I'm trying to get all C. elegans genes from Wormbase programmatically, as well as all of their alternative gene names. To do this, I'm using intermine.

I was able to obtain all genes, but not ALL alternative names. The code below retrieves the genes' primary identifiers, and their "secondary identifiers."

from intermine.webservice import Service
service = Service("http://intermine.wormbase.org/tools/wormmine/service")

# 6239 is the taxonId for C. elegans

all_wormbase_genes_symbol = list()
all_wormbase_genes_sID = list()

for row in query.rows(start=0):
    # get primary symbol/ID
    # get secondary ID

I tried to look for other keys in row that might contain this information by first retrieving the list of all possible keys:

k = set()
for row in query.rows(start=0):

but none have what I want:

  • $\begingroup$ I don't know via intermine, but you can download a file with this information from the FTP at /pub/wormbase/releases/WS287/species/c_elegans/PRJNA13758/annotation/c_elegans.PRJNA13758.WS287.geneOtherIDs.txt.gz (changing to the appropriate WSxxx version) $\endgroup$
    – Alexlok
    Mar 30 at 19:50


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