IPNI LSID's mentioned in Sally's post. Thanks to Nicky Nicolson for sending me her modifications to my code so that it plays nice with the IPNI server. Regards Rod ------------------------------------------------------------------------ ---------------------------------------- Professor Roderic D. M. Page Editor, 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 Search for taxon names: http://darwin.zoology.gla.ac.uk/~rpage/portal/ Find out what we know about a species: http://ispecies.org Rod's rants on phyloinformatics: http://iphylo.blogspot.com

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[Tdwg-guid] ipni BETA LSID resolution service up
by Sally Hinchcliffe 25 May '06

25 May '06

Hi everyone We now have the IPNI lsid server working - it's still just a development project, hasn't been rigorously tested and may still be subject to change, but please have a look Best way is to go to the wiki and follow the links. I've added some discussion about what we have/haven't done there as well http://wiki.gbif.org/guidwiki/wikka.php?wakka=LSIDResolverForTaxonName sIPNI You can also get at LSIDs from our beta web server - http://www.uk.ipni.org:90 Sally *** Sally Hinchcliffe *** Computer section, Royal Botanic Gardens, Kew *** tel: +44 (0)20 8332 5708 *** S.Hinchcliffe(a)rbgkew.org.uk

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[tdwg-tapir] TAPIR SVN layout
by "Döring, Markus" 19 May '06

19 May '06

Hi Charles, I'd like to inform you about the status and layout of the TAPIR SVN repository. The metadata response related modifications during the last weeks are over and the current TRUNK is yours to be documented. The trunk will be stable now and if you have any questions about the SVN please let me know. -- Markus The following parts currently exist in the SVN: +++++++++ WORK IN PROCESS ++++++++++++ * TRUNK http://ww2.biocase.org/svn/tapir/trunk/protocol/ The trunk is not being edited anymore by me, renato or javier and is left to you to update the inline schema documentation. * BRANCH protocol_edits_during_documentation http://ww2.biocase.org/svn/tapir/branches/protocol_edits_during_documentati… I've created a new branch of the current trunk (rev534) that will allow me or renato to apply little modifications to the schema without disturbing your documentation process. After you have completed the docs we will be able to merge back this branch into the trunk. +++++++++ TAGGED VERSIONS (not meant for editing) ++++++++++++ * PRE_DOCUMENTATION http://ww2.biocase.org/svn/tapir/tags/protocol/pre_documentation/ The current trunk version (rev534) tagged so you can always refer to it after you have started applying modifications to the trunk. * MADRID (outdated) http://ww2.biocase.org/svn/tapir/tags/protocol/madrid/ the schema alone with the modifications agreed on in Madrid2005 * PROPOSAL_2004 (outdated) http://ww2.biocase.org/svn/tapir/tags/protocol/proposal_2004/ This is the first proposal renato and myself presented at TDWG2004

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