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Question: OMA BROWSER ID MAPPING
1
gravatar for kozhaki.seq
3.0 years ago by
kozhaki.seq • 50
Korea, Republic Of
kozhaki.seq • 50 wrote:

OMA browser( http://omabrowser.org/oma/home/) is very useful for my work of ortholog analysis. However, I face an issue regarding ID mapping. I searched the identifier mapping files but couldnt success. Specifically, how can I convert a big list of Oryza sativa uniprot id (for ex, Q10M50 ) to RGAP id (for ex, LOC_Os03g20700)? Thanks..!!
oryza sativa rgap id mapping oma orthologs • 1.2k views
ADD COMMENT • link •
modified 3.0 years ago by adrian.altenhoff • 400 • written 3.0 years ago by kozhaki.seq • 50
2
gravatar for adrian.altenhoff
3.0 years ago by
adrian.altenhoff • 400
Switzerland
adrian.altenhoff • 400 wrote:

On the OMA browser there is no direct mapping between UniProtKB/TrEMBL accessions and RGAP ids. However, you can download two mapping files in the download section of the current release plant mapping and mapping to UniProt. By combining the two mappings based on the common OMA-ID you can establish a direct mapping from uniprot to rgap. In python you could do something like this to produce a mapping file from uniprot ids to the plant ids:

import csv
import collections
up2plant = collections.defaultdict(list)
with open('oma-uniprot.txt', 'r') as up, open('oma-plants.txt', 'r') as plant, open('up-plants.txt', 'w') as out:
    up_reader = csv.reader((row for row in up if not row.startswith('#')), delimiter='\t')
    plant_reader = csv.reader((row for row in plant if not row.startswith('#')), delimiter='\t')
    out_writer = csv.writer(out, delimiter='\t')
    up2oma = collections.defaultdict(list)
    for row in up_reader:
        up2oma[row[0]].append(row[1])
    for row in plant_reader:
        if row[0] in up2oma:
            for up_id in up2oma[row[0]]:
                out_writer.writerow([up_id, row[1]])
ADD COMMENT • link modified 3.0 years ago • written 3.0 years ago by adrian.altenhoff • 400

Thanks @adrian.altenhoff. It was the source files I was looking for.!!

ADD REPLY • link written 3.0 years ago by kozhaki.seq • 50
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