GO Annotations from geneontology.org

Question

[anu014]

Hello Biostars!

Can anyone tell me how to get GO Ontology (Molecular function, Cellular Component & Biological process ) along with genes involved in it from GAF (go-annotation-file) or geneontology.org for a particular species?

Right now I'm getting from GAF:

Column  Content     Required?   Cardinality     Example
1   DB  required    1   UniProtKB
2   DB Object ID    required    1   P12345
3   DB Object Symbol    required    1   PHO3
4   Qualifier   optional    0 or greater    NOT
5   GO ID   required    1   GO:0003993
6   DB:Reference (|DB:Reference)    required    1 or greater    SGD_REF:S000047763|PMID:2676709
7   Evidence Code   required    1   IMP
8   With (or) From  optional    0 or greater    GO:0000346
9   Aspect  required    1   F
10  DB Object Name  optional    0 or 1  Toll-like receptor 4
11  DB Object Synonym (|Synonym)    optional    0 or greater    hToll|Tollbooth
12  DB Object Type  required    1   protein
13  Taxon(|taxon)   required    1 or 2  taxon:9606
14  Date    required    1   20090118
15  Assigned By     required    1   SGD
16  Annotation Extension    optional    0 or greater    part_of(CL:0000576)
17  Gene Product Form ID    optional    0 or 1  UniProtKB:P12345-2

Please help..Thank you. :)

Answer 1

[EagleEye]

You can try GeneSCF,

Example: A: How to look up GO terms associated to a certain organism?

[anu014]

Hello EagleEye. Thanks for suggestion! But for custom database/ non-model organisms I've to create GO/KEGG files as explained by you here - A: GO enrichment analysis using a Text file with all the genes and GO ids associat . Again, I've to go to the source such as 'geneontology.org' to get GO entries & their associated Genes.. Is there any way I just give taxid & get associated Geneontology?

[EagleEye]

Hi, in 'gene ontology' which closest organism are you looking for ? You can use organism code (3. Preparing database) in GeneSCF to retrieve the terms and genes specific to an organism of interest.

[anu014]

Right now, I'm dealing with 'mycobacterium tuberculosis h37rv' & 'mus musculus'. For mouse, I see GO & KEGG codes but for mycobacterium tuberculosis h37rv I'm just getting KEGG code.. How is this even possible, KEGG but no GO ?