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[bioontology-support] [BioPortal] Feedback from Michal Lijowski

John Graybeal jgraybeal at stanford.edu
Mon Jun 1 14:53:08 PDT 2020


Michael,

Sorry for this trouble, thanks for calling it to our attention.

With respect to NCIT, it appears the ontology was re-parsed on May 26 but that the indexing failed. We are digging in to confirm that, and will index it and report back as soon as we have something more to report.

I can't speak to the 'similar cases', not knowing what they are, but the two most significant sources of discrepancies are an error in parsing the most recent version, such as the indexing error above; or a different in ontology versions. For example, UMLS just came out with release 2020AA of their vocabularies; we have not yet installed this version although we will be doing so soon. (Sometimes the version discrepancy is in the other direction; if a term is removed or deprecated, it can still be in an older version of the ontology but not be served in the current BioPortal version.)

We'll have a look at some of the other ontologies, but any specific citations you can offer about missing classes will help us zero in on the problem ontologies.

John



On Jun 1, 2020, at 7:34 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Michal Lijowski

Email: michal.lijowski at essential-soft.com<mailto:michal.lijowski at essential-soft.com>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fsearch%3Futf8%3D%25E2%259C%2593%26query%3Dtreatment%2Bvehicle%2Bvolume%26button%3D

Feedback:

I am very curious about some of the terms disappearing from Bioportal.
For example, treatment vehicle volume http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C93697.
This term is in NCI Thesaurus but it does not show up when
I query Bioportal for this term. There are more similar cases
involving other ontologies.

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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360



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