sssom-py
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mapping-commons
Python toolkit for SSSOM mapping format
``` sssom parse uberon-base.json --input-format obographs-json --metadata metadata.yml --prefix-map-mode merged --output uberon.sssom.tsv ``` VHOG VHOG_RETIRED
sssom parse should extract "replace by" correctly and print an error if the target is not well formed.
Rather than strings like "mapping_justification".
This ensures that multivalued items are treated correctly.
RDF and OWL serialisations of SSSOM in the test data contain: ``` sssom:mapping_justification "semapv:LexicalMatching" ; ``` These should be: ``` sssom:mapping_justification semapv:LexicalMatching ; ``` This is not a bug with...
## Description I've written an exporter for FHIR ConceptMap [R4](https://fhir-ru.github.io/conceptmap.html) JSON. But there are additional tasks to complete over time. Exporter is part of conversion / converter from SSSOM TSV...
## Description I've written an exporter for FHIR ConceptMap [R4](https://fhir-ru.github.io/conceptmap.html) JSON. It would be best practice to also write an importer for it, so we're going to do that. Importer...
Is this how it should work? ``` sssom parse ontologies/ro.json -I obographs-json | sssom dosql -Q "SELECT * FROM df WHERE subject_id LIKE \"%ro%\"" -o mappings/ro.ols.sssom.tsv ``` Results in ```...
I am worried that copying mapping sets around will result in lazy behaviour like: 1) I get the mondo mappings 2) I remove the OMIM mappings from the mondo mappings...
Fixes #249 Origin: - https://github.com/mapping-commons/sssom-py/pull/249 - https://github.com/mapping-commons/sssom-py/pull/217 - [ ] what is the difference between parse and convert? - [ ] https://mapping-commons.github.io/sssom-py/cli_usage.html?highlight=merge#sssom-py-sparql - give an example - https://mapping-commons.github.io/sssom-py/sphinx_documentation.html * [...
