WebHints

**About Phenotypes** Phenotypes are a combination of an **Entity**, such as an anatomical structure, with a **Quality**, a description of some qualitative aspect of the entity such as shape, color, or size. Some qualities describe aspects of one entity relative to another: these use the optional **Related Entity** term.

**Find a Specific Term** Search using any valid term (taxon, gene, etc.) in the Knowledgebase. **You must choose a matched value from the drop-down list before you can search.**

**Browse All Phenotypes** View all phenotypes used within annotations. Narrow results by taxa, anatomical entity, phenotypic quality, or gene classification.

**Browse Taxa** Browse the taxonomic hierarchy and view detailed information about each term.

**Browse Anatomical Entities** Browse the anatomy ontology hierarchy and view detailed information about each term.

**Browse Phenotypic Qualities** Browse the phenotypic quality ontology hierarchy and view detailed information about each term.

**Browse Genes** TODO

**Browse Comparative Publications** TODO

**Query Phenotype Annotations To Taxa** Find **phenotypes** associated with particular **taxa**; filter by publication.

**Query Phenotype Annotations To Genes** Find **phenotypes** associated with particular **genes**.

**Query Taxa** Find the **taxa** associated with a particular phenotype or publication.

**Query Genes** Find a list of **genes** associated with a particular phenotype.

**Query Comparative Publications** Find **publications** that contain descriptions of particular taxa or phenotypes.

**Query Phenotypes** Find a list of **phenotypes** associated with a particular taxon, gene, or publication.

**Visualize Phenotypic Profile Tree** Visualize the extent to which a specified set of phenotypes is exhibited within and between taxa.

**Visualize Phenotypic Variation Tree** Visualize the taxonomic distribution of a specified phenotype.

**Apply higher taxon annotations to all included species** Using this option, phenotypes annotated to a higher taxon (e.g., Vertebrata) are assumed to apply to all organisms within that group. For example, searching for 'basihyal bone absent' would return a list of all catfish (Siluriformes) species because this phenotype has been annotated at the level of the Siluriformes.

**Add to workspace** When viewing query results, check the box to the left of any result to add it to the workspace. On the workspace page, you can combine saved items into new queries.

**Choose a specific term** Use this button to choose a specific term to jump to, rather than narrowing down via the ontology hierarchy links.

**Phenotype Profiles** A phenotype profile is a set of phenotypes exhibited by a taxon. Taxa in the tree are displayed in groups exhibiting a common phenotype profile. A given phenotype may appear in multiple profiles—select a phenotype in the table to see in which profiles in the tree it is present.

**Entity term** An anatomical structure or other item ("basihyal bone", "tooth", "head").

**Quality term** A qualitative aspect of the entity, such as shape, size, or color.

**Related Entity term** A second entity which further species the quality term: may be another structure to which the first is attached.

**Query Phenotypes** View distinct phenotypes meeting the query criteria. To view intersections (AND) of phenotypes, use the pulldown menu to choose a query for either **Taxa**, **Genes**, or **Publications**.

**Query Phenotype annotations to taxa** View distinct annotations of phenotypes to taxa which meet the query criteria. To view intersections (AND) of phenotypes, use the pulldown menu to choose a query for either **Taxa**, **Genes**, or **Publications**.

**Query Phenotype annotations to genes** View distinct annotations of phenotypes to genes which meet the query criteria. To view intersections (AND) of phenotypes, use the pulldown menu to choose a query for either **Taxa**, **Genes**, or **Publications**.

**Query Taxa** View taxa which meet the query criteria.

**Query Genes** View genes which meet the query criteria.

**Query Comparative publications** View comparative publications which meet the query criteria. These publications contain the evolutionary data matrices annotated by Phenoscape.