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,
[EMAIL PROTECTED] 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 - [EMAIL PROTECTED]
