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A comment on Ontology for the life sciences: genes, proteins, diseases, all expressed in OWL.

Re:Ontology for the life sciences: genes, proteins, diseases... by killjoywashere on Monday January 20, 2020 @06:14PM (#22102861)
Why does this not include the clinically relevant ontologies like ICD9, ICD10, SNOMED, LOINC, and CPT?

Also, folks may find this article interesting: Classification, Ontology, and Precision Medicine (1)

(1) https://www.nejm.org/doi/full/10.1056/NEJMra1615014

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Re:Ontology for the life sciences: genes, proteins, diseases... by dan_fornika on Monday January 20, 2020 @06:26PM (#22102918)
The OBOFoundry has a set of principles[0] that not all ontologies conform to. An ontology project can register with the OBOFoundry through their GitHub site [1] if they follow the principles.

[0] http://obofoundry.org/principles/fp-001-open.html

[1] https://github.com/OBOFoundry/OBOFoundry.github.io

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Re:Ontology for the life sciences: genes, proteins, diseases... by jerven on Tuesday January 21, 2020 @02:00AM (#22104848)
It is a combination of licensing. Snomed-CT is there in part via ULMS. But these days there is an official Snomed and Loinc via FHIR maintained by their hosting organizations.
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Re:Ontology for the life sciences: genes, proteins, diseases... by veritas3241 on Monday January 20, 2020 @08:00PM (#22103410)
At one point when I was at another company I was working on a graph database that connected all of the ontologies you mentioned and then some. It was really cool to be able to traverse the entire chain all the way from an analyte and see how it was linked through genes up to and including specific tests that were available for said gene.

I'm glad I don't work in healthcare anymore though... CPT is such a nightmare!

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Re:Ontology for the life sciences: genes, proteins, diseases... by i_am_nomad on Monday January 20, 2020 @07:33PM (#22103267)
One thought about this, ICD9/10 are medical coding standards. They have only a very shallow semantic depth to them, they’re more about completeness and specificity. They don’t map well to what OWL tries to do.
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Re:Ontology for the life sciences: genes, proteins, diseases... by tejtm on Tuesday January 21, 2020 @05:17AM (#22105644)
In particular the ICD evolved as insurance billing codes so the structures they resemble is office paperwork.

The Human Phenotype Ontology (HPO) on the other hand is made to represent observable characteristics at various granularities.

[hpo] https://hpo.jax.org/app/

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Re:Ontology for the life sciences: genes, proteins, diseases... by jerven on Tuesday January 21, 2020 @01:57AM (#22104839)
ICD11 is at least going the semantic way ;) e.g. http://id.who.int/icd/entity/1435254666
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Re:Ontology for the life sciences: genes, proteins, diseases... by meej on Wednesday January 22, 2020 @02:11AM (#22115315)
These are all part of the UMLS Metathesaurus. https://www.nlm.nih.gov/research/umls/knowledge_sources/meta...

BioPortal ingests the UMLS twice a year, you can also find them there: http://bioportal.bioontology.org/ontologies

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Re:Ontology for the life sciences: genes, proteins, diseases... by mnemonicsloth on Monday January 20, 2020 @06:40PM (#22103002)
1. Good link

2. I wish I could answer your question about the other projects. All I can say is that I saw this on Friday in a bioinformatics lecture. I'm not a bioinformatician. I don't know all the various projects relate to each other, although there should be some kind of liaison effort (right?). I do think I remember something about SNOMED, but the rest are blanks.

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