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obophenotype / uberon

An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
http://obophenotype.github.io/uberon/
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IRI typos in phenoscape-ext #218

Closed balhoff closed 11 years ago

balhoff commented 11 years ago

There are many instances of "purl.obolibrary.obo" in phenoscape-ext where it should be "purl.obolibrary.org". Example:

Declaration(Class(http://purl.obolibrary.obo/obo/UBERON_1500000)) AnnotationAssertion(http://www.geneontology.org/formats/oboInOwl#created_by http://purl.obolibrary.obo/obo/UBERON_1500000 "PERSON: Alex Dececchi"^^xsd:string) AnnotationAssertion(http://purl.obolibrary.org/obo/IAO_0000115 http://purl.obolibrary.obo/obo/UBERON_1500000 "Enlarged and broad extension of the scapula distal to the glenoid region that conforms to the contour of the ribs. Origin for the major shoulder muscles including the deltoid group."^^xsd:string) AnnotationAssertion(rdfs:label http://purl.obolibrary.obo/obo/UBERON_1500000 "scapular blade"^^xsd:string)

Can these be updated or must they all be obsoleted and replaced? Some may have been obsoleted already.

cmungall commented 11 years ago

Looks like a problem with the entity creation preferences - Alex your terms shouldn't be in the 1.5k range anyway

On Mar 14, 2013, at 9:55 AM, Jim Balhoff wrote:

There are many instances of "purl.obolibrary.obo" in phenoscape-ext where it should be "purl.obolibrary.org". Example:

Declaration(Class(http://purl.obolibrary.obo/obo/UBERON_1500000)) AnnotationAssertion(http://www.geneontology.org/formats/oboInOwl#created_by http://purl.obolibrary.obo/obo/UBERON_1500000 "PERSON: Alex Dececchi"^^xsd:string) AnnotationAssertion(http://purl.obolibrary.org/obo/IAO_0000115 http://purl.obolibrary.obo/obo/UBERON_1500000 "Enlarged and broad extension of the scapula distal to the glenoid region that conforms to the contour of the ribs. Origin for the major shoulder muscles including the deltoid group."^^xsd:string) AnnotationAssertion(rdfs:label http://purl.obolibrary.obo/obo/UBERON_1500000 "scapular blade"^^xsd:string)

Can these be updated or must they all be obsoleted and replaced? Some may have been obsoleted already.

— Reply to this email directly or view it on GitHub.

cmungall commented 11 years ago

Revision 3890, Fixed #218

On Mar 14, 2013, at 9:55 AM, Jim Balhoff wrote:

There are many instances of "purl.obolibrary.obo" in phenoscape-ext where it should be "purl.obolibrary.org". Example:

Declaration(Class(http://purl.obolibrary.obo/obo/UBERON_1500000)) AnnotationAssertion(http://www.geneontology.org/formats/oboInOwl#created_by http://purl.obolibrary.obo/obo/UBERON_1500000 "PERSON: Alex Dececchi"^^xsd:string) AnnotationAssertion(http://purl.obolibrary.org/obo/IAO_0000115 http://purl.obolibrary.obo/obo/UBERON_1500000 "Enlarged and broad extension of the scapula distal to the glenoid region that conforms to the contour of the ribs. Origin for the major shoulder muscles including the deltoid group."^^xsd:string) AnnotationAssertion(rdfs:label http://purl.obolibrary.obo/obo/UBERON_1500000 "scapular blade"^^xsd:string)

Can these be updated or must they all be obsoleted and replaced? Some may have been obsoleted already.

— Reply to this email directly or view it on GitHub.

cmungall commented 11 years ago

This is fixed

_everyone check your protege entity creation preferences_

The url should be .org, not .obo

On Mar 14, 2013, at 9:55 AM, Jim Balhoff wrote:

There are many instances of "purl.obolibrary.obo" in phenoscape-ext where it should be "purl.obolibrary.org". Example:

Declaration(Class(http://purl.obolibrary.obo/obo/UBERON_1500000)) AnnotationAssertion(http://www.geneontology.org/formats/oboInOwl#created_by http://purl.obolibrary.obo/obo/UBERON_1500000 "PERSON: Alex Dececchi"^^xsd:string) AnnotationAssertion(http://purl.obolibrary.org/obo/IAO_0000115 http://purl.obolibrary.obo/obo/UBERON_1500000 "Enlarged and broad extension of the scapula distal to the glenoid region that conforms to the contour of the ribs. Origin for the major shoulder muscles including the deltoid group."^^xsd:string) AnnotationAssertion(rdfs:label http://purl.obolibrary.obo/obo/UBERON_1500000 "scapular blade"^^xsd:string)

Can these be updated or must they all be obsoleted and replaced? Some may have been obsoleted already.

— Reply to this email directly or view it on GitHub.

cmungall commented 11 years ago

we really need ID profiles for protege....similar to oboedit.

On Mar 15, 2013, at 2:23 PM, Chris Mungall wrote:

This is fixed

_everyone check your protege entity creation preferences_

The url should be .org, not .obo

On Mar 14, 2013, at 9:55 AM, Jim Balhoff wrote:

There are many instances of "purl.obolibrary.obo" in phenoscape-ext where it should be "purl.obolibrary.orghttp://purl.obolibrary.org/". Example:

Declaration(Class(http://purl.obolibrary.obo/obo/UBERON_1500000)) AnnotationAssertion(http://www.geneontology.org/formats/oboInOwl#created_by http://purl.obolibrary.obo/obo/UBERON_1500000 "PERSON: Alex Dececchi"^^xsd:string) AnnotationAssertion(http://purl.obolibrary.org/obo/IAO_0000115 http://purl.obolibrary.obo/obo/UBERON_1500000 "Enlarged and broad extension of the scapula distal to the glenoid region that conforms to the contour of the ribs. Origin for the major shoulder muscles including the deltoid group."^^xsd:string) AnnotationAssertion(rdfs:label http://purl.obolibrary.obo/obo/UBERON_1500000 "scapular blade"^^xsd:string)

Can these be updated or must they all be obsoleted and replaced? Some may have been obsoleted already.

— Reply to this email directly or view it on GitHubhttps://github.com/cmungall/uberon/issues/218.

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Dr. Melissa Haendel

Assistant Professor Ontology Development Group, OHSU Library http://www.ohsu.edu/library/ Department of Medical Informatics and Epidemiology Oregon Health & Science University haendel@ohsu.edumailto:haendel@ohsu.edu skype: melissa.haendel 503-407-5970