Dear Brooke,
I asked you a few months ago a question regarding obtaining a list of genes
for various organisms. Your answer then was very helpful, so I hope that
it's okay I am replying back to you, as I have a follow-up question on the
same matter.
You previously suggested that I use RefSeq genes rather the KnownGenes (as
it applies to a wider variety of organisms), and indeed I did so. However,
I'm interested in obtaining more information per gene than what is present
in the table schema. For example, I want the summary and description of a
gene, as can be obtained in the page of the following sort:
http://genome.cse.ucsc.edu/cgi-bin/hgGene?org=Human&hgg_gene=NM_007294&hgg_chrom=none&db=hg18
<http://genome.cse.ucsc.edu/cgi-bin/hgGene?org=Human&hgg_gene=NM_007294&hgg_chrom=none&db=hg18>I
want to be able to automatically obtain such a url given organism, gene and
build, so that I can then automatically parse the web-page. For example in
human and mouse I succssfully create the url as follows:
"http://genome.ucsc.edu/cgi-bin/hgGene?org="; + ORGANISM_NAME + "&hgg_gene="
+ GENE_NAME + "&hgg_chrom=none&db=" + BUILD
However, this didn't work in other organisms, such as chicken, zebrafish,
drosophila, etc.
Could you please suggest how I can obtain this information in a manner
applicable to all organisms?
I hope my explanation was clear enough :)
Thank you very much for you help,
Best regards,
Adam
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