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owlcollab / oboformat

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subsetdefs name underscores get mangled in OBO2OWL2OBO roundtrip #35

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
If subset names specified in subsetdef tags have underscores, they lose 
everything after the underscore following OBO2OWL2OBO roundtrip.  This seems to 
come from rolling a URI using the subset name prefixed by FBbt_ and then using 
the standard conversion for OWL URIs to OBO:

e.g.- 

subsetdef: FB_gloss "terms for FlyBase glossary page"

OBO2OWL =>

   <!-- http://purl.obolibrary.org/obo/FBbt_FB_gloss -->

    <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/FBbt_FB_gloss">
        <rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_subsetdef"/>
        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">terms for FlyBase glossary page</rdfs:label>
    </owl:NamedIndividual>

OWL2OBO =>

subsetdef: FB "terms for FlyBase glossary page"

Note - the same issue afflicts synonymtypedefs.

Original issue reported on code.google.com by dosu...@gmail.com on 20 Jun 2011 at 1:12

GoogleCodeExporter commented 9 years ago 
Note, implementing http://code.google.com/p/oboformat/issues/detail?id=37 
should fix this.

Original comment by dosu...@gmail.com on 20 Jun 2011 at 7:40

GoogleCodeExporter commented 9 years ago 
Added RoundTripFlyAnatomyTest to junits

Original comment by cmung...@gmail.com on 13 Jul 2011 at 8:20

GoogleCodeExporter commented 9 years ago 
fixed. Here is the header, post-roundtrip:

ontology: FBbt
date: 17:06:2011 16:17
saved-by: djs93
auto-generated-by: OBO-Edit 2.1-beta3
subsetdef: FlyTed "Testis slim"
subsetdef: RD "terms for rd test ontology"
subsetdef: EmbDevSlim "EmbDevSlim"
subsetdef: FT_new "FlyTed temp subset for edit tracking purposes"
subsetdef: FB_gloss "terms for FlyBase glossary page"
subsetdef: cur "cur"
subsetdef: hidden_assertion "Stanza contains hidden assertion."
subsetdef: olfactory_system_draft "adult olfactory system model"
subsetdef: deprecated "warning of impending obsoletion"
subsetdef: BrainName "BrainName project terms"
subsetdef: BrainName_Embargo "Terms to hold back pending BrainName paper 
publication."
subsetdef: larval_OF "larval olfactory system"
synonymtypedef: BRAND_NAME "BRAND NAME"
synonymtypedef: INN "INN"
synonymtypedef: SMILES "SMILES"
synonymtypedef: InChI "InChI"
synonymtypedef: IUPAC_NAME "IUPAC NAME"
synonymtypedef: systematic_synonym "Systematic synonym" EXACT
synonymtypedef: BRAIN_NAME_ABV "BrainName official abbreviation"
synonymtypedef: InChIKey "InChIKey"
synonymtypedef: FORMULA "FORMULA"
default-namespace: fly_anatomy.ontology
remark: Release version: 1.43; Derived from fly_anatomy_XP.obo version 1.16. 
Uses helpers:  CHEBI - datestamp = 03:06:2011 16:30; GO - datestamp = 
14:06:2011 19:30 ; cvs version: $Revision: 1.43 $; PATO - datestamp = 
13:06:2011 11:15.
property_value: namespace-id-rule * FBbt:$sequence(8,7000,17000)$ !

Original comment by cmung...@gmail.com on 15 Jul 2011 at 9:52

GoogleCodeExporter commented 9 years ago

Original comment by cmung...@gmail.com on 15 Jul 2011 at 9:53