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[bioontology-support] [BioPortal] Feedback from Nicolas Joannin

Michael Dorf mdorf at stanford.edu
Wed Oct 17 11:44:33 PDT 2018


Hi Nicolas,

Thank you for bringing this to our attention. We don’t offer actual download files for UMLS ontologies (unless you supply us your UMLS license, offline), but I definitely see what you mean when looking at the user interface that displays these terms:

http://bioportal.bioontology.org/ontologies/ICD9CM/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FICD9CM%2F386.00&jump_to_nav=true<http://bioportal.bioontology.org/ontologies/ICD9CM/?p=classes&conceptid=http://purl.bioontology.org/ontology/ICD9CM/386.00&jump_to_nav=true>

Roughly twice per year the UMLS [1] publishes a release of a group of ontologies, which we import into BioPortal.  ICD9CM and ICD10CM is one of the ontologies that’s pulled in when we do the UMLS imports.  At this point, I am not sure exactly where in the import process the wrong encoding gets introduced. I’ve logged this as an issue in our Github tracker:

https://github.com/ncbo/umls2rdf/issues/28

Thanks again for your report!

Michael

[1] https://www.nlm.nih.gov/research/umls/



On Oct 15, 2018, at 1:51 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Nicolas Joannin

Email: nicolas.joannin at linguamatics.com<mailto:nicolas.joannin at linguamatics.com>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FICD9CM

Feedback:

Encoding problems with your ICD9CM and ICD10CM TTL files:

Hello,

The files you provide for ICD9CM and ICD10CM have erroneous characters, e.g. "Ménière's disease" instead of "Ménière's disease".

This type of character replacement is typical when a UTF-8 encoded source file is read as a Windows-1252 encoded file (probably the default encoding of the machine used to process the data).

I would suggest that when next updating these files you consider updating your script to read the source data with the proper encoding.

Cheers,
Nicolas

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