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owlcollab / oboformat

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Roundtrip for synonyms without a scope #58

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
A roundtrip (obo2owl + owl2obo) for synonyms without a scope in the original 
OBO file adds the scope RELATED in the generated OBO file.

Is this an intended behavior or is this a bug?

Original issue reported on code.google.com by HDie...@lbl.gov on 20 Oct 2011 at 5:02

GoogleCodeExporter commented 9 years ago 
scope is required, so a file that lacks this is invalid. As a courtesy we 
"repair" the file and related is the safest. This should be documented as 
optional behavior in the spec so I'll leave this open just now. But the 
behavior of the parser/translator is fine.

Which input ontology were you using?

Original comment by cmung...@gmail.com on 21 Oct 2011 at 5:41

GoogleCodeExporter commented 9 years ago 
The missing scope was an error of termgenie (which is now fixed).

The current 1.4 draft states that the scope for a synonym is optional:
"The value consists of a quote enclosed synonym text, an optional scope 
identifier, an optional synonym type name, and an optional dbxref list"

Does this need to be changed?

Original comment by HDie...@lbl.gov on 21 Oct 2011 at 3:30

GoogleCodeExporter commented 9 years ago 
Fixed the guide.

(note that they are optional in synonymtypedef and required in synonym. The 
spec and the guide should now be consistent on this point)

Original comment by cmung...@gmail.com on 17 Dec 2011 at 12:41

GoogleCodeExporter commented 9 years ago

Original comment by HDie...@lbl.gov on 12 Jan 2012 at 11:21