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ORDO docs updates #497

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Apr 23, 2024
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ORDO docs updates #497

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ORDO docs
joeflack4 Apr 18, 2024
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Update src/ontology/metadata/ordo.yml
joeflack4 Apr 22, 2024
78f0c6b
Update docs/sources/ordo.md
joeflack4 Apr 22, 2024
c450f91
Update docs/sources/ordo.md
joeflack4 Apr 22, 2024
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Update src/ontology/metadata/ordo.yml
joeflack4 Apr 22, 2024
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Update src/ontology/metadata/ordo.yml
joeflack4 Apr 22, 2024
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7 changes: 5 additions & 2 deletions docs/sources/ordo.md
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Expand Up @@ -7,9 +7,12 @@

**Homepage:** http://www.orphadata.org/

**Comments about this source:** ORDO is not really OWL in the strict sense. For example, disease 2 gene relationships follow the 'some, some' logic (a disease may have basis in the mutation of one of these), while the OWL interpretation of these axioms is that the disease has basis in the mutation of all of them. Example: ramona wartz disease can have a mutation in _any_ (not all) of the genes recorded in ORDO. This is why great care needs to be taking interpreting diesease 2 gene relationships during ingest!

**Comments about this source:**
ORDO is not really OWL in the strict sense. For example, disease 2 gene relationships follow the 'some, some' logic (a disease may have basis in the mutation of one of these), while the OWL interpretation of these axioms is that the disease has basis in the mutation of all of them. Example: ramona wartz disease can have a mutation in _any_ (not all) of the genes recorded in ORDO. This is why great care needs to be taking interpreting diesease 2 gene relationships during ingest!

About certain prefixes
- **ICD10EXP**: is when ORDO uses expressions over ICD10 codes, for example to express a range of codes. It is specific to Orphanet use cases and will never be aligned in Mondo, but could give some “useful” information for curators about the intentions of a group of disorders term.
- **ICD9 and ICD9CM**: As we do not seek to align with ICD9, these are just prefixes in ORDO and DOID we dont really care about other other than for documentative purposes.

## Preprocessing:
* **EntityRemoval**:
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6 changes: 6 additions & 0 deletions src/ontology/metadata/ordo.yml
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Expand Up @@ -71,3 +71,9 @@ comment: >
recorded in ORDO. This is why great care needs to be taking interpreting diesease 2 gene relationships during ingest!
base_prefix_map:
Orphanet: http://www.orpha.net/ORDO/Orphanet_
comments_about_this_source: >
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comments_about_this_source in ordo.yml

As decided in #481. The relevance of this will kick in moreso when that issue is completed.

ORDO is not really OWL in the strict sense. For example, disease 2 gene relationships follow the 'some, some' logic (a disease may have basis in the mutation of one of these), while the OWL interpretation of these axioms is that the disease has basis in the mutation for all of them. Example: ramona wartz disease can have a mutation in _any_ (not all) of the genes recorded in ORDO. This is why great care needs to be taking interpreting disease 2 gene relationships during ingest!

About certain prefixes
- **ICD10EXP**: is when ORDO uses expressions over ICD10 codes, for example to express a range of codes. It is specific to Orphanet use cases and will never be aligned in Mondo, but could give some “useful” information for curators about the intentions of a group of disorders term.
- **ICD9 and ICD9CM**: As we do not seek to align with ICD9, these are just prefixes in ORDO and DOID we dont really care about other other than for documentative purposes.