Terminology

Phenotype

An Entity-Quality (EQ) statement. Semantically, a phenotype is_a PATO:quality AND inheres_in some entity.

Taxon phenotype

A phenotype that has been used in a taxon phenotype annotation. A taxon phenotype may correspond to part or whole of a described character state (i.e. a character state may be decomposed into multiple phenotypes).

Gene phenotype: A phenotype that has been used in a gene phenotype annotation.

Distinct phenotype: Property of a set of phenotypes. A distinct phenotype differs from others in entity, quality, related entity (where present), relation, or post-composition.

Distinct taxon phenotype

Phenotype assigned to taxon that is 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 for alternative character states (e.g., when annotating at high level of PATO granularity). The number of distinct taxon phenotype annotations is typically lower than the total number of taxon phenotype annotations.

Distinct gene phenotype

Phenotype assigned to gene that is unique.

Phenotype annotation (synonym

phenotype assertion): The connection of a phenotype to a taxon or gene.

Taxon phenotype annotation

EQ statement associated with a taxon.

Gene phenotype annotation

EQ statement associated with a gene.

Attribute

High-level PATO quality term.

Phenotype profile

The union of phenotypes that are asserted for a particular gene or a particular taxon. Washington et al. (2009) defined a phenotypic profile or gene phenotype profile as 'the sum-total of the EQ descriptions for an individual genotype'.

Character

Presumably homologous feature of an organism that varies across taxa.

Character state

Variant of a character; assigned a code in a phylogenetic analysis.

Composite character

A character state with more than one phenotype.

Phenotyped character

A character with one or more states assigned to a phenotype.

Taxa:

Publication (Taxon) Name

The taxon name used in a publication from which we have curated data.

Incompletely Identified Taxon

A taxon that is identified in a publication less specific than genus and species. Typically, these are of the form "Genus sp. (Author Year)", where (Author Year) cites the publication in which it appears.

Valid Taxon Name

The name of a taxon that is currently valid, according to an authoritative naming source (e.g., Catalog of Fishes) that is used in construction of the Taxonomy Ontology under consideration. This may or may not be the same as the Publication Taxon Name.

Total (Number of) Publication Taxon Names

Count of the total number of taxon names used in the publications that have annotations. The same publication taxon name used in different publications is counted multiple times.

Distinct (Number of) Publication Taxon Names

Count of the unique number of taxon names used in the publications that have annotations. The same taxon name used in different publications is counted only once.

Distinct (Number of) 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 incompletely identified taxa (which we cite to the publication in which it appears, such as Danio sp. (Smith 1992)).

Total (Number of) Mismatches

Count of the total number of mismatches between publication taxon names and their corresponding valid taxon names. Each mismatch, including the same mismatch in different publications, is counted for the total. This count excludes incompletely identified taxa (such as Danio sp. in Smith 1992).

Distinct (Number of) Mismatches

Count of the unique mismatches between publication names and valid taxon names. The same mismatche occurring in different publications is counted only once. This count excludes incompletely identified taxa (such as Danio sp. in Smith 1992).

Total (Number of) Publication-Specific Names

Count of the unique valid taxon names that are incompletely identified in (and thus specific to) a publication (such as Danio sp. in Smith 1992). - used in Curation paper