Difference between revisions of "Terminology"

Revision as of 22:07, 1 March 2012

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.

Phenotype annotation (synonym: phenotype assertion): The connection of a phenotype to a taxon or gene.

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.

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

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

@@ Line 3: / Line 3: @@
 ;   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.
+; 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 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.