Question: Gene ontology question: Creating annotation file (gaf) to match an existing .obo file
0
gravatar for Leklahein
2.3 years ago by
Leklahein0
Leklahein0 wrote:

I have an .obo file (EMAPA.obo to be exact). It's format-version 1.2. Here's an example of the contents:

[Term] id: EMAPA:16037 name: 4-8 cell stage embryo namespace: anatomical_structure comment: order=2 for EMAPA:25765. synonym: "4-8 cell embryo" RELATED [] synonym: "four-to-eight cell embryo" RELATED [] is_a: EMAPA:36032 ! early embryo relationship: ends_at TS03 ! TS03 relationship: part_of EMAPA:36063 ! 4-8 cell stage conceptus relationship: starts_at TS03 ! TS03

I'm trying to pass it into various web servers, like VLAD and LAGO, but I require an annotation (gaf) file to go with it. I have a file, gene_association.mgi which seems to be consistent with the obo file. Here's an example of the contents:

MGI MGI:1920971 1110017D15Rik GO:0005737 MGI:MGI:3794006|PMID:18163442 IDA C RIKEN cDNA 1110017D15 gene Cbe1|Smrp1 protein taxon:10090 20081211 MGI part_of(EMAPA:17972),part_of(CL:0000018)

However, when I pass them together to various servers, it doesn't work. I either get no results or a crash. I know my gene lists should generate SOME gene ontology terms. Many genes in the gaf file don't have any EMAPA listing, and I've generated a file in which all non-EMAPA genes are excluded. This one works when I pass it to the servers. However, by doing that, haven't I wiped out my entire background of genes?

Can anyone provide some guidance?

Lekla

gene • 864 views
ADD COMMENTlink modified 2.2 years ago by Biostar ♦♦ 20 • written 2.3 years ago by Leklahein0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1179 users visited in the last hour