NCBI can't keep up with dbs?

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Alan Ruttenberg

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Apr 28, 2009, 12:36:06 AM4/28/09

to shared...@googlegroups.com

Came across http://www.ncbi.nlm.nih.gov/protein/32699780?report=GenPept

Note that there are a number of dbxrefs that aren't linked, e.g.

GenomeReviews:AL591688_GR,
KEGG:sme:SMc02793,
HOGENOM:Q92TF2,
BioCyc:SMEL266834:SMC02793-MON,
HAMAP:MF_01062
Pfam:PF03618

Some notes:

Google finds a link for the first:
http://www.genomereviews.ebi.ac.uk/GR/contigview?chr=AL591688_GR but
it is dead. Wayback machine doesn't have an archive.

Kegg and BioCyc links have 2 parameters, a taxon and and id. The NCBI
list of prefixes has just a few of the many organism types that Kegg
has (almost 1000): KEGG_ec, KEGG_hsa, KEGG_mmu, KEGG_rno. It doesn't
have a prefix for "sme".

See http://sharedname.org/page/Issue/ProviderPartitions/NormalizeTaxon

HOGENOM:Q92TF2 and HAMAP:MF_01062 - interesting exercise for the reader

HAMAP:MF_01062 is (it appears) http://expasy.org/unirules/MF_01062
(there's a tag for it in the NCBI list, but no prefix)

No idea why the Pfam isn't linked it's
http://pfam.sanger.ac.uk/family/PF03618 (there's also tag for it in
the NCBI list, but no prefix)