March 2007 - tdwg-tag - lists.tdwg.org

[tdwg-tapir] Output model & query template repository
by Renato De Giovanni 29 Mar '07

29 Mar '07

Dear all, Since the last TAPIR meeting I took the liberty to reorganize the TDWG repository of output models, mainly by creating subfolders for each version of each conceptual schema and by normalizing the output models. By output model normalization I mean removing the inline response structure definition from the output model, putting it somewhere else and just referencing it. This seems good practice because response structures tend to be exactly the same, regardless the conceptual schema that was used in the mapping. So the root folder for the repository is: http://rs.tdwg.org/tapir/cs/ Inside this folder you can find subfolders for each conceptual schema, then subfolders for each version and then a "model" and a "template" folder. So far I could only test dwc/1.4 with TapirLink, which still doesn't work with the ABCD output model (due to the lack of some type definitions in the ABCD XML Schema) and with the taxonCoordinates.xml (due to unsupported schema constructs). This last one I suppose was created for Biomoby tests and I'm not sure if it's being (or will be) used. And as I said, a new folder was created to store response structures: http://rs.tdwg.org/tapir/rs/ Not all structures are there. For instance, canonical Darwin and ABCD are hosted under their own domains. Please let me know if you have any comments or suggestions. There may still be some changes to make, but I really hope that this way of organizing things will remain stable for the next centuries. Best Regards, -- Renato

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[tdwg-tapir] Mapping to CNS file
by Roger Hyam 28 Mar '07

28 Mar '07

Hi Folks, I have been doing some thinking about mapping to the ontology. We have a way of defining TAPIR concepts as paths through the ontology. I have written a script to generate a CNS file from a particular view onto the ontology i.e. starting at a root class and following all the links in the RDF to extinction but not allowing recursion on any one path. It needs a little work to include the common and external properties but seems to run OK. I attach an example CNS if it will make it through the mail server. How can we use such as CNS file to configure the configurators of the wrappers and is this desirable? I believe the current configurators assume that the full name of the concepts is resolvable to the documentation for the concept. The concept paths generated form the ontology are not resolvable in this way. I could write a script that generated a documentation page when it was passed one of these paths. Would this be a reasonable thing to do? There are lots of concepts in this file (138) and it will get a lot bigger when I add in the general properties. We really need a way of organizing the mapping process into a hierarchy browsing process. Could we have a pre-mapping phase where someone browses the ontology and creates a list of concepts that they want to map. They could then use this much shorter list in the configurator. Would this be more productive? I have started mocking something up along these lines but will abandon it if there is another way forward. I was thinking of writing a script to automate the production of output model structures in much the same way as creating the CNS but I ran into an interesting problem with preventing recursion. When building paths for the CNS any one path can't include the same class twice - which is easy to do when you are only thinking about paths but when you are building a series of XML Schemas it becomes more complex. A --includes--> B --includes--> C --includes--> A Can be detected and C can contain a link instead of the include. A --includes--> B --includes--> C --linksTo--> A So we avoid recursion when building the concepts in the CNS. But if we have to consider multiple paths and possible loops then we end in situations where we can't make choices automatically. If B can include C and C can include B for example. A --includes--> B --includes--> C --linksTo-->B A --includes--> C --includes--> B --linksTo -->C There are two definitions of B here, one with a link to C and one which includes C. We can't do this in XML Schema because we have to have two definitions of the same thing in the same namespace. When you reference the element in the schema for A it couldn't know which one you meant. Please correct me if I am wrong - I'd like to be. This example is likely to arise more often than you might think as there are lots of circular links in the ontology. just think of synonymy and basionyms and hierarchies etc. So a decision still has to be made - by a human I guess - about which is the optimum combination of links and includes for a useful output structure. It makes me think a convention on namespace substitution is the easiest way forward for building output models - but that might be just because we are getting near the end of the day here.... What do you think? Roger

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[tdwg-guid] RDF-TCS Location
by peter.hollas＠thomson.com 25 Mar '07

25 Mar '07

Dear All, Could someone please enlighten me as to where the current TCS-RDF ontology is hosted? I've looked through the TDWG wiki, but only found it referenced from hyam.net, which is offline. I am looking at using it as a vocab for LSID metadata responses from organismnames.com. Many thanks, Peter. Peter Hollas Software Engineer / Systems Administrator Zoological Record Thomson Scientific Innovation Centre, York Science Park Heslington, York YO10 5DG United Kingdom Tel +44 (0)1904 435218 Fax +44 (0)1904 435114 peter.hollas(a)thomson.com http://scientific.thomson.com Better Decisions Faster

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Re: [tdwg-guid] BioGUID
by Roderic Page 21 Mar '07

21 Mar '07

Dear Chris, Damn, I was hoping nobody would ask about specifics as that would expose the fact that I've not thought much (any) of this through. My instinct is that for those bits that will interact with existing publishers (e.g., will be cited in lists of references in papers), then DOIs are the logical choice. Hence, article and monograph-level would get DOIs. This would satisfy the desire to make taxonomic literature as visible to readers. It would also not require CrossRef to change any metadata that they serve. For within-monograph (e.g., pages), then I guess the issue boils down to (a) cost, and (b) what metadata would be served? Here, I'd be happy with Handles (there's nothing stopping us having Handles for the articles and monographs as well as DOIs). So, we could have Article: DOI:xxxxxx HDL:yyyyyyyy Monograph: DOI:xxxxxxx HDL:yyyyyyyyy p. 1 HDL:yyyyyyyy.1 p. 2 HDL:yyyyyyyy.2 . . p. n HDL:yyyyyyyy.n In some ways it would be ideal to have a single GUID, but if DOIs are too costly then I still think we need DOIs for integration. I also wonder whether we need DOIs for page elements. When are they going to be used? I suspect, only in the context of (a) old literature being marked up, or new online taxonomic publications (say if BMC published a journal). In both cases, the underlying XML could be structured in such a way to recognise Handles. Hope this makes sense. My instinct is that authors of a paper in Science, say, just want to cite a monograph or article, but somebody doing a taxonomic revision may want a much finder degree of citation, and in an ideal world they would be doing this electronically online. Regards Rod On 20 Mar 2007, at 17:37, Chris Freeland wrote: > Rod, > > Fascinating stuff, as always. DOIs have come up time and again in > discussing the Biodiversity Heritage Library and I wondered if you had > any thoughts about DOIs for historic literature. You were fairly > adamant at the EoL meeting in Woods Hole in February that DOIs were > critical for BHL, which we can all agree, but the unresolved question > is > at what level(s) we need DOIs. For serials it makes sense to assign at > the article level, but what about as detailed as page-level DOI or as > broad as title-level DOI? What then of monographs - would you want a > DOI at the page for protologue linking? Looking forward to your > thoughts, > > Chris > ******************************* > Chris Freeland > Application Development Manager > Missouri Botanical Garden > (314) 577-9548 > > -----Original Message----- > From: tdwg-guid-bounces(a)lists.tdwg.org > [mailto:tdwg-guid-bounces@lists.tdwg.org] On Behalf Of Roderic Page > Sent: Tuesday, March 20, 2007 9:15 AM > To: tdwg-tag(a)lists.tdwg.org; tdwg-guid(a)lists.tdwg.org > Cc: Simon Rycroft; Vince Smith; David Remsen; Donat Agosti; William > Piel > Subject: [tdwg-guid] BioGUID > > Dear All, > > I've put together a web site called http://bioguid.info which, rather > grandly, is an attempt to bootstrap the biodiversity Semantic Web by > providing resolvable URIs for biological objects, such as publications, > > taxonomic names, nucleotide sequences, and specimens. > > These URIs (or "GUIDs") can be resolved by a web browser to display > HTML, but under the hood are resolved to RDF (which you can see by > viewing the source of the web page you get for a URI). > > The web interface is really window dressing, I just wanted a way to > display RDF that wouldn't frighten people (me included). For some URIs > all I do is grab XML and reformat it (e.g., DOIs). For GenBank records, > > all manner of agony is involved in trying to extract specimen and > publication links. > > A good place to get a sense of what bioguid.info is about is to start > with this Pubmed record: http://bioguid.info/pmid:17079492 > > From this, you can get a list of sequences. If you click on one of > those, you'll see a link to a specimen, which you can then look at > (you'll need Firefox 1.5, Camino, Webkkit, or a browser with a SVG > plugin for the full effect). > > What I'm hoping to do is start doing things like taking a TreeBASE > record, getting the linked sequences, running these through > bioguid.info to extract georeferenced specimen links, so with minimal > effort we get a map (and eventually a Google Earth tree a la Bill > Piel). > > The glue to make this happen comprises HTTP URIs that are > dereferenceable to RDF. This is my mantra for the day. > > 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 > > _______________________________________________ > tdwg-guid mailing list > tdwg-guid(a)lists.tdwg.org > http://lists.tdwg.org/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

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BioGUID
by Roderic Page 20 Mar '07

20 Mar '07

Dear All, I've put together a web site called http://bioguid.info which, rather grandly, is an attempt to bootstrap the biodiversity Semantic Web by providing resolvable URIs for biological objects, such as publications, taxonomic names, nucleotide sequences, and specimens. These URIs (or "GUIDs") can be resolved by a web browser to display HTML, but under the hood are resolved to RDF (which you can see by viewing the source of the web page you get for a URI). The web interface is really window dressing, I just wanted a way to display RDF that wouldn't frighten people (me included). For some URIs all I do is grab XML and reformat it (e.g., DOIs). For GenBank records, all manner of agony is involved in trying to extract specimen and publication links. A good place to get a sense of what bioguid.info is about is to start with this Pubmed record: http://bioguid.info/pmid:17079492 From this, you can get a list of sequences. If you click on one of those, you'll see a link to a specimen, which you can then look at (you'll need Firefox 1.5, Camino, Webkkit, or a browser with a SVG plugin for the full effect). What I'm hoping to do is start doing things like taking a TreeBASE record, getting the linked sequences, running these through bioguid.info to extract georeferenced specimen links, so with minimal effort we get a map (and eventually a Google Earth tree a la Bill Piel). The glue to make this happen comprises HTTP URIs that are dereferenceable to RDF. This is my mantra for the day. 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] TapirLink 0.2
by Renato De Giovanni 11 Mar '07

11 Mar '07

Dear all, I just wanted to say that version 0.2 of TapirLink is now available for download. It contains several bugfixes since the last release and also some new features: XSLT skins, TAPIR environment variables, enhancements in XML Schema parsing and it's now also fully compatible with all changes proposed in the last workshop. It can be downloaded from the same place: https://sourceforge.net/project/showfiles.php?group_id=38190&package_id=217… Search operations were tested with "canonical darwin", kml_simple and rss2 output models. Best Regards, -- Renato

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[tdwg-tapir] Role of TAPIR in Architecture Diagram
by Roger Hyam 08 Mar '07

08 Mar '07

Hi Folks, I have been doing some work on the TAG wiki pages and tutorial material for explaining how the TDWG Standards Architecture works. As part of that I have produced a single summary diagram. This contains some of what we talked about at the TAPIR developers meeting so I thought I would run it past the TAPIR list to see if it fits with the TAPIR world view. http://wiki.tdwg.org/twiki/bin/view/TAG/WebHome I'd be grateful for your thoughts on this diagram. What would make it clearer? Where are the mistakes. Many thanks, Roger **************************************** Roger Hyam <roger(a)tdwg.org> Biodiversity Information Standards ****************************************

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Re: [tdwg-tapir] tapir clients?
by Kevin Richards 06 Mar '07

06 Mar '07

I will be working on a Microsoft .NET server implementation of TAPIR. Also, how LSID resolution fits in with TAPIR providers. And looking at hooking up different data sources (other than DBs) at the TAPIR server end. I will put more details on the TAPIR web site when things are more definite and I get the chance. Kevin Richards >>> Dave Vieglais <vieglais(a)ku.edu> 28/02/2007 11:52:06 a.m. >>> Hi Tapirologists, There's the PyWrapper and TapirLink for the server side of the protocol, but I was wondering if: a) there's other server implementations and b) what client implementations are out there It might be worthwhile starting a "Software" page on the wiki to provide pointers to the various projects implementing TAPIR. cheers, Dave V. _______________________________________________ tdwg-tapir mailing list tdwg-tapir(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-tapir ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 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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