[Bioperl-l] [OT] ISO guide to human genomics DBs

[Horvath, Monica (NIH/NIEHS)]

If I were you, I would find yourself a copy of the database issue of NAR--
usually in January of each year.

Also, I would check out all of the gene symbol/mappings provided as options
(e.g. ensmart) or tables within the ensembl and ucsc genome browser
systems-- this would give you an idea of the type of mappings typically
desired by biologists.

I would make your application as flexible as possible to accept additional
code portions to accommodate new identification schemes because this stuff
changes constantly.

Monica M. Horvath, Ph.D.
Laboratory of Molecular Genetics
Environmental Genomics Group
111 T.W. Alexander Drive
P.O. Box 12233 MD C3-03
Research Triange Park, NC 27709-2333
+1 919-541-3266

-----Original Message-----
From: kynn at panix.com [mailto:kynn at panix.com] 
Sent: Monday, August 22, 2005 3:30 PM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] [OT] ISO guide to human genomics DBs






Hi!  Does anyone know of a high-level guide to the various Human
genomics databases?  Basically, I want to make my software as flexible
as possible regarding the kinds of human gene identifiers it will
recognize, but I'm having a hard time figuring out the various naming
schemes.  I'm (vaguely) aware of

  Entrez
  IPI
  Ensembl
  SwissProt/UniProt
  RefSeq
  LocusLink
  "gene symbols" (e.g. GHC1_HUMAN)
  "gi numbers"

though I'm not sure these are strictly comparable.  (Am I missing any
major ones?)

>From what I've seen at sites like http://harvester.embl.de it looks
like a huge mess, but maybe this is only a reflection of my ignorance.
Any pointers would be much appreciated!

kj

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