Error when importing all terminologies

Posted by Kim Tang on
URL: http://owlready.306.s1.nabble.com/Error-when-importing-all-terminologies-tp3344.html

Hello Jiba,

I would like to make use of the MedMentions dataset by gathering all synonyms for each CUI in the dataset.
MedMentions was created 2017 so I am using the umls-2017AA-full release.

Based on the PyMedTermino2 installation instructions, I set up PyMedTermino2 with the terminologies "ICD10", "SNOMEDCT_US", "CUI" as shown in the documentation (https://owlready2.readthedocs.io/en/latest/pymedtermino2.html#installation).

But unfortunately errors occured, when I tried to query several CUIs.

For instance the CUI "C0847557" with

CUI['C0847557']

 can not be found and returns:

CUI["C0847557"] # None

I checked for a handful of concepts, for which the querying failed, in which terminologies they are:

Terminologies with some concepts for which querying failed:
- ICPC2P (C0847557)
- NCI (C1708520)
- CPM (C1254354)
- CHV · AOD (C0683579, C0680954)
- ICD10AM (C0845989)
- CHV · MDR · MDRSPA · MDRDUT · MDRFRE · MDRGER · MDRITA · MDRJPN (C0858354)
- MEDCIN (C3646020)

My assumption is that only CUIs of concepts occuring in any of the defined terminologies are imported (e.g. if only SNOMED-CT is provided as a terminology, then only CUIs linking to concepts in SNOMED-CT are stored and retrievable? (Was not clear to me based on the documentation but makes sense)

So that would mean I need to import all terminologies, since I don't know beforehand to which terminology a CUI belongs to.

I went ahead and omitted the terminologies parameter according to the instructions to load all terminologies, but unfortunately, after a while of letting "import_umls" run (created file is 31.9 GB large) and processing the UMLS zip, it fails with following error:





How can I fix this issue and load PyMedtermino2 properly with all terminologies?

Kind regards
Kim Tang