Reference type (extension point)

Identifier

ru.biosoft.access.referenceType

Plugin

ru.biosoft.access

Registry

ReferenceTypeRegistry

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:

• Type can be assigned to user-imported tables;
• Type can be autodetected based on table IDs pattern;
• IDs in the table may be displayed as links to an external database (e.g. Ensembl);
• You can create an analysis method which will restrict input tables to given type;
• You can create matching BioHub to convert identifiers from your type to other types and vice versa via Convert table analysis;
• You can assign this type to your database collections and use this for Annotate table analysis.

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

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.

Notes

• Your reference type class must implement ru.biosoft.access.biohub.ReferenceType interface. It's highly recommended to subclass ru.biosoft.access.biohub.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.