Difference between revisions of "Reference type (extension point)"

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(Reference types information is moved to separate page.)
 
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{{Extension point|referenceType|ru.biosoft.access|registry=ru.biosoft.access.biohub.ReferenceTypeRegistry}}
 
{{Extension point|referenceType|ru.biosoft.access|registry=ru.biosoft.access.biohub.ReferenceTypeRegistry}}
 
=== Description ===
 
=== Description ===
This extension point allows you to define new type of references which may appear in tables and other places. An example of reference type is Ensembl gene ID (like ENSG00000000003). The following features are available when you define the reference type:
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This extension point allows you to define new [[reference type]] which may appear in tables and other places.
* Type can be assigned to user-imported tables;
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* Type can be autodetected based on table IDs pattern;
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* IDs in the table may be displayed as links to an external database (e.g. Ensembl);
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* You can create an [[method (extension point)|analysis method]] which will restrict input tables to given type;
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* You can create [[matching BioHub]] to convert identifiers from your type to other types and vice versa via [[Convert table (analysis)|Convert table]] analysis;
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* You can assign this type to your database collections and use this for [[Annotate table (analysis)|Annotate table]] analysis.
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=== Configuration Markup ===
 
=== Configuration Markup ===

Latest revision as of 10:36, 15 May 2013

Identifier
ru.biosoft.access.referenceType
Plugin
ru.biosoft.access
Registry
ReferenceTypeRegistry

[edit] Description

This extension point allows you to define new reference type which may appear in tables and other places.

[edit] Configuration Markup

<!ELEMENT type>
<!ATTLIST type
     typeClass     CDATA #REQUIRED
     urlTemplate   CDATA #IMPLIED
>
typeClass
Fully-qualified name of the reference type class.
urlTemplate
Template for the URL to the external database describing elements of this type. Two options are available here:
  • Complete URL where $id$ will be expanded to the identifier: https://www.affymetrix.com/LinkServlet?probeset=$id$
  • Internal BioUML URL pointing to some database like "de:databases/MyDatabase/genes/$id$"
  • MIRIAM DB link like MIR:00000003

[edit] Example

<extension id="EnsemblGeneTableType" point="ru.biosoft.access.referenceType">
   <type typeClass="biouml.plugins.ensembl.tabletype.EnsemblGeneTableType" urlTemplate="MIR:00000003"/>
</extension>

This extension registers type for Ensembl Gene using MIRIAM URL template.

[edit] Notes

  • Your reference type class must implement ReferenceType interface. It's highly recommended to subclass ReferenceTypeSupport abstract class.
  • If URLs for your type has more complex structure and cannot be generated using the urlTemplate parameter, you may omit urlTemplate and override getURL method in your ReferenceType class to generate URLs in custom way.
  • You can specify @ClassIcon annotation for your reference type class pointing to the icon file. This icon will be used to represent the tables of given type.
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