W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > July 2006

Re: LSID lookup details: help? [was: All about the LSID URI/URN]

From: <jbarkley@nist.gov>
Date: Mon, 31 Jul 2006 15:27:05 -0400
Message-ID: <1154374025.44ce5989a17ad@webmail.nist.gov>
To: Dan Connolly <connolly@w3.org>
Cc: Sean Martin <sjmm@us.ibm.com>, public-semweb-lifesci@w3.org, Alan Ruttenberg <alanruttenberg@gmail.com>, Noah Mendelsohn <noah_mendelsohn@us.ibm.com>, "Henry S. Thompson" <ht@inf.ed.ac.uk>

dan,

I recall reading that the PDB Resolver is offline pending 
upgrades.

You might try urn:lsid:gdb.org:GenomicSegment:GDB132938 
which does work with the BioPathways Resolver:

http://lsid.biopathways.org/resolver/urn:lsid:gdb.org:Genom
icSegment:GDB132938

jb



Quoting Dan Connolly <connolly@w3.org>:

> 
> In today's call, I learned a bit about how LSID lookup
> works:
> 
>  (1) try to find an SRV record using the domain in the
> LSID
>  (2) fall back to a DDDS lookup and NAPTR and such
> 
> Option (2) depends on some NAPTR stuff in the "arpa"
> parts
> of DNS space that OMG is expected to install but hasn't
> gotten around to, largely for lack of urgent need, I
> gather.
> 
> I'm trying to verify my understanding from some code.
> I found some perl code[2], and I got it installed
> with "All tests successful." But when I run it,
> using an example from the LSID spec[1]:
> 
>   URN:LSID:rcsb.org:PDB:1D4X:22
> 
> I get "Unable to resolve authority to SRV record:
> NXDOMAIN".
> 
> 
> Any clues? A full trace is below:
> 
> > ~/src/lsid-perl-1.1.4$ perl
> examples/client/lsid_client.pl
> > URN:LSID:rcsb.org:PDB:1D4X:22
> Client settings:
> Cleaning cache:
>         no
> 
> LSID Given:
>         URN:LSID:rcsb.org:PDB:1D4X:22
> 
> Canonicalized LSID:
>         urn:lsid:rcsb.org:PDB:1D4X:22
> 
> Unable to resolve authority.
>  -> Unable to resolve authority to SRV record: NXDOMAIN
> 
> Stack trace at LS/Locator.pm line 230
>        
> LS::Locator::resolveAuthority('LS::Locator=HASH
(0x824e900)',
> 'LS::ID=SCALAR(0x823f7cc)') called at
> LS/Client/BasicResolver.pm line
> 138
> 
> LS::Client::BasicResolver::resolve
('LS::Client::BasicResolver=HASH(0x824e4b0)',
> 'lsid', 'LS::ID=SCALAR(0x823f7cc)') called at
> examples/client/lsid_client.pl line 165
>         main::resolveLSID('LS::ID=SCALAR(0x823f7cc)',
> 'undef', 'undef')
> called at examples/client/lsid_client.pl line 125
> 
> 
> Stack trace at LS/Client/BasicResolver.pm line 143
> 
> LS::Client::BasicResolver::resolve
('LS::Client::BasicResolver=HASH(0x824e4b0)',
> 'lsid', 'LS::ID=SCALAR(0x823f7cc)') called at
> examples/client/lsid_client.pl line 165
>         main::resolveLSID('LS::ID=SCALAR(0x823f7cc)',
> 'undef', 'undef')
> called at examples/client/lsid_client.pl line 125
> 
> > 
> [1] http://www.omg.org/cgi-bin/doc?dtc/04-05-01
> [2] 
> http://easynews.dl.sourceforge.net/sourceforge/lsid/lsid-
perl-1.1.4.tar.gz
>  <- http://lsid.sourceforge.net/
> 
> -- 
> Dan Connolly, W3C http://www.w3.org/People/Connolly/
> D3C2 887B 0F92 6005 C541  0875 0F91 96DE 6E52 C29E
> 
> 
> 
Received on Monday, 31 July 2006 19:27:24 GMT

This archive was generated by hypermail 2.3.1 : Tuesday, 26 March 2013 18:00:44 GMT