Classification hub - Revision history

Lan@dote.ru: Implementation via SqlCachedFunctionalHubSupport

2013-07-03T09:13:10Z

Implementation via SqlCachedFunctionalHubSupport

Lan@dote.ru: +{{Stub}}

2013-07-03T05:37:34Z

+{{Stub}}

Lan@dote.ru: 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..."

2013-07-01T05:43:47Z

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..."

New page

'''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)|biouml.plugins.enrichment]] plugin and used for two analysis methods: [[File:Data-Functional-classification-icon.png]] [[Functional classification (analysis)|Functional classification]] and [[File:Data-Enrichment-analysis-icon.png]] [[Enrichment analysis]]. Currently only [[File:ReferenceType-EnsemblGeneTableType-icon.png]] [[Genes - Ensembl|Ensembl genes]] are accepted for classification via classification hubs. If you have other type of identifiers, consider using [[File:Data-Convert-table-icon.png]] [[Convert table (analysis)|Convert table]] analysis.

An example of classification hub is the {{Class|biouml.plugins.enrichment.FunctionalGOHub}}, which classifies supplied genes via [[Gene Ontology]] categories.

=== Implementation details ===
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.

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 {{Class|biouml.plugins.enrichment.RepositoryHub}} is used.

[[Category:Development]]
[[Category:BioHub]]

← Older revision		Revision as of 05:37, 3 July 2013
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	=== 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.

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 === Implementation details ===
 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.
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 When user selects "Repository folder" as the classification hub, then {{Class|biouml.plugins.enrichment.RepositoryHub}} is used.
 [[Category:Development]]
 [[Category:BioHub]]