This revision is driven by the concrete use-case needs for expressing phyloreferences that have come out of the curation effort. This revision may not (and most likely will not) solve all those needs, but takes a stab at addressing those that initially appear most important and evident.
In summary, this includes the following changes:
Adds new property excludes_TU as a property chain over excludes_lineage_to and cdao:represents_TU, This is designed as the main property by which to declare taxon concepts to be excluded in a clade definition, and honors the fact that the vast majority of clade definitions out there reference taxon concepts for exclusion and inclusion.
Adds new property includes_TU, as a superproperty of cdao:represents_TU and a property chain over has_Descendant and cdao:represents_TU.
Adds annotation property newick_expression for annotating a cado:Tree instance with the Newick-format of the tree.
Adds a property 'matches_TU' that links one cdao:TU to another, and property chains that extend excludes_TU and includes_TU over matches_TU. This will need more work in the future, including, if possible, alignment with TDWG's taxon concept vocabulary, and the RCC5 vocabulary in the OpenBiodiv-O ontology.
Asserts cdao:belongs_to_Tree_as_Root as a subproperty of cdao:belongs_to_Tree. (This axiom is a candidate for being pushed down to CDAO.)
Adds property chain axiom of cdao:has_Parent o cdao:belongs_to_Tree -> cdao:belongs_to_Tree. (This axiom is a candidate for being pushed down to CDAO.)
Imports 'is_specified_input_of', 'is_specified_output_of' and their inverses from OBI. Also imports 'prediction' from OBI. Using these is the designated model I propose for identifying the node in a (reference) tree to which a phyloreference is expected to resolve.
Adds ExpectedNode defined as a cdao:Node that obi:is_specified_output_of some (obi:prediction and ro:has_participant some Phyloreference). Note that obi:has_specified_input is a subproperty of ro:has_participant.
Imports class evidence from ECO, and 'has evidence'/'is evidence for' properties from RO. Adds a subclass hierarchy extending from eco:evidence as PhylogeneticEvidence > PhylogenyEvidence > ReferencePhylogenyEvidence. Using these is the designated model I propose for identifying the reference phylogeny for a phyloreference, as Phyloreference and ro:'has evidence' value .
Also included are removals of the following entities for which a clear need has not surfaced.
Removes class 'SpecifiedGroup' and property 'has_specifier'. At least for now, the need for specifiers as their own concepts apart from TUs, and with their own properties lacks clear evidence.
Removes 'has_Progenitor' property. There is currently no evidence that this is needed.
Removes 'includes_group' property. See icludes_TU.
hlapp
commented
5 years ago
This revision is driven by the concrete use-case needs for expressing phyloreferences that have come out of the curation effort. This revision may not (and most likely will not) solve all those needs, but takes a stab at addressing those that initially appear most important and evident.
In summary, this includes the following changes:
cdao:has_Parent o cdao:belongs_to_Tree -> cdao:belongs_to_Tree. (This axiom is a candidate for being pushed down to CDAO.)Also included are removals of the following entities for which a clear need has not surfaced.