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mapping-commons / sssom-py

Python toolkit for SSSOM mapping format
https://mapping-commons.github.io/sssom-py/index.html#
MIT License
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Bug?: `--mapping-predicate-filter` only accepting URI, not CURIE #457

Open joeflack4 opened 11 months ago

joeflack4 commented 11 months ago

Overview

I tried --mapping-predicate-filter omoprel:Mapped_from and it did not work, but --mapping-predicate-filter https://w3id.org/cpont/omop/relations/Mapped_from did.

Details

Command

Syntax: f'sssom parse {obograph_path} -I obographs-json -o {outpath_sssom} -m {metadata_path}' Actual: sssom parse /Users/joeflack4/projects/owl-on-fhir/test/output/test_defaults/RxNorm.owl.obographs.json -I obographs-json -o /Users/joeflack4/projects/owl-on-fhir/test/output/test_defaults/RxNorm.sssom.tsv -m /Users/joeflack4/projects/owl-on-fhir/test/output/test_defaults/temp-metadata.sssom.yml

Inputs

  1. Obographs JSON: RxNorm.owl.obographs.json
  2. SSSOM Metadata YML: temp-metadata.sssom.yml 
    curie_map:
OMOP: https://athena.ohdsi.org/search-terms/terms/
omoprel: https://w3id.org/cpont/omop/relations/

Additional details

Context:

matentzn commented 10 months ago

I think this is a good idea. With @cthoyt huge improvements on handling prefixmaps you could simply use the msdf.converter right after it is created to expand(passthru=true) all the values provided! One line of code if I think of this correctly.