Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Question: OMA BROWSER ID MAPPING
1
gravatar for kozhaki.seq
3.7 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 • 1.4k views
ADD COMMENT • link •
modified 3.7 years ago by adrian.altenhoff • 520 • written 3.7 years ago by kozhaki.seq • 50
2
gravatar for adrian.altenhoff
3.7 years ago by
adrian.altenhoff • 520
Switzerland
adrian.altenhoff • 520 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 3.7 years ago • written 3.7 years ago by adrian.altenhoff • 520

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

ADD REPLY • link written 3.6 years ago by kozhaki.seq • 50
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1227 users visited in the last hour