[Genome] table X-Ref & aliases

[Fan Hsu]

Hi Chris,

Our kgAlias and kgXref tables are UCSC Genes (formally known as UCSC Known
Genes) centric.
But since UCSC Genes (available for hg18 and mm9) covers more than 99% of
RefSeq, our alias and xref tables covers most of RefSeqs (and more).

Besides these two tables, you may consider our knownToXXXX tables (more than
a dozen) too.  There is another xref table in our proteome database,
hgncXref, which is derived from HGNC DB.

As you know, when you start using alias, often things become fuzzy and you
start loosing the precise definition of a gene/transcript.

Fan.
-----Original Message-----
From: genome-bounces at soe.ucsc.edu [mailto:genome-bounces at soe.ucsc.edu]On
Behalf Of Chris Zaleski
Sent: Tuesday, October 30, 2007 6:27 AM
To: genome at soe.ucsc.edu
Subject: [Genome] table X-Ref & aliases


Greetings,

I'm hoping you can help me with a general question. This is applicable to
most
any species/assembly combination, however please assume hg17 as context. I'm
using many of the annotation tables from your databases in our own system.
We
allow lookup of IDs/accessions to find the corresponding loci. For
instance - a
user can paste a list of RefSeq accessions, we'll find them in the "refGene"
table, and return the gene coordinates, exons, UTRS, whatever.
I now need to allow for cross-reference lookup, so the user need not match
the
exact table ID (eg: they can enter a gene name, alias, 'friendly name'). I
know
that tables already exist for this purpose - I've found them for knownGene
specifically - kgAlias, kgXref, etc.

However, here's my question:
Do these cross-reference/alias tables exist only for specific data sets -
such
as knownGene? (For instance, the examples I gave above specifically link
everything back to knownGene). Or are there tables which link
names/aliases/IDs
between many other tables, which are not specific to one context? Like:
refSeqID -> ensemblID -> knownGeneID -> swissProtID -> geneName -> alias

Thanks very much for your help,
Chris Zaleski
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