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?