Package org.bridgedb
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.
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Interface Summary Interface Description 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.XrefIterator -
Class Summary Class Description 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.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 multipleIDMapper's in a stack.Xref Stores an id +DataSourcecombination, which represents an unique gene product. -
Exception Summary Exception Description IDMapperException for all exceptions thrown by IDMapper interface.