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)
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 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 Comparative Publications
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.
Find the taxa associated with a particular phenotype or publication.
Find a list of genes associated with a particular phenotype.
Query Comparative Publications
Find publications that contain descriptions of particular taxa or 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.
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.
An anatomical structure or other item ("basihyal bone", "tooth", "head").
A qualitative aspect of the entity, such as shape, size, or color.
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.
View taxa which meet the query criteria.
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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