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htn_owl's Issues

Use hsapdv for age ranges

Consider re-using classes from http://obofoundry.org/ontology/hsapdv

VSO classes do not resolve

Looks like VSO was never registered:

http://obofoundry.org/ontology/vso

Add obofoundry topic to repo metadata

The OBO Foundry has recently created a topics page at https://github.com/topics/obofoundry. It would be great if you could add the obofoundry topic to your repository, since it's currently listed as active in the OBO Foundry. If you're not sure how to do that, follow the instructions here. The main issue for this task is at OBOFoundry/OBOFoundry.github.io#1538 in case you want some more context or to join the larger discussion.

Family members

Model family members to accommodate finding mentions of family members in clinical text.

Import classes

The following classes come from "Lemoniz-ing" our annotated corpus

DRON_00000034
DRON_00020576
DRON_00023851
DRON_00025157
DRON_00059567
EFO_0004303
ERO_0000383
GO_0008217
HP_0000001
HP_0000822
HP_0002615
HP_0003124
HP_0011009
HP_0012826
MONDO_0002280
MONDO_0004981
MONDO_0005010
MONDO_0005015
MONDO_0005147
MONDO_0005240
MONDO_0005300
MONDO_0005350
MONDO_0007455
MONDO_0020438
OGMS_0000029
OGMS_0000057
PATO_0000461
SYMP_0000682

Provide OBO export

Hi, would you please provide an OBO version of this ontology? Thanks!

statement

obstructive sleep apnea predisposes toward cvd

'role in human social processes' (OMRSE:00000024) has been deprecated and replaced

In the future we plan on reaching out to developers of ontologies that import our classes to get their input prior to making such changes, but we have replaced this class with another one with the same label: 'role in human social processes' (OMRSE:00002072). The only change to the class was to the subClassOf axiom, which we changed from "inheres-in only human or organization" to "inhere-in only 'material entity'."

Syntactic issues with htn.owl prevent loading into Protege

when parsing the owlapi throws:

2019-05-16 22:46:08,310 WARN  (OWLOntologyManagerImpl:1299) Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/IDO_0000664 in punning not allowed [Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IDO_0000664>)), Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/IDO_0000664>))]
2019-05-16 22:46:08,312 WARN  (OWLOntologyManagerImpl:1299) Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0000092 in punning not allowed [Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0000092>)), Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0000092>))]
2019-05-16 22:46:08,313 WARN  (OWLOntologyManagerImpl:1299) Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/IAO_0000039 in punning not allowed [Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000039>)), Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/IAO_0000039>))]
2019-05-16 22:46:08,313 WARN  (OWLOntologyManagerImpl:1299) Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/OBI_0000295 in punning not allowed [Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/OBI_0000295>)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/OBI_0000295>))]
2019-05-16 22:46:08,313 WARN  (OWLOntologyManagerImpl:1299) Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/BFO_0000113 in punning not allowed [Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000113>)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/BFO_0000113>))]
2019-05-16 22:46:08,314 WARN  (OWLOntologyManagerImpl:1299) Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0000053 in punning not allowed [Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0000053>)), Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0000053>))]
2019-05-16 22:46:08,314 WARN  (OWLOntologyManagerImpl:1299) Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0000086 in punning not allowed [Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0000086>)), Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0000086>))]
2019-05-16 22:46:08,315 WARN  (OWLOntologyManagerImpl:1299) Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/IAO_0000142 in punning not allowed [Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/IAO_0000142>)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000142>))]
2019-05-16 22:46:08,315 WARN  (OWLOntologyManagerImpl:1299) Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/OBI_0000312 in punning not allowed [Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/OBI_0000312>)), Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/OBI_0000312>))]

When loading into Protege I get:

Ontology already exists. OntologyID(OntologyIRI(<https://raw.githubusercontent.com/aellenhicks/htn_owl/master/htn.owl>) VersionIRI(<null>))

Normalising RO relations

Hey; we are on a mission to unify ID space/ PURL usage across OBO ontologies;

You are using two relations:

http://purl.org/obo/owl/OBO_REL#exists_during
http://purl.org/obo/owl/obo#towards

That should be changed to their correct RO ids;

RO ids usually look something like "http://purl.org/obo/owl/RO_0000001"

here is some more context:
https://github.com/orgs/OBOFoundry/projects/5

http://purl.obolibrary.org/obo/OBI_0000295 is_specified_input_of
http://purl.obolibrary.org/obo/OBI_0000312 is_specified_output_of
http://purl.obolibrary.org/obo/RO_0000086 has_quality
http://purl.obolibrary.org/obo/IDO_0000664 has_material_basis_in
http://purl.obolibrary.org/obo/IAO_0000142 mentions

Ontology contains a class _undefined_primitive_term

looks like a mistake:

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