Campaign to standardize synonym types

[cthoyt]

This is an "epic" issue, just as a placeholder to reference various efforts towards standardizing synonym type definitions across the OBO Foundry

Background

These are the two precursor discussions in the OMO tracker where we talked about starting to encode synonym type definitions in OMO:

1. Standardising some of the synonym types information-artifact-ontology/ontology-metadata#70
2. provide URIs for synonym types within OMO information-artifact-ontology/ontology-metadata#122

Updating OMO

Here are issues/PRs where we added standards to OMO:

• Nested Synonym Types information-artifact-ontology/ontology-metadata#151
• Add some synonym types information-artifact-ontology/ontology-metadata#124
• Add new synonym types for misnomer and misspelling information-artifact-ontology/ontology-metadata#133
• Add previous name synonym type information-artifact-ontology/ontology-metadata#140
• Request for adding property 'Latin term' to OMO information-artifact-ontology/ontology-metadata#146 / Add OMO:0003011 "latin term" information-artifact-ontology/ontology-metadata#152
• Request for adding property brand name to OMO information-artifact-ontology/ontology-metadata#148
• Add INN synonym type information-artifact-ontology/ontology-metadata#150
• Add acronym synonym type information-artifact-ontology/ontology-metadata#159

Specifically, see the template: https://github.com/information-artifact-ontology/ontology-metadata/blob/master/src/templates/annotation_properties.tsv

Ontology Issues/Updates

Ontology updates/issues, where we updated an ontology to conform to the standard

Uberon

• Add OMO import to UBERON obophenotype/uberon#3058 / Standardise annotation property: 'plural form' (UBERON) obophenotype/uberon#3080 (duplicate issue) / Replace type definition for plural form synonyms obophenotype/uberon#3083
• Standardise annotation property: abbreviation (UBERON) obophenotype/uberon#3079 / Replace type definition for abbreviation synonyms obophenotype/uberon#3082
• Replace type definition for dubious synonyms obophenotype/uberon#3077
• Replace type definition for latin term synonyms obophenotype/uberon#3113

CL

• Standardise annotation property: abbreviation obophenotype/cell-ontology#2150 / Addresses #2150 Standardise annotation property: abbreviation obophenotype/cell-ontology#2159

ZFA

• Standardize synonym type definition for PLURAL ZFIN/zebrafish-anatomical-ontology#173

NCBITaxon

• Use OMO for synonym type predicates obophenotype/ncbitaxon#88

ENVO

• Standardize ad-hoc definition of plural synonym EnvironmentOntology/envo#1465

XAO

• Standardize ad-hoc plural synoynm type xenopus-anatomy/xao#62

PO

• Standardize ad-hoc plural synoynm type Planteome/plant-ontology#722

HP

• Standardize http://purl.obolibrary.org/obo/hp#layperson to OMO:0003003 obophenotype/human-phenotype-ontology#10140 / Replace ad hoc synonym type "layperson" with OMO:0003003 obophenotype/human-phenotype-ontology#10241

ChEBI

• https://gitlab.ebi.ac.uk/chembl/chebi/chebi-2.0/chebi-ontology-generator/-/issues/27

[cmungall]

Thank you!!!

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On Sat, Sep 23, 2023 at 4:00 AM Charles Tapley Hoyt < ***@***.***> wrote: This is an "epic" issue, just as a placeholder to reference various efforts towards standardizing synonym type definitions across the OBO Foundry These are the two precursor discussions in the OMO tracker where we talked about starting to encode synonym type definitions in OMO: 1. information-artifact-ontology/ontology-metadata#70 <information-artifact-ontology/ontology-metadata#70> 2. information-artifact-ontology/ontology-metadata#122 <information-artifact-ontology/ontology-metadata#122> Here are issues/PRs where we added standards to OMO: - information-artifact-ontology/ontology-metadata#124 <information-artifact-ontology/ontology-metadata#124> - information-artifact-ontology/ontology-metadata#133 <information-artifact-ontology/ontology-metadata#133> - information-artifact-ontology/ontology-metadata#140 <information-artifact-ontology/ontology-metadata#140> Specifically, see the template: https://github.com/information-artifact-ontology/ontology-metadata/blob/master/src/templates/annotation_properties.tsv Ontology updates/issues, where we updated an ontology to conform to the standard: - obophenotype/ncbitaxon#88 <obophenotype/ncbitaxon#88> - obophenotype/uberon#3077 <obophenotype/uberon#3077> - obophenotype/cell-ontology#2150 <obophenotype/cell-ontology#2150> — Reply to this email directly, view it on GitHub <#2450>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAMMOLU3KKR35W45D4JS2LX326MBANCNFSM6AAAAAA5EDX7SQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[matentzn]

I need some methodological help here, how I can weigh the arguments of @hoganwr on #148 ("universal or near universal substitutabilty") against yours "useful for X, eg Chebi"?

In other words, how will we decide, moving forward, what is a valid synonym type to avoid overloading the concept? In the current sense, even "first name" could become a synonym type. Can we have a clear definition of synonym type before we move on to add all these?

[cthoyt]

We are only two ontologies away from being done with my initial list! HPO needs some more hand-holding, and ChEBI will be possible if we can decide to push through the synonym types they need to encode different kinds of chemical synonyms.

There's still more to do. For example, PRO and NCBITaxon both require some more work since they have a big variety of synonyms, some of which could probably be ontologized differently (or really would never make sense as a "standardized" or "externalized" synonym). PO is misusing synonyms to denote languages. There are probably other things floating around too!

[cthoyt]

I need some methodological help here, how I can weigh the arguments of @hoganwr on #148 ("universal or near universal substitutabilty") against yours "useful for X, eg Chebi"?

I want to counter this wrt the BRAND_NAME discussion, since many ontologies import chebi and therefore accidentally mint their own version, I think that there is always a case to be made for externalizing synonym types, and anyone who wants to be a stakeholder can participate in the discussion board here when someone proposes one

[hoganwr]

It occurs to me here that there are term "types", and there are "synonym" types. What are we discussing here specifically? Brand name is suitable as a term type, but it is not a good synonym type. Bill

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On Wed, Feb 21, 2024 at 5:54 AM Charles Tapley Hoyt < ***@***.***> wrote: I need some methodological help here, how I can weigh the arguments of @hoganwr <https://github.com/hoganwr> on #148 <#148> ("universal or near universal substitutabilty") against yours "useful for X, eg Chebi"? I want to counter this wrt the BRAND_NAME discussion, since many ontologies import chebi and therefore accidentally mint their own version, I think that there is always a case to be made for externalizing synonym types, and anyone who wants to be a stakeholder can participate in the discussion board here when someone proposes one — Reply to this email directly, view it on GitHub <#2450 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJR55QEZOJSNVZAF5U4SRLYUXN7ZAVCNFSM6AAAAAA5EDX7SSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNJWGQ4DSNZXGU> . You are receiving this because you were mentioned.Message ID: ***@***.***>