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[bioontology-support] FW: NCBO bioportal - SO

Colin Batchelor BatchelorC at rsc.org
Wed Mar 24 07:47:30 PDT 2010


Hello Natasha,

Yes, please take down the first one.

Something has gone very wrong with the Explore option, though.  sequence_feature should be one of the root terms and I can't see it.

Best wishes,
Colin.

-- 
Dr Colin Batchelor MChem MRSC, Senior Informatics Analyst, Informatics R&D 
Informatics Department, 
Royal Society of Chemistry, Thomas Graham House, Cambridge UK CB4 0WF 
batchelorc at rsc.org t: +44 1223 432280 

> -----Original Message-----
> From: Natasha Noy [mailto:noy at stanford.edu]
> Sent: 23 March 2010 20:01
> To: Colin Batchelor
> Cc: 'support at bioontology.org'; 'Michel Dumontier'; Trish Whetzel
> Subject: Re: [bioontology-support] FW: NCBO bioportal - SO
> 
> Colin,
> 
> Just to clarify: you are referring to the Sequence Ontology being
> listed twice on this page:
> http://bioportal.bioontology.org/ontologies
> 
> Right?
> 
> I  think the first one (http://bioportal.bioontology.org/ontologies/36782
> ) was pulled from OBO Foundry a while ago, but then something probably
> changed in its metadata and it got migrated into the second one
> (http://bioportal.bioontology.org/ontologies/42321
> ).
> 
> The second one seems to be the correct and the active one. According
> to out logs,  both were uploaded automatically through our OBO Pull
> process.
> 
> Should we just  take down the first one
> (http://bioportal.bioontology.org/ontologies/36782
> ) entirely?
> 
> Natasha
> 
> 
> On Mar 23, 2010, at 2:21 AM, Colin Batchelor wrote:
> 
> > Hello support!
> >
> > Do you know why the Sequence Ontology is in twice?
> >
> > http://bioportal.bioontology.org/visualize/42321/
> >
> > Which URL are you taking as the source?
> >
> > best wishes,
> > Colin.
> >
> >
> > --
> > Dr Colin Batchelor MChem MRSC, Senior Informatics Analyst,
> > Informatics R&D
> > Informatics Department,
> > Royal Society of Chemistry, Thomas Graham House, Cambridge UK CB4 0WF
> > batchelorc at rsc.org t: +44 1223 432280
> >
> > ________________________________________
> > From: Trish Whetzel [mailto:plwhetzel at gmail.com]
> > Sent: 22 March 2010 18:05
> > To: Colin Batchelor
> > Cc: Michel Dumontier
> > Subject: Re: NCBO bioportal - SO
> >
> > I'm at a meeting today. Would you mind sending to
> support at bioontology.org
> > ?
> >
> > Thanks!
> > Trish
> >
> > On Mon, Mar 22, 2010 at 9:24 AM, Colin Batchelor
> > <BatchelorC at rsc.org> wrote:
> > Hello,
> >
> > Yes---we haven't had the top-level term SO:0000000 in ages and ages,
> > so #1 should go go go.
> >
> > Odd about #2.  Trish: are you working from so.obo or so-xp.obo?  The
> > latter is the canonical one with the formal definitions, the former
> > is the "toy" one.
> >
> > There are disjoint_from relations between the high-level classes---
> > could that be causing trouble?
> >
> > Colin.
> >
> > --
> > Dr Colin Batchelor MChem MRSC, Senior Informatics Analyst,
> > Informatics R&D
> > Informatics Department,
> > Royal Society of Chemistry, Thomas Graham House, Cambridge UK CB4 0WF
> > batchelorc at rsc.org t: +44 1223 432280
> >
> > ________________________________________
> > From: Michel Dumontier [mailto:michel.dumontier at gmail.com]
> > Sent: 22 March 2010 16:15
> > To: Trish Whetzel; Colin Batchelor
> > Subject: NCBO bioportal - SO
> >
> > Hello,
> >   I'm trying to figure out what's going on with the NCBO bioportal
> > rendering of SO.
> >
> > First, I see two entries:
> >
> > 1. Sequence Ontology (SO)
> > 2. Sequence types and features (SO)
> >
> > looks like the second is newer, so should the first one disappear?
> >
> > Second, the rendering of 2. appears incomplete, even though i can
> > search and find terms:
> >
> > http://bioportal.bioontology.org/visualize/42321/
> >
> >
> > m.
> >
> > --
> > Michel Dumontier
> > Associate Professor of Bioinformatics
> > Carleton University
> > http://dumontierlab.com
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