Terminology

Phenotype: An EQ statement. A phenotype, i.e. EQ statement, 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. - used in all papers

Distinct phenotype: Phenotype that differs from others in entity, quality, related entity (where present), relation, or postcomposition (order of parens) not used

'Phenotype assertion' 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 os- tariophysan fishes. '

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...'

Mutant phenotype: - used in SB paper, not defined

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.'

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.

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. - used in Curation paper

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