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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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tax restrict: #8815

Closed gocentral closed 9 years ago

gocentral commented 13 years ago

See below no tetrahydrobiopterin biosynthetic process for fungi Val

>> >> >> >> folic acid-containing compound biosynthetic process seems that tetrahydrobiopterin biosynthesis is only valid for vertebrates, whereas in fungi it is the first enzyme in the biosynthetic pathway leading to folic acid. I changed the KW from 'Tetrahydrobiopterin biosynthesis' to 'Folate biosynthesis', which will trigger GO:0046656; folic acid biosynthetic process. this ok?

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/8603

gocentral commented 13 years ago

Original comment by: paolaroncaglia

gocentral commented 13 years ago

Hi Val,

My apologies, but I'm not sure I understand your request and comment. Would you like us to add a taxon constraint to limit GO:0006729 tetrahydrobiopterin biosynthetic process to Vertebrata? If so, could you please provide a reference to support this? Chris has been asking for them. I'm also not sure what keywords you are referring to... sorry! I can't see any recent changes to any of those terms in QuickGO, so I assume this is in some other file?

Thanks, Paola

Original comment by: paolaroncaglia

gocentral commented 13 years ago

Hi Paola,

Sorry for the incomplete explanation. This item was transferred from another tracker.

The restriction was to have been "Not fungi" rather than only present in vertebrates, but I now see that the pathway is present in N. crassa.

So for now I am not confident about this although I believe the pathway is absent from fission yeast. The mapping which generated the annotation erroneously has now been removed so this will be dealt with another way.

It will usually be difficult to supply a reference for taxonomic restrictions though. They are usually "common knowledge" like "photosynthesis is not present in yeast"......

Val

Original comment by: ValWood

gocentral commented 13 years ago

Hi Val,

Thanks for providing more details - that's quite helpful! Since it looks like we can't be sure that this term should be restricted (or even "never in some taxon"), and you solved the issue anyway, I'd close this item for now, but feel free to comment more or to place a new request in the future. I agree with you that it might be difficult to provide references for all taxon rules...

Thanks, Paola

Original comment by: paolaroncaglia

gocentral commented 13 years ago

Original comment by: paolaroncaglia

gocentral commented 13 years ago

Original comment by: mah11