Terminology

Character:

Character state: variant of a Character, assigned a code in a phylogenetic analysis

Phenotype: An EQ version of a part or whole character state (i.e. a character state may have multiple phenotypes). Semantically, a phenotype is_a PATO:quality AND inheres_in some entity.

Distinct Phenotype: Phenotype that differs from others in entity, quality, related entity (where present), relation, or postcomposition (order of parens)

Composite character: character state with more than one phenotype.

Phenotyped character: Character with one or more states assigned to a phenotype

Phenotype-taxon assertion: Phenotype that is assigned to a taxon

Distinct phenotype-taxon assertions: phenotypes assigned to taxa that are unique. For example, the same taxon might be assigned the same phenotype (EQ) in different papers or the same taxon may be assigned the same phenotype (EQ) for alternative character states (when annotating at high level of PATO granularity, e.g.). Thus the number of distinct phenotype assertions is lower than the number of phenotype assertions.

Attribute: Higher level PATO quality term used to group "value qualities"

Value qualities: Nodes at a lower level than 'Attribute' in the PATO hierarchy

Phenotype Group: combination of an attribute with some entity, such as basihyal bone shape, tooth count, etc.

Taxa:

Total Publication Names: Count of the total number of taxa used in the publications that have annotations. Includes repeated uses of the same publication name in different publications. [*side note not for report: should be around 3,400 for 47 publications]

Distinct Publication Names: Count of the unique number of publication taxa used in the publications that have annotations. The same publication name used in different publications is counted only once.

Distinct Valid Taxon Names: Count of unique Valid Taxon names appearing in publications. The same valid taxon name used in different publications is counted only once. This includes 'publication-specific' names, meaning those referring to Author and Year in parentheses.

Total Mismatches: Count of the total number of mismatches between Total Publication Names and Valid Taxon names. Each mismatch, including the same mismatch in different publications, is counted for the total. Also, do not count any 'publication-specific' names, meaning those refering to Author and Year in parentheses.

Distinct Mismatches: Count of the unique mismatches between publication names and valid taxon names. The same publication name used in different publications is counted only once. Also, do not count any 'publication-specific' names, meaning those referring to Author and Year in parentheses.

Total Publication-Specific Names: Count of the unique Valid Taxon names that refer to the Author and Year in parentheses. For example, 'Danio sp. (Smith 1992)' is counted as a publication-specific name.