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Axioms not being translated from OWL to OBO. #28

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GoogleCodeExporter opened this issue Mar 12, 2015 · 4 comments
Closed

Axioms not being translated from OWL to OBO. #28

GoogleCodeExporter opened this issue Mar 12, 2015 · 4 comments
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Axioms are being lost in translation from OWL to OBO.  It looks like only one 
relationship and one intersection (the genus) per stanza get translated.

Example of dropped relationship

ontology: test

[Term]
id: FBbt:00000457
name: midgut constriction
def: "Constriction forming in the embryonic midgut between stage 15 and 16 
caused by contraction of the mesoderm which, as a result, penetrates the 
underlying endoderm." [FlyBase:FBrf0051566]
subset: cur
is_a: FBbt:00007010 ! multi-tissue structure
relationship: BFO:0000050 FBbt:00005333 ! late embryo
relationship: BFO:0000050 FBbt:00005628 ! embryonic midgut chamber

[Typedef]
id: BFO:0000050
name: part_of
is_transitive: true
is_a: RO:0002131

> OWL > OBO =>

ontology: test

[Term]
id: FBbt:00000457
name: midgut constriction
def: "Constriction forming in the embryonic midgut between stage 15 and 16 
caused by contraction of the mesoderm which, as a result, penetrates the 
underlying endoderm." [FlyBase:FBrf0051566]
subset: cur
is_a: FBbt:00007010
relationship: BFO:0000050 FBbt:00005333

[Typedef]
id: BFO:0000050
name: part_of
is_transitive: true
is_a: RO:0002131

-----

Example of dropped intersection clause:

    <owl:Class rdf:about="&obo;CARO_0000006">
        <rdfs:label rdf:datatype="&xsd;string">material anatomical entity</rdfs:label>
        <owl:equivalentClass>
            <owl:Class>
                 <owl:intersectionOf rdf:parseType="Collection">
                    <rdf:Description rdf:about="&obo;CARO_0000000"/>
                    <owl:Restriction>
                        <owl:onProperty rdf:resource="&obo;CARO_has_quality"/>
                        <owl:someValuesFrom rdf:resource="&obo;PATO_0000125"/>
                    </owl:Restriction>
                </owl:intersectionOf>
            </owl:Class>
        </owl:equivalentClass>

>

[Term]
id: CARO:0000006
name: material anatomical entity
def: "Anatomical entity that has mass." [CARO:MAH]
intersection_of: CARO:0000006

ie. missing:
intersection_of: has_quality* PATO:0000125

(Note, don't worry about details of how relation is translated here - this will 
be the subject of a future ticket.)

Original issue reported on code.google.com by dosu...@gmail.com on 26 May 2011 at 8:22
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Original comment by shahid.m...@gmail.com on 26 May 2011 at 2:15

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It is fixed now.

Original comment by shahid.m...@gmail.com on 26 May 2011 at 8:50

  • Changed state: Fixed

@GoogleCodeExporter
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Hi Shahid - thanks for fixing so quickly. But note - fixed for relationships 
(OWL SubClassOf), but not for intersections.  In fact, something weirder seems 
to be going on with intersections - 

------
ontology: test

[Term]
id: FBbt:00000457
name: midgut constriction
def: "Constriction forming in the embryonic midgut between stage 15 and 16 
caused by contraction of the mesoderm which, as a result, penetrates the 
underlying endoderm." [FlyBase:FBrf0051566]
subset: cur
intersection_of: FBbt:00007010 ! multi-tissue structure
intersection_of: BFO:0000050 FBbt:00005333 ! late embryo
intersection_of: BFO:0000050 FBbt:00005628 ! embryonic midgut chamber

[Typedef]
id: BFO:0000050
name: part_of
is_transitive: true
is_a: RO:0002131
------
-> OBO2OWL -> OWL2OBO =>
------
ontology: test

[Term]
id: FBbt:00000457
name: midgut constriction
def: "Constriction forming in the embryonic midgut between stage 15 and 16 
caused by contraction of the mesoderm which, as a result, penetrates the 
underlying endoderm." [FlyBase:FBrf0051566]
subset: cur
intersection_of: FBbt:00000457

[Typedef]
id: BFO:0000050
name: part_of
is_transitive: true
is_a: RO:0002131
------

Note, after conversion - intersection_of: self.  Intermediate OWL looks fine to 
me.

Original comment by dosu...@gmail.com on 27 May 2011 at 9:27

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The translation of the intersection_of tag is fixed.

Original comment by smanzoor...@lbl.gov on 2 Jun 2011 at 5:09

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