add Synonyms

[chung88]

entityid	value
BAO_0000165	caspase activity
BAO_0000165	caspase activity assay
BAO_0000165	caspase apoptosis assay
BAO_0000165	caspase activity measurements
BAO_0000165	caspase-3 activation
BAO_0000165	caspase-3 and caspase-8 activity
BAO_0002041	cell cycle analysis
BAO_0002189	toxicology assay
BAO_0002189	tox assay
BAO_0002438	gene knockdown siRNA
BAO_0010083	paracellular permeability assay
BAO_0010083	transcellular permeability assay
BAO_0010190	inhibition of bile salt export pump
BAO_0010190	bile salt export pump inhibition
BAO_0010245	reactive metabolite assay

id	module
BAO_0000165	vocabulary_method
BAO_0002041	vocabulary_assay
BAO_0002189	vocabulary_assay
BAO_0002438	vocabulary_method
BAO_0010083	vocabulary_assay
BAO_0010190	vocabulary_assay
BAO_0010245	vocabulary_assay

[chung88]

slack discussion on 1/26/2023 at 4:20 PM Term IRI: http://purl.obolibrary.org/obo/IAO_0000118 linikujp: has_broad / narrow /exact / related synonym seems a set of GO annotation terms. Alternative term is an IAO term. See https://www.ebi.ac.uk/ols/ontologies/iao/properties?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000118 I think you would use alternative term more strictly as exact match (semantically). But instead of GO sets broad, narrow, related synonym, you could just use SKOS The GO set of the concepts are not having any context description as IAO or SKOS. SKOS is becoming complicated now, but SKOS:broader, narrower, exact, related are used quite popularly. https://www.w3.org/TR/2008/WD-skos-reference-20080829/skos.html You could make IAO_0000118 and skos:exact to be equivalent properties <--- can we do that in OWL? Can some engineer check? (I think theoretically it should be fine) sschurer: Thank you I suggest “alternative term” we are not at a point where we really can define the level of detail of broad, narrow, related etc synonyms

[chung88]

visser (email 1/30/2023): An alternative term is an annotation term without consequences for the reasoner. A synonym usually will have implications with regard to reasoning engines, but not all reasoning engines calculate synonyms.

OWL as a language defines two ways for the definition of synonyms:

1. Different IRIs. It is possible to have two different IRIs that represent the same concept.

2. Same IRI, different labels. The other way to indicate that an IRI can have multiple names but still represents the same concept is to have different labels.

Now, this is the language only. It depends on the reasoner if synonyms are calculated (like with any other OWL concept to be honest).

What you might want to look at is SKOS. Lately, people are using SKOS (Simple Knowledge Organization System) vocabulary instead of OWL vocabulary. SKOS provides more sophisticated ways to show entities are similar or related without necessarily being exact synonyms.

In order to denote that you have a synonym (or for humans: an alternative term) one usually goes with rdfs:label. SKOS adds three sub-properties to rdfs:label:

1.) The skos:prefLabel property has the highest priority to display an OWL entity. (That would be your synonym or alternative term) 2.) The skos:altLabel property is usually the lowest priority. It is used when none of the other label properties have a value. 3.) The skos:hiddenLabel is for literals that are used to find an entity but not to display it, e.g., for common misspellings.

So, if you want to model “Country” as an entity, you can use skos:prefLabel for “Country” and skis:altLabel for “Nation”, and skos:hiddenLabel for “Countries” or any other word derivate.

[sschurer]

Our situation it is 2 - the simpler one. We may have cases logical synonyms with different IRIs, but nothing tp worry now. Good point to use SKOS altLabel instead to IAO. Stephan

[chung88]

BAO PROD bao_qaqc actioncase bao_ext_id actioncomment actiondate status 1 BAO_0010238 obo deprecation; module: vocabulary_assay 11/15/2022 2:46:59 PM BAO v2.7.4 2 NCIT_C18079 remove; external: NCIT 11/15/2022 2:46:59 PM BAO v2.7.4 8 BAO_0000009 rename label from ADMET to ADME 11/15/2022 3:10:55 PM BAO v2.7.4 11 BAO_0000165 add Synonym 1/31/2023 12:36:32 PM BAO v2.7.4 11 BAO_0002041 add Synonym 1/31/2023 12:36:32 PM BAO v2.7.4 11 BAO_0002189 add Synonym 1/31/2023 12:36:32 PM BAO v2.7.4 11 BAO_0002438 add Synonym 1/31/2023 12:36:32 PM BAO v2.7.4 11 BAO_0010083 add Synonym 1/31/2023 12:36:32 PM BAO v2.7.4 11 BAO_0010190 add Synonym 1/31/2023 12:36:32 PM BAO v2.7.4 11 BAO_0010245 add Synonym 1/31/2023 12:36:32 PM BAO v2.7.4