Related concepts, terms, and synonyms (long-term refinement)

[matuskalas]

This is a long-term, conceptual enhancement issue that is common between EDAM-bioimaging and the mainline EDAM.

More in the following comments...

[matuskalas]

(A placeholder for this issue in the EDAM repo is edamontology/edamontology#350)

[matuskalas]

Terms

N.B.: Terms consist of a textual label.

• oboInOwl:hasExactSynonym == alternative term or a variation of the primary term, with exactly the same meaning
• oboInOwl:hasNarrowSynonym == as above but with a somewhat narrower (more specific) meaning*
• oboInOwl:hasBroadSynonym == as above but with a somewhat broader (more generic) meaning*
• oboInOwl:hasRelatedSynonym == as above, with major overlap but neither strictly broader nor narrower meaning*
  *However, without the need for including as a separate concept in EDAM; but important for searching and text mining.
• relatedTerm° == out-of-scope term that is relevant for searching and|or giving context
  °for implementations|viewers compatibility purpose defined as a specialisation of oboInOwl:hasRelatedSynonym

Concepts

N.B.: Concepts contain a persistent, dereferenceable URI (ideally a 'cool URL') of a concept (from another ontology, vocabulary, taxonomy, or Wikipedia).

N.B.: Relations between different concepts within EDAM are covered by EDAM relations (has_topic, is_format_of, is_identifier_of, has_input, has_output).

• rdfs:seeAlso == additional information and|or additional context about|of this concept (e.g. a Wikipedia article)
• skos:closeMatch == well-overlapping concept from another ontology|taxonomy|vocabulary (maybe incl. Wikipedia)
  Can be narrower, broader, or neither, but must have a major overlap.
• skos:relatedMatch == partially overlapping and partically different-scope concept
• Let us define also a relatedConcept for out-of-scope related concepts that are, however, relevant for providing more information or context°°
  °°in the fashion of relatedTerm. Maybe also defined as a specialisation of skos:relatedMatch, if useful for implementations|viewers.

Probably not to be used in EDAM:

• skos:exactMatch -- concepts can be used interchangeably
  (we could maybe start using this in EDAM in case we need distinction from rdfs:seeAlso (for human information) and more granularity under|than skos:closeMatch. But we would have to constantly keep checking consistency of definitions & relations, what is unlikely feasible)
• owl:equivalentClass -- similar to skos:exactMatch, but with extra OWL reasoning
• owl:sameAs == an alternative ID (URI) of the same concept
  (we can use this in EDAM if necessary, i.e. where alternative EDAM IDs need to be recorded)

N.B.: The proposed usage is closely matching the usage within the EUCLID project.

[matuskalas]

Thanks to Sophie Aubin and Claire Nédellec for sharing the gist clarifying the concept relations from the EUCLID perspective.:

Hi,

Sophie Aubin would could not attend the meeting this morning gave me
this link to the Euclid project about linked data:
http://euclid-project.eu/modules/chapter3.html

_The property _owl:sameAs is used to express that two URI references
actually refer to the same thing.

_The property _rdfs:seeAlso__indicates that more relevant information
can be found by following the link.

skos:closeMatch expresses that two concepts are sufficiently similar
that they could possibly be used interchangeably
skos:exactMatch expresses that two concepts can be used
interchangeably. This property is transitive.
skos:relatedMatch expresses that there is an associative mapping
between the two concepts

http://euclid-project.eu/modules/chapter2.html

INFERENCES BASED ON EQUIVALENCE AMONG TERMS
owl:sameAs : It provides a means by which datasets with different
naming conventions can be connected.
owl:equivalentClass: Stating that two classes, or two properties, have
the same meaning,

More on the website.

Best,

Claire