Don't find some GO IDs in GO ontology

Question

[animesh_10kuet]

I stacked at some position to understand the GO ontology. I do not find some GO ID now but this GO ID was there some time ago. I got those GO ID from a paper.

I use this link for finding the GO IDs.

Those GO IDs are: GO:0006350, GO:0007047, GO:0006118, GO:0006519, GO:0016044.

I don't understand the reasons. Is there new IDs for this GO IDs? If yes, where I can get that.

Please help.

Answer 1

[Philipp Bayer]

Some of those GO-terms are "alternative IDs" - for example, GO:0006350 is an alternative ID/synonym for GO:0006351. These don't work in the URL but they do work in amigo's search system: http://amigo.geneontology.org/amigo/search/ontology?q=GO:0006350

Other terms are still in amigo but have been made "obsolete" for various reasons - like http://amigo.geneontology.org/amigo/term/GO:0006118.

You should be able to use QuickGO to always see the "main" ID for each of the alternative IDs or a reason why the ID is obsolete, amiGO (as far as I know) does not do that automatically.

Trying the above GO:0006350 in QuickGO automatically redirects to the page for GO:0006351: http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0006350

Same goes for GO:0016044: http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0016044

You see obsolete or alternative IDs in papers when people use GO-annotation tools that use older versions of the GO datasets, like DAVID did until recently, or agriGO still does.