#1140 beta 16 removing Xref and DBXref information

[RFoulger]

Hi Nomi,

When I save the GO obo file in beta16, it strips out all of the ISBN names in the DBxref section, and Reactome X-ref names.

So my diff gives:

> def: "The chemical reactions and pathways resulting in the formation of D-glucarate, the D-enantiomer of glucarate." [GOC:jsg, GOC:mah, ISBN:0198506732]
234793c234795
< def: "The chemical reactions and pathways resulting in the breakdown of D-glucarate, the D-enantiomer of glucarate." [GOC:jsg, GOC:mah, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"]

< xref: Reactome:1252989 "Pyrimidine biosynthesis"
< xref: Reactome:1279920 "Pyrimidine biosynthesis"
---
> xref: Reactome:1252989
> xref: Reactome:1279920

etc etc

I don't get this when I save with 2.0.

Does anyone else have this problem?
Thanks
Becky

[RFoulger]

Okay- not a bug but rather a fix requested in a previous bug report: http://sourceforge.net/tracker/?func=detail&aid=2679772&group_id=36855&atid=418257

I've emailed the ontology editors to see if they need the Reactome X-ref descriptions to remain in the GO .obo file.

Nomi says: if you want to save descriptions for xrefs but not definition xrefs: that is doable (but may have to wait a bit--I'm in Vienna now for BOSC).

[Nomi Harris]

Fixed in 2.1-b17
When saving, include the description for xrefs but not for definition and synonym dbxrefs
(this behavior was agreed to by the GO committee).

Might eventually want this behavior to be user-configurable.