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[bioontology-support] BioPortal: Questions

Samson Tu swt at stanford.edu
Tue Jul 10 17:15:23 PDT 2018


Hi,

On Jul 10, 2018, at 11:25 AM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:


some time ago (2018-04-24) I added some notes to International Classification of Diseases, Version 10 (ICD10), because I found out that some classes are missing. As I noticed that these classes are not yet added, could you please enlighten me on the correct procedure to correct an  ontology?

We provided the notes capabiity as a service to ontology authors, some of whom use it to inform changes to ontologies; and also to other users of the ontology. In many other cases, ontologies are considered fixed once released, and will not be changed. ICD10 is one of these, as it goes through a major revision cycle that takes many years, and the underlying model is often changed considerably as well. For the last several years the authoring community has been working on ICD11, which is likely to be a major overhaud of ICD10.

To answer your specific question, what I will do if I see a concern with an ontology is to see the contact email on the summary page for that ontology, and send an email to that address with my concern. If I get no information back or can't reach that address, I will look up the ontology in Google to see if I can determine where and how it is maintained; many are maintained on GitHub or have their own web sites, often with issue trackers or contact information. If those methods fail, the BioPortal support list is a reasonable last-ditch effort to find the current status and owners of an ontolog, and determine whether issue reports are likely to be addressed.

I hope these answers help,


Bioportal got its ICD-10 resource from UMLS. This is probably a problem with UMLS rather with WHO’s ICD-10. If you search WHO’s online ICD-10 browser [1], 'Primary thrombophilia' and 'Other thrombophilia' are subcategories of ‘Other coagulation defects’.  ICD-10CM, as published by the National Center for Health Statistics, also contains these two concepts. However, UMLS 2018AA doesn’t seem to have these two terms as part of ICD-10 (according to the Metathesaurus Browser hosted at NLM). I find this discrepancy rather surprising. It’s up to whoever maintains UMLS to explain or correct these missing concepts.

With best regards,
Samson

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