Question: Is There A Human Annotation Resource Using The Sequence Ontology (So) ?
2
gravatar for Alex Stoddard
7.5 years ago by
Alex Stoddard190
Wisconsin, USA
Alex Stoddard190 wrote:

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?

ADD COMMENTlink written 7.5 years ago by Alex Stoddard190
4

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.

ADD REPLYlink written 7.5 years ago by Bert Overduin3.6k
1

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

ADD REPLYlink written 7.5 years ago by Bert Overduin3.6k

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

ADD REPLYlink written 7.5 years ago by Sean Davis25k
0
gravatar for Dm Church
7.0 years ago by
Dm Church30
United States
Dm Church30 wrote:

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

ADD COMMENTlink written 7.0 years ago by Dm Church30
2

Alex is asking about SO, not GO.

ADD REPLYlink written 7.0 years ago by Khader Shameer18k

Sorry for the misread on that.

ADD REPLYlink written 7.0 years ago by Dm Church30
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