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Published 20 hours ago • verified publisher icon eggnogdb

obsolete GOs

Open nhartwic opened this issue 4 years ago • 2 comments

I've been getting some Obsolete GO terms in my results. I'm curious as to how they get there and what if anything should be done about them.

I'm using version 2.0.1 of eggnog-mapper from conda. Example output featuring an obsolete go "GO:0005623" below...

lm5633.a03.1.g00020_p1  4432.XP_010243210.1     2.3999999999999994e-175 621.7   Streptophyta    AXS2    GO:0000166,GO:0003674,GO:0003824,GO:0005488,GO:0005575,GO:0005576,GO:0005622,GO:0005623,GO:0005737,GO:0005829,GO:0006139,GO:0006725,GO:0006807,GO:0008150,GO:0008152,GO:0009058,GO:0009225,GO:0009226,GO:0009987,GO:0016829,GO:0016830,GO:0016831,GO:0018130,GO:0019438,GO:0034641,GO:0034654,GO:0036094,GO:0044237,GO:0044238,GO:0044249,GO:0044271,GO:0044281,GO:0044424,GO:0044444,GO:0044464,GO:0046483,GO:0048037,GO:0048040,GO:0048046,GO:0050662,GO:0051287,GO:0055086,GO:0071704,GO:0097159,GO:1901135,GO:1901137,GO:1901265,GO:1901360,GO:1901362,GO:1901363,GO:1901576                ko:K12449       ko00520,ko01100,map00520,map01100               R01384,R01386   RC00508,RC01811 ko00000,ko00001                         Viridiplantae   37PXX@33090,3GDPQ@35493,COG0451@1,KOG1429@2759  NA|NA|NA        GM      UDP-D-apiose UDP-D-xylose synthase

Any help/input is, as always, appreciated. Thanks in advance.

nhartwic avatar Feb 01 '21 19:02 nhartwic

I have the same question. Is there a way to find out which release of the GO database is used in a version of eggnog mapper?

Shellfishgene avatar Jun 10 '22 13:06 Shellfishgene

Hi,

There is currently no way, that I know of, to track the version of annotation sources (besides PFAM). We hope to add and update such info in future versions of the eggNOG-mapper DB.

Best, Carlos

Cantalapiedra avatar Jun 13 '22 09:06 Cantalapiedra