Inside LSID

This post is my notes about LSID but it has nothing todo with the current "LSID wars".

There is no or no good documentation about the life science identifiers(LSID). Did you just try to read the specs ? houch... I'm a biologist not a network engineer. Fortunately the sources of the firefox add-on for LSID where very informative. It shows what happen when you enter a LSID in the browser. (Note: Roderic Page has also implemented is own firefox extension for LSID, see http://lsid.mozdev.org/))

Say, you have a LSID identifier:

urn:lsid:ubio.org:namebank:11815

The third part of this uri (ubio.org) is called the authority. By default the plugin looks at http://ubio.org:9090/authority to find a "WSDL" file.

OK, and this is where I've got a problem: the default behavior of the firefox add-on failed in most cases I've tested.
For instance, dcc.hapmap.org:9090/authority does not work with urn:LSID:dcc.hapmap.org:Individual:JA18942:1. So I guess that there must be a way to find this authority from the LSID itself (biomoby?) but I still have not find how.

Here I added the server http://www.ubio.org/authority in the preferences of the add-ons just because I found the URL by chance

Here is the WSDL file found at http://www.ubio.org/authority:

<?xml version="1.0"?>
<wsdl:definitions xmlns:tns="http://www.hyam.net/lsid/Authority"
targetNamespace="http://www.hyam.net/lsid/Authority"
xmlns:wsdl="http://schemas.xmlsoap.org/wsdl/"
xmlns:xsd="http://www.w3.org/2001/XMLSchema"
xmlns:httpsns="http://www.omg.org/LSID/2003/AuthorityServiceHTTPBindings">

<import namespace="http://www.omg.org/LSID/2003/AuthorityServiceHTTPBindings" location="LSIDAuthorityServiceHTTPBindings.wsdl" />

<wsdl:service name="MyAuthorityHTTPService">
<wsdl:port name="MyAuthorityHTTPPort" binding="httpsns:LSIDAuthorityHTTPBinding">
<httpsns:address location="http://www.ubio.org/authority/index.php" />
</wsdl:port>
</wsdl:service>

</wsdl:definitions>

Tthe prefix associated with the namespace http://www.omg.org/LSID/2003/AuthorityServiceHTTPBindings is then searched (There may be other bindings than HTTP: SOAP, FTP...). Here it is httpsns. The <wsdl:port> element having an attribute binding containing httpsns:LSIDAuthorityHTTPBinding" contains a child element with an attribute "location". Here the value of "location" is "http://www.ubio.org/authority/index.php". We then ask some informations about our LSID from this URL by adding a parameter "lsid=[the-lsid]" at the end of the URL: http://www.ubio.org/authority/index.php?lsid=urn:lsid:ubio.org:namebank:11815. The result is, again a WSDL file:

<?xml version="1.0"?>
<definitions xmlns:tns="http://www.example.org/SampleDataServices"
targetNamespace="http://www.example.org/SampleDataServices"
xmlns:xsd="http://www.w3.org/2001/XMLSchema"
xmlns="http://schemas.xmlsoap.org/wsdl/"
xmlns:http="http://schemas.xmlsoap.org/wsdl/http/"
xmlns:httpsns="http://www.omg.org/LSID/2003/DataServiceHTTPBindings"
>

<import namespace="http://www.omg.org/LSID/2003/DataServiceHTTPBindings" location="LSIDDataServiceHTTPBindings.wsdl" />

<!-- Example HTTP GET Services (urlEncoding) -->
<service name="MyDataHTTPService">
<port name="MyDataServiceHTTPPort" binding="httpsns:LSIDDataHTTPBinding">
<http:address location="http://www.ubio.org/authority/data.php" />
</port>
</service>
<service name="MyMetadataHTTPService">
<port name="MyMetadataServiceHTTPPort" binding="httpsns:LSIDMetadataHTTPBinding">
<http:address location="http://www.ubio.org/authority/metadata.php" />
</port>
</service>
</definitions>

Again, from this xml file, we obtain two URLs: http://www.ubio.org/authority/data.php and http://www.ubio.org/authority/metadata.php are the URL respectively used to fetch the data and the metadata about the LSID.

http://www.ubio.org/authority/data.php?lsid=urn:lsid:ubio.org:namebank:11815 returns
http://www.ubio.org/authority/data.php?lsid=urn:lsid:ubio.org:namebank:11815 (???)

Here is the Metadata/RDF file fetched from http://www.ubio.org/authority/metadata.php?lsid=urn:lsid:ubio.org:namebank:11815

<?xml version="1.0" encoding="utf-8"?>
<rdf:RDF
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:ubio="urn:lsid:ubio.org:predicates:"
xmlns:gla="urn:lsid:lsid.zoology.gla.ac.uk:predicates:"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">

<rdf:Description rdf:about="urn:lsid:ubio.org:namebank:11815">
<dc:identifier>urn:lsid:ubio.org:namebank:11815</dc:identifier>
<dc:creator rdf:resource="http://www.ubio.org"/>
<dc:subject>Pternistis leucoscepus (Gray, GR) 1867</dc:subject>
<ubio:taxonomicGroup>Aves</ubio:taxonomicGroup>
<ubio:recordVersion>4</ubio:recordVersion>
<ubio:canonicalName>Pternistis leucoscepus</ubio:canonicalName>
<dc:title>Pternistis leucoscepus</dc:title>
<dc:type>Scientific Name</dc:type>
<ubio:lexicalStatus>Unknown (Default)</ubio:lexicalStatus>
<gla:rank>Species</gla:rank>
<gla:vernacularName rdf:resource="urn:lsid:ubio.org:namebank:954940"/>
<gla:vernacularName rdf:resource="urn:lsid:ubio.org:namebank:954941"/>
<gla:vernacularName rdf:resource="urn:lsid:ubio.org:namebank:1564236"/>
<gla:vernacularName rdf:resource="urn:lsid:ubio.org:namebank:783787"/>
<gla:vernacularName rdf:resource="urn:lsid:ubio.org:namebank:1580313"/>
<gla:mapping rdf:resource="http://starcentral.mbl.edu/microscope/portal.php?pagetitle=classification&amp;BLCHID=12-4498"/>
<gla:mapping rdf:resource="http://www.cbif.gc.ca/pls/itisca/next?v_tsn=553857&amp;taxa=&p_format=&p_ifx=cbif&p_lang="/>
<gla:hasBasionym rdf:resource="urn:lsid:ubio.org:namebank:12292"/>
<gla:objectiveSynonym rdf:resource="urn:lsid:ubio.org:namebank:12292"/>
<gla:objectiveSynonym rdf:resource="urn:lsid:ubio.org:namebank:1762007"/>
<gla:objectiveSynonym rdf:resource="urn:lsid:ubio.org:namebank:1762032"/>
<gla:objectiveSynonym rdf:resource="urn:lsid:ubio.org:namebank:1762051"/>
<gla:objectiveSynonym rdf:resource="urn:lsid:ubio.org:namebank:3408791"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:1116259"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:1137821"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:1173817"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:1174615"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:1416177"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:1672192"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:2233032"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:12798879"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:1909656"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:2304281"/>
<dcterms:bibliographicCitation>Sclater, W.L., Systema Avium Æthiopicarum, p. 91</dcterms:bibliographicCitation>
</rdf:Description>
</rdf:RDF>