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OntologyClass for ICD-O?
The Disease
object references OntologyClass
for ICD-O values used for primary_site
annotations.
Which ICD-O ontology implementation does this refer to? While the codes themselves are well defined/known, It is no clear which (public) source for CURIEs would be recommended (in fact, exists).
Thanks for pointing this out. The documentation in the protobuf file needs to be revised to say "such as" -- in no place do we want to proscribe a specific ontology. I agree it is hard to access ICD-O terms, but this is one option (https://apps.who.int/iris/handle/10665/96612). It would also be acceptable to use UBERON or NCIT terms here. @julesjacobsen
@pnrobinson We have coded to ICD-O for ~20ys; and my original interest in ontologies w/ CURIEs started from the lack of those for ICD-O, when writing the OntologyTerm use into the GAGH metadata schema.
There is a representation in SNOMED, but this isn't correct & also not OA. So ICD-O became the driver for us to code the ICD-O (morphology + topography) doublets to NCIt while using a modified code representation:
- https://progenetix.org/service-collection/ontologymaps/
- https://progenetix.org/services/ontologymaps?filters=NCIT,icdom,icdot for term groupings
We've worked on getting this into MONDO last year (w/ @cmungall and @nicolevasilevsky).
Still, for practical purposes (i.e. talking to pathologists ...) we still code ICD-O and NCIt in parallel.
@pnrobinson @julesjacobsen As much as I love ICD-O, I would drop it here since it requires coding of 2 arms & does not exist in a "ontologized" form. You can document/point out that when using standards like the current ICD-O the codes should be converted to a suitable ontologyClass.
@pnrobinson @mbaudis Can you recommend an NCIT root term for this? NCIT:C12219?
@julesjacobsen For Cancer it is NCIT:C3262 (I don't have to look this up :-)
I.e. "Neoplasm" root term, which covers also benign neoplasms.
Thank @mbaudis. However, isn't Neoplasm
better placed in the Biosample.histological diagnosis
? The Disease.primary_site
ought to be an anatomy term. In the case below this should be cervix uteri
- NCIT:C12311 == UBERON:0000002
[
{
"id": "NCIT:C4028",
"label": "Cervical Squamous Cell Carcinoma, Not Otherwise Specified"
},
{
"id": "icdom-80703",
"label": "Squamous cell carcinoma, NOS"
},
{
"id": "icdot-C53.9",
"label": "cervix uteri"
}
],
[
{
"id": "NCIT:C4029",
"label": "Cervical Adenocarcinoma"
},
{
"id": "icdom-81403",
"label": "Adenocarcinoma, NOS"
},
{
"id": "icdot-C53.9",
"label": "cervix uteri"
}
]
@julesjacobsen Correct - my original comment led then a to a more general drift... We're using in parallel 1x NCIt neoplasm <=> 2x ICD-O, and recode ICD-O Topo to UBERON. So, yes, NCIt Neoplasm subtree for Biosample.histological_diagnosis
(we actually use it this way), and primary_site
UBERON or a corresponding code.
Just for emphasis: For the cancer use, I still think that the ICD-O Topo coding is in principle the best match and has a widespread use. It is just that I'm not aware of a representation in a well structured ontology with CURIEs, to point to. This may (have) change(d) - I would be glad ...
@balhoff can you comment