Re: [SO-devel] SO in Genbank/INSDC feature table files?

[Murphy, T. (NIH/NLM/N. [C] <mur...@nc...>]

Hi Jim,

It doesn't look like there are any examples of SO terms submitted to INSDC, at least not as db_xrefs. Most INSDC features map 1:1 with a SO term, and NCBI uses internal mapping tables to convert between INSDC and SO feature types when reading and writing GFF3 files, so providing SO terms as db_xrefs would typically be redundant (or potentially conflict with our mapping table, so we'd need to add validation if anyone ever did submit annotation to INSDC with SO terms). There are a few areas where the INSDC feature options are a bit lacking and SO has something more specific, but those are rarely seen in INSDC submissions so I think the issue just hasn't come up.

-Terence



From: Jim Hu [mailto:ji...@ta...]
Sent: Monday, September 07, 2015 2:22 PM
To: SO developers <son...@li...>
Subject: [SO-devel] SO in Genbank/INSDC feature table files?

Are there examples I can use for teaching where SO terms are incorporated in Genbank records? Would they be xrefs?

Thanks,

Jim
=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054