org.bridgedb.bio
Class BioDataSource

java.lang.Object
  org.bridgedb.bio.BioDataSource

public class BioDataSource
extends java.lang.Object

Definition of many common biological DataSources. Meta data about these Data Sources, such as URL templates, are read from a bundled text file. Call the init() method at the start of your program to initialize all meta data.

Field Summary

static DataSource	AFFY
static DataSource	AGILENT
static DataSource	BIOCYC
static DataSource	BIOGRID
static DataSource	CAS
static DataSource	CCDS
static DataSource	CHEBI
static DataSource	CHEMSPIDER
static DataSource	CINT
static DataSource	CODELINK
static DataSource	ECOLI
static DataSource	EMBL
static DataSource	ENSEMBL Deprecated. use one of the organism-specific system codes instead
static DataSource	ENSEMBL_BSUBTILIS
static DataSource	ENSEMBL_CELEGANS
static DataSource	ENSEMBL_CHICKEN
static DataSource	ENSEMBL_CHIMP
static DataSource	ENSEMBL_COW
static DataSource	ENSEMBL_DOG
static DataSource	ENSEMBL_ECOLI
static DataSource	ENSEMBL_FRUITFLY
static DataSource	ENSEMBL_HORSE
static DataSource	ENSEMBL_HUMAN
static DataSource	ENSEMBL_MOSQUITO
static DataSource	ENSEMBL_MOUSE
static DataSource	ENSEMBL_MTUBERCULOSIS
static DataSource	ENSEMBL_RAT
static DataSource	ENSEMBL_SCEREVISIAE
static DataSource	ENSEMBL_XENOPUS
static DataSource	ENSEMBL_ZEBRAFISH
static DataSource	ENTREZ_GENE
static DataSource	ENZYME_CODE
static DataSource	FLYBASE
static DataSource	GENBANK
static DataSource	GENE_ONTOLOGY
static DataSource	GENE_WIKI
static DataSource	GRAMENE_ARABIDOPSIS
static DataSource	GRAMENE_GENES_DB
static DataSource	GRAMENE_LITERATURE
static DataSource	GRAMENE_PATHWAY
static DataSource	GRAMENE_RICE
static DataSource	HMDB
static DataSource	HSGENE
static DataSource	HUGO
static DataSource	ILLUMINA
static DataSource	INTERPRO
static DataSource	IPI
static DataSource	IRGSP_GENE
static DataSource	KEGG_COMPOUND
static DataSource	KEGG_GENES
static DataSource	MAIZE_GDB
static DataSource	MGI
static DataSource	MIRBASE
static DataSource	NASC_GENE
static DataSource	NUGOWIKI
static DataSource	OMIM
static DataSource	ORYZA_BASE
static DataSource	OTHER
static DataSource	PDB
static DataSource	PFAM
static DataSource	PLANTGDB
static DataSource	PUBCHEM
static DataSource	REFSEQ
static DataSource	RFAM
static DataSource	RGD
static DataSource	RICE_ENSEMBL_GENE
static DataSource	SGD
static DataSource	SNP
static DataSource	TAIR
static DataSource	TIGR
static DataSource	UCSC
static DataSource	UNIGENE
static DataSource	UNIPROT
static DataSource	WHEAT_GENE_CATALOG
static DataSource	WHEAT_GENE_NAMES
static DataSource	WHEAT_GENE_REFERENCES
static DataSource	WIKIGENE
static DataSource	WIKIPEDIA
static DataSource	WORMBASE
static DataSource	ZFIN

Constructor Summary

BioDataSource()

Method Summary

static DataSource	getSpeciesSpecificEnsembl(Organism org)
static void	init() Call this to initialize the BioDataSource.XXX constants.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

TAIR

public static final DataSource TAIR

AGILENT

public static final DataSource AGILENT

BIOGRID

public static final DataSource BIOGRID

BIOCYC

public static final DataSource BIOCYC

CINT

public static final DataSource CINT

CCDS

public static final DataSource CCDS

CAS

public static final DataSource CAS

CHEBI

public static final DataSource CHEBI

HMDB

public static final DataSource HMDB

KEGG_COMPOUND

public static final DataSource KEGG_COMPOUND

PUBCHEM

public static final DataSource PUBCHEM

CHEMSPIDER

public static final DataSource CHEMSPIDER

SGD

public static final DataSource SGD

ENZYME_CODE

public static final DataSource ENZYME_CODE

ECOLI

public static final DataSource ECOLI

EMBL

public static final DataSource EMBL

ENSEMBL

public static final DataSource ENSEMBL

Deprecated. use one of the organism-specific system codes instead

ENSEMBL_MOSQUITO

public static final DataSource ENSEMBL_MOSQUITO

GRAMENE_ARABIDOPSIS

public static final DataSource GRAMENE_ARABIDOPSIS

ENSEMBL_BSUBTILIS

public static final DataSource ENSEMBL_BSUBTILIS

ENSEMBL_COW

public static final DataSource ENSEMBL_COW

ENSEMBL_CELEGANS

public static final DataSource ENSEMBL_CELEGANS

ENSEMBL_DOG

public static final DataSource ENSEMBL_DOG

ENSEMBL_FRUITFLY

public static final DataSource ENSEMBL_FRUITFLY

ENSEMBL_ZEBRAFISH

public static final DataSource ENSEMBL_ZEBRAFISH

ENSEMBL_ECOLI

public static final DataSource ENSEMBL_ECOLI

ENSEMBL_CHICKEN

public static final DataSource ENSEMBL_CHICKEN

ENSEMBL_HUMAN

public static final DataSource ENSEMBL_HUMAN

ENSEMBL_MOUSE

public static final DataSource ENSEMBL_MOUSE

ENSEMBL_MTUBERCULOSIS

public static final DataSource ENSEMBL_MTUBERCULOSIS

GRAMENE_RICE

public static final DataSource GRAMENE_RICE

ENSEMBL_CHIMP

public static final DataSource ENSEMBL_CHIMP

ENSEMBL_HORSE

public static final DataSource ENSEMBL_HORSE

ENSEMBL_RAT

public static final DataSource ENSEMBL_RAT

ENSEMBL_SCEREVISIAE

public static final DataSource ENSEMBL_SCEREVISIAE

ENSEMBL_XENOPUS

public static final DataSource ENSEMBL_XENOPUS

FLYBASE

public static final DataSource FLYBASE

GENBANK

public static final DataSource GENBANK

CODELINK

public static final DataSource CODELINK

GRAMENE_GENES_DB

public static final DataSource GRAMENE_GENES_DB

GRAMENE_LITERATURE

public static final DataSource GRAMENE_LITERATURE

GRAMENE_PATHWAY

public static final DataSource GRAMENE_PATHWAY

GENE_WIKI

public static final DataSource GENE_WIKI

HUGO

public static final DataSource HUGO

HSGENE

public static final DataSource HSGENE

INTERPRO

public static final DataSource INTERPRO

ILLUMINA

public static final DataSource ILLUMINA

IPI

public static final DataSource IPI

IRGSP_GENE

public static final DataSource IRGSP_GENE

KEGG_GENES

public static final DataSource KEGG_GENES

ENTREZ_GENE

public static final DataSource ENTREZ_GENE

MGI

public static final DataSource MGI

MIRBASE

public static final DataSource MIRBASE

MAIZE_GDB

public static final DataSource MAIZE_GDB

NASC_GENE

public static final DataSource NASC_GENE

NUGOWIKI

public static final DataSource NUGOWIKI

OTHER

public static final DataSource OTHER

ORYZA_BASE

public static final DataSource ORYZA_BASE

OMIM

public static final DataSource OMIM

RICE_ENSEMBL_GENE

public static final DataSource RICE_ENSEMBL_GENE

PDB

public static final DataSource PDB

PFAM

public static final DataSource PFAM

PLANTGDB

public static final DataSource PLANTGDB

REFSEQ

public static final DataSource REFSEQ

RGD

public static final DataSource RGD

RFAM

public static final DataSource RFAM

UNIPROT

public static final DataSource UNIPROT

SNP

public static final DataSource SNP

GENE_ONTOLOGY

public static final DataSource GENE_ONTOLOGY

TIGR

public static final DataSource TIGR

UNIGENE

public static final DataSource UNIGENE

UCSC

public static final DataSource UCSC

WORMBASE

public static final DataSource WORMBASE

WIKIGENE

public static final DataSource WIKIGENE

WIKIPEDIA

public static final DataSource WIKIPEDIA

WHEAT_GENE_CATALOG

public static final DataSource WHEAT_GENE_CATALOG

WHEAT_GENE_NAMES

public static final DataSource WHEAT_GENE_NAMES

WHEAT_GENE_REFERENCES

public static final DataSource WHEAT_GENE_REFERENCES

AFFY

public static final DataSource AFFY

ZFIN

public static final DataSource ZFIN

Constructor Detail

BioDataSource

public BioDataSource()

Method Detail

getSpeciesSpecificEnsembl

public static DataSource getSpeciesSpecificEnsembl(Organism org)

Parameters:

org - an organism

Returns:

the species-specific Ensembl DataSource corresponding to a given organism, or null if there isn't one known.

init

public static void init()

Call this to initialize the BioDataSource.XXX constants. You should call this before using any of these constants, or they may be undefined.