Matching BioHub - Revision history

Lan@dote.ru: Sections level changed

2013-07-03T08:57:23Z

Sections level changed

Lan@dote.ru: Sections level changed

2013-07-03T08:57:07Z

Sections level changed

Lan@dote.ru: Notes on SQL connection, subsections /* Implementation of SQL-based matching hub */

2013-07-03T08:56:42Z

Notes on SQL connection, subsections - ‎Implementation of SQL-based matching hub

Lan@dote.ru: Technical details and implementation via SqlBasedHub added

2013-07-03T05:23:08Z

Technical details and implementation via SqlBasedHub added

Lan@dote.ru: Created page with "{{Stub}} '''Matching BioHub''' is a kind of BioHub which allows you to match a list of identifiers from one reference type to another..."

2013-05-14T04:03:18Z

Created page with "{{Stub}} '''Matching BioHub''' is a kind of BioHub which allows you to match a list of identifiers from one reference type to another..."

New page

{{Stub}}

'''Matching BioHub''' is a kind of [[BioHub]] which allows you to match a list of identifiers from one [[Reference type (extension point)|reference type]] to another (including if necessary cross-species matching). In [[BioUML]] code matching BioHub is a Java class which implements {{Class|ru.biosoft.access.biohub.BioHub}} interface.

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

@@ Line 55: / Line 55: @@
 If this algorithm doesn't satisfy you, you may override this method to create the {{Class|java.sql.Connection}} in a custom way.
-=== See also ===
+== See also ==
 *[[Biohub (host object)]]
 [[Category:Development]]
 [[Category:BioHub]]

@@ Line 1: / Line 1: @@
 '''Matching BioHub''' is a kind of [[BioHub]] which allows you to match a list of identifiers from one [[Reference type (extension point)|reference type]] to another (including if necessary cross-species matching). In [[BioUML]] code matching BioHub is a Java class which implements {{Class|ru.biosoft.access.biohub.BioHub}} interface.
-=== Technical details ===
+== Technical details ==
 There's a '''matching graph''' defined where each node is a combination of [[reference type]] and species and each edge is a matching procedure implemented by matching hub. Usually edges connect nodes of single species, but cross-species hubs are also possible and used in [[File:Data-Convert-table-via-homology-icon.png]] [[Convert table via homology (analysis)|Convert table via homology]] analysis.
@@ Line 13: / Line 13: @@
 Each matching hub can define several matching edges. When you request a matching between given nodes using {{Method|ru.biosoft.access.biohub.BioHubRegistry.getMatchingPath(Properties, Properties)}}, it performs a Dijkstra search within matching graph looking for the path with minimal matching qualities product.
-=== Debugging matching graph ===
+== Debugging matching graph ==
 You may debug matching graph using the [[Biohub (host object)|biohub]] JavaScript host object in [[script viewpart]]. Use <code>getReachableTypes</code> method to retrieve all [[reference type]]s reachable from given node. Use <code>getMatchingPlan</code> method to retrieve list of optimal matching steps between given nodes. The <code>matchDebug</code> method will provide a verbose output for matching procedure of given identifier between given nodes.

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 You may debug matching graph using the [[Biohub (host object)|biohub]] JavaScript host object in [[script viewpart]]. Use <code>getReachableTypes</code> method to retrieve all [[reference type]]s reachable from given node. Use <code>getMatchingPlan</code> method to retrieve list of optimal matching steps between given nodes. The <code>matchDebug</code> method will provide a verbose output for matching procedure of given identifier between given nodes.
-=== Implementation of SQL-based matching hub ===
+== Implementation of SQL-based matching hub ==
-The easiest way to implement your own matching hub is to prepare a special MySQL database and subclass {{Class|ru.biosoft.access.biohub.SQLBasedHub}}. The database schema is the following:
+The easiest way to implement your own matching hub is to prepare a special MySQL database and subclass {{Class|ru.biosoft.access.biohub.SQLBasedHub}}.
   CREATE TABLE `hub` (
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 So two tables called '''hub''' and '''hub_terms''' must present. Of course, you can use the same database for other purposes as well. The '''input_type''', '''output_type''' and '''specie''' fields refer to the terms in '''hub_terms''' table via '''hub_terms.id''' field. The '''input_type''' and '''output_type''' fields must refer to [[reference type]] stable name (usually the reference type class simple name; see {{Method|ru.biosoft.access.biohub.ReferenceTypeSupport.getStableName()}}). The '''specie''' field must refer to the Latin name of the species. The '''input''' and '''output''' fields contains the identifier of the input type and the converted identifier of the output type respectively.
 After creating the database you must subclass the {{Class|ru.biosoft.access.biohub.SQLBasedHub}} class providing the {{Method|ru.biosoft.access.biohub.SQLBasedHub.getMatchings()}} method implementation. This method must return an array of {{Class|ru.biosoft.access.biohub.SQLBasedHub.Matching}} objects which are constructed via the following parameters:
 * '''inputType''': ReferenceType class for the input type.
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 * '''forward''': if false, then matching will be performed in backwards direction, thus input id will be looked in '''hub.output''' field and output id will be returned from '''hub.input''' field.
 * '''quality''': the quality of given matching (between 0 and 1).
 === See also ===