September 2006 - tdwg-tag - lists.tdwg.org

[Tdwg-guid] Jena examples?
by peter.hollas＠thomson.com 03 Oct '06

03 Oct '06

Hi Everyone, Does anyone have/or know of any good examples of using Jena to output RDF metadata with non-typical namespaces such as TCS/RDF? Currently I have the following code for my metadata method(I know it's wrong!). String TN_NS = "http://tdwg.org/2006/03/12/TaxonNames/"; ByteArrayOutputStream byteStream = new ByteArrayOutputStream(); Model model = ModelFactory.createDefaultModel(); Resource res = model.createResource("http://test"); res.addProperty(model.createProperty(TN_NS,"testProperty"),"test"); model.write(byteStream, "RDF/XML-ABBREV"); return new MetadataResponse(new ByteArrayInputStream(byteStream.toByteArray()),null,MetadataResponse.RDF _FORMAT); ...which gives me. <rdf:RDF xmlns:j.0="http://tdwg.org/2006/03/12/TaxonNames/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="http://test"> <j.0:testProperty >test</j.0:testProperty> </rdf:Description> </rdf:RDF> ...whereas I could really do with something along the lines of the IPNI metadata. <rdf:RDF xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:tn="http://tdwg.org/2006/03/12/TaxonNames/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">  <tn:TaxonName rdf:about="urn:lsid:ipni.org:names:30000959-2:1.1.2.1"> <tn:nomenclaturalCode rdf:resource="&tn;#botanical" /> <dc:title>Amaryllidaceae J.St.-Hil.</dc:title> <dcterms:created>2004-01-20 00:00:00.0</dcterms:created> <dcterms:modified>2005-06-23 15:45:33.0</dcterms:modified> <tn:rankString>fam.</tn:rankString> <tn:nameComplete>Amaryllidaceae</tn:nameComplete> <tn:uninomial>Amaryllidaceae</tn:uninomial> <tn:authorship>J.St.-Hil.</tn:authorship> <tn:publishedIn>Expos. Fam. Nat. 1: 134. 1805 [Feb-Apr 1805]</tn:publishedIn> <tn:year>1805</tn:year> <tn:typifiedBy> <tn:NomenclaturalType> <dc:title>Amaryllis Linnaeus, nom. cons.</dc:title> </tn:NomenclaturalType> </tn:typifiedBy> </tn:TaxonName> I think the main problem I have is creating resources that aren't defined as vocabularies within Jena already. I can't seem to find a way to create that <tn:TaxonName root resource element. I'm starting to think that just outputting vanilla text could be the best option here, or am I barking up the wrong tree? Many thanks, Peter. Peter Hollas MSc BSc(hons) (Peter.Hollas(a)thomson.com) Software Engineer /Systems Administrator Thomson Zoological Innovation Centre York Science Park Heslington York YO10 5DG Tel: 01904-435113 Fax: 01904-435114

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Re: [Tdwg-guid] Which TCS/RDF?
by "Döring, Markus" 28 Sep '06

28 Sep '06

Rod, I am not saying a service should provide different formats. I was simply curious to know what the LSID specs suggest. I couldn't recall a discussion on what format would be most useful for clients. Markus -----Original Message----- From: tdwg-guid-bounces(a)mailman.nhm.ku.edu [mailto:tdwg-guid-bounces@mailman.nhm.ku.edu] On Behalf Of Roderic Page Sent: Donnerstag, 28. September 2006 15:50 To: Döring, Markus Cc: tdwg-guid(a)mailman.nhm.ku.edu Subject: Re: [Tdwg-guid] Which TCS/RDF? I'm, struggling a little to see why this is an issue. Surely a provider would aim to serve the format that is most use to consumers -- in which case, RDF/XML seems the obvious choice to me, given the availability of tools for handling XML (including web browsers). Translating RDF/XML into alternative formats would simply require a XSL style sheet. For example, I use XSL to transform RDF into colour-coded XML, and HTML in my LSID tester. It should be trivial to convert RDF/XML into N-triple, for example. If consumers need N-triples, they can do the translation at their end. There are examples of this here http://www.semanticplanet.com/library/Main/RdfToTriplesStylesheet and here http://www.w3.org/2001/12/rubyrdf/xsltrdf/README.html. Why not keep things simple? Providers serve the most generally useful format, and consumers massage that if necessary. Regards Rod On 28 Sep 2006, at 11:49, Döring, Markus wrote: > Roger, > I was rather thinking about different ways of serializing RDF. RDF/XML > is just one way of expressing RDF and I would like to know if LSIDs > (or TDWG) specifies that RDF/XML should be used. If a service is free > to pick, a RDF framework, in contrast to templates, could probably > easily return different formats for the same RDF graph. > > Markus > >> -----Original Message----- >> From: rogerhyam(a)googlemail.com [mailto:rogerhyam@googlemail.com] On >> Behalf Of Roger Hyam >> Sent: Donnerstag, 28. September 2006 11:53 >> To: Döring, Markus >> Cc: Steve Perry; peter.hollas(a)thomson.com; >> tdwg-guid(a)mailman.nhm.ku.edu >> Subject: Re: [Tdwg-guid] Which TCS/RDF? >> >> Hi Markus, >> >> The LSID spec suggests that RDF is the default return type but you >> can request different formats. We would just need to agree on names >> for the formats. >> >> Thinking from a clients point of view consistency is the most >> important thing I guess especially if the data is going to be mixed >> with data from other sources. It would be far easier to write a >> client to handle just RDF than to handle RDF plus arbitrary other >> formats - perhaps with a plug in infrastructure etc etc. >> >> All the best, >> >> Roger >> >> >> >> On 9/28/06, "Döring, Markus" <m.doering(a)bgbm.org> wrote: Hi, >>> I was wondering if the LSID specs require you to return RDF/XML. >>> Could a service also return (or even request?) Turtle, N-Triple, >>> RDFa or whatever comes next year? >>> >>> It would be costly to switch formats using a templating system, so I >>> am just curious. >>> >>> Markus >>> >>> >>> -----Original Message----- >>> From: tdwg-guid-bounces(a)mailman.nhm.ku.edu >>> [mailto:tdwg-guid-bounces@mailman.nhm.ku.edu] On Behalf Of Steve >>> Perry >>> Sent: Dienstag, 26. September 2006 18:12 >>> To: peter.hollas(a)thomson.com >>> Cc: tdwg-guid(a)mailman.nhm.ku.edu >>> Subject: Re: [Tdwg-guid] Which TCS/RDF? >>> >>> >>> Hi Peter, >>> >>> I was just writing a response to your question about Jena, but I'll >>> scrap it now. Unfortunately there's no standard representation for >>> TCS >>> in RDF at this time. Hopefully there will be one in the near future. >>> >>> Jena is well suited to consuming RDF metadata, but I agree with you >>> that >>> it's a bit heavyweight if all you want to do is produce many >>> instances >>> of a single class. >>> >>> Visualizing the problem as one of templating and using Spring MVC is >>> a >>> neat approach. I use Spring mostly for dependency injection and >>> hadn't >>> considered that it might be used to isolate this kind of software >>> from >>> changes in the schema. >>> >>> -Steve >>> >>> >>> >>> peter.hollas(a)thomson.com wrote: >>> > Hi, >>> > >>> > Could someone advise on which TCS/RDF ontology would be the best >>> > to implement for metadata coming from nomenclatural sources such >>> > as ZooBank? I've yet to come across anything other than a TCS XML >>> Schema >>> > in public circulation. >>> > >>> > I've decided to do away with using the Jena API altogether for >>> > returning metadata responses from ZooBank; it seems to be rather >>> heavy >>> > handed approach to returning what is basically a simple structured >>> > text document. A much more flexible way to go is with a page >>> > templating system, especially when the schemata are in constant >>> flux. >>> > A Spring Framework MVC/JSTL endpoint will allow for schemata >>> changes >>> > to be implemented without recompilation. The LSID metadata class >>> will >>> > just act as a façade/decorator to the templating system. >>> > >>> > Many thanks, Peter. >>> > >>> > _______________________________________________ >>> > TDWG-GUID mailing list >>> > TDWG-GUID(a)mailman.nhm.ku.edu >>> > http://mailman.nhm.ku.edu/mailman/listinfo/tdwg-guid >>> > >>> >>> >>> _______________________________________________ >>> TDWG-GUID mailing list >>> TDWG-GUID(a)mailman.nhm.ku.edu >>> http://mailman.nhm.ku.edu/mailman/listinfo/tdwg-guid >>> >>> _______________________________________________ >>> TDWG-GUID mailing list >>> TDWG-GUID(a)mailman.nhm.ku.edu >>> http://mailman.nhm.ku.edu/mailman/listinfo/tdwg-guid >> >> >> >> -- >> ------------------------------------- >> Roger Hyam >> Technical Architect >> Taxonomic Databases Working Group >> ------------------------------------- >> http://www.tdwg.org >> roger(a)tdwg.org >> +44 1578 722782 >> ------------------------------------- >> > _______________________________________________ > TDWG-GUID mailing list > TDWG-GUID(a)mailman.nhm.ku.edu > http://mailman.nhm.ku.edu/mailman/listinfo/tdwg-guid > ------------------------------------------------------------------------ ---------------------------------------- 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 _______________________________________________ TDWG-GUID mailing list TDWG-GUID(a)mailman.nhm.ku.edu http://mailman.nhm.ku.edu/mailman/listinfo/tdwg-guid

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ontology &TCS RDF
by Kennedy, Jessie 28 Sep '06

28 Sep '06

Hi Folks For info, as Steve mentioned we (Rob, Robert and me)have been working on a draft ontology for TDWG that the subgroups were involved in and which was reported briefly at the last GUID meeting. The agreement was to present the results of this at TDWG after we did some testing in a mini project over the summer to see how usable it was. We're still finishing off the documentation and no doubt there will be things to discuss and changes to be made to the ontology but if you really want to look at the ontology (in OWL) we used in the project you can see it at http://tdwg.napier.ac.uk/ontology/ We had UML diagrams of the design - which I need to check to make sure they are in agreement with the OWL, but you can look at the UML diagrams on http://wiki.tdwg.org/twiki/bin/view/TAG/TDWGOntology unfortunately these don't go down to the level of detail being discussed and it is our domain ontology that really lets you represent for example an actual name. We'll make the some sample RDF available in due course with the software. See you all at TDWG - hopefully with everything documented by then ;-) Jessie > -----Original Message----- > From: tdwg-guid-bounces(a)mailman.nhm.ku.edu [mailto:tdwg-guid- > bounces(a)mailman.nhm.ku.edu] On Behalf Of Steve Perry > Sent: 26 September 2006 15:16 > To: S.Hinchcliffe(a)kew.org > Cc: tdwg-guid(a)mailman.nhm.ku.edu > Subject: Re: [Tdwg-guid] Jena examples? > > Hi Sally, > > No problem. The task was to create a prototype LSID resolver, not to > solve all the KR issues surrounding taxon concepts. However, I do think > it's time we start talking about these issues. I worry that the > prototype resolvers we set up will become de facto reference > implementations, that other people will start to construct services > modeled on the prototypes without us ever having gone back to talk about > what worked and what didn't. > > I know there are several versions of TCS-in-RDF floating around. I > think Roger's is an RDFS document. Rob Gales created an OWL-DL version > for the GBIF demonstration project that Jessie and he worked on this > summer. Early this year I created a partial implementation in OWL-Lite > (that I've since discarded). While each one is "TCS", they're all > substantially different in the way they represent TCS classes and > properties, in part because the different representation languages > (RDFS, OWL-Lite, OWL-DL) have different language features and expressive > powers. > > It would be nice if we could devise one standard RDF implementation of > TCS. I don't care which one we use, but I would like to narrow the > field to one so we can get the details sorted out. I'm talking about > details like resolvable namespaces, typed versus non-typed literals, the > use of anonymous resources, and serialization issues like the > references-to-resources problem that cropped up in the IPNI example > Peter Hollas is working from. These details are quite important because > certain decisions taken here can effect the larger network of linked > data providers. > > Take the anonymous resources issues: If you look at the example Peter > cites, the typifiedBy property refers to an anonymous NomenclaturalType > that has a dc:title. Within a single data provider, this is no big deal > because many different data objects can refer to this > NomenclaturalType. However the use of anonymous resources can cause big > problems when you try to harvest and index the data from multiple > providers. It also causes problems for the caching use case. > > It would be nice to discuss some of these things, perhaps within TAG. > > -Steve > > > Sally Hinchcliffe wrote: > > Hi Steve /all > > > > We took that syntax straight from Roger's RDF/TCS examples. I think > > Roger was going to do more work on tidying up those sorts of loose > > ends. I have to admit that my knowledge of RDF and particularly RDFS > > is pretty superficial > > > > We can switch to either the shorter format or the safer fully > > qualified URI - what do people think would be better? > > > > Sally > > > > > > > >> By the way, the IPNI example you cite has an error: > >> > >> <tn:nomenclaturalCode rdf:resource="&tn;#botanical" /> > >> > >> Many RDF/XML parsers will see &tn; as an entity which cannot be > >> resolved. Since I don't have a copy of the ontology (and > >> http://tdwg.org/2006/03/12/TaxonNames does not resolve), I can only > take > >> a guess that it should look something like: > >> > >> <tn:nomenclaturalCode rdf:resource="tn:botanical" /> > >> > >> However, using XML namespace prefixes in resource references inside > >> RDF/XML documents tends to cause problems because not all RDF/XML > >> parsers are smart enough to dereference the namespace prefix and build > a > >> fully-qualified resource URI. A safer form of the above would be the > >> fully qualified resource URI which looks like: > >> > >> <tn:nomenclaturalCode > rdf:resource="http://tdwg.org/2006/03/12/TaxonNames/botanical" /> > >> > >> > >> -Steve > >> > >> > > *** 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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Re: [Tdwg-guid] TDWG-GUID Digest, Vol 4, Issue 16
by Bart Van Brabant 28 Sep '06

28 Sep '06

Ik ga de trein van 17h nemen, ok? Dan ben ik tegen 18h15 thuis. -----Original Message----- From: tdwg-guid-bounces(a)mailman.nhm.ku.edu [mailto:tdwg-guid-bounces@mailman.nhm.ku.edu] On Behalf Of tdwg-guid-request(a)mailman.nhm.ku.edu Sent: donderdag 28 september 2006 15:22 To: tdwg-guid(a)mailman.nhm.ku.edu Subject: TDWG-GUID Digest, Vol 4, Issue 16 Send TDWG-GUID mailing list submissions to tdwg-guid(a)mailman.nhm.ku.edu To subscribe or unsubscribe via the World Wide Web, visit http://mailman.nhm.ku.edu/mailman/listinfo/tdwg-guid or, via email, send a message with subject or body 'help' to tdwg-guid-request(a)mailman.nhm.ku.edu You can reach the person managing the list at tdwg-guid-owner(a)mailman.nhm.ku.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of TDWG-GUID digest..." Today's Topics: 1. Re: Which TCS/RDF? (Roger Hyam) 2. Re: Which TCS/RDF? (D?ring, Markus) 3. Re: Which TCS/RDF? (Roderic Page) ---------------------------------------------------------------------- Message: 1 Date: Thu, 28 Sep 2006 10:53:23 +0100 From: "Roger Hyam" <roger(a)tdwg.org> Subject: Re: [Tdwg-guid] Which TCS/RDF? To: " D?ring, Markus " <m.doering(a)bgbm.org> Cc: tdwg-guid(a)mailman.nhm.ku.edu Message-ID: <414e0a4f0609280253x42e254d9y16af515e6a6e0715(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hi Markus, The LSID spec suggests that RDF is the default return type but you can request different formats. We would just need to agree on names for the formats. Thinking from a clients point of view consistency is the most important thing I guess especially if the data is going to be mixed with data from other sources. It would be far easier to write a client to handle just RDF than to handle RDF plus arbitrary other formats - perhaps with a plug in infrastructure etc etc. All the best, Roger On 9/28/06, "D?ring, Markus" <m.doering(a)bgbm.org> wrote: > > Hi, > I was wondering if the LSID specs require you to return RDF/XML. Could a > service also return (or even request?) Turtle, N-Triple, RDFa or whatever > comes next year? > > It would be costly to switch formats using a templating system, so I am > just curious. > > Markus > > > -----Original Message----- > From: tdwg-guid-bounces(a)mailman.nhm.ku.edu [mailto: > tdwg-guid-bounces(a)mailman.nhm.ku.edu] On Behalf Of Steve Perry > Sent: Dienstag, 26. September 2006 18:12 > To: peter.hollas(a)thomson.com > Cc: tdwg-guid(a)mailman.nhm.ku.edu > Subject: Re: [Tdwg-guid] Which TCS/RDF? > > > Hi Peter, > > I was just writing a response to your question about Jena, but I'll > scrap it now. Unfortunately there's no standard representation for TCS > in RDF at this time. Hopefully there will be one in the near future. > > Jena is well suited to consuming RDF metadata, but I agree with you that > it's a bit heavyweight if all you want to do is produce many instances > of a single class. > > Visualizing the problem as one of templating and using Spring MVC is a > neat approach. I use Spring mostly for dependency injection and hadn't > considered that it might be used to isolate this kind of software from > changes in the schema. > > -Steve > > > > peter.hollas(a)thomson.com wrote: > > Hi, > > > > Could someone advise on which TCS/RDF ontology would be the best to > > implement for metadata coming from nomenclatural sources such as > > ZooBank? I've yet to come across anything other than a TCS XML Schema > > in public circulation. > > > > I've decided to do away with using the Jena API altogether for > > returning metadata responses from ZooBank; it seems to be rather heavy > > handed approach to returning what is basically a simple structured > > text document. A much more flexible way to go is with a page > > templating system, especially when the schemata are in constant flux. > > A Spring Framework MVC/JSTL endpoint will allow for schemata changes > > to be implemented without recompilation. The LSID metadata class will > > just act as a fa?ade/decorator to the templating system. > > > > Many thanks, Peter. > > > > _______________________________________________ > > TDWG-GUID mailing list > > TDWG-GUID(a)mailman.nhm.ku.edu > > http://mailman.nhm.ku.edu/mailman/listinfo/tdwg-guid > > > > > _______________________________________________ > TDWG-GUID mailing list > TDWG-GUID(a)mailman.nhm.ku.edu > http://mailman.nhm.ku.edu/mailman/listinfo/tdwg-guid > > _______________________________________________ > TDWG-GUID mailing list > TDWG-GUID(a)mailman.nhm.ku.edu > http://mailman.nhm.ku.edu/mailman/listinfo/tdwg-guid > -- ------------------------------------- Roger Hyam Technical Architect Taxonomic Databases Working Group ------------------------------------- http://www.tdwg.org roger(a)tdwg.org +44 1578 722782 -------------------------------------

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Re: [Tdwg-guid] Which TCS/RDF?
by "Döring, Markus" 28 Sep '06

28 Sep '06

Roger, I was rather thinking about different ways of serializing RDF. RDF/XML is just one way of expressing RDF and I would like to know if LSIDs (or TDWG) specifies that RDF/XML should be used. If a service is free to pick, a RDF framework, in contrast to templates, could probably easily return different formats for the same RDF graph. Markus -----Original Message----- From: rogerhyam(a)googlemail.com [mailto:rogerhyam@googlemail.com] On Behalf Of Roger Hyam Sent: Donnerstag, 28. September 2006 11:53 To: Döring, Markus Cc: Steve Perry; peter.hollas(a)thomson.com; tdwg-guid(a)mailman.nhm.ku.edu Subject: Re: [Tdwg-guid] Which TCS/RDF? Hi Markus, The LSID spec suggests that RDF is the default return type but you can request different formats. We would just need to agree on names for the formats. Thinking from a clients point of view consistency is the most important thing I guess especially if the data is going to be mixed with data from other sources. It would be far easier to write a client to handle just RDF than to handle RDF plus arbitrary other formats - perhaps with a plug in infrastructure etc etc. All the best, Roger On 9/28/06, "Döring, Markus" <m.doering(a)bgbm.org> wrote: Hi, I was wondering if the LSID specs require you to return RDF/XML. Could a service also return (or even request?) Turtle, N-Triple, RDFa or whatever comes next year? It would be costly to switch formats using a templating system, so I am just curious. Markus -----Original Message----- From: tdwg-guid-bounces(a)mailman.nhm.ku.edu [mailto:tdwg-guid-bounces@mailman.nhm.ku.edu] On Behalf Of Steve Perry Sent: Dienstag, 26. September 2006 18:12 To: peter.hollas(a)thomson.com Cc: tdwg-guid(a)mailman.nhm.ku.edu Subject: Re: [Tdwg-guid] Which TCS/RDF? Hi Peter, I was just writing a response to your question about Jena, but I'll scrap it now. Unfortunately there's no standard representation for TCS in RDF at this time. Hopefully there will be one in the near future. Jena is well suited to consuming RDF metadata, but I agree with you that it's a bit heavyweight if all you want to do is produce many instances of a single class. Visualizing the problem as one of templating and using Spring MVC is a neat approach. I use Spring mostly for dependency injection and hadn't considered that it might be used to isolate this kind of software from changes in the schema. -Steve peter.hollas(a)thomson.com wrote: > Hi, > > Could someone advise on which TCS/RDF ontology would be the best to > implement for metadata coming from nomenclatural sources such as > ZooBank? I've yet to come across anything other than a TCS XML Schema > in public circulation. > > I've decided to do away with using the Jena API altogether for > returning metadata responses from ZooBank; it seems to be rather heavy > handed approach to returning what is basically a simple structured > text document. A much more flexible way to go is with a page > templating system, especially when the schemata are in constant flux. > A Spring Framework MVC/JSTL endpoint will allow for schemata changes > to be implemented without recompilation. The LSID metadata class will > just act as a façade/decorator to the templating system. > > Many thanks, Peter. > > _______________________________________________ > TDWG-GUID mailing list > TDWG-GUID(a)mailman.nhm.ku.edu > http://mailman.nhm.ku.edu/mailman/listinfo/tdwg-guid > _______________________________________________ TDWG-GUID mailing list TDWG-GUID(a)mailman.nhm.ku.edu http://mailman.nhm.ku.edu/mailman/listinfo/tdwg-guid _______________________________________________ TDWG-GUID mailing list TDWG-GUID(a)mailman.nhm.ku.edu http://mailman.nhm.ku.edu/mailman/listinfo/tdwg-guid -- ------------------------------------- Roger Hyam Technical Architect Taxonomic Databases Working Group ------------------------------------- http://www.tdwg.org roger(a)tdwg.org +44 1578 722782 -------------------------------------

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Re: [Tdwg-guid] Which TCS/RDF?
by "Döring, Markus" 28 Sep '06

28 Sep '06

Hi, I was wondering if the LSID specs require you to return RDF/XML. Could a service also return (or even request?) Turtle, N-Triple, RDFa or whatever comes next year? It would be costly to switch formats using a templating system, so I am just curious. Markus -----Original Message----- From: tdwg-guid-bounces(a)mailman.nhm.ku.edu [mailto:tdwg-guid-bounces@mailman.nhm.ku.edu] On Behalf Of Steve Perry Sent: Dienstag, 26. September 2006 18:12 To: peter.hollas(a)thomson.com Cc: tdwg-guid(a)mailman.nhm.ku.edu Subject: Re: [Tdwg-guid] Which TCS/RDF? Hi Peter, I was just writing a response to your question about Jena, but I'll scrap it now. Unfortunately there's no standard representation for TCS in RDF at this time. Hopefully there will be one in the near future. Jena is well suited to consuming RDF metadata, but I agree with you that it's a bit heavyweight if all you want to do is produce many instances of a single class. Visualizing the problem as one of templating and using Spring MVC is a neat approach. I use Spring mostly for dependency injection and hadn't considered that it might be used to isolate this kind of software from changes in the schema. -Steve peter.hollas(a)thomson.com wrote: > Hi, > > Could someone advise on which TCS/RDF ontology would be the best to > implement for metadata coming from nomenclatural sources such as > ZooBank? I've yet to come across anything other than a TCS XML Schema > in public circulation. > > I've decided to do away with using the Jena API altogether for > returning metadata responses from ZooBank; it seems to be rather heavy > handed approach to returning what is basically a simple structured > text document. A much more flexible way to go is with a page > templating system, especially when the schemata are in constant flux. > A Spring Framework MVC/JSTL endpoint will allow for schemata changes > to be implemented without recompilation. The LSID metadata class will > just act as a façade/decorator to the templating system. > > Many thanks, Peter. > > _______________________________________________ > TDWG-GUID mailing list > TDWG-GUID(a)mailman.nhm.ku.edu > http://mailman.nhm.ku.edu/mailman/listinfo/tdwg-guid > _______________________________________________ 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] (Fwd) Fwd: [TDWG] Announce: Proposal for "microformat" for mar
by Sally Hinchcliffe 28 Sep '06

28 Sep '06

Hi all This is probably on the wrong list (Maybe TAG?) but it strikes me that what this guy needs is an ontology that he can use in his microformats ... Possibly an example of a real world need for ontologies ? Sally ------- Forwarded message follows ------- Date sent: Tue, 26 Sep 2006 09:34:04 -0000 To: <sh00kg(a)rbgkew.org.uk> Subject: Fwd: [TDWG] Announce: Proposal for "microformat" for marking-up taxonomic names in HTML: comments and contributions sought From: <M.Jackson(a)kew.org> Send reply to: M.Jackson(a)rbgkew.org.uk Sally, Do you think you might respond to this? Just curious what you think. Mark ---- Forwarded From: Andy Mabbett <andy(a)pigsonthewing.org.uk> > > Hello - my first post to this mailing list. > > I'm not a taxonomist, but I've been told by one that you might be > interested in recent proposals for a formula (a "microformat" > <http://microformats.org>) for marking-up, in HTML, the names of species > (and other ranks, varieties, hybrids, etc.). > > Microformats are a way of adding additional, simple markup to > human-readable data items on web pages, using common and open HTML > standards, so that the information can be extracted by software and > indexed, searched for, saved, cross-referenced or aggregated. > Microformats are also open standards, freely available for anyone to > use. > > The proposed format respects all existing biological taxonomies, and is > not intended to change or supplant any of them - it merely provides > webmasters with a method of either: > > 1) marking-up a taxonomical name (or taxon-common name pair) in > such a way that its components can be recognised by computers > > or > > 2) marking up a common name, so as to associative with it a > taxonomical name, in such a way that the latter's components can > be recognised by computers > > For instance, if I mark up a list of common names on a page I maintain: > > <http://www.westmidlandbirdclub.com/staffs/tittesworth/latest.htm> > > using that microformat, a visitor might have browser tool which lists > all the species on the page, sorted into alphabetical order within > taxonomic class, or in taxonomic order, and then creates links to, say > (for Joe Public) their entries in Wikipedia, or the British Trust for > Ornithology, or (for scientists) some academic database of the users > choosing. > > Early thoughts on the format are on an editable "wiki", here: > > <http://microformats.org/wiki/species> > > Please feel free to participate - the proposal needs both messages of > support (particularly from people or organisations who have websites on > which they might use them) and, especially, comments and constructive > criticisms - does the proposal understand and use taxonomy correctly; is > the terminology right, are there any omissions or overlooked, unusual > naming conventions? > > You can use the above wiki, or the microformats mailing list: > > <http://microformats.org/wiki/mailing-lists> > > and/ or please feel free to pass this e-mail to other interested > parties. > > Thank you. > > -- > Andy Mabbett > Birmingham, England > > _______________________________________________ > TDWG mailing list > TDWG(a)mailman.nhm.ku.edu > http://mailman.nhm.ku.edu/mailman/listinfo/tdwg > -- ------- End of forwarded message -------*** Sally Hinchcliffe *** Computer section, Royal Botanic Gardens, Kew *** tel: +44 (0)20 8332 5708 *** S.Hinchcliffe(a)rbgkew.org.uk

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Off List for a few days
by Roger Hyam 27 Sep '06

27 Sep '06

Dear TAG List, I probably won't be responding to messages over the next few days - not because I don't want to but because I am moving house (which includes moving my office and family). I should be back to normal middle of next week. Don't hold back though. I'll soon catch up. All the best, Roger -- ------------------------------------- Roger Hyam Technical Architect Taxonomic Databases Working Group ------------------------------------- http://www.tdwg.org roger(a)tdwg.org +44 1578 722782 -------------------------------------

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Update on GUID/LSID work
by Ricardo Pereira 26 Sep '06

26 Sep '06

Dear GUID and TAG members, We would like to update you about the GUID/LSID work. Since the 2nd GUID workshop in Edinburgh, the GUID group have been working on documents targeted at different audiences interested in LSIDs- * An LSID primer for biologists (http://www.tdwg.gbif.org/uploads/media/LSIDs_for_Biologists.pdf) * An executive summary on LSID (for 'Managers') (http://www.tdwg.gbif.org/uploads/media/LSIDs_for_Managers.pdf) * An annotated summary of LSID resources on the Internet for software developers (http://www.tdwg.gbif.org/uploads/media/LSID_Resources.pdf) * An LSID Applicability Statement (in prep). This is planed to serve as guideline for implementation of LSID resolvers in biodiversity information applications. This specification will summarize all agreed decisions by the GUID group. * An LSID 'Roadmap' (in prep). This roadmap describes our priorities for the next ~6 months for LSID work. The list containing all these documents can be found at this temporary URL: http://www.tdwg.gbif.org/subgroups/guid/documents-reports/ During the TDWG 2006 Annual Meeting, several presentations will address GUIDs and LSIDs. Kevin Richards with help from Ricardo Pereira will be running a hands-on LSID tutorial/workshop that will demonstrate various aspects of a running LSID resolver and help interested parties to set up their own resolvers. Hopefully, end-users will get an idea on how LSIDs can help them. As the TDWG 2006 Annual Meeting approaches, we will be spending more time establishing the basic infrastructure to support a more integrated data sharing environment for biodiversity information applications and will be encouraging the deployment of LSID clients and resolvers in our community. We will keep you posted on any new developments. Best regards, The TDWG Infrastructure Team (TIP)

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Re: [tdwg-tag] Re: [Tdwg-guid] Jena examples?
by Roger Hyam 26 Sep '06

26 Sep '06

Hi Kevin, Thanks for your thoughts. It does seem a bit of a hack the way I am suggesting - more elegant solutions are welcome but I am not sure we can get the hierarchy in the namespace. The classes would still be part of a regular inheritance hierarchy but you wouldn't see it in the namespace. The only way you would see the hierarchy is if you had namespaces that went something like this: http://rs.tdwg.org/ontology/BaseThing/MyClass/MySubclass/MySubSubClass/mypr… Kind of like an xpath down the hierarchy for every concept. I am not sure how you would then handle targetNamespaces in XML Schema. I believe most people in the semantic world seem to have a namespace per ontology and no indication of the class structure within the ontology from the namespaces. I am curious about what a huge list of classes is - I have a general question in the back of my mind about how big people think the TDWG ontology needs to be. But that is a question for another day! Thanks, Roger Kevin Richards wrote: > My only thought is that it seems a bit like a hack and may be too > restrictive when trying to categorise classes. Ie it looks like you > intend to have ALL RDF classes under the namespace > http://rs.tdwg.org/ontology/ (correct me if I am wrong). This will > result in a huge list of classes at the one level, and hence, again > diminishing the human readability of the ontology. I wouldnt know, but > it sounds like it also might cause ontology management headaches later > on? > > Kevin > > >>>> Roger Hyam <roger(a)tdwg.org> 09/26/06 8:49 PM >>> >>>> > > Hi Everyone, > > In the not very comforting words of software vendors these are "known > issues" and will be resolved in the next release ;) > > But seriously.The namespaces in the TCS names vocabulary do not resolve > because we didn't have a policy at that time. The use if entity > references was 'borrowed' from an example (probably Protege output) and > I wouldn't mind doing away with it. > > I have been thinking long and hard about the namespace issues in the > last few weeks and believe I have a solution that I will propose at TDWG > > St Louis. It would be good to have face to face discussions about it and > > make a decision there. > > To briefly summarize: The issue is getting a namespace convention that > will work across technologies. Suppose we want to serve data in a > technology that "isn't very good at namespaces". As an example - if we > were to have separate namespaces for TaxonNames, TaxonConcepts, > Specimens, Metadata, GeospatialStuff, Collections and we wanted to > validate a document using XML Schema that contained all these things it > would require 6 independent schemas each with it's own target namespace. > > If you have ever tried to debug something like this you will know what > total madness it is. We can't just abandon XML Schema because it would > rule out not only our existing technologies but GML and probably > others... It may also be desirable to express our ontology in things > that aren't even XML. > > The only solution I can think is that for the TDWG Ontology we should > have a single formal namespace of: http://rs.tdwg.org/ontology/ > > Within the ontology we have a convention for concepts that goes like > this. > > A class would be: http://rs.tdwg.org/ontology/tdwg123_MyClass > > where 123 is the internal id of the class and MyClass is the class name > > A property in MyClass would be: > http://rs.tdwg.org/ontology/tdwg123_myProperty > > where 123 is the *class* id not the property id and myProperty is the > property name. > > An instance would be http://rs.tdwg.org/ontology/tdwg123_789 > > where 123 is the *class* id and 789 is the instance id (there is nothing > > stable about an instance that we could use as an identifier unless we > force a label property and make it immutable). > > In a way this is using the part before the _ as a pseudo namespace. > > I think this hits the balance between something that is technology > independent and something that will produce reasonably human readable > documents. > > It is radical which is why I thought it would be good to talk about it. > > Any one got an alternative? > > We have to have a solution for this by the end of the St Louis meeting > as it is critical path for ontology work. > > Most grateful for you patience and any thoughts you have. > > Roger > > > Sally Hinchcliffe wrote: > >> Hi Steve /all >> >> We took that syntax straight from Roger's RDF/TCS examples. I think >> Roger was going to do more work on tidying up those sorts of loose >> ends. I have to admit that my knowledge of RDF and particularly RDFS >> is pretty superficial >> >> We can switch to either the shorter format or the safer fully >> qualified URI - what do people think would be better? >> >> Sally >> >> >> >> >>> By the way, the IPNI example you cite has an error: >>> >>> <tn:nomenclaturalCode rdf:resource="&tn;#botanical" /> >>> >>> Many RDF/XML parsers will see &tn; as an entity which cannot be >>> resolved. Since I don't have a copy of the ontology (and >>> http://tdwg.org/2006/03/12/TaxonNames does not resolve), I can only >>> > take > >>> a guess that it should look something like: >>> >>> <tn:nomenclaturalCode rdf:resource="tn:botanical" /> >>> >>> However, using XML namespace prefixes in resource references inside >>> RDF/XML documents tends to cause problems because not all RDF/XML >>> parsers are smart enough to dereference the namespace prefix and >>> > build a > >>> fully-qualified resource URI. A safer form of the above would be the >>> > > >>> fully qualified resource URI which looks like: >>> >>> <tn:nomenclaturalCode >>> > rdf:resource="http://tdwg.org/2006/03/12/TaxonNames/botanical" /> > >>> -Steve >>> >>> >>> >> *** 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 >> >> >> > > > -- ------------------------------------- Roger Hyam Technical Architect Taxonomic Databases Working Group ------------------------------------- http://www.tdwg.org roger(a)tdwg.org +44 1578 722782 -------------------------------------

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