ICD11 --> ORDO mappings

[joeflack4]

Overview

Produce some mappings.

[joeflack4]

@twhetzel Nico asked for this as a subtask of #10 back in January I think. For now I put it as 'very high'; This should come up at our check-in w/ Nico when we look at the board.

• ICD11 --> ORDO mappings #10

I don't actually know what this might entail other than running a SSSOM command on icd11foundation.owl.

[joeflack4]

FYI, I saw this during build-mondo-ingest. IDK what goal threw these warnings, but I take it that the reason is that the namespace does not exist in our Orphanet component. IDK for sure but I would imagine that this is not a new thing.

Example: ERROR:root:Skipping statements(subject=Orphanet:1560,predicate=oio:hasDbXref,object=None,value=ICD-11:1F70 ,datatype=None,language=None,); ValueError: ICD-11:1F70 is not a valid URI or CURIE

Full log

ERROR:root:Skipping statements(subject=Orphanet:1560,predicate=oio:hasDbXref,object=None,value=ICD-11:1F70 ,datatype=None,language=None,); ValueError: ICD-11:1F70  is not a valid URI or CURIE
ERROR:root:Skipping statements(subject=Orphanet:2073,predicate=oio:hasDbXref,object=None,value=ICD-11:7A20.0 ,datatype=None,language=None,); ValueError: ICD-11:7A20.0  is not a valid URI or CURIE
ERROR:root:Skipping statements(subject=Orphanet:2380,predicate=oio:hasDbXref,object=None,value=ICD-11:FB82.1 ,datatype=None,language=None,); ValueError: ICD-11:FB82.1  is not a valid URI or CURIE
ERROR:root:Skipping statements(subject=Orphanet:2582,predicate=oio:hasDbXref,object=None,value=ICD-11:4A43.Y ,datatype=None,language=None,); ValueError: ICD-11:4A43.Y  is not a valid URI or CURIE
ERROR:root:Skipping statements(subject=Orphanet:2764,predicate=oio:hasDbXref,object=None,value=ICD-11:FB82.1 ,datatype=None,language=None,); ValueError: ICD-11:FB82.1  is not a valid URI or CURIE
ERROR:root:Skipping statements(subject=Orphanet:293202,predicate=oio:hasDbXref,object=None,value=ICD-11:2B5F.2 ,datatype=None,language=None,); ValueError: ICD-11:2B5F.2  is not a valid URI or CURIE
ERROR:root:Skipping statements(subject=Orphanet:3005,predicate=oio:hasDbXref,object=None,value=ICD-11:LD24.1Y ,datatype=None,language=None,); ValueError: ICD-11:LD24.1Y  is not a valid URI or CURIE
ERROR:root:Skipping statements(subject=Orphanet:33276,predicate=oio:hasDbXref,object=None,value=ICD-11:2B57.1 ,datatype=None,language=None,); ValueError: ICD-11:2B57.1  is not a valid URI or CURIE
ERROR:root:Skipping statements(subject=Orphanet:36236,predicate=oio:hasDbXref,object=None,value=ICD-11:EA50.2 ,datatype=None,language=None,); ValueError: ICD-11:EA50.2  is not a valid URI or CURIE
ERROR:root:Skipping statements(subject=Orphanet:47045,predicate=oio:hasDbXref,object=None,value=ICD-11:4A60.1 ,datatype=None,language=None,); ValueError: ICD-11:4A60.1  is not a valid URI or CURIE
ERROR:root:Skipping statements(subject=Orphanet:521,predicate=oio:hasDbXref,object=None,value=ICD-11:2B33.2 ,datatype=None,language=None,); ValueError: ICD-11:2B33.2  is not a valid URI or CURIE
ERROR:root:Skipping statements(subject=Orphanet:545,predicate=oio:hasDbXref,object=None,value=ICD-11:2A80 ,datatype=None,language=None,); ValueError: ICD-11:2A80  is not a valid URI or CURIE
ERROR:root:Skipping statements(subject=Orphanet:572,predicate=oio:hasDbXref,object=None,value=ICD-11:4A01.12 ,datatype=None,language=None,); ValueError: ICD-11:4A01.12  is not a valid URI or CURIE
ERROR:root:Skipping statements(subject=Orphanet:67,predicate=oio:hasDbXref,object=None,value=ICD-11:1A36.00 ,datatype=None,language=None,); ValueError: ICD-11:1A36.00  is not a valid URI or CURIE
ERROR:root:Skipping statements(subject=Orphanet:69665,predicate=oio:hasDbXref,object=None,value=ICD-11:JA65.0 ,datatype=None,language=None,); ValueError: ICD-11:JA65.0  is not a valid URI or CURIE
ERROR:root:Skipping statements(subject=Orphanet:97360,predicate=oio:hasDbXref,object=None,value=ICD-11:LD24.A ,datatype=None,language=None,); ValueError: ICD-11:LD24.A  is not a valid URI or CURIE

[matentzn]

FYI, I saw this during build-mondo-ingest. IDK what goal threw these warnings, but I take it that the reason is that the namespace does not exist in our Orphanet component. IDK for sure but I would imagine that this is not a new thing.

Dont worry about that error - I added a SPARQL query to add basically just copy that specific xref to one that is legal:
https://github.com/monarch-initiative/mondo-ingest/blob/8bcce8eeba57982128fd384e0ac55cdc053bd297/src/sparql/fix_xref_prefixes.ru#L38

You can ignore that warning.

ORDO mappings: I don't actually know what this might entail other than running a SSSOM command on icd11foundation.owl.

You need to do some research.

• 1. Check if ORDO contains ICD11 mappings - there should be a lot of them. Look at the file (components/ordo.owl) and convince yourself that the mappings are exact.
• 2. Write a SPARQL query that reads ICD11 xrefs and asserts SKOS exact matches (there should be some sparql queries that already do this)
• 3. Compare the mappings to whatever you can find in https://www.orphadata.com/alignments/

Alternatively, you can email Julie T from Orphanet, and ask her:

"What is the easiest way to get exact mappings between ORDO and ICD11 Foundation?"

[matentzn]

(Also - make sure that whatever you look it is really ICD 11 foundation, and not linearization)

[joeflack4]

I checked off (1 - 3) above:

1. They're there, but to get foundation terms requires more work: Temp: ORDO mappings analysis #11 (comment)
2. SPARQL query alone won't suffice. Going to ignore that for now. Also, we have ordo-replace-annotation-based-mappings.ru, which seems like it's supposed to be inserting skos mapping annotations, but I don't see those actually appearing on components/ordo.owl; it appears the query is broken. Also, I didn't end up needing the query. I was able to query the nomenclature file directly.
3. Done. Here's a report: Temp: ORDO mappings analysis #11 (comment)