WebHints

This page is an easily editable source for help popups in the Phenoscape web UI. Each entry below should be contained in a block element (DIV) with a mnemonic ID.

NOTE that there may be other wiki pages that also appear in the Phenoscape web UI, e.g. http://phenoscape.org/wiki/Knowledgebase:File_formats_(for_data_downloads)

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.

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