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Re: Hosted Triple Store Oracle RDF DM - and access to BioRDF examples in general

From: Sean Martin <sjmm@us.ibm.com>
Date: Mon, 22 Jan 2007 09:11:19 -0500
To: public-semweb-lifesci@w3.org
Message-ID: <OFB9FB5650.B35C6938-ON8525726B.004A659A-8525726B.004DF0F2@us.ibm.com>
Hello Bill,

public-semweb-lifesci-request@w3.org wrote on 01/22/2007 06:21:19 AM:

> 
> William Bug wrote:
> > Also - for loading remote LSID resources:

> > It installed just fine, but when I try to access:
> > urn:lsid:uniprot.org:keywords:462
> > 
> > I get an error back claiming "unknown protocol".

As Eric says this may be because there is no resolver for Uniprot id's 
provided by uniprot.org and you cannot expect to get any data for an LSID 
if nobody is providing service for it :-( OR when you have not cached a 
copy of it when they were. Of course if there actually had ever been data 
for urn:lsid:uniprot.org:keywords:462, one of your colleagues or someone 
on the net might have a copy of it that you are now capable of asking for 
by name.

> Maybe this has something to do with the fact that we never set up a 
> resolver, but other identifiers don't seem to work, either:
> 
> lsidres:urn:lsid:ncbi.nlm.nih.gov:pubmed:12571434 returns "false"
> lsidres:urn:lsid:ncbi.nlm.nih.gov.lsid.biopathways.org:pubmed:12441807 
> returns "Error retreiving authority WSDL"
> lsidres:urn:lsid:pdb.org:1AFT:1 returns "Error retreiving authority 
WSDL"
> 
> Maybe a simpler resolution mechanism may not be a bad idea after all ;-)

Why not go to the URL-LSID gateway at http://lsid-info.org/ and try 
resolving LSIDs that are actually backed by servers? It worked ok for me.

urn:lsid:gdb.org:GenomicSegment:GDB132938
urn:lsid:ncbi.nlm.nih.gov.lsid.biopathways.org:pubmed:12571434
urn:lsid:ncbi.nlm.nih.gov.lsid.biopathways.org:genbank:30350027

The one valid one that Eric tried works fine for me, both for data and 
metadata.

http://lsid-info.org/urn:lsid:ncbi.nlm.nih.gov.lsid.biopathways.org:pubmed:12441807? 
returns:

<rdf:RDF xmlns:j.0="urn:lsid:ncbi.nlm.nih.gov.lsid.biopathways.org:types:" 
xmlns:j.1="urn:lsid:ncbi.nlm.nih.gov.lsid.biopathways.org:pubmed-classes:" 
xmlns:j.2="urn:lsid:ncbi.nlm.nih.gov.lsid.biopathways.org:pubmed-predicates:" 
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" 
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" 
xmlns:dc="http://purl.org/dc/elements/1.1/">
<rdf:Description rdf:nodeID="A0">
<rdf:type 
rdf:resource="urn:lsid:ncbi.nlm.nih.gov.lsid.biopathways.org:pubmed-classes:MeshHeading" 
/> 
<j.2:qualifierName 
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">genetics</j.2:qualifierName> 

<j.2:descriptorName 
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">HIV-1</j.2:descriptorName> 

</rdf:Description>
<rdf:Description rdf:nodeID="A1">... etc

To see which LSIDs are backed by servers you can use the following URL 
syntax:

http://lsid-info.org/host/<LSID> 

The message "500 Server Error: Unable to resolve authority." means that a 
particular LSID has no resolving service. You get back a WSDL with 
resolution service data and metadata endpoints listed if it finds a 
service for that LSID. e.g. 
http://lsid-info.org/host/urn:lsid:ncbi.nlm.nih.gov.lsid.biopathways.org:pubmed:12441807

Kindest regards, Sean
Received on Monday, 22 January 2007 14:11:30 UTC

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