Latest vocab lacks Novel 2019 Coronavirus terms & concepts

[mikedemick]

Describe the bug
The most current data download: biomedicus-3.0b4-umls-license-required-data does not contain Novel 2019 Coronavirus / Covid-19 terms added to the UMLS Metathesaurus vocabs, such as Snomed and MSH, in early 2020. Without these updates the tool does not support analysis on Covid-19 related EHR histories.

To Reproduce
Extractions on documents containing references to Covid-19/ Wuhan Virus/ Novel 2019 Coronavirus, etc., and related terms are not detected by the dataset available.

Expected behavior
Dataset should be amended to include the newer terms summarized here: https://metamap.nlm.nih.gov/Covid19Terms.shtml.

Terminal Output
N/A
EnvironmentN/A
N/A
Additional context
Add any other context about the problem here.

[benknoll-umn]

I'm updating our vocabularies to 2020AA and will have a release out this week.

[benknoll-umn]

New version got pushed on Wednesday, go ahead and give it a try.

[mikedemick]

Thanks, really appreciate it, especially the quick turnaround. Still doing some testing, noticing some terms are found, 'wuhan virus', whereas others, 'covid-19' don't seem to get a proper match. Will continue to work with this version-- thanks again. Mike Demick 919-414-6590

…

On Fri, Aug 14, 2020 at 1:57 PM Ben Knoll ***@***.***> wrote: New version got pushed on Wednesday, go ahead and give it a try. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#64 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AQFH73FDDBUI37ART6OJCUTSAV3IXANCNFSM4PY4K3MA> .

[benknoll-umn]

From looking at 2019 AA it may not include those MSH terms listed in the file. I'll confirm and if they aren't I'll manually add them to the UMLS before building the concepts dictionary.