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OBO format issues detected by ONTO-perl tools #2

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GoogleCodeExporter opened this issue Mar 28, 2015 · 6 comments
Closed

OBO format issues detected by ONTO-perl tools #2

GoogleCodeExporter opened this issue Mar 28, 2015 · 6 comments
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@GoogleCodeExporter
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What steps will reproduce the problem?
Using ONTO-perl (http://search.cpan.org/dist/ONTO-PERL/) tools with the 
envo.obo (r6) and envo-basic.obo (r6) files available in this repository.

The results are available here:
https://github.com/dbcls/bh12/wiki/Integrate-deploy-perl-modules-for-obo-formatt
ed-ontologies
NB: The results include those from CHEBI and MIREOT-ed ontologies

Please provide any additional information below.

The analysis was run by Erick Antezana. Most of the issues appear to be the 
definition of synonyms. EA stated that if the term in another 
vocabulary/onotology is syntactically and semantically equivalent, then an xref 
is more appropriate than a synonym. Also, there are cases where the same 
synonym appears multiple times due only to a different xref. A list of xrefs, 
e.g. "[MEAT:00324, BACONBASE:03021]", is more appropriate unless there's a 
reason not to do so. Thoughts?

Original issue reported on code.google.com by p.buttig...@gmail.com on 6 Sep 2012 at 9:06
@GoogleCodeExporter
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1. I'm not sure the date tag is actually wrong - when was the last content edit 
to ENVO?
2. This is a false positive. The .obo is fine
3. Some of this should be punted to CHEBI. Rest of it is really a stylistic 
question
4. Agreed
5. Agreed
6. Should be fixed. The first is a mere redundancy, the 2nd a logic error
7. Arose from OORT mireoting process - punt to Oort

Original comment by cmung...@gmail.com on 6 Sep 2012 at 4:15

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@GoogleCodeExporter
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Points 4 and 5 have been addressed by a revision of terrestrial biomes (and a 
number of obsoletions) in revision 55 of envo-edit.obo. 
Details here: 
https://envo.googlecode.com/svn/releases/2013-05-02/diffs/envo-obo-diff.html

There are still definitions to add and relations to create before this goes 
into a release.

Original comment by p.buttig...@gmail.com on 3 May 2013 at 11:16

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@GoogleCodeExporter
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Experimental "has_condition" relations added in revision 61 of envo-edit.obo. 
This links "environmental conditions" with the relevant "biomes".

Original comment by p.buttig...@gmail.com on 8 May 2013 at 8:03

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@GoogleCodeExporter
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Evangelos Pafilis (Environments-EOL) and Erick Antezana added in CC.

Original comment by p.buttig...@gmail.com on 8 May 2013 at 8:07

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@GoogleCodeExporter
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Regarding 6: Stream sediment issue fixed in envo-edit.obo, revision 156. Stream 
sediment is now adjacent_to stream.

The karst field vs plain issue was attended to some time ago, but I'm still not 
sure about this. The current state is that a karst field is a plain located_in 
karst, which I think works.

Original comment by p.buttig...@gmail.com on 25 Apr 2014 at 8:35

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Original comment by cmung...@gmail.com on 18 Feb 2015 at 2:04

  • Changed state: Fixed
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