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

Stefan Kirov skirov at utk.edu
Mon Aug 22 16:28:19 EDT 2005

You certainly have missed HGNC (http://www.gene.ucl.ac.uk/nomenclature/) 
and HUGO in particular. By the way EntrezGene substituted LocusLink few 
months ago... Affy mapping is also useful for some things. Aceview 
(http://www.ncbi.nih.gov/IEB/Research/Acembly/index.html?human), MIM 
(Mendelian Inheritance in Man, though it is not just human anymore...) 
and GRIF (Gene Reference Into Function) are also of some relevance I 
guess, though you can access these through EntrezGene. There are bunch 
of others more specialized DBs out there as well, depends what you want 
to do.
By the way you can search for most relationships you have mentioned 
through EnsMART and BioMART or through GeneKeyDB 
(genereg.ornl.gov/gkdb),  the last being developed by me so this is not 
unbiased :-) ...

kynn at panix.com wrote:

>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!
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>Bioperl-l at portal.open-bio.org

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