Is There A Human Annotation Resource Using The Sequence Ontology (So) ?

Question

[Alex Stoddard]

The Sequence Ontology provides a rich description of well defined and interrelated genome annotation terms. However it seems to be adopted only by the model organisms community and not the human genome annotation groups - at least as far as I can tell from the SO resources page.

Is there a resource for human genome annotation, specifically genes ands transcripts (including lncRNAs, miRNAs, transcribed pseudo-genes etc.) which has been annotated using the sequence ontology?

[Bert Overduin]

No, Ensembl does not use SO terms for its gene annotation. Afaik there has been talk about this, but the fact that the many different gene and transcript types that are distinguished by the manual annotators of the Vega/Havana team cannot straightforwardly be mapped to the SO terms, makes this a complex undertaking. So, I have no idea if this is going to happen in the foreseeable future, I am afraid. Ensembl does use SO terms for the description of variant consequence types, though. Hope this helps.

[Bert Overduin]

In addition, I am not aware of any human gene annotation resource that does use SO terms.

[Sean Davis]

You might take a look at Ensembl. If things are unclear, you can always write to their email list.

Answer 1

[Dm Church]

You can get a file mapping GO terms to Gene IDs from Entrez Gene: ftp://ftp.ncbi.nih.gov/gene/DATA/ gene2go.gz

[Khader Shameer]

Alex is asking about SO, not GO.

[Dm Church]

Sorry for the misread on that.