Terminology

Phenotype: An Entity-Quality statement. A phenotype corresponds to 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: Property of a set of phenotypes. Phenotype that differs from others in entity, quality, related entity (where present), relation, or postcomposition (order of parentheses). Property of a set of phenotypes.

Phenotype assertion: not defined, used in TAO paper only

• • 'Another alternative would take advantage of phenotype annotations to infer a taxonomically variable relationship. In thiscase, a rule could be constructed that would allow a reasoner to infer from the (separately asserted) presence of Weberian apparatus in a taxon (e.g., Otophysi) that vertebra 1 is a Weberian vertebra in that taxon. Because the presence of the Weberian apparatus is a morphological character state and as such a phenotype, this strategy would use phenotype assertions to inject additional and taxon-specific relationships into the anatomy ontology, without the need for an ontology curator to maintain those separately.'

Annotation: part of title of Phenex paper, not defined; defined in TAO paper: 'One common use of ontologies is the annotation or “tagging” of objects or observations, such as genetic sequences, gene expression patterns, or whole organism phenotypes, with ontology terms. The convention used by model organism databases to annotate mutant phenotypes is entity-quality (EQ) syntax in which an entity from an anatomical ontology is combined with a quality or nontaxon specific modifier (Gkoutos et al. 2004; Sprague et al. 2008). The Phenoscape project has adopted and extended EQ to annotate evolutionary phenotypes, specifically systematic characters for ostariophysan fishes. '

Asserted annotation: used in Phenoscape paper

Inferred annotation: used in Phenoscape paper

Phenotype annotation: - used in all papers, not defined!

• • From SB paper: 'Because the active use of ontologies is relatively new to evolutionary biology in general and systematics in particular, the biological research project currently driving development of TAO is the phenotype annotation of the systematic literature for teleost fishes by the Phenoscape project.'

• • From SB paper: 'For example, a character state might be “Antorbital, triangular.” This phenotype can be expressed using the TAO term antorbital and the PATO term triangular. Such phenotype annotations corresponding to systematic characters require the association of the anatomical term with a taxonomic name. Thus, TAO terms are associated with species or higher taxa through annotations to teleost scientific names from the Teleost Taxonomy On- tology (www.phenoscape.org; OBO CVS repository: http://obofoundry.org).'

• • From Phenex paper:'Here, we address this problem at its root by development of a configurable software tool that employs standard ontologies and syntax to create computable phenotype annotations .'

• • 'Specialized software has been developed to assist human curators in annotating the phenotypes of mutant genotypes using EQ syntax...'

Gene phenotype: used in Phenoscape paper to describe the phenotypes associated with genes in the zebrafish database. See kb where we use 'Gene phenotype annotations' and 'Complex query for: annotated genes'. We use 'mutant phenotypes' in the TAO paper (not defined). The Washington et al. paper uses 'zebrafish phenotypes' or 'mutant phenotypes' (but they only use the mutant data, vs. we are using also morpholino data). KB reports also uses 'Count of genotype-phenotype assertions (including morpholinos as genotypes)' and report delivered says 'genotype annotations'. KB reports uses 'Count of distinct gene-phenotype assertions (implied by genotype assertions)' and report delivered says 'gene annotations'.

• • Zebrafish phenotype annotations: - used currently in Phenoscape paper to mean 'Zebrafish phenotypes' or Zebrafish EQ statements' E.g.: 'Zebrafish phenotype annotations recorded in the ZFIN database (21,476 as of 13 Jan 2011) are associated with genes (3,865) that are mutated or knocked down using morpholinos'

Phenotype-taxon assertion (=Taxon-Phenotype annotations?): Phenotype that is assigned to a taxon - not used in Phenex, TAO, or Curation papers, however, 'Taxon-Phenotype annotation used in Phenex paper:

• • 'From this knowledgebase, similar taxon–phenotype annotations can be easily discovered by searching higher level anatomical or quality terms.'

Taxon phenotype (used synonymously with Taxon phenotype annotations in current Phenoscape paper). Used in the same sense as 'Taxon-phenotype annotations' above in Phenex paper. We have discussed the use of the term Evolutionary phenotype. See kb for our use of 'Taxonomic phenotype annotations' -- but then we also use 'taxon phenotype annotations'.

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. - not used

Attribute: Higher level PATO quality term used to group "value qualities". NOTE: In current Phenoscape paper we define as 'Attributes are relatively high-level nodes in the PATO quality ontology, such as shape, position, etc.'

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.- not used -- PM recommends getting rid of this

Phenotype profile: union of phenotypes that are asserted for a particular gene or a particular taxon. Washington et al. define phenotypic profile as 'the sum-total of the EQ descriptions for an individual genotype' (but they also refer to gene phenotype profile.

Character:

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

Composite character: character state with more than one phenotype. - used in Curation paper, Phenex paper

Phenotyped character: Character with one or more states assigned to a phenotype - not used

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 the Teleost Taxonomy Ontology and the taxonomic authorities it is based on. 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 taxa used in the publications that have annotations. Includes repeated uses of the same taxon name in different publications.
[*side note not for report: should be around 3,400 for 47 publications]

Distinct (Number of) Publication Taxon Names

Count of the unique number of publication taxa 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