matentzn
commented
11 months ago One terminological thing here: a mapping is not a relationship. Its a correspondence between two terms. The lines between the two are very hazy in practice, but in our minds we should draw them, because otherwise sssom becomes another ontology formalism (basically able to publish all possible triples). This must be avoided.
In your case, did you try to use the https://mapping-commons.github.io/sssom-py/cli_usage.html#sssom-parse method with the --F/--filter-mapping-predicates option?
joeflack4
Overview
I'm working on a PR to add FHIR ConceptMaps to the TIMS OMOP/OWL to FHIR conversion tooling.
I am stuck on an issue where when I convert OMOP -> OWL -> Obographs -> SSSOM TSV, the TSV does not contain any mappings.
Command & main inputs / outputs of concern
Command:
f'sssom parse {obograph_path} -I obographs-json -o {outpath_sssom} -m {metadata_path}'(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:
Output: RxNorm.sssom.tsv
Discussion
RxNorm.owl is a subset of the OMOP content. It's only 472 lines.
Includes namespaces:
Example class snippet (truncated)
```owl
hepatitis B immune globulin 200 UNT/ML Injectable Solution
Clinical Drug
412674
Drug
S
2099-12-31
1970-01-01
RxNorm
OMOP:41148125
OMOP:19110172
OMOP:2026202
OMOP:2035461
OMOP:35139038
OMOP:501346
OMOP:501346
OMOP:19082103
OMOP:36223599
```
I expect / want every object property declaration from the second half of the snippet to be a single row in my SSSOM TSV.
When I convert to Obographs, it looks like this:
Obographs snippet
```json }, { "id" : "https://athena.ohdsi.org/search-terms/terms/501346", "lbl" : "hepatitis B immune globulin 200 UNT/ML Injectable Solution", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "https://athena.ohdsi.org/search-terms/terms/concept_class_id", "val" : "Clinical Drug" }, { "pred" : "https://athena.ohdsi.org/search-terms/terms/concept_code", "val" : "412674" }, { "pred" : "https://athena.ohdsi.org/search-terms/terms/domain_id", "val" : "Drug" }, { "pred" : "https://athena.ohdsi.org/search-terms/terms/standard_concept", "val" : "S" }, { "pred" : "https://athena.ohdsi.org/search-terms/terms/valid_end_date", "val" : "2099-12-31" }, { "pred" : "https://athena.ohdsi.org/search-terms/terms/valid_start_date", "val" : "1970-01-01" }, { "pred" : "https://athena.ohdsi.org/search-terms/terms/vocabulary_id", "val" : "RxNorm" }, { "pred" : "https://w3id.org/cpont/omop/relations/Available_as_box", "val" : "OMOP:41148125" }, { "pred" : "https://w3id.org/cpont/omop/relations/Consists_of", "val" : "OMOP:19110172" }, { "pred" : "https://w3id.org/cpont/omop/relations/Has_marketed_form", "val" : "https://athena.ohdsi.org/search-terms/terms/2026202" }, { "pred" : "https://w3id.org/cpont/omop/relations/Has_marketed_form", "val" : "OMOP:2026526" }, { "pred" : "https://w3id.org/cpont/omop/relations/Has_quantified_form", "val" : "OMOP:42919946" }, { "pred" : "https://w3id.org/cpont/omop/relations/Has_tradename", "val" : "OMOP:2035461" "pred" : "https://w3id.org/cpont/omop/relations/Mapped_from", "val" : "OMOP:501346" }, { "pred" : "https://w3id.org/cpont/omop/relations/Maps_to", "val" : "OMOP:501346" }, { "pred" : "https://w3id.org/cpont/omop/relations/RxNorm_has_dose_form", "val" : "OMOP:19082103" }, { "pred" : "https://w3id.org/cpont/omop/relations/RxNorm_is_a", "val" : "OMOP:36223599" } ] } }, { ```
In that snippet, you can see some of the relationship mappings:
In the top of these 2 mappings, I manually edited the JSON to replace the CURIE with a URI to test if that would work, but it didn't.
These namespaces exist in my metadata YML, so why aren't any mappings being generated?
Additional info
For reference, I looked at how OMIM is being converted to Obographs and SSSOM to double check what I was doing was correct. The [PR](https://github.com/HOT-Ecosystem/owl-on-fhir/pull/7) has a test case for this, FYI.