Sequence Ontology functional annotation doc fixes

[heuermh]

I have added links to the Sequence Ontology MISO browser for all the SO terms used in the functional annotation documentation.

In doing so I found a few errors (e.g. feature elongation should be feature_elongation, non_coding_exon_variant should be non_coding_transcript_exon_variant) and at least one term that I could not correct (nc_transcript_variant).

I haven't looked at the GEMINI code yet to see if the same corrections need to be made there, or if these were just documentation errors.

[arq5x]

Fantastic - thanks very much for this, Michael!

We will correct the errors you kindly identified.

[udp3f]

Hi,
Hi Michael,

Thanks for adding links to SO terms. As a note, GEMINI stores VEP impacts, the way they are returned/documented by VEP, since they intend to use SO terminology. But for terms like non_coding_exon_variant (rightfully: http://www.sequenceontology.org/browser/current_svn/term/SO:0001792) and nc_transcript_variant (rightfully: http://www.sequenceontology.org/browser/current_svn/term/SO:0001619) they seem to be not returning the correct terms. Since this is a VEP issue, I guess these could be left as such in the documentation, but with the right links in place.
I will try getting in touch with the VEP guys to correct this.
-Uma

[udp3f]

Hi,
Following up on the above mentioned impacts, these would be fixed in the next release of Ensembl/VEP.
-Uma