Clinical Measurement Ontology (CMO) maintained by RGD

Home Page: https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology

clinical-measurements cmo human laboratory-measurements model-organisms obo obofoundry ontology owl semantic-web

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cmo-clinical-measurement-ontology's Issues

CMO completely broken right now due to parsing issues

Hello!

Right now CMO cannot be processed at all:

Broken object property:
Many broken xrefs like <oboInOWL:xref rdf:resource="http://purl.obolibrary.org/obo/Wikipedia#_http\://en.wikipedia.org/wiki/Waist-hip_ratio"/>
Or <oboInOWL:xref rdf:resource="http://purl.obolibrary.org/obo/MedicineNet#_http\://www.medicinenet.com"/>

As a minimum, please try to use ROBOT with the OWL release file (which is the most important one):

robot convert -i cmo.owl -f ofn -o cmo.ofn

Or open it with Protege!

CMO has multiple syntactic issues

There are a number of major syntactic issues with the CMO obo and owl releases. This causes many parsers to break, as was reported in #5.

Even in cases where parsers don't break, the results of the parse give unintended results

For example, virtually all ontology browsers and tools do not correctly interpret the definitions, because they are encoded in OBO as a property_value:

id: CMO:0003022
name: hemoglobin distribution width
is_a: CMO:0000508 ! hemoglobin measurement
property_value: created:by "sjwang" xsd:string
property_value: creation:date 2019-01-29T15:15:44Z xsd:string
property_value: hasExactSynonym "HDW" xsd:string
property_value: http://purl.obolibrary.org/obo/def "The distribution width of erythrocytes by their cellular (individual) hemoglobin concentrations. It is a measurement of the heterogeneity of the red cell hemoglobin concentration." xsd:string {http://www.geneontology.org/formats/oboInOWL#xref="PMID:PMID\\:3411196"}

This should be:

id: CMO:0003022
name: hemoglobin distribution width
is_a: CMO:0000508 ! hemoglobin measurement
created_by: "sjwang"
creation_date: 2019-01-29T15:15:44Z
synonym: "HDW" EXACT []
def: "The distribution width of erythrocytes by their cellular (individual) hemoglobin concentrations. It is a measurement of the heterogeneity of the red cell hemoglobin concentration." [PMID:3411196]

The OWL that gets generated from the current obo is both syntactically incorrect, and even when parsed, information gets missed. For example on OLS:

https://www.ebi.ac.uk/ols/ontologies/cmo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCMO_0003022

The definition doesn't show up where it should:

It looks like at some point in the past you passed the obo through a troundtrip with a very old obo to owl converter.

If you like I can provide a PR that fixes CMO. I assume this is the source file: https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology/blob/master/clinical_measurement.obo

or I can provide support to a developer to fix this

ID for definition is not IAO:0000115

CMO uses http://purl.obolibrary.org/obo/def for definitions. These should be updated to http://purl.obolibrary.org/obo/IAO_0000115.

Clarify license

According to the obo foundry link the license for this ontology is CC0 1.0 Universal (CC0 1.0). Since there is no mention of the license in the readme and I could not find a license file in the git repository I am a bit unsure whether this is true.

Would it be possible to add the license information to the readme file?

Wrong use of oboInOwl Id space

http://www.geneontology.org/formats/oboInOWL#hasAlternativeId
http://www.geneontology.org/formats/oboInOWL#hasBroadSynonym
http://www.geneontology.org/formats/oboInOWL#hasExactSynonym
http://www.geneontology.org/formats/oboInOWL#hasNarrowSynonym
http://www.geneontology.org/formats/oboInOWL#hasRelatedSynonym
http://www.geneontology.org/formats/oboInOWL#xref

Should be:

http://www.geneontology.org/formats/oboInOwl#hasExactSynonym

(note capitalisation).

Note that:
http://www.geneontology.org/formats/oboInOWL#xref

Is wrong in general. Should be:
http://www.geneontology.org/formats/oboInOwl#hasDbXref

Context: Our grand OBO wide ID normalisation effort.
https://github.com/orgs/OBOFoundry/projects/5

Related:
OPMI/opmi#9

NTR: relative maximal oxygen consumption

Hello, I have a use case that is interested in a new CMO term:

term: 'relative maximal oxygen consumption'
parent: 'maximal oxygen consumption' (CMO:0000135)
definition: Maximum capacity of an individual's body to transport and utilize oxygen, usually measured during exercise as volume of oxygen per unit of time, relative to an individual's body weight.
synonyms: relative VO2 peak, relative VO2 max

Issue with "part of" object property in released OWL file

There is a strange IRI in the object properties of CMO when retrieved from http://purl.obolibrary.org/obo/cmo.owl:

Optional.of(http://purl.obolibrary.org/obo/cmo.obo)#part_of

Then, there is also a "part of" named individual:

http://purl.obolibrary.org/obo/part_of

Was this intended to be part of?

The file is able to be opened in Protege, but this is causing issues with other tools.

new term requests?

are you taking new term requests or would you prefer we ask OBI? the terms needed are:
erythrocyte sedimentation rate (ESR)
and
blood myoglobin level
thanks

Term with ID "CMO:0002948" has invalid definition declaration

I'm unable to load this ontology using the OWL API due to an invalid def declaration for the term "renal tubulointerstitial score". The def for this term starts with a double quotation mark:

[Term]
id: CMO:0002948
name: renal tubulointerstitial score
def: ""A semiquantitative evaluation of the renal interstitium using a grading system with a score of 0 to 4+, which assesses the tubules and the interstitium for the presence of (1) tubular atrophy, (2) tubular dilatation, (3) interstitial inflammatory cell infiltrates, and (4) interstitial fibrosis. A score of 0 indicates no lesion (normal kidney), 1+ indicates a single, small focal lesion with very minimal tubular alterations and interstitial inflammatory cell infiltration, and 2+ to 4+ indicated increasing severity of tubular lesions, interstitial inflammatory cell infiltration, and/or fibrosis. A score of 4+ indicates involvement of approximately 50% or more of the renal parenchyma or interstitium." [PMID:PMID\:9369281]
...

... which causes a parsing error:

org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing file:/Users/jvendetti/Development/IntelliJ_Projects/owlapi-example-code/src/test/resources/clinical_measurement.obo
Could not parse ontology.  Either a suitable parser could not be found, or parsing failed.  See parser logs below for explanation.
The following parsers were tried:
1) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@5990e6c5


Detailed logs:
--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@5990e6c5
    Stack trace:
LINENO: 26701 - expected newline or end of line but found: A semiquantitative evaluation of the renal interstitium using a grading system with a score of 0 to 4+, which assesses the tubules and the interstitium for the presence of (1) tubular atrophy, (2) tubular dilatation, (3) interstitial inflammatory cell infiltrates, and (4) interstitial fibrosis. A score of 0 indicates no lesion (normal kidney), 1+ indicates a single, small focal lesion with very minimal tubular alterations and interstitial inflammatory cell infiltration, and 2+ to 4+ indicated increasing severity of tubular lesions, interstitial inflammatory cell infiltration, and/or fibrosis. A score of 4+ indicates involvement of approximately 50% or more of the renal parenchyma or interstitium." [PMID:PMID\:9369281]
LINE: def: ""A semiquantitative evaluation of the renal interstitium using a grading system with a score of 0 to 4+, which assesses the tubules and the interstitium for the presence of (1) tubular atrophy, (2) tubular dilatation, (3) interstitial inflammatory cell infiltrates, and (4) interstitial fibrosis. A score of 0 indicates no lesion (normal kidney), 1+ indicates a single, small focal lesion with very minimal tubular alterations and interstitial inflammatory cell infiltration, and 2+ to 4+ indicated increasing severity of tubular lesions, interstitial inflammatory cell infiltration, and/or fibrosis. A score of 4+ indicates involvement of approximately 50% or more of the renal parenchyma or interstitium." [PMID:PMID\:9369281]        org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:67)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:221)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1293)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1233)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1184)
        edu.stanford.ncbo.bioportal.SimpleLoadTest.testLoadCMOOntology_WithDocumentFormat(SimpleLoadTest.java:415)
        java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        java.base/java.lang.reflect.Method.invoke(Method.java:566)

Would it be possible to have this corrected? We're currently unable to successfully load this ontology in BioPortal as a result (https://bioportal.bioontology.org/ontologies/CMO).

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.

Wikipedia URIs are not valid.

When I attempt to load CMO into a RDFlib graph:

import rdflib
g = rdflib.Graph()
g.load('http://purl.obolibrary.org/obo/cmo.owl',format="xml")

I get the following error:

http://purl.obolibrary.org/obo/Wikipedia#_http\://en.wikipedia.org/wiki/Waist-hip_ratio does not look like a valid URI, trying to serialize this will break.
http://purl.obolibrary.org/obo/MedicineNet#_http\://www.medicinenet.com does not look like a valid URI, trying to serialize this will break.

I recommend using the direct URL in question, or rewrite the URL to not include the escape character. Ideally, you should refer to the actual web page directly without escaping it.

rat-genome-database / cmo-clinical-measurement-ontology Goto Github PK

cmo-clinical-measurement-ontology's People

Contributors

Stargazers

Watchers

Forkers

cmo-clinical-measurement-ontology's Issues

CMO completely broken right now due to parsing issues

CMO has multiple syntactic issues

ID for definition is not IAO:0000115

Clarify license

Wrong use of oboInOwl Id space

NTR: relative maximal oxygen consumption

Issue with "part of" object property in released OWL file

new term requests?

Term with ID "CMO:0002948" has invalid definition declaration

Add obofoundry topic to repo metadata

Wikipedia URIs are not valid.

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