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Bug?: Obographs parser: metadata not utilized; getting 0 mappings #456

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joeflack4 opened this issue Oct 7, 2023 · 4 comments
Closed

Bug?: Obographs parser: metadata not utilized; getting 0 mappings #456

joeflack4 opened this issue Oct 7, 2023 · 4 comments

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@joeflack4
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joeflack4 commented Oct 7, 2023 •
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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:

  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/

Output: RxNorm.sssom.tsv

Discussion

RxNorm.owl is a subset of the OMOP content. It's only 472 lines.

Includes namespaces:

     xmlns:OMOP="https://athena.ohdsi.org/search-terms/terms/"
     xmlns:omoprel="https://w3id.org/cpont/omop/relations/">
Example class snippet (truncated) 

    <owl:Class rdf:about="https://athena.ohdsi.org/search-terms/terms/501346">
        <rdfs:label>hepatitis B immune globulin 200 UNT/ML Injectable Solution</rdfs:label>
        <OMOP:concept_class_id>Clinical Drug</OMOP:concept_class_id>
        <OMOP:concept_code>412674</OMOP:concept_code>
        <OMOP:domain_id>Drug</OMOP:domain_id>
        <OMOP:standard_concept>S</OMOP:standard_concept>
        <OMOP:valid_end_date>2099-12-31</OMOP:valid_end_date>
        <OMOP:valid_start_date>1970-01-01</OMOP:valid_start_date>
        <OMOP:vocabulary_id>RxNorm</OMOP:vocabulary_id>

        <omoprel:Available_as_box>OMOP:41148125</omoprel:Available_as_box>
        <omoprel:Consists_of>OMOP:19110172</omoprel:Consists_of>
        <omoprel:Has_marketed_form>OMOP:2026202</omoprel:Has_marketed_form>
        <omoprel:Has_tradename>OMOP:2035461</omoprel:Has_tradename>
        <omoprel:Has_tradename>OMOP:35139038</omoprel:Has_tradename>
        <omoprel:Mapped_from>OMOP:501346</omoprel:Mapped_from>
        <omoprel:Maps_to>OMOP:501346</omoprel:Maps_to>
        <omoprel:RxNorm_has_dose_form>OMOP:19082103</omoprel:RxNorm_has_dose_form>
        <omoprel:RxNorm_is_a>OMOP:36223599</omoprel:RxNorm_is_a>
    </owl:Class>

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 

    }, {
      "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:

          "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"

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 has a test case for this, FYI.
joeflack4 added a commit to timsbiomed/owl-on-fhir that referenced this issue Oct 7, 2023
@joeflack4
1.1.0: ConceptMap
353683a 
ConceptMaps Feature
Added output for FHIR ConceptMap JSON.
Currently having some issues, mapping-commons/sssom-py#456, so have added param include_concept_map to toggle off.
- Add: Dependency: sssom
- Add: test/ directory, and initialized with inputs and test case
- Add: Scripting for this work

General
- Delete: Support for SemanticSQL intermediary
@matentzn
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matentzn commented Oct 8, 2023

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
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joeflack4 commented Oct 8, 2023 •
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Great point; this is another case where I missed the forest for the trees. It all makes perfect sense now. Should've been totally obvious to check the docs.

-F / ----mapping-predicate-filter is working for me. Gonna close this issue, but I'm wondering about opening 1-3 more issues, what do you think?:

New issues

1. Docs about the nature of mappings?

I glanced through the SSSOM docs but I didn't see anything about what a mapping is and isn't. Im' guessing it has something to do with the concept of "degree of equivalence / shared properties". Is this in scope for the docs? I'm not sure.

Could also include short list of preds SSSOM considers by default (I'm guessing something like skos exact/broad/narrow/close/related & oio hasDbXref).

2. Bug?: --mapping-predicate-filter only accepting URI, not CURIE

I tried --mapping-predicate-filter omoprel:Mapped_from (using the metadata YML posted in the OP) and it did not work, but --mapping-predicate-filter https://w3id.org/cpont/omop/relations/Mapped_from did.

3. Which OMOP relationships are mappings?

Not really scope for SSSOM, at least not at this point. Maybe for mapping-commons, or some of the OMOP or FHIR working groups. Not sure who I ought to engage with about this, but I can start with Davera Gabriel. OMOP has ~450 different relationships. So the task would be to go through and determine which are mapping relationships.

@joeflack4 joeflack4 closed this as not planned Won't fix, can't repro, duplicate, stale Oct 8, 2023
joeflack4 added a commit to timsbiomed/owl-on-fhir that referenced this issue Oct 8, 2023
@joeflack4
1.1.0: ConceptMap
50b157f 
ConceptMaps Feature
Added output for FHIR ConceptMap JSON.
Currently having some issues, mapping-commons/sssom-py#456, so have added param include_concept_map to toggle off.
- Add: Dependency: sssom
- Add: test/ directory, and initialized with inputs and test case
- Add: Scripting for this work

General
- Delete: Support for SemanticSQL intermediary
joeflack4 added a commit to timsbiomed/owl-on-fhir that referenced this issue Oct 9, 2023
@joeflack4
1.1.1: ConceptMap
bcd3688 
ConceptMaps Feature
Added output for FHIR ConceptMap JSON.
Currently having some issues, mapping-commons/sssom-py#456, so have added param include_concept_map to toggle off.
- Add: Dependency: sssom
- Add: test/ directory, and initialized with inputs and test case
- Add: Scripting for this work

General
- Delete: Support for SemanticSQL intermediary
joeflack4 added a commit to timsbiomed/owl-on-fhir that referenced this issue Oct 9, 2023
@joeflack4
1.1.1: ConceptMap
b624d0e 
ConceptMaps Feature
Added output for FHIR ConceptMap JSON.
Currently having some issues, mapping-commons/sssom-py#456, so have added param include_concept_map to toggle off.
- Add: Dependency: sssom
- Add: test/ directory, and initialized with inputs and test case
- Add: Scripting for this work

General
- Delete: Support for SemanticSQL intermediary
@matentzn
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matentzn commented Oct 9, 2023

You should turn 1) into issue on sssom repo, 2) into issue on sssom-py (both very good requests) and (3) could be made into an "example paragraph of (1)

This was referenced Oct 14, 2023
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@joeflack4
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joeflack4 commented Oct 14, 2023 •
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Done!

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