4 ms·

Why does this not include the clinically relevant ontologies like ICD9, ICD10, SNOMED, LOINC, and CPT? Also, folks may find this article interesting: Classific

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 https://www.nejm.org/doi/full/10.1056/NEJMra1615014

dan_fornika 7y ago
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 http://obofoundry.org/principles/fp-001-open.html [1] https://github.com/OBOFoundry/OBOFoundry.github.io https://github.com/OBOFoundry/OBOFoundry.github.io
- jerven 7y ago
  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.
mnemonicsloth 7y ago
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.
i_am_nomad 7y ago
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.
- jerven 7y ago
  ICD11 is at least going the semantic way ;) e.g. http://id.who.int/icd/entity/1435254666 http://id.who.int/icd/entity/1435254666
- tejtm 7y ago
  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/ https://hpo.jax.org/app/
veritas3241 7y ago
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!
meej 7y ago
These are all part of the UMLS Metathesaurus. https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/index.html 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 http://bioportal.bioontology.org/ontologies

dan_fornika 7y ago

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 http://obofoundry.org/principles/fp-001-open.html [1] https://github.com/OBOFoundry/OBOFoundry.github.io https://github.com/OBOFoundry/OBOFoundry.github.io

jerven 7y ago
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.

mnemonicsloth 7y ago

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.

i_am_nomad 7y ago

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.

jerven 7y ago
ICD11 is at least going the semantic way ;) e.g. http://id.who.int/icd/entity/1435254666 http://id.who.int/icd/entity/1435254666
tejtm 7y ago
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/ https://hpo.jax.org/app/

veritas3241 7y ago

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!

meej 7y ago

These are all part of the UMLS Metathesaurus. https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/index.html 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 http://bioportal.bioontology.org/ontologies