Difference between revisions of "WebHints"

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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.
 
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)
 +
 +
<div id="WhatArePhenotypes" style="border: 2px dashed silver;">
 +
'''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.
 +
</div>
  
  
 
<div id="FindSpecificTerm" style="border: 2px dashed silver;">
 
<div id="FindSpecificTerm" style="border: 2px dashed silver;">
−
===Find a Specific Term===
+
'''Find a Specific Term'''
  
−
Use this tool to 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.'''
+
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.'''
 
</div>
 
</div>
  
  
 
<div id="BrowseAllPhenotypes" style="border: 2px dashed silver;">
 
<div id="BrowseAllPhenotypes" style="border: 2px dashed silver;">
−
====Browse All Phenotypes====
+
'''Browse All Phenotypes'''
  
−
You can browse all phenotypes. (This hint uses a smaller heading than ''Find a Specific Term''.)
+
View all phenotypes used within annotations. Narrow results by taxa, anatomical entity, phenotypic quality, or gene classification.
 
</div>
 
</div>
  
  
 
<div id="BrowseTaxa" style="border: 2px dashed silver;">
 
<div id="BrowseTaxa" style="border: 2px dashed silver;">
−
This is a more compact style of hint that does not use a heading.
+
'''Browse Taxa'''
  
−
It should, however, have two paragraphs.
+
Browse the taxonomic hierarchy and view detailed information about each term.
 
</div>
 
</div>
  
  
−
<div id="BrowseAnatomicalEntities">
+
<div id="BrowseAnatomicalEntities" style="border: 2px dashed silver;">
 
'''Browse Anatomical Entities'''
 
'''Browse Anatomical Entities'''
  
−
Now we're using a simple bolded paragraph instead of a heading. Does this give better margins?
+
Browse the anatomy ontology hierarchy and view detailed information about each term.
 
</div>
 
</div>
  
−
<div id="BrowsePhenotypicQualities">
+
 
 +
<div id="BrowsePhenotypicQualities" style="border: 2px dashed silver;">
 
'''Browse Phenotypic Qualities'''
 
'''Browse Phenotypic Qualities'''
 +
 +
Browse the phenotypic quality ontology hierarchy and view detailed information about each term.
 +
</div>
 +
 +
 +
<div id="BrowseGenes" style="border: 2px dashed silver;">
 +
'''Browse Genes'''
  
 
TODO
 
TODO
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−
<div id="BrowseGenes">
+
<div id="BrowseComparativePublications" style="border: 2px dashed silver;">
−
'''Browse Genes'''
+
'''Browse Comparative Publications'''
  
 
TODO
 
TODO
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−
<div id="BrowseComparitivePublications">
+
<div id="QueryPhenotpyeAnnotationsToTaxa" style="border: 2px dashed silver;">
−
    ===Browse Comparitive Publications===
+
'''Query Phenotype Annotations To Taxa'''
−
    TODO
+
 
 +
Find '''phenotypes''' associated with particular '''taxa'''; filter by publication.
 +
</div>
 +
 
 +
 
 +
<div id="QueryPhenotpyeAnnotationsToGenes" style="border: 2px dashed silver;">
 +
'''Query Phenotype Annotations To Genes'''
 +
 
 +
Find '''phenotypes''' associated with particular '''genes'''.
 +
</div>
 +
 
 +
 
 +
<div id="QueryTaxa" style="border: 2px dashed silver;">
 +
'''Query Taxa'''
 +
 
 +
Find the '''taxa''' associated with a particular phenotype or publication.
 +
</div>
 +
 
 +
 
 +
<div id="QueryGenes" style="border: 2px dashed silver;">
 +
'''Query Genes'''
 +
 
 +
Find a list of '''genes''' associated with a particular phenotype.
 +
</div>
 +
 
 +
 
 +
<div id="QueryCompatarivePublications" style="border: 2px dashed silver;">
 +
'''Query Comparative Publications'''
 +
 
 +
Find '''publications''' that contain descriptions of particular taxa or phenotypes.
 +
</div>
 +
 
 +
 
 +
<div id="QueryPhenotpyes" style="border: 2px dashed silver;">
 +
'''Query Phenotypes'''
 +
 
 +
Find a list of '''phenotypes''' associated with a particular taxon, gene, or publication.
 +
</div>
 +
 
 +
 
 +
<div id="VisualizePhenotypicProfileTree" style="border: 2px dashed silver;">
 +
'''Visualize Phenotypic Profile Tree'''
 +
 
 +
Visualize the extent to which a specified set of phenotypes is exhibited within and between taxa.
 +
</div>
 +
 
 +
 
 +
<div id="VisualizePhenotypicVariationTree" style="border: 2px dashed silver;">
 +
'''Visualize Phenotypic Variation Tree'''
 +
 
 +
Visualize the taxonomic distribution of a specified phenotype.
 +
</div>
 +
 
 +
 
 +
<div id="AboutInferredAnnotations" style="border: 2px dashed silver;">
 +
'''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.
 +
</div>
 +
 
 +
 
 +
<div id="AboutTheWorkspace" style="border: 2px dashed silver;">
 +
'''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.
 +
</div>
 +
 
 +
 
 +
<div id="ChooseTermForFacet" style="border: 2px dashed silver;">
 +
'''Choose a specific term'''
 +
 
 +
Use this button to choose a specific term to jump to, rather than narrowing down via the ontology hierarchy links.
 +
</div>
 +
 
 +
 
 +
<div id="PhenotypeProfiles" style="border: 2px dashed silver;">
 +
'''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.
 
</div>
 
</div>
  
  
−
<div id="QueryPhenotpyeAnnotationsToTaxa">
+
<div id="Entity" style="border: 2px dashed silver;">
−
    ===Query PhenotpyeAnnotations To Taxa===
+
'''Entity term'''
−
    TODO
+
 
 +
An anatomical structure or other item ("basihyal bone", "tooth", "head").
 
</div>
 
</div>
  
  
−
<div id="QueryPhenotpyeAnnotationsToGenes">
+
<div id="Quality" style="border: 2px dashed silver;">
−
    '''Query Phenotpye Annotations To Genes'''
+
'''Quality term'''
−
    TODO
+
 
 +
A qualitative aspect of the entity, such as shape, size, or color.
 
</div>
 
</div>
  
  
−
<div id="QueryTaxa">
+
<div id="RelatedEntity" style="border: 2px dashed silver;">
−
    '''Query Taxa'''
+
'''Related Entity term'''
−
    TODO
+
 
 +
A second entity which further species the quality term: may be another structure to which the first is attached.
 
</div>
 
</div>
  
 +
<div id="PhenotypeQueryResults" style="border: 2px dashed silver;">
 +
'''Query Phenotypes'''
  
−
<div id="QueryGenes">
+
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 Genes===
 
−
    TODO
 
 
</div>
 
</div>
  
  
−
<div id="QueryCompatarivePublications">
+
<div id="TaxonPhenotypeAnnotationQueryResults" style="border: 2px dashed silver;">
−
    ===Query Compatarive Publications===
+
'''Query Phenotype annotations to taxa'''
−
    TODO
+
 
 +
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'''.
 
</div>
 
</div>
  
  
−
<div id="VisualizePhenotypicProfileTree">
+
<div id="GenePhenotypeAnnotationQueryResults" style="border: 2px dashed silver;">
−
    ===Visualize Phenotypic Profile Tree===
+
'''Query Phenotype annotations to genes'''
−
    TODO
+
 
 +
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'''.
 
</div>
 
</div>
  
  
−
<div id="VisualizePhenotypicVariationTree">
+
<div id="TaxaQueryResults" style="border: 2px dashed silver;">
−
    ===Visualize Phenotypic Variation Tree===
+
'''Query Taxa'''
−
    TODO
+
 
 +
View taxa which meet the query criteria.
 +
</div>
 +
 
 +
 
 +
<div id="GenesQueryResults" style="border: 2px dashed silver;">
 +
'''Query Genes'''
 +
 
 +
View genes which meet the query criteria.
 
</div>
 
</div>
  
 +
 +
<div id="ComparativePublicationsQueryResults" style="border: 2px dashed silver;">
 +
'''Query Comparative publications'''
 +
 +
View comparative publications which meet the query criteria. These publications contain the evolutionary data matrices annotated by Phenoscape.
 +
</div>
  
 
Add more entries here...
 
Add more entries here...

Latest revision as of 18:39, 19 March 2012


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.

Add more entries here...

Retrieved from "https://wiki.phenoscape.org/wg/phenoscape/index.php?title=WebHints&oldid=9753"