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

From: William Bug <William.Bug@DrexelMed.edu>
Date: Mon, 22 Jan 2007 10:07:10 -0500
Message-Id: <9AD2E45C-13E8-485C-A26A-C9C665257435@DrexelMed.edu>
Cc: public-semweb-lifesci@w3.org
To: Sean Martin <sjmm@us.ibm.com>
Many thanks, Sean.

I understand the need for a resolver, but I'd thought I'd remembered  
last Spring actually using this LSID plugin to look at the fruits of  
all that wonderful work Eric had done on RDFizing UniProt, but I  
guess that's just a memory phantom.  ;-)

By the way, I'm still not able to simply paste these lsid's into my  
Firefox URL line.  I just noticed in the LSID plugin Preferences I'm  
set to "Use Biopathways for DNS lookup".  Do I need to add Authority  
Mappings in order to reach the proper resolvers for those "working"  
LSIDs?

Thanks again for the remedial assistance.  I'm trying to move many  
tasks forward in parallel here and have to pick my troubleshooting  
battles carefully.  ;-)

Cheers,
Bill


On Jan 22, 2007, at 9:11 AM, Sean Martin wrote:

>
> 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

Bill Bug
Senior Research Analyst/Ontological Engineer

Laboratory for Bioimaging  & Anatomical Informatics
www.neuroterrain.org
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA    19129
215 991 8430 (ph)
610 457 0443 (mobile)
215 843 9367 (fax)


Please Note: I now have a new email - William.Bug@DrexelMed.edu





Received on Monday, 22 January 2007 15:07:32 UTC

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