Package org.bridgedb

BridgeDb is a java library intended for dealing with identifiers for biological entities such as genes, proteins, metabolites.

See:
Description

Interface Summary

AttributeMapper	AttributeMapper knows about attributes for Xrefs.
Driver	A Driver knows how to create an IDMapper instance.
IDMapper	Base interface for all id mapping methods.
IDMapperCapabilities	Describes capabilities of an IDMapper.

Class Summary

AbstractIDMapper	Contains default implementation of some IDMapper methods.
AbstractIDMapperCapabilities	Simple implementation of IDMapperCapabilities, which assumes that the supported datasources are the same for target and source, and that the supported data sources and properties are static and known at creation time.
BridgeDb	Central access point for connecting to IDMappers.
DataSource	contains information about a certain DataSource, such as It's full name ("Ensembl") It's system code ("En") It's main url ("http://www.ensembl.org") Id-specific url's ("http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=" + id) The DataSource class uses the extensible enum pattern.
DataSource.Builder	Uses builder pattern to set optional attributes for a DataSource.
DataSourcePatterns	Contains regular expression patterns for identifiers Can be used to guess the BioDataSource of an identifier of unknown origin.
IDMapperStack	combines multiple IDMapper's in a stack.
Xref	Stores an id + DataSource combination, which represents an unique gene product.

Exception Summary

IDMapperException

for all exceptions thrown by IDMapper interface.

Package org.bridgedb Description

BridgeDb is a java library intended for dealing with identifiers for biological entities such as genes, proteins, metabolites.

In BridgeDb, a DataSource defines an online resource such as Ensembl or Entrez.

An Xref is the combination of an identifier and a particular resource, and thus uniquely defines a single biological entity. It is often possible to generate a URL to an online description of this biological entity.

Identifiers are preferably not descriptive. A descriptive name such as INSR (Insulin Receptor) instead of Entrez Gene 3643 can be useful. In BridgeDb we refer to this as a Symbol. Because of the ambiguous nature, Symbols are not the primary means for identifying

Usually, different DataSources describe the same biological entities. Cross references are stored in so called Synonym databases. IDMapper has facilities for mapping cross-references and mapping between different DataSources.