Question: How/Where do I find mapped GO terms in EggNOG (preferably via FTP download)?
0
gravatar for 17th Level Botanist
21 months ago by
17th Level Botanist30 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 21 months ago • written 21 months ago by 17th Level Botanist30
0
gravatar for 17th Level Botanist
21 months ago by
17th Level Botanist30 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.

Hallelujah.

ADD COMMENTlink written 21 months ago by 17th Level Botanist30
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: 1153 users visited in the last hour