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phyloref / phyloref-ontology

Phyloreferencing Ontology and OWL DL reasoning with phyloreferences
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A new OWL class for Taxonomic Unit matches #9

Closed gaurav closed 3 years ago

gaurav commented 6 years ago

Proposed term: TUMatch (class) Superclass: testable hypothesis? Definition: An assertion that two taxonomic units overlap to some extent, which can be used to store information on the match. See also: scratch ontology

Competency questions:

gaurav commented 5 years ago

In Model 2.0, taxonomic units are directly included in Phyloref logical expressions. For example:

:phyloref1 owl:equivalentClass ( phyloref:excludes_TU some (
  (TaxonConcept:hasName some (TaxonName:nomenclaturalCode value ICZN)
  and (dwc:scientificName value "Tomistoma schlegii")) and ... )

They are also directly noted on a phylogeny node:

:node1 rdf:type ( obo:CDAO_0000187 [= cdao:represents_TU] some (
   TaxonConcept:hasName some (
    obo:NOMEN_0000107 [= nomen:ICZN] and (dwc:scientificName value "Tomistoma schlegii"))))

The CDAO_0000187 annotation (represents_TU) could furthermore have annotations indicating who made this assertion and on what evidence, and can be used multiple times if a single node represents multiple taxonomic units in a phylogeny -- for example, a node labeled "Homo sapiens" in a particular phylogeny might represent the species Homo sapiens, the genus Homo and the family Hominidae in a particular phylogeny if no other hominids are included elsewhere in that phylogeny. We can also assert relationships between names if we need to record a synonymy, and then annotate that assertion with the evidence used to make that assertion.

Since we no longer need taxonomic unit matches, I propose that we close this issue as resolved.

hlapp commented 5 years ago

I anticipate that we will use GCIs to represent TU matches, not using a TUmatch class. So in principle I'm in agreement, but would like to keep this as an open issue until have an example with a corresponding reference model documented, and convinced ourselves that the logic works as intended.

hlapp commented 3 years ago

As of today we decided to close this issue due to lack of a supporting use-case. Once a use-case does surface, we'll reopen it.