February 2008 - tdwg-tag - lists.tdwg.org

[tdwg-guid] Testing TCS and some ideas on GUIDs and ontologies: ranking synomymies
by Robert Huber 28 Feb '08

28 Feb '08

Dear all, I just have finished a TCS XML demo page at: http://taxonconcept.stratigraphy.net/taxon_tcs?taxid=793 which is a TCS representation of synonym list (concepts) data on the taxon 'Subbotina patagonica' published by Berggren & Norris (1997) and Pearson et al. (2006), see a html output here: http://taxonconcept.stratigraphy.net/taxon_details?taxid=793 The XML valdates against the schema, but of course, what I have implemented is a 'interpretation' of the standard, e.g. I have now summarized the two synonymies to one DataSet, and I am not sure if this granularity makes sense. So I would like to ask you to check if the output looks reasonable. I was really happy to see how good TCS fits to my data and after I have seen the first results I realized how good this fits to an experiment I was trying some months ago: I tried to apply the Google PageRank algorithm to synonymies and as a first attempt I calculated what I called TaxonRank. I have provided some more info on this here: http://stratigraphynet.blogspot.com/2008/01/how-taxonrank-works.html (+ my geoinformatics community prepared a special volume on ontologies etc and I have also submitted a paper to Computers&Geosciences which will be published soon). After seeing the TCS XML output and reading many RDF and ontology related mailing list contributions I wonder if anybody has ever thought about doing something like this before? My tests are on synonymy list (concepts) only, but I think similar approaches could lead to interesting results also if applied to e.g. genetics. And..wouldn't be ranking based on such ontologies a killer application for GUIDs? apologies for cross posting.. Robert -- Dr. Robert Huber, WDC-MARE / PANGAEA - www.pangaea.de 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(a)wdc-mare.org

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[tdwg-tapir] CNS file
by Renato De Giovanni 22 Feb '08

22 Feb '08

Dear all, The last change in the protocol (inclusion of concept datatypes) made things more complicated when dealing with CNS files. As you probably know, a CNS file is a kind of configuration file that can be used by TAPIR networks and TAPIR software. This is the current official version: http://rs.tdwg.org/tapir/cns/alias.txt The idea is to have a one-stop place from where we can get basic information about conceptual schemas and other things like available output models and query templates. Initially we decided to use a simple textual format (key-value pairs with sections) for quick and easy prototyping. The problem now is that this format doesn't allow us to store datatypes, unless we start using ugly tricks with additional custom formating and logic. And if we don't store datatypes it won't be a one-stop place anymore, forcing software to parse conceptual schemas. I think this is a good opportunity to change the CNS file and I would like to suggest the following XML format which is already being used by the output model builder under development: http://rs.tdwg.org/tapir/cns/alias.xml Regarding the datatypes, we could simply add a new subelement to <concept>. Another thing I would like to suggest is to completely decouple protocol and CNS. The CNS would become an external convention, probably still mentioned in the documentation as an example or recommendation, but not defined by the spec and not bound to capabilities responses as it can be now. The first reason is that if providers can declare and point to a CNS in capabilities, this means that once created and made public, a CNS should never change. Otherwise it may conflict with providers that may already be referencing it. This is clearly unpractical since we will need to be constantly changing the file. Moreover, after all changes since the first version of the protocol, almost all information in a CNS can also be declared in capabilities responses. This goes against the "DRY principle" (http://c2.com/cgi/wiki?DontRepeatYourself) and can easily cause problems. So the other suggestion I would like to make is to remove the optional <conceptNameServers> element from capabilities responses. Does anybody know of any software that uses this specific element? Is there any TAPIR software that currently depends on the CNS file besides provider software? In anyway, we could keep the original alias.txt file available for tools that would still depend on it. Please let me know if you have any comments, suggestions or objections. Best Wishes, -- Renato

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[tdwg-guid] LSID Tester paper
by Roderic Page 18 Feb '08

18 Feb '08

A short note on my LSID Tester tool (http://linnaeus.zoology.gla.ac.uk/~rpage/lsid/tester ) has been published in the Open Access journal Source Code for Biology and Medicine. The article has just come out so the DOI (doi:10.1186/1751-0473-3-2) isn't live yet, the direct link is http://www.scfbm.org/content/3/1/2/. Source code for the tester is available from Google Code. Thanks to those who have used the tool and provided feedback, and the reviewers who were anonymous but I suspect reside on this list ;-) 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-guid] LSID Authority Setup Guides
by Ricardo Scachetti Pereira 17 Feb '08

17 Feb '08

Dear list subscribers, The TDWG Secretariat and the TDWG Globally Unique Identifiers (GUID) Task Group announce the availability of the LSID Authority Setup Guides- http://www.tdwg.org/activities/guid/documents/lsid-setup-guides/ These guides were written by Richard Pyle, Kevin Richards and myself to help system administrators avoid common pitfalls in setting up their own LSID authorities. We hope that they will be useful to those interested in assigning LSIDs to their biodiversity information data records. Any feedback would be appreciated. Best regards, Ricardo Pereira Software Engineer TDWG Globally Unique Identifiers Task Group

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[tdwg-guid] taxon concepts in dublin core
by Robert Huber 13 Feb '08

13 Feb '08

Dear all, This is a bit OT, but at least about metadata: I am curently preparing some data in TCS schema and I plan to set up a OAI interface for data exchange. According to the OAI specifications the use of dublin (NOT darwin..) core formatted metadata is obligatory, so I will also try to offer oai_dc metadata. I would like to ask the group if there have been any discussions on mapping TCS to DC before? Do you know of any attempts to model concept or name metadata with DC? many thanks in advance, Robert -- Dr. Robert Huber, WDC-MARE / PANGAEA - www.pangaea.de 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(a)wdc-mare.org

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[tdwg-tapir] New schema & spec version
by Renato De Giovanni 07 Feb '08

07 Feb '08

Dear all, I've just released a new version of the specification to incorporate the changes that we discussed during the last months: http://www.tdwg.org/dav/subgroups/tapir/1.0/docs/TAPIRSpecification_2008-02… You can find a changelog in the end of the document. As you could see, one of the changes required a small modification in the schema (inclusion of a new "datatype" attribute for mapped concepts). I thought it was better not to enforce any controlled vocabulary for datatypes in the schema. The reason is that if we decide to change this in the future, the schema will remain the same. However, the specification mandates that the values should be limited to XML Schema primitive datatypes. Please let me know if you have any comments or suggestions. Best Regards, -- Renato

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[tdwg-tapir] r1364 - tapir/dev/schema
by svn＠rs.tdwg.org 07 Feb '08

07 Feb '08

Author: RenatoDeGiovanni Date: 2008-02-07 14:14:28 +0100 (Thu, 07 Feb 2008) New Revision: 1364 Modified: tapir/dev/schema/tapir.xsd Log: Added new attribute "datatype" to mapped concepts in capabilities responses. Modified: tapir/dev/schema/tapir.xsd =================================================================== --- tapir/dev/schema/tapir.xsd 2008-02-07 12:57:34 UTC (rev 1363) +++ tapir/dev/schema/tapir.xsd 2008-02-07 13:14:28 UTC (rev 1364) @@ -8,7 +8,7 @@ xmlns:geo="http://www.w3.org/2003/01/geo/wgs84_pos#" xmlns:vcard="http://www.w3.org/2001/vcard-rdf/3.0#" elementFormDefault="qualified" - attributeFormDefault="unqualified" version="1.0.5" xml:lang="EN" > + attributeFormDefault="unqualified" version="1.0.6" xml:lang="EN" > <xsd:annotation> <xsd:documentation xml:lang="en"> TAPIR XML Schema. TAPIR is an acronym for TDWG Access Protocol for Information Retrieval. @@ -1054,6 +1054,7 @@ <xsd:attribute name="searchable" type="xsd:boolean" use="optional" default="true"/> <xsd:attribute name="required" type="xsd:boolean" use="optional" default="false"/> <xsd:attribute name="alias" type="xsd:string" use="optional"/> + <xsd:attribute name="datatype" type="xsd:string" use="optional" default="http://www.w3.org/2001/XMLSchema#string"/> </xsd:extension> </xsd:complexContent> </xsd:complexType>

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Fwd: Request for Comments: Best Practice Recipes for Publishing RDF Vocabularies
by Kevin Richards 03 Feb '08

03 Feb '08

May be useful. Kevin >>> Diego Berrueta <diego.berrueta(a)fundacionctic.org> 1/02/2008 9:48 p.m. >>> A new working draft of "Best Practice Recipes for Publishing RDF Vocabularies" was published on 23 January, 2008. The W3C Semantic Web Deployment Working Group (SWD WG) invites you to comment on this document: http://www.w3.org/TR/2008/WD-swbp-vocab-pub-20080123/ This document describes best practice recipes for publishing vocabularies or ontologies on the Web (in RDF Schema or OWL). The features of each recipe are described in detail, so that vocabulary designers may choose the recipe best suited to their needs. Each recipe introduces general principles and an example configuration for use with an Apache HTTP server (which may be adapted to other environments). The recipes are all designed to be consistent with the architecture of the Web as currently specified. W3C Working Drafts provide opportunities for public comment during the development of a specification. Please send comments to the public mailing list: public-swd-wg(a)w3.org; please include the text "comment recipes" in the subject line. Thank you in advance for your comments, Diego Berrueta and Jon Phipps, editors. -- Diego Berrueta R&D Department - CTIC Foundation E-mail: diego.berrueta(a)fundacionctic.org Phone: +34 984 29 12 12 Parque Científico Tecnológico Gijón-Asturias-Spain www.fundacionctic.org

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