Difference between revisions of "Classification hub"
Tagir Valeev (Talk | contribs) (Created page with "'''Classification hub''' is a kind of BioHub which used to classify the genes into several groups. This BioHub type is defined in [[Biouml.plugins.enrichment (plugin)|biou...") |
Tagir Valeev (Talk | contribs) (+{{Stub}}) |
||
| Line 4: | Line 4: | ||
=== Implementation details === | === Implementation details === | ||
| + | {{Stub|information about implementation via SqlCachedFunctionalHubSupport}} | ||
To mark BioHub as classification hub, its {{Method|ru.biosoft.access.biohub.BioHub.getPriority}} method should return positive priority when <code>"FunctionalClassification"</code> {{Class|ru.biosoft.access.biohub.TargetOptions.CollectionRecord}} is supplied. The easiest way to implement such hub is to subclass {{Class|biouml.plugins.enrichment.SqlCachedFunctionalHubSupport}} abstract class. | To mark BioHub as classification hub, its {{Method|ru.biosoft.access.biohub.BioHub.getPriority}} method should return positive priority when <code>"FunctionalClassification"</code> {{Class|ru.biosoft.access.biohub.TargetOptions.CollectionRecord}} is supplied. The easiest way to implement such hub is to subclass {{Class|biouml.plugins.enrichment.SqlCachedFunctionalHubSupport}} abstract class. | ||
Revision as of 12:37, 3 July 2013
Classification hub is a kind of BioHub which used to classify the genes into several groups. This BioHub type is defined in biouml.plugins.enrichment plugin and used for two analysis methods: 
Functional classification and 
Enrichment analysis. Currently only 
Ensembl genes are accepted for classification via classification hubs. If you have other type of identifiers, consider using 
Convert table analysis.
An example of classification hub is the FunctionalGOHub, which classifies supplied genes via Gene Ontology categories.
Implementation details
| This page or section is a stub. Please add information about implementation via SqlCachedFunctionalHubSupport here! |
To mark BioHub as classification hub, its BioHub.getPriority method should return positive priority when "FunctionalClassification" CollectionRecord is supplied. The easiest way to implement such hub is to subclass SqlCachedFunctionalHubSupport abstract class.
When classification hub is requested to provide the matching, it must provide some additional information including total number of Ensembl genes participating in classification; total number of genes in the individual groups and number of input genes which participate in classifications. Also some additional group annotation fields can be added. These fields will appear in the analysis output table.
When user selects "Repository folder" as the classification hub, then RepositoryHub is used.
