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

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

Hi Michal,

Our INSDC <--> SO mapping is all buried in C++ code. If you want to see the absolute current mappings, you can go to the source code here:

http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/SeqFeatData_8cpp_source.html
see lines 405-502, to map CSeqFeatData::eSubtype to INSDC feature types

and here:
http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/sofa__map_8cpp_source.html
to map eSubtype to SO terms

I went ahead and joined the two and made a simple table of our current mappings (see attached file, if attachments work with the forum). It looks like we’ve picked up a few holes in our mapping which I’ll try to fill in. Currently anything with no term listed in the SO column is converted to “region”.

Let me know if you have any more questions and I’d be glad to help.

-Terence



From: Michal Galdzicki [mailto:mga...@gm...]
Sent: Tuesday, September 08, 2015 1:40 PM
To: SO developers <son...@li...>
Subject: Re: [SO-devel] SO in Genbank/INSDC feature table files?

That's interesting, do you know if those NCBI mapping tables are available anywhere?  I'd like to suggest that table for the SBOL effort I participate on.

thanks for any help locating those,
Michal Galdzicki
Arzeda, Corp.

On Tue, Sep 8, 2015 at 5:05 AM Murphy, Terence (NIH/NLM/NCBI) [C] <mur...@nc...<mailto:mur...@nc...>> wrote:
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...<mailto:ji...@ta...>]
Sent: Monday, September 07, 2015 2:22 PM
To: SO developers <son...@li...<mailto: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

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