OMOP2OBO
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OMOP2OBO: A Python Library for mapping OMOP standardized clinical terminologies to Open Biomedical Ontologies
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Currently, the mappings generated by omop2obo do not respect the semantic constraints of all participating ontologies (which makes some sense because of the significant negative impact on performance). For example,...
## Basic description Feature request. Allow option for mappings outputs to be in SSSOM format. **Action:** Generate mapping outputs. **Output:** Rather than the existing output format, this would output mappings...
test_string_similarity failed for me because the nltk download isn't working. I found a way to get the download to work here: https://stackoverflow.com/questions/38916452/nltk-download-ssl-certificate-verify-failed After failing to get the solutions that fix...
Now it shows a friendlier message "Error: Missing option '--clinical_domain'."
**Describe the bug** running without a mrconso file creates an error **To Reproduce** Steps to reproduce the behavior: (test_env) CARD-CRoeder:OMOP2OBO christopherroeder$ time ./main.py --clinical_domain condition --clinical_data resources/clinical_data/sample_conditions.csv **Expected behavior** no...
for issue #63
**Describe the bug** If you run with no arguments (as you very likely would not) you get: "ValueError: 'default' must be a list when 'multiple' is true." **To Reproduce** Steps...
Add a requirements.txt to make it easier to create an environment with required libs.