Comments (17)
Bit unsure where to draw the line. Maybe for now a simple python script that imports SSSOM mapping and mapping sets and just do it externally? I told @joeflack4 to add the ICD10-snomed mapping parser to SSSOM py but I am not sure. Maybe yes, adding it to parsers would be an option. For now the answer is: python, in whatever way you like. But perhaps having a method from_ncit() in parsers.py would be awesome.
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It's confusing but bare with me:
- Broader than: skos:narrowMatch
- Narrower than skos:broadMatch
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Related to : skos:relatedMatch
We don't need synonym unless the object of synonym is a code and not a label. What about "equivalent"?
from disease-mappings.
Use skos:exactMatch in these cases
from disease-mappings.
- Can you double-check that ncit.owl contains the ICD 10 mappings mentioned here:
https://ncit.nci.nih.gov/ncitbrowser/pages/mapping_search.jsf?nav_type=mappings
from disease-mappings.
You mean NCIt_Maps_To_ICD10_2016 (22.01e) and NCIt_Maps_To_ICD10CM_2017 (22.01e) ?
from disease-mappings.
Yeah, maybe.. Not sure. I guess I am wondering whether ncit.owl contains the mappings mentioned on this page, and if the page is mentioning these two, then yes.
I would love these mappings, especially the newest one, to be included here!
from disease-mappings.
So ncit.owl has just the mention of ICD10 2017
in them. Does not seem to have the actual ICD10 code. Although the mapping tables linked above have the mapping: 800 (ICD10 2017), 15 (ICD10 2016) and have the corresponding NCIT code.
from disease-mappings.
Perfect, thank you for checking. In this case, let's build an ingest into SSSOM for these!
from disease-mappings.
So do you mean having a new method in sssom-py
that accommodates for external mapping files?
from disease-mappings.
Alright, for the time being I'll just do an external JOIN
so to speak to include it in the SSSOM mappings as a quick-n-dirty solution. We can discuss a generic solution down the road after having experience with the different scenarios.
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Sounds good!
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ICD mapping column:
RELATIONSHIP_TO_TARGET
Broader Than
Related To
Has Synonym
Narrower Than
Which one would be appropriate?
"Broader Than": "skos:broader",
"Related To": "skos:relatedMatch",
"Has Synonym": "skos:altLabel",
"Narrower Than": "skos:related",
or
"Broader Than": "oboInOwl:hasBroadSynonym",
"Related To": "oboInOwl:hasRelatedSynonym",
"Has Synonym": "oboInOwl:hasExactSynonym",
"Narrower Than": "oboInOwl:hasNarrowSynonym",
from disease-mappings.
Maybe synonym is equivalent
from disease-mappings.
- skos:closeMatch,
- skos:exactMatch,
- owl:sameAs,
- owl:equivalentClass,
- owl:equivalentProperty
from https://www.w3.org/TR/skos-reference/#L4858
from disease-mappings.
Just for recording (no need to concern yourself): NCIT versions can be found here: https://stars.renci.org/var/NCIt/releases/)
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https://thesaurus.cancer.gov/ncitbrowser/pages/mapping_search.jsf?nav_type=mappings&b=0&m=0
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Related Issues (17)
- Integrate other mapping sources (drop links)
- Prefix maps do not exist HOT 1
- Ingest Mondo mappings
- Document ICD10 mapping sources HOT 3
- Ingest OMOP2OBO mappings HOT 3
- Build ingest pipeline for SNOMED-ICD10 mappings HOT 3
- Boomer pipeline prototype implementation for Mondo ICD10CM mapping HOT 4
- Capturing confidence levels from the side of the registry
- Basic progress monitor for mappings HOT 3
- Include Meddra mappings from Open Targets
- Change default license HOT 1
- Review general mapping rules for diseases and phenotypes HOT 6
- Rules for disease mappings
- Add mapping sets to disease mapping commons
- Slurp Medgen HPO mappings HOT 1
- UMLS - HPO Mappings HOT 1
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