April 2007 - tdwg-tag - lists.tdwg.org

[tdwg-guid] URN, URI and http
by Markus Döring 25 Apr '07

25 Apr '07

Dear all, I don't really intend to fire up a new discussion about GUIDs, but I came across some pretty good documents about URIs I thought I share with you. They adress pretty much all of our needs for persistent and resolvable identifiers in these texts. (1) http://www.dfki.uni-kl.de/dfkidok/publications/TM/07/01/tm-07-01.pdf "Cool URIs for the Semantic Web" by Leo Sauermann DFKI GmbH, Richard Cyganiak Freie Universität Berlin (D2R author), Max Völkel FZI Karlsruhe The authors of this document come from the semantic web community and discuss what kind of URIs should be used for RDF resources. (2) http://www.w3.org/2001/tag/doc/URNsAndRegistries-50 This one here is written by the W3C and addresses the questions "When should URNs or URIs with novel URI schemes be used to name information resources for the Web?" The answers given are "Rarely if ever" and "Probably not". Common arguments in favor of such novel naming schemas are examined, and their properties compared with those of the existing http: URI scheme. best wishes, Markus Döring

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[tdwg-tapir] Darwin & RDF
by Renato De Giovanni 23 Apr '07

23 Apr '07

Dear all, This is clearly a crosscutting issue and I thought about using the TAPIR mailing list for the following reasons: 1) The main people involved with DarwinCore are subscribed here; 2) This issue raised from a TAPIR use case; 3) It can affect all existing TAPIR/DarwinCore providers, as well as all output models based on DarwinCore. As you know, there was a recent release of TapirLink which includes an LSID authority that serves an RDF representation of DarwinCore by default. Everything seems to be working fine, but when I parse the resulting RDF in the W3C validator, I see that the predicates are being displayed as: http://rs.tdwg.org/dwc/dwcoreGenus While in the semantic world the "expected" representation would be something like: http://rs.tdwg.org/dwc/dwcore#Genus Apparently it seems just a cosmetic thing, but after some quick research this "unexpected representation" can cause problems depending on usage and tools: for instance, if it's necessary to perform RDF/XML round-tripping, then semantic web tools may not work if there's no clear separation between the namespace URI and local names, which is normally done by using the fragment identifier. If you're interested, you can find a similar discussion here: http://www.imc.org/atom-syntax/mail-archive/msg16476.html Which has this interesting follow-up: http://www.imc.org/atom-syntax/mail-archive/msg16480.html Since the new DarwinCore version and its extensions are not yet a TDWG standard and may even be subject to other changes, I'm proposing to add the fragment identifier to all Darwin namespaces. Better to do this as soon as possible if we're going to need this in the future. Please let me know if you have any comments, ideas or concerns... It may be the case that this change will affect other things (like the new GBIF REST service) although probably not as much as TAPIR/DarwinCore providers which will need to re-map their databases. Best Regards, -- Renato

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Re: [tdwg-guid] URN, URI and http
by Roderic Page 21 Apr '07

21 Apr '07

Two more resources that may be useful come from the HCLS and Science Commons communities. See http://tinyurl.com/y5tmud and http://tinyurl.com/38fhan. Interestingly, these resources are not thrilled with LSIDs, nor with the 303 redirect solution to the problem of distinguishing between a thing and an information resource. I wonder if TDWG should enage with these communities because they are dealing with similar issues -- and are making progress. 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 iChat: aim://rodpage1962 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 Rod's rants on ants: http://semant.blogspot.com

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[tdwg-tapir] PyWrapper 3.1.0alpha released
by Markus Döring 20 Apr '07

20 Apr '07

Hi Tapiris, I've just released the alpha version of PyWrapper 3.1 that finally supports all the TAPIR protocol changes we agreed upon during the last developer meeting at GBIF. It now also runs with the latest version of Python2.5. Download & installation instructions can be found here as usual: http://trac.pywrapper.org/pywrapper/wiki/Downloads The final 3.1 release will add some minor bug fixes and most innovative a new LSID resolver written by Kevin Richards. The missing steps until the final 3.1 release can be found here: http://trac.pywrapper.org/pywrapper/milestone/3.1.0 http://trac.pywrapper.org/pywrapper/query? status=new&status=assigned&status=reopened&milestone=3.1.0 If you encounter any bugs in pywrapper, please issue a ticket on pywrapper.org If you prefer to write emails, feel free to send them to me or this mailing list. For those of you who can't be bothered to install a TAPIR service, here is a demo service running at the BGBM, please be kind: http://search.biocase.org/tapir/ Cheers Markus -- Markus Döring Botanic Garden and Botanical Museum Berlin Dahlem, Dept. of Biodiversity Informatics Königin-Luise-Str. 6-8, D-14191 Berlin +49 (30) 83850-284 m.doering(a)bgbm.org

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[tdwg-tapir] darin core rdf model
by Markus Döring 20 Apr '07

20 Apr '07

hi there, I am getting error with the darwin core rdf model and I found out thats because the structure schema does not allow for any unbounded elements anywhere. So I took the liberty to change the schema to support multiple rdf:Description elements. Please let me know if I missed something. -- Markus model http://rs.tdwg.org/tapir/cs/dwc/1.4/model/dw_rdf_record.xml schema http://rs.tdwg.org/tapir/rs/dw_v14_rdf_record.xsd

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[tdwg-tapir] r1015 - tapir/dev/schema
by svn＠rs.tdwg.org 20 Apr '07

20 Apr '07

Author: RenatoDeGiovanni Date: 2007-04-20 02:49:55 +0200 (Fri, 20 Apr 2007) New Revision: 1015 Modified: tapir/dev/schema/vcard.xsd tapir/dev/schema/w3c_geo.xsd Log: Removed xs:appinfo element to avoid validation problems. Modified: tapir/dev/schema/vcard.xsd =================================================================== --- tapir/dev/schema/vcard.xsd 2007-04-20 00:44:32 UTC (rev 1014) +++ tapir/dev/schema/vcard.xsd 2007-04-20 00:49:55 UTC (rev 1015) @@ -19,15 +19,10 @@ The xml namespace is prefixed xml which seems to be reuired for the standard xml namespace. Otherwise the schema wouldnt validate This schema is based on the Representing vCard Objects in RDF/XML at the W3C http://www.w3.org/TR/vcard-rdf - </documentation> + More information: http://xml.coverpages.org/draft-dawson-vcard-xml-dtd-19981027.txt - <appinfo xmlns:dc="http://purl.org/dc/elements/1.1/"> - <dc:title>vCard XML Schema</dc:title> - <dc:creator>Tom Habing, thabing(a)uiuc.edu</dc:creator> - <dc:relation>http://www.w3.org/TR/vcard-rdf</dc:relation> - <dc:relation>ftp://ftp.isi.edu/in-notes/rfc2426.txt</dc:relation> - <dc:relation>http://xml.coverpages.org/draft-dawson-vcard-xml-dtd-19981027.txt</dc:relation> - </appinfo> + See also: ftp://ftp.isi.edu/in-notes/rfc2426.txt + </documentation> </annotation> Modified: tapir/dev/schema/w3c_geo.xsd =================================================================== --- tapir/dev/schema/w3c_geo.xsd 2007-04-20 00:44:32 UTC (rev 1014) +++ tapir/dev/schema/w3c_geo.xsd 2007-04-20 00:49:55 UTC (rev 1015) @@ -5,16 +5,12 @@ elementFormDefault="qualified" version="1.0"> <xs:annotation> <xs:documentation xml:lang="en"> - W3C Basic Geo Vocabulary XML Schema. + W3C Basic Geo Vocabulary XML Schema. + Created by Markus Döring, m.doering(a)bgbm.org This schema represents the Geo vocabulary for RDF in the XML schema language. - Its developed for the use in TAPIR + It was developed for the use in TAPIR. + More information: http://www.w3.org/2003/01/geo/ </xs:documentation> - - <xs:appinfo xmlns:dc="http://purl.org/dc/elements/1.1/"> - <dc:title>W3C Basic Geo Vocabulary XML Schema</dc:title> - <dc:creator>Markus Döring, m.doering(a)bgbm.org</dc:creator> - <dc:relation>http://www.w3.org/2003/01/geo/</dc:relation> - </xs:appinfo> </xs:annotation>  @@ -56,4 +52,4 @@ </xs:simpleType> -</xs:schema> \ No newline at end of file +</xs:schema>

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[tdwg-tapir] r1014 - tapir/dev/schema
by svn＠rs.tdwg.org 20 Apr '07

20 Apr '07

Author: RenatoDeGiovanni Date: 2007-04-20 02:44:32 +0200 (Fri, 20 Apr 2007) New Revision: 1014 Modified: tapir/dev/schema/tapir.xsd Log: Moved the TAPIR website address to the xsd:documentation element and removed xsd:appinfo to avoid validation problems. Modified: tapir/dev/schema/tapir.xsd =================================================================== --- tapir/dev/schema/tapir.xsd 2007-04-18 14:17:34 UTC (rev 1013) +++ tapir/dev/schema/tapir.xsd 2007-04-20 00:44:32 UTC (rev 1014) @@ -16,11 +16,8 @@ stateless, HTTP transmittable, XML-based request and response protocol for accessing structured data that may be stored on any number of distributed databases of varied physical and logical structure. + More information: http://www.tdwg.org/activities/tapir/ </xsd:documentation> - <xsd:appinfo> - <dc:title>TAPIR XML Schema</dc:title> - <dc:relation>http://www.tdwg.gbif.org/subgroups/tapir/</dc:relation> - </xsd:appinfo> </xsd:annotation>

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[tdwg-tapir] TapirLink 0.3
by Renato De Giovanni 13 Apr '07

13 Apr '07

Dear all, It's still not Friday 13th here so I think I can safely make and announce the release of TapirLink 0.3. This version contains a number of bugfixes, one of them will require existing instances to regenerate the capabilities configuration file for each resource (otherwise capabilities responses will not validate against the protocol schema). This can easily be done by just saving the local mapping again using the configurator (this process can be automated in future versions). The main new feature is that now TapirLink can be used as an LSID authority, resolving LSIDs metadata through the TAPIR service (many thanks to Kevin Richards for the code!). The default metadata representation provided is an RDF version of DarwinCore, which can also be easily changed through configuration. You can download TapirLink from: https://sourceforge.net/project/showfiles.php?group_id=38190&package_id=217… Happy data sharing, -- Renato

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[tdwg-tapir] Re: PyWrapper test
by Markus Döring 05 Apr '07

05 Apr '07

Renato, with the change of the CNS file layout some time ago the alias.txt wasn't updated and pointed to no longer existing models and templates. that caused the errors in the http://search.biocase.org/tapir installation when doing searches. I've fixed the alias.txt file http://rs.tdwg.org/tapir/cns/alias.txt So the above installation works now for ABCD models. But it still has problems with DarwinCore models, cause they already use the new prefixed qualified paths. and that I havent found time to implement yet. I will try tonight, hopefully I manage. and the errors should be a bit more meaningfull too... Its because when downloading the wrong models I didnt check the returned http code and you do get back a file. A http 404 not found error page as HTML. But that is really not a TAPIR model. so dont eat too many eggs my friend! cheers. -- Markus On 04.04.2007, at 21:56, Renato De Giovanni wrote: > Hi Markus, > > I'm implementing a TAPIR driver to read occurrences for the biogeosdi > prototype. I tried to made it compatible with both DarwinCore1.4 and > ABCD2.06 providers, but I couldn't really test with you demo provider > without knowing any scientific name there. The following request > returns > an error: > > http://search.biocase.org/tapir/pywrapper? > dsa=training&op=inventory&concept=FullScientificName@abcd206 > > Error: Response preparation and data retrieval error > (GENERATING_CONTENT_FAILED) > > Not sure what went wrong... > -- > Renato > >

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TAG Spring News Letter?
by Roger Hyam 05 Apr '07

05 Apr '07

Dear Fellow TAG Member, The TAG mailing list has been quiet recently which may give the impression that there has been little action in terms of the new standards architecture. This is far from the truth. By its nature the TAG runs across almost all of the activities in TDWG and progress has been made in many separate areas that is contributing to the implementation of the overall vision as outlined in last years roadmap document: http://www.tdwg.org/uploads/media/TAG_Roadmap_01.doc This is a (possibly one off) news letter that summarizes some of the activities. Please shout out if I have missed anything or misrepresented anything. Ontology and LSID Vocabularies. An initial high level ontology for TDWG was presented at St Louis meeting. This is a useful overview of the TDWG domain across the existing schemas and standards. http://wiki.tdwg.org/twiki/bin/view/TAG/TDWGOntology Since that meeting the focus has been on developing application level classes within the ontology that can be used to define the metadata returned by LSID providers that are coming on line this year. These classes have been termed the LSID Vocabularies: http://wiki.tdwg.org/twiki/bin/view/TAG/LsidVocs The relationship between these 10 or so application level classes and the higher level ontology is being left somewhat vague at this point to allow the development of deployable systems now. Future changes in the ontology to more tightly integrate the LSID Vocabularies will be required to allow for inference across the data in the future but should not require significant changes of instance data (the deployed base) as the classes are insulated in their own namespaces. The tool presented in St Louis to allow collaborative editing of the ontology has been abandoned in favor of the use of regular IDEs to produce RDF/OWL documents a Subversion repository. The need to port the ontology into many different technologies was not supported by further investigation but LSID Vocabularies will be presented in XML Schema so that they can be integrated with the TAPIR data providers - see below. LSID Adoption By the end of the year it is planned that LSID providers will include IPNI, Index Fungorum and ZooBank for TaxonName objects. Species2000/ Catalogue of Life annual checklist for TaxonConcepts, Herb IMI for Specimens. There will be a toolkit available for publishing Collections data in LSID Vocabulary format and issuing LSIDs for them. Many data sources will either be LSID enabled or in a position to deliver data as RDF based on the TDWG ontology - thanks to a combination of the TAPIR protocol/provider software and the LSID Vocabularies. Progress with TAPIR protocol and providers. The TAPIR protocol is now ready to enter the new TDWG standards track as Version 1 and two wrapper implementations are available -PyWrapper and TAPIRLink. It has been established (at a very successful TAPIR developers meeting in Copenhagen) that TAPIR will support delivery of RDF data based on the ontology. This mechanism is currently being refined through the use of avowed XML Schemas. TAPIR providers are being rolled out in the USA and Europe this year and with them will go the ability to map to the ontology and exchange data in RDF. A diagram summarizing the standards architecture is on the home page of the TAG Wiki http://wiki.tdwg.org/twiki/bin/view/TAG/WebHome New charter for the new organisation structure. TDWG was re-organized at the St Louis meeting. There is now a hierarchy of subgroups consisting of Interest Groups that contain Task Groups. All subgroups were asked to re-submit their charters and this has now been done for the TAG. The new charter is on the TAG Wiki home page. There are few changes from the previous charter. There seems to be general agreement that the TAPIR subgroup and the GUID subgroup will become Task Groups within the TAG Interest Group but this can't happen until the executive have reviewed and accepted the TAG charter. How about a meeting? The dates have now been set for the TDWG 2007 meeting (16-23 September 2007 - Bratislava, Slovakia). By that date the TAG needs to put together a new Roadmap document describing the outlook for 2007/8. Funding may be available (from the TDWG Infrastructure Project) to hold a meeting of key individuals within the TAG at some point over the northern summer to help put that documents together. We would need to put a good case together to get it funded as we would be in competition with other groups. Whether or not we have a meeting I would like to hear opinions on how the TAG should be represented at the Bratislava meeting. Should we have a session within the main meeting? Should we have a pre-meeting? Your input required The TAG seems to be operating as a network of individuals rather than a single conversation. This is a good thing in that people don't have to spend a lot of time sifting through stuff that doesn't effect them. It is a bad thing in that it is easy for people to feel left out of the process. If you would like to be more involved or think we should be looking at something we are not please let me know, bring it up on the mailing list or start a page on the wiki. All the best for Easter and the coming Spring/Autumn depending on you hemisphere. Roger ____________________________________________________________ Roger Hyam <roger(a)tdwg.org> Biodiversity Information Standards: http://www.tdwg.org/ ____________________________________________________________ TDWG Standards Architecture: http://wiki.tdwg.org/twiki/bin/view/TAG LSID RDF Vocabularies: http://wiki.tdwg.org/twiki/bin/view/TAG/ LsidVocs ____________________________________________________________

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