Question: How/Where do I find mapped GO terms in EggNOG (preferably via FTP download)?
0
gravatar for 17th Level Botanist
2.6 years ago by
17th Level Botanist40 wrote:

Hello.

I am looking for a download from the EggNOG FTP site for the most current mapping of orthologous groups (NOGs) to their Gene Ontology (GO) terms.

I see where I can query for the Go terms if I know the NOG number, but I am working in the other direction: I have GO terms and want to know to which NOGs they correspond.

Additionally, I see where mapper is useful if I want to get GO terms for a previously unmapped group of sequences. However, I am wanting to work with NOGs in the EggNOG, so those should already be mapped and mapping them again seems unnecessary and inefficient.

Help is appreciated! And thanks.

ADD COMMENTlink modified 8 months ago by sapuizait0 • written 2.6 years ago by 17th Level Botanist40

Thank you, I ve been looking for that for some time now and it was driving me crazy!

still cannot find the KEGG identifiers, they mention that it should be there but I cant see it - it could be that its right in front of me and I dont see :)

thanks again

ADD REPLYlink modified 7 weeks ago by zx87549.6k • written 8 months ago by sapuizait0
1
gravatar for 17th Level Botanist
2.6 years ago by
17th Level Botanist40 wrote:

After several hours of downloading and checking through files from the EggNOG FTP, I finally found this one:

http://eggnogdb.embl.de/download/eggnog_4.5/all_OG_annotations.tsv.gz

The file just under 1G and seems to contain mappings to other annotation type databases.

One line of data contains as follows and is available in a compressed tab-delimited file.

> 0RWQ4   homNOG  4       RNA binding motif protein 43    [u'B'] 
> {"Molecular Function":[["GO:0097159","organic cyclic compound
> binding","IEA",4,"100","100"],["GO:0000166","nucleotide
> binding","IEA",4,"100","100"],["GO:0036094","small molecule
> binding","IEA",4,"100","100"],["GO:0005488","binding","IEA",4,"100","100"],["GO:1901363","heterocyclic
> compound binding","IEA",4,"100","100"],["GO:1901265","nucleoside
> phosphate binding","IEA",4,"100","100"],["GO:0003676","nucleic acid
> binding","IEA",3,"75","98.4"],["GO:0003723","RNA
> binding","IEA",1,"25","92.5"]]}        []     
> {"SMART":[["RRM",3,"75","98.4"]]}      
> 9601.ENSPPYP00000014337,9606.ENSP00000331211,9593.ENSGGOP00000008646,9598.ENSPTRP00000021421

The "0RWQ4" is the EggNOG unique identifier for the protein OG. As we might predict, not all OGs have GO mappings.

ADD COMMENTlink modified 7 weeks ago by zx87549.6k • written 2.6 years ago by 17th Level Botanist40
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