This question is based on a question on BioStars posted >2 years ago by user jack.
It describes a very frequent problem of generating GO annotations for non-model organisms. While it is based on some specific format and single application (Ontologizer), it would be useful to have a general description of the pathway to getting to a GAF file.
Note, that the input format is lacking a bit of essential information, like how it was obtained. Therefore, it is har to assign evidence code. Therefore, lets assume that the assignments of GO terms were done automagically.
I want to do the Gene enrichment using Ontologizer without a predefined association file(it's not model organism).
I have parsed a file with two columns for that organism like this :
geneA GO:0006950,GO:0005737 geneB GO:0016020,GO:0005524,GO:0006468,GO:0005737,GO:0004674,GO:0006914,GO:0016021,GO:0015031 geneC GO:0003779,GO:0006941,GO:0005524,GO:0003774,GO:0005516,GO:0005737,GO:0005863 geneD GO:0005634,GO:0003677,GO:0030154,GO:0006350,GO:0006355,GO:0007275,GO:0030528
I have downloaded the .ob file from Gene ontology file which contain this information (from here) :
! ! GO IDs (primary only) and name text strings ! GO:0000000 [tab] text string [tab] F|P|C ! where F = molecular function, P = biological process, C = cellular component ! GO:0000001 mitochondrion inheritance P GO:0000002 mitochondrial genome maintenance P GO:0000003 reproduction P GO:0000005 ribosomal chaperone activity F GO:0000006 high affinity zinc uptake transmembrane transporter activity F GO:0000007 low-affinity zinc ion transmembrane transporter activity F GO:0000008 thioredoxin F GO:0000009 alpha-1,6-mannosyltransferase activity F GO:0000010 trans-hexaprenyltranstransferase activity F GO:0000011 vacuole inheritance P
What I need as output is .gaf file in the following format (in the format of the files here):
!gaf-version: 2.0 !Project_name: Leishmania major GeneDB !URL: http://www.genedb.org/leish !Contact Email: email@example.com GeneDB_Lmajor LmjF.36.4770 LmjF.36.4770 GO:0003723 PMID:22396527 ISO GeneDB:Tb927.10.10130 F mitochondrial RNA binding complex 1 subunit, putative LmjF36.4770 gene taxon:347515 20120910 GeneDB_Lmajor GeneDB_Lmajor LmjF.36.4770 LmjF.36.4770 GO:0044429 PMID:20660476 ISS C mitochondrial RNA binding complex 1 subunit, putative LmjF36.4770 gene taxon:347515 20100803 GeneDB_Lmajor GeneDB_Lmajor LmjF.36.4770 LmjF.36.4770 GO:0016554 PMID:22396527 ISO GeneDB:Tb927.10.10130 P mitochondrial RNA binding complex 1 subunit, putative LmjF36.4770 gene taxon:347515 20120910 GeneDB_Lmajor GeneDB_Lmajor LmjF.36.4770 LmjF.36.4770 GO:0048255 PMID:22396527 ISO GeneDB:Tb927.10.10130 P mitochondrial RNA binding complex 1 subunit, putative LmjF36.4770 gene taxon:347515 20120910 GeneDB_Lmajor
How to create your own GO association file (gaf)?