MONDO:omim_formerly
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MONDO:omim_formerly
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- Update: f-endities.md with an entry for MONDO:omim_formerly
joeflack4
requested review from
sabrinatoro,
twhetzel and
nicolevasilevsky
as code owners
twhetzel
reviewed
Oct 18, 2024
docs/editors-guide/f-entities.md
Outdated
| @@ -193,6 +193,7 @@ MONDO:entailed | An inferred superclass (which is a redundant axiom) | subc | |||
| MONDO:equivalentObsolete | Used for cases where we have exact 1:1 matches between a live class in Mondo and an obsolete class in the source ontology. We want to avoid making an equivalence axiom (MONDO:equivalentTo) here. | xrefs | N | MONDO:0020499 'Nipah virus disease' database_cross_reference: Orphanet:1239 (was obsoleted in Orphanet) {source=MONDO:equivalentObsolete} | |||
| MONDO:equivalentTo | This is interpreted strongly as an OWL equivalence axiom, meaning the two terms are considered to be exactly the same. This can be added to any xref where this is true. | xrefs | N | MONDO:0100087 'familial Alzheimer disease' database_cross_reference: GARD:0000632 (refers to the disease in GARD) {source=MONDO:equivalentTo} | |||
| MONDO:includedEntryInOMIM | This indicates a term is an 'included' entry in OMIM, for example https://omim.org/entry/233910 | xrefs | N | MONDO:0100167 'dystonia, dopa-responsive, with or without hyperphenylalaninemia, autosomal recessive' | |||
| MONDO:omim_formerly | Used on OMIM synonyms whose labels end with ", formerly", denoting a status similar to `owl:deprecated`. | synonyms | N | | |||
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I am not sure this is the correct description, e.g. "status similar to owl:deprecated". An example could be an OMIM that contains ", formerly".
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- @joeflack4 An example could be an OMIM that contains ", formerly".
- Done!
- @twhetzel / curators: Confirm/review notes on curator description of "formerly".
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@joeflack4 the definition of omim_formerly is something you can check on during a Mondo Tech call since curators are at the meeting
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Just noticed this, I think the casing should be MONDO:omimFormerly.
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suggested updated definition:
Used on OMIM synonyms that have been deprecated in OMIM; in OMIM, these synonyms end with ", formerly".
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@twhetzel Done!
- Updated w/ Sabrina's verbiage.
- Changed to camel case.
twhetzel
reviewed
Oct 18, 2024
- Update: Added example to entry in f-entities.md
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- Update: Changed to camel case - Update: Changed verbiage (thanks @sabrinatoro)
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joeflack4
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Dec 16, 2024
| @@ -193,6 +193,7 @@ MONDO:entailed | An inferred superclass (which is a redundant axiom) | subc | |||
| MONDO:equivalentObsolete | Used for cases where we have exact 1:1 matches between a live class in Mondo and an obsolete class in the source ontology. We want to avoid making an equivalence axiom (MONDO:equivalentTo) here. | xrefs | N | MONDO:0020499 'Nipah virus disease' database_cross_reference: Orphanet:1239 (was obsoleted in Orphanet) {source=MONDO:equivalentObsolete} | |||
| MONDO:equivalentTo | This is interpreted strongly as an OWL equivalence axiom, meaning the two terms are considered to be exactly the same. This can be added to any xref where this is true. | xrefs | N | MONDO:0100087 'familial Alzheimer disease' database_cross_reference: GARD:0000632 (refers to the disease in GARD) {source=MONDO:equivalentTo} | |||
| MONDO:includedEntryInOMIM | This indicates a term is an 'included' entry in OMIM, for example https://omim.org/entry/233910 | xrefs | N | MONDO:0100167 'dystonia, dopa-responsive, with or without hyperphenylalaninemia, autosomal recessive' | |||
| MONDO:omimFormerly | Used on OMIM synonyms that have been deprecated in OMIM; in OMIM, these synonyms end with ", formerly". | synonyms | N | [OMIM:101000](https://omim.org/entry/101000?search=FORMERLY&highlight=formerly), Schwannomatosis, vestibular (Acoustic schwannomas, bilateral, formerly) | |||
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@twhetzel Nico said I don't need to have MONDO:omimFormerly or MONDO:omimIncluded on the entities page, because he doesn't think they should be used as either values or annotation properties, but instead should be synonym types, and those don't belong here.
Gonna close. If Nico is mistaken, feel free to re-open!
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This is related to new synonym annotations coming from:
This is an update to the Axiom Annotations Summary Table.
I'm not sure what to add in the "examples" column. Perhaps I could simply add a link to an OMIM term, and one of the labels? E.g.:
Changes
MONDO:omim_formerly