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bioDBnet: Documentation: Network Nodes

Descriptions for all the nodes in bioDBnet

This page lists all the identifiers/nodes in bioDBnet. Every identifier is associated with a name, description, examples and url. In addition if we download and maintain the whole database at the Advanced Biomedcal Computing Center then it's status is mentioned in the main database field, with an yes meaning it is downloaded, parsed and loaded into our relational tables. For each of these main databases additional fields are included to give more details on the coverage of these databases.

( * - not a node in bioDBnet )

Name: Affy ID
Description: Identifier for affymetrix probe set
Main Database: Yes - Affy
   Complete: No - only annotation files for 3'IVT expression analysis arrays. Affy IDs included in the Ensembl and dbSNP database are also included. These do not have any annotations yet.
   Species specific: Yes - human, mouse, rat, dog, cow and monkey
Examples: 1007_s_at, 1053_at, 117_at
URL: http://www.affymetrix.com/
Name: Affy Annotation
Details: Information on the affymetrix array, probe target, alignments
  
Name: Agilent ID
Description: identifier for the Agilent arrays
Main Database: No - information obtained from cross references in Ensembl and H-Inv
Examples: A_14_P111876, A_23_P11531, A_44_P253268
URL: http://www.chem.agilent.com/
  
Name: ApiDB_CryptoDB ID
Description: identifier for the Cryptosporidium Genome Resource, a part of ApiDB which is a portal for accessing genome-scale datasets associated with the protozoan parasites in the phlyum Apicomplexa
Main Database: No - information obtained from cross references in Gene
Examples: cgd1_3140, cgd1_2980, cgd1_3080
URL: http://cryptodb.org/cryptodb/
  
Name: Allergome Code
Description: identifier for Allergome, which contains information on allergenic molecules causing allergic diseases like asthma, rhinitis, urticaria, anaphylaxis
Main Database: No - information obtained from cross references in UniProt
Examples: 3115, 7653, 3149
URL: http://www.allergome.org
  
Name: BIND ID
Description: identifier for BIND, the Biomolecular Interaction Network Database
Main Database: No - information obtained from cross references in H-Inv
Examples: 133599, 130942
URL: http://www.bind.ca
  
Name: Biocarta Pathway Name
Description: name of the pathway in biocarta
Main Database: Yes - Biocarta
   Complete: Yes
   Species specific: Yes - human and mouse
Examples: h_MITRPathway, m_aktPathway
URL: http://www.biocarta.com/
Name: Biocarta Pathway Title
Details: one line description of the biocarta pathway
  
Name: BioCyc ID
Description: identifier for BioCyc, a collection of pathway/genome databases
Main Database: No - information obtained from cross references in UniProt
Examples: HDUC233412:HD_0947-MONOMER, BJAP224911:BSR3237-MONOMER
URL: http://www.biocyc.org
  
Name: CCDS ID
Description: identifier for the Consensus Coding DNA Sequence project, an effort to identify consistently annotated, high quality human and mouse protein coding regions
Main Database: No - information obtained from cross references in H-Inv and Ensembl
Examples: CCDS34794, CCDS4072, CCDS13870
URL: http://www.ncbi.nlm.nih.gov/CCDS/
  
Name: ChEBI ID
Description: identifier for Chemical Entities of Biological Interest (ChEBI) is a dictionary of molecular entities focused on 'small' chemical compounds.
Main Database: No - information obtained from cross references in DrugBank
Examples: 30860. 15699
URL: http://www.ebi.ac.uk/chebi/
  
Name: Chromosomal Location
Description: information on the chromosome and base pair location for an identifier
Main Database: No - information obtained from Ensembl
  
Name: CleanEx ID
Description: identifier for CleanEx, a database that provides access to public gene expression data
Main Database: No - information obtained from cross references in UniProt
Examples: HS_NME3, HS_HLA-C, MM_KRT14, MM_BIRC5
URL: http://www.cleanex.isb-sib.ch
  
Name: CodeLink ID
Description: identifier for the CodeLink arrays from GE Healthcare
Main Database: No - information obtained from cross references in Ensembl
Examples: GE21784, GE1138666, GE882321
URL: http://www4.gelifesciences.com/APTRIX/upp01077.nsf/content/codelink_site
  
Name: COG Term
Description: term names for Clusters of Orthologous Groups of proteins
Main Database: No - information obtained from the mappings in GO
URL: http://www.ncbi.nlm.nih.gov/COG/
  
Name: COSMIC ID
Description: mutation identifier for COSMIC, a Catalogue Of Somatic Mutations In Cancer
Main Database: No - information obtained from cross references in Ensembl
Examples: COSM45944, COSM46103
URL: http://www.sanger.ac.uk/genetics/CGP/cosmic/
  
Name: CYGD ID
Description: identifier for the Comprehensive Yeast Genome Database
Main Database: No - information obtained from cross references in UniProt
Examples: YDL033c, YML124c, YDR518w
URL: http://mips.gsf.de/genre/proj/yeast/
  
Name: DPD DIN
Description: Drug Indentification Number for the Health Canada Drug Proiduct Database
Main Database: No - information obtained from cross references in DrugBank
Examples: 01970631, 00687405
URL: http://www.hc-sc.gc.ca/dhp-mps/prodpharma/databasdon/index-eng.php
  
Name: dbSNP ID
Description: identifier for the Single Nucleotide Polymorphism database
Main Database: Yes - dbSNP
   Complete: No
   Species specific: Yes - human and mouse
Examples: rs4875950, rs749822
URL: www.ncbi.nlm.nih.gov/projects/SNP/
Name: SNP Info
Details: INformation on the alleles, chromosome, organism and refseq accessions for the dbSNP ID
  
Name: dictyBase ID
Description: identifier for DictyBase, a Dictyostelium discoideum genomic database
Main Database: No - information obtained from cross references in UniProt
Examples: DDB0233219, DDB0188621, DDB0206225
URL: http://dictybase.org/
  
Name: DIP ID
Description: identifier for the nodes/proteins in Database of Interacting Proteins
Main Database: No - information obtained from cross references in UniProt
Examples: DIP:3299N, DIP:3398N, DIP:24582N
URL: http://dip.doe-mbi.ucla.edu/
  
Name: DisProt ID
Description: identifier for the Database of Protein Disorder
Main Database: No - information obtained from cross references in UniProt
Examples: DP00348, DP00022, DP00119
URL: http://www.disprot.org/
  
Name: DrugBank Drug *
Description: a resource that combines drug data with comprehensive drug target information
Main Database: Yes - DrugBank
   Complete: Yes
   Species specific: Yes - Human
URL: http://www.drugbank.ca/
Name: DrugBank Drug ID
Details: identifier for DrugBank database Ex: DB00001, BTD00010, APRD00714
Name: DrugBank Drug Name
Details: Generic and brand names of drugs used in DrugBank Ex: Aspirin, Lepirudin, Refludan
Name: DrugBank Drug Info
Details: Information on the drug name, type and category
Name: DrugBank Drug Target ID
Details: Identifier for the drug target Ex: 1102, 54
Name: DrugBank Drug Enzyme ID
Details: Identifier for the enzyme for the drug Ex: 5718, 4118
  
Name: EC Number
Description: the Enzyme Commission number is a numerical classification scheme for enzymes
Main Database: No - information obtained from KEGG, GO, UniProt and H-Inv
Examples: EC 1.6.5.3, EC 1.11.1.6, EC 6.3.4.3
URL: http://www.chem.qmul.ac.uk/iubmb/enzyme/
  
Name: EchoBASE ID
Description: identifier for EchoBASE, an integrated post-genomic database for Escherichia coli
Main Database: No - information obtained from cross references in UniProt
Examples: EB1114, EB2433, EB2470
URL: http://www.york.ac.uk/res/thomas/
  
Name: ECO2DBASE ID
Description: identifier for the Escherichia coli 2-D gel gene-protein database
Main Database: No - information obtained from cross references in UniProt
Examples: D026.3, I065.0, D049.9
URL: http://pcsf.brcf.med.umich.edu/eco2dbase/
  
Name: EcoGene ID
Description: identifier for EcoGene, a database of Escherichia coli sequence and function
Main Database: No - information obtained from cross references in UniProt and Gene
Examples: EG12560, EG11277, EG10817
URL: www.ecogene.org
  
Name: Ensembl*
Description: Identifiers for Ensembl
Main Database: Yes - Ensembl
   Complete: Yes
   Species specific: No
URL: http://www.ensembl.org
Name: Ensembl Gene ID
Details: Ensembl gene identifier Ex: ENSG00000182196, ENSMUSG00000040855
Name: Ensembl Transcript ID
Details: Ensembl transcript identifier Ex: ENST00000262112, ENSMUST00000167991
Name: Ensembl Protein ID
Details: Ensembl protein identifier Ex: ENSP00000356130, ENSMUSP00000003035
Name: Ensembl Biotype
Details: The biotype of a gene or a protein Ex: protein-coding, ncRNA
  
Name: FlyBase*
Description: Identifiers for FlyBase
Main Database: No - information obtained from cross references in UniProt, Ensembl and Gene
URL: www.flybase.org
Name: FlyBase Gene ID
Details: gene identifier for FlyBase, a database of Drosophila genes and genomes Ex: FBgn0083414, FBgn0084466
Name: FlyBase Transcript ID
Details: Transcript identifier for FlyBase Ex: FBtr0089256, FBtr0078166
Name: FlyBase Protein ID
Details: Protein identifier for FlyBase Ex: FBpp0077824, FBpp0088316
  
Name: FunCatDB ID
Description: Identifier for the MIPS Functional Catalogue Database
Main Database: No - information obtained from external mappings in GO
Examples: 01.01.03.01.01, 20.01.01.07.05
URL: http://mips.gsf.de/projects/funcat
  
Name: GenBank Nucleotide Accession
Description: mRNA accession for the Entrez Nucleotide database at NCBI
Main Database: Yes - genbank
   Complete: Yes
   Species specific: No
Examples: AB190745, DQ337540, X06117
URL: http://www.ncbi.nlm.nih.gov/sites/entrez?db=nuccore
Name: GenBank Nucleotide GI
Details: GI number for the nucleotide sequences in GenBank
Name: GenBank Nucleotide Info
Details: Information on the length, organism and definition of the GenBank Nucleotide Accession
  
Name: GenBank Protein Accession
Description: protein accession for the NCBI protein sequence database
Main Database: Yes - Genpept
   Complete: Yes
   Species specific: No
Examples: BAA21795, AF041837, AAC72404
URL: http://www.ncbi.nlm.nih.gov/sites/entrez?db=protein
Name: GenBank Protein GI
Details: GI number for the protein sequences in GenBank
Name: GenBank Protein Info
Details: Information on the length, molecular weight, PI, organism and definition of the GenBank Protein Accession
  
Name: Gene ID
Description: identifier for a gene as assigned by the Entrez gene project
Main Database: Yes - Gene
   Complete: Yes
   Species specific: No
Examples: 3702, 1, 401285
URL: http://www.ncbi.nlm.nih.gov/sites/entrez?db=Gene
Name: Gene Info
Details: detailed information of a particular gene, contains gene id, gene symbol, gene synonyms, locustag, chromosome, cytoband location, description and gene type
Name: Gene Symbol
Details: Current symbolic representation of a gene Ex: repA2, A1BG
Name: Gene Synonyms
Details: Gene symbol aliases
Name: Gene Symbol+Synonyms
Details: Current Gene symbol and its aliases
  
Name: GeneDB_Spombe ID
Description: identifier for GeneDB, a database containing information on all genes and RNA's of Schizosaccharomyces pombe
Main Database: No - information obtained from cross references in UniProt
Examples: SPBC13E7.08c, SPCC320.11c, SPBC3B8.06
URL: http://www.genedb.org/genedb/pombe/
  
Name: GeneFarm ID
Description: identifier for GeneFarm, a database of structural and functional annotation of plant gene and protein families
Main Database: No - information obtained from cross references in UniProt
Examples: 1910, 3510, 4745
URL: http://urgi.versailles.inra.fr/Genefarm/
  
Name: GenomeReviews ID
Description: identifier for Genome Reviews, a comprehensive annotated view of the genomic sequence of organisms with completely deciphered genomes
Main Database: No - information obtained from cross references in UniProt
Examples: SPBC13E7.08c, SPCC320.11c, SPBC3B8.06
URL: http://www.ebi.ac.uk/GenomeReviews/
  
Name: GI Number
Description: a numeric sequence identifer used at NCBI
Main Database: Yes - complete GenBank and RefSeq databases are stored
Examples: 22958901, 186973032
URL: http://www.ncbi.nlm.nih.gov/sites/gquery
  
Name: GO*
Description: identifier for gene ontology, a project which annotates genes and gene products
Main Database: Yes
   Complete: Yes
   Species specific: No
Examples: GO:0016787, GO:0005739, GO:001602
URL: www.geneontology.org
Name: GO Annotation
Details: Information on the definition and type of GO term
Name: GO - Biological Process
Details: GO biological process identifiers
Name: GO - Cellular Component
Details: GO cellular component identifiers
Name: GO - Molecular Function
Details: GO molecular function identifiers
  
Name: GSEA*
Description: Gene Set Enrichment Analysis
Main Database: Yes
   Complete: Yes
   Species specific: Yes - human, mouse, rat, chimpanzee, pig, dog, zebra fish, rhesus
URL: http://www.broad.mit.edu/gsea/
Name: GSEA Group Members
Details: all the members belonging to a group as determined by GSEA Ex: STK3, EGFR
Name: GSEA Standard Name
Details: the standard name for a GSEA cluster Ex: UVC_XPCS_ALL_DN, KERATINOCYTEPATHWAY
  
Name: H-Inv*
Description: Human-invitational Database, an integrated database of human genes and transcripts
Main Database: Yes
   Complete: Yes
   Species specific: Yes - Human
URL: http://www.h-invitational.jp/
Name: H-Inv Info
Details: detailed information on the chromosome loaction for H-Inv identifiers
Name: H-Inv Locus ID
Details: cluster identifier for H-Inv database Ex: HIX0016996, HIX0057233
Name: H-Inv Transcript ID
Details: transcript identifier for H-Inv database Ex: HIT000022181, HIT000000123
Name: H-Inv Protein ID
Details: protein identifier for H-Inv database Ex: HIP000042367, HIP000087930
  
Name: HAMAP ID
Description: identifier for High-quality Automated and Manual Annotation of microbial Proteomes(HAMAP)
Main Database: No - information obtained from cross references in GO and UniProt
Examples: MF_01351, MF_00472, MF_01200
URL: http://ca.expasy.org/sprot/hamap/
  
Name: HGNC ID
Description: identifier for the Human Gene Nomenculature Committee
Main Database: No - information obtained from cross references in UniProt, Ensembl and Gene
Examples: HGNC:7851, HGNC:4933, HGNC:32309
URL: http://www.genenames.org/
  
Name: HMDB Metabolite
Description: Human Metabolome Database, a database about small molecule metabolites found in human body
Main Database: Yes
   Complete: Yes
   Species specific: Yes - Human
Examples: 1-Methylhistidine, Cortexolone
URL: http://www.hmdb.ca/
Name: HMDB Metabolite Desc
Details: detailed description of the metabolite
Name: HMDB Enzyme - Gene Symbol
Details: Gene Symbol of the enzyme for the metabolite
Name: HMDB Enzyme - UniProt Entry Name
Details: UniProt Entry Name of the enzyme for the metabolite
  
Name: HomoloGene ID
Description: identifier for HomoloGene, an automated detection system for homologs among the annotated genes of several eukaryotic genomes
Main Database: Yes - HomoloGene
   Complete: Yes
   Species specific: No
Examples: 4, 6, 7
URL: http://www.ncbi.nlm.nih.gov/sites/entrez?db=homologene
Name: Homolog - Human Gene ID
Details: Gene ID homolog in human
Name: Homolog - Human Ens Gene ID
Details: Ensembl Gene ID homolog in human
Name: Homolog - Human Protein Acc
Details: RefSeq Protein Accession homolog in human
Name: Homolog - Human Ens Protein ID
Details: Ensembl Protein ID homolog in human
Name: Homolog - Mouse Gene ID
Details: Gene ID homolog in mouse
Name: Homolog - Mouse Ens Gene ID
Details: Ensembl Gene ID homolog in mouse
Name: Homolog - Mouse Protein Acc
Details: RefSeq Protein Accession homolog in mouse
Name: Homolog - Mouse Ens Protein ID
Details: Ensembl Protein ID homolog in mouse
Name: Homolog - Rat Gene ID
Details: Gene ID homolog in rat
Name: Homolog - Rat Ens Gene ID
Details: Ensembl Gene ID homolog in rat
Name: Homolog - Rat Protein Acc
Details: RefSeq Protein Accession homolog in rat
Name: Homolog - Rat Ens Protein ID
Details: Ensembl Protein ID homolog in rat
Name: Homolog - All Gene ID
Details: All the gene homologs along with the corresponding Taxon ID's
Name: Homolog - All Ens Gene ID
Details: All the ensembl gene homologs along with the corresponding Taxon ID's
Name: Homolog - All Protein Acc
Details: All the protein homologs along with the corresponding Taxon ID's
Name: Homolog - All Ens Protein ID
Details: All the Ensembl Protein ID homologs along with the corresponding Taxon ID's
  
Name: HPA ID
Description: identifier for the Human Protein Atlas which shows expression and protein localization in human tissues, cancer cells and cell lines with the aid of immunohistochemistry images
Main Database: No - information obtained from cross references in UniProt
Examples: HPA007415, CAB008374, HPA001589
URL: http://www.proteinatlas.org/
  
Name: HPRD ID
Description: identifier for the Human Protein Reference Database
Main Database: Yes - HPRD
   Complete: Yes
   Species specific: Yes - Human
Examples: 06590, 12335, 15886
URL: http://www.hprd.org/
Name: HPRD Protein Interactor
Details: RefSeq Protein Accession of the interacting protein from HPRD
Name: HPRD Protein Complex
Details: RefSeq Protein Accession of the protein forming a complex from HPRD
Name: HPRD Non Protein Interactor
Details: Identifier for the non protein interactor from HPRD
Name: HPRD Protein Feature
Details: Features of the protein along with position in the sequence from HPRD
Name: HPRD Protein Modification
Details: Post translational modifications of the protein from HPRD
  
Name: Illumina ID
Description: Identifier for Illumina microarrays
Main Database: No - information obtained from cross references in Ensembl
Examples: scl020955.1_87-S, ILMN_32172
URL: http://www.illumina.com/
  
Name: IMGT/GENE-DB ID
Description: Database of Immunoglobulin and T-cell receptor genes in IMGT (ImMunoGeneTics Information system)
Main Database: No - information obtained from cross references in Gene and Ensembl
Examples: TRBVA/OR9-2, TRAV4D-4, IGLC3
URL: http://imgt.cines.fr/IMGT_GENE-DB/GENElect?livret=0
  
Name: IntAct ID
Description: identifier for IntAct, a protein interaction database from the European Bioinformatics Institute
Main Database: No - information obtained from cross references in H-Inv
Examples: EBI-754597, EBI-754606
URL: http://www.ebi.ac.uk/intact
  
Name: InterPro ID
Description: identifier for InterPro, a database of protein families, domains and functional sites
Main Database: No - information obtained from cross references in GO, Ensembl, H-Inv, UniProt and Gene
Examples: IPR002891, IPR000318, IPR007110
URL: http://www.ebi.ac.uk/interpro/
  
Name: IPI ID
Description: International Protein Index identifier
Main Database: No - information obtained from cross references in Ensembl
Examples: IPI00000001, IPI00596060, IPI00695306
URL: http://www.ebi.ac.uk/IPI
  
Name: KEGG Pathway ID
Description: Pathwy identifier for Kyoto Encyclopedia of Genes and Genomes (KEGG)
Main Database: Yes - KEGG
   Complete: Yes
   Species specific: No
Examples: hsa00521, mmu00710
URL: http://www.genome.jp/kegg/
Name: KEGG Pathway Title
Details: the title for kegg pathways
Name: KEGG Compound ID
Details: Identifier for kegg compounds Ex: C02170, C00263
Name: KEGG Compound Name
Details: Names of kegg compounds Ex: Acetate, Chondroitin-D-glucuronate, H2S
Name: KEGG Disease ID
Details: Identifier for the disease in KEGG medicus
Name: KEGG Disease Info
Details: Details on the disease from KEGG medicus
Name: KEGG Drug ID
Details: Identifier for the drug in KEGG medicus
Name: KEGG Drug Name
Details: Name of the drug from KEGG medicus
Name: KEGG Drug Info
Details: Details on the drug from KEGG medicus
Name: KEGG Gene ID
Details: identifier for kegg_genes Ex: hsa:27159, mmu:100041337, aae:aq_001
Name: KEGG Reaction ID
Details: identifier for kegg reactions Ex: R00858, R00299
  
Name: LegioList ID
Description: identifier for LegioList, a database for the analysis of Legionella pneumophilia genomes
Main Database: No - information obtained from cross references in UniProt
Examples: lpl1455, lpp2666, lpl2673
URL: http://genolist.pasteur.fr/LegioList/
  
Name: Leproma ID
Description: identifer for Leproma, a database for the analysis of Mycobacterium leprae genome
Main Database: No - information obtained from cross references in UniProt
Examples: ML0608, ML2227, ML0224
URL: http://genolist.pasteur.fr/Leproma/
  
Name: MaizeGDB ID
Description: identifier for MaizeGDB, the Maize Genetics and Genomics Database
Main Database: No - information obtained from cross references in UniProt
Examples: 403201, 131629, 887762
URL: http://www.maizegdb.org/
  
Name: MEROPS ID
Description: identifier for MEROPS, database of peptidases and the proteins that inhibit them
Main Database: No - information obtained from cross references in Ensembl and UniProt
Examples: C19.087, S01.011, A01.003
URL: http://merops.sanger.ac.uk/
  
Name: MetaCyc Reaction
Description: reaction name/identifier for MetaCyc, an encyclopedia of metabolic pathways
Main Database: No - information obtained from external mappings in GO
URL: http://metacyc.org/
  
Name: MGC(ZGC/XGC) ID
Description: identifier for Mammalian Gene Collection, a trans-NIH inititaive providing access to full-length protein-coding cDNA clones. Also includes ZGC (Zebrafish Gene Collection) and XGC (Xenopus Gene Collection)
Main Database: Yes - MGC, ZGC and XGC
   Complete: Yes
   Species specific: Yes - human, mouse, rat, cow, Zebrafish, Xenopus laevis and Xenopus tropicalis
Examples: 140383,179411,127219
URL: http://mgc.nci.nih.gov/
Name: MGC(ZGC/XGC) Image ID
Details: Image ID for the MGC/XGC/ZGC clone
Name: MGC(ZGC/XGC) Info
Details: Information on the Image ID, status, library, GenBank accession, length and GenBank definition
  
Name: MGI ID
Description: identifier for Mouse Genome Informatics
Main Database: No - information obtained from cross references in Ensembl, UniProt and Gene
Examples: MGI:2385297, MGI:1346098, MGI:97309
URL: http://www.informatics.jax.org
  
Name: MIM ID
Description: identifier for the Mendelian Inheritance in Man, a catalog of human genes and genetic disorders
Main Database: Yes - MIM
   Complete: Yes
   Species specific: No
Examples: 603785, 115665, 172430
URL: http://www.ncbi.nlm.nih.gov/sites/entrez?db=OMIM
Name: MIM Info
Details: Title and chromosomal location for the MIM ID
  
Name: MINT ID
Description: identifier for the Molecular INTeraction database
Main Database: No - information obtained from cross references in H-Inv
Examples: MINT-66692, MINT-66913
URL: http://mint.bio.uniroma2.it/mint/
  
Name: miRBase ID
Description: identifier for the miRNA sequences at miRBase
Main Database: No - information obtained from cross references in Ensembl
Examples: MI0000060, MI0000557, MI0007150
URL: http://microrna.sanger.ac.uk/
  
Name: MultiFun ID
Description: identifier to MultiFun, a classification system for cellular/physiological roles of E.coli gene products from GenProtEC
Main Database: No - information obtained from external mappings in GO
Examples: 1.1.1.8, 2.3.2
URL: http://genprotec.mbl.edu/files/MultiFun.html
  
Name: NCIPID*
Description: Pathway Interaction Database from NCI, containing curated information about known biomolecular interactions and key cellular processes assembled into signaling pathways
Main Database: Yes - NCIPID
   Complete: Yes
   Species specific: Yes - Human
URL: http://pid.nci.nih.gov/
Name: NCIPID Pathway
Details: Pathway name from NCIPID
Name: NCIPID Protein Complex Interactor
Details: UniProt Entry Name for the protein forming the complex from NCIPID
Name: NCIPID Protein Interactor
Details: UniProt Entry Name for the interacting protein from NCIPID
Name: NCIPID Protein Modification
Details: Post translational modifications of the protein from NCIPID
  
Name: Orphanet ID
Description: identifier for orphanet, a database of rare diseases and orphan drugs
Main Database: No - information obtained from cross references in UniProt
Examples: 1452, 69712, 88
URL: http://www.orpha.net/consor/cgi-bin/home.php?Lng=GB
  
Name: PANTHER ID
Description: identifier for Protein ANalysis THrough Evolutionary Relationships, a resource that classifies genes by their functions
Main Database: No - information obtained from cross references in UniProt
Examples: PTHR11264, PTHR21060:SF11, PTHR18804
URL: http://www.pantherdb.org/
  
Name: Paralog*
Description: paralogs of the input identifiers
Main Database: No - information obtained from cross references in Ensembl
Name: Paralog Ens Gene ID
Details: Ensembl Gene idenitifer for the paralog of the input identifier
Name: Paralog Ens Protein ID
Details: Ensembl Protein idenitifer for the paralog of the input identifier
  
Name: PBR ID
Description: Identifier for the Poxvirus Bioinformatics Resource center
Main Database: No - information obtained from cross references in Gene
Examples: 42477, 42573
URL: http://www.poxvirus.org/
  
Name: PDB ID
Description: identifier for Protein Data Bank, a repository of protein and nucleic-acid 3-D structures
Main Database: No - information obtained from cross references in Ensembl, UniProt and H-Inv
Examples: 1J5I, 1NCO, 2CBT
URL: http://www.rcsb.org/pdb
  
Name: PeroxiBase ID
Description: identifier for the peroxidase database
Main Database: No - information obtained from cross references in UniProt
Examples: 4426, 4352, 100
URL: http://peroxibase.isb-sib.ch/
  
Name: Pfam ID
Description: identifier for Pfam, a database of protein families
Main Database: No - information obtained from cross references in GO, Ensembl and UniProt
Examples: PF07654, PF00059, PF07974
URL: http://pfam.sanger.ac.uk/
  
Name: PharmGKB ID
Description: identifier for the Pharmacogenetics and Pharmacogenomics Knowledge Base, an integrated resource about how human gentics variation leads to variation in response to drugs
Main Database: No - information obtained from cross references in UniProt
Examples: PA31656, PA35057, PA134899667
URL: http://www.pharmgkb.org/
  
Name: PIR ID
Description: identifier for Protein Information Resource(PIR)
Main Database: No - information obtained from cross references in UniProt
Examples: A59028, S57591, D86338
URL: http://pir.georgetown.edu/
  
Name: PIRSF ID
Description: identifier for PIRSF, a protein family classification system
Main Database: No - information obtained from cross references in UniProt and Ensembl
Examples: PIRSF002276, PIRSF000110, PIRSF000735
URL: http://pir.georgetown.edu/pirsf/
  
Name: PptaseDB ID
Description: Identifier for the Prokaryotic Protein Phosphatase Database
Main Database: No - information obtained from cross references in UniProt
Examples: P3D0409136, P3D040487, P3D0410139
URL: http://vigen.biochem.vt.edu/p3d/p3d.htm
  
Name: PRINTS ID
Description: identifier for PRINTS, a database consisting of protein fingerprints
Main Database: No - information obtained from cross references in GO, Ensembl and UniProt
Examples: PR00662, PR00353, PR00079
URL: http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/
  
Name: ProDom ID
Description: identifier for ProDom, a database of protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases
Main Database: No - information obtained from cross references in GO and UniProt
Examples: PD000050, PD001018, PD001129
URL: http://prodom.prabi.fr
  
Name: PROSITE ID
Description: identifier for prosite, a database of protein domains, families and functional sites
Main Database: No - information obtained from cross references in Ensembl, GO and UniProt
Examples: PS50835, PS01186, PS00615
URL: http://ca.expasy.org/prosite/
  
Name: PseudoCAP ID
Description: identifier for the Psuendomonas Genome Database
Main Database: No - information obtained from cross references in UniProt
Examples: PA4174, PA1977, PA4774
URL: http://www.pseudomonas.com/
  
Name: PubChem ID
Description: identifier for PubChem, database of chemical structures of small organic molecules
Main Database: No - information from KEGG medicus (drug)
Examples: 96026227, 17397569
URL: http://pubchem.ncbi.nlm.nih.gov/
  
Name: PubMed ID
Description: identifier for PubMed, a search engine offering access to the MEDLINE database of citations and abstracts of biomedical research articles
Main Database: No - information obtained from Gene and H-Inv
Examples: 10984505, 8655511
URL: http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed
  
Name: Reactome ID
Description: identifier for Reactome, a curated knowledgebase of biological pathways
Main Database: No - information obtained from cross references in GO and UniProt
Examples: REACT_6840, REACT_1698, REACT_7970
URL: http://www.reactome.org
  
Name: REBASE ID
Description: identifier for the Restriction Enzyme Database
Main Database: No - information obtained from cross references in UniProt
Examples: 13433, 3523, 13642
URL: http://rebase.neb.com/rebase/rebase.html
  
Name: RefSeq Genomic Accession
Description: genomic accession for RefSeq, a collection of comprehensive, integrated, non-redundant set of nucleotide and protein sequences
Main Database: Yes - Refseq Genomic
   Complete: Yes
   Species specific: No
Examples: NW_001094801, NW_908862, NW_001257098
URL: http://www.ncbi.nlm.nih.gov/RefSeq/
Name: RefSeq Genomic GI
Details: GI number for the RefSeq genomic sequences
  
Name: RefSeq *RNA Accession
Description: RNA accession for RefSeq, a collection of comprehensive, integrated, non-redundant set of nucleotide and protein sequences
Main Database: Yes - Refseq Nucleotide
   Complete: Yes
   Species specific: No
URL: http://www.ncbi.nlm.nih.gov/RefSeq/
Name: RefSeq mRNA Accession
Details: mRNA accession for RefSeq Ex: NM_116243, XM_965655, NM_001100597
Name: RefSeq ncRNA Accession
Details: non coding RNA accession for RefSeq Ex: NR_030888, NR_031225
Name: RefSeq Nucleotide GI
Details: GI number for the RefSeq nucleotide sequences
Name: RefSeq mRNA Info
Details: Information on the length, organism and definition of the RefSeq mRNA Accession
  
Name: RefSeq Protein Accession
Description: protein accession for RefSeq, a collection of comprehensive, integrated, non-redundant set of nucleotide and protein sequences
Main Database: Yes - Refseq Protein
   Complete: Yes
   Species specific: No
Examples: NP_355517, YP_001544266, XP_971211
URL: http://www.ncbi.nlm.nih.gov/RefSeq/
Name: RefSeq Protein GI
Details: GI number for the RefSeq protein sequences
Name: RefSeq Protein Info
Details: Information on the length, organism and definition of the RefSeq Protein Accession
  
Name: Rfam ID
Description: identifier for the RNA families database of alignments and covariance models
Main Database: No - information obtained from mappings in GO
Examples: RF00004, RF00257, RF00397
URL: http://www.sanger.ac.uk/Software/Rfam/
  
Name: RGD ID
Description: identifier for the Rat Genome Database
Main Database: No - information obtained from cross references in Ensembl, UniProt and Gene
Examples: 1298474, 1300033
URL: http://rgd.mcw.edu/
  
Name: SCOP ID
Description: identifier for Structural Classification of Proteins
Main Database: No - information obtained from cross references in H-Inv
Examples: a.87.1.1, g.52.1.1, b.36.1.1
URL: http://scop.mrc-lmb.cam.ac.uk/scop/
  
Name: SGD ID
Description: identifier for Saccharomyces Genome Database (SGD)
Main Database: No - information obtained from cross references in Ensembl, UniProt and Gene
Examples: S000000575, S000000533
URL: http://www.yeastgenome.org/
  
Name: SMART ID
Description: identifier for the Simple Modular Architecture Research Tool which allows the identification and annotation of genetically mobile domains and the analysis of domain architectures
Main Database: No - information obtained from cross references in GO and UniProt
Examples: SM00034, SM00407, SM00456
URL: http://smart.embl-heidelberg.de/
  
Name: SP Keywords Accession
Description: accessions for the keywords and categories used in UniProt
Main Database: No - information obtained from mappings in GO
Examples: KW-0008, KW-0458, KW-0862
URL: ftp://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/keywlist.txt
  
Name: SP Subcellular Location Acc
Description: accessions for the controlled vocabulary of subcellular locations used in UniProt
Main Database: No - information obtained from mappings in GO
Examples: SL-0021, SL-0194, SL-0268
URL: ftp://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/subcell.txt
  
Name: TAIR ID
Description: identifier for The Arabidopsis Information Resource
Main Database: No - information obtained from cross references in UniProt and Gene
Examples: AT2G01031, AT2G01440
URL: http://www.arabidopsis.org/
  
Name: Taxon ID
Description: identifier for the NCBI taxonomy database which contains the names of all organisms that are represented in the genetic databases with atleast one nucleotide or protein sequence
Main Database: Yes - Taxon
   Complete: Yes
   Species specific: No
Examples: 9606, 3702, 10090
URL: http://www.ncbi.nlm.nih.gov/Taxonomy/
Name: Organism Scientific Name
Details: the scientific name of an organism Ex: Homo sapiens, Mus musculus, Oryza granulata
  
Name: TCDB ID
Description: the identifier for the Transporter Classification Database
Main Database: No - information obtained from cross references in UniProt
Examples: 3.A.1.201.8, 8.A.17.1.1
URL: http://www.tcdb.org
  
Name: TIGRFAMs ID
Description: the identifier for the TIGR protein families
Main Database: No - information obtained from cross references in Ensembl, GO and UniProt
Examples: TIGR01029, TIGR00403, TIGR00871
URL: http://www.tigr.org/TIGRFAMs/
  
Name: TubercuList ID
Description: identifier for TubercuList, a database for the analysis of tubercle bacilli genomes
Main Database: No - information obtained from cross references in UniProt
Examples: Rv0069c, Rv0089, Rv0382c
URL: http://genolist.pasteur.fr/TubercuList/
  
Name: UCSC ID
Description: UCSC identifier for known genes in human and mouse
Main Database: No - information obtained from cross references in Ensembl
Examples: uc009uyv.2, uc009uyw.1, uc001ach.1
URL: http://genome.cse.ucsc.edu/knownGeneList
  
Name: UM-BBD Enzyme ID
Description: identifier for the enzymes in University of Minnesota's Biocatalysis/Biodegradation Database
Main Database: No - information obtained from mappings in GO
Examples: e0005, e0242, e0350
  
Name: UM-BBD Pathway ID
Description: identifier for the pathways in University of Minnesota's Biocatalysis/Biodegradation Database
Main Database: No - information obtained from mappings in GO
Examples: 2,4-d, benz, pha3
  
Name: UniGene ID
Description: identifier representing a unigene cluster, a set of transcript sequences that appear to come from the same transcription locus
Main Database: Yes - Unigene
   Complete: Yes
   Species specific: No
Examples: Cpo.1, Aae.30, Hs.656020
URL: http://www.ncbi.nlm.nih.gov/sites/entrez?db=UniGene
Name: UniGene Sequence Accession
Details: GenBank/EMBL/DDBJ accession number of the unigene sequence
Name: EST Accession
Details: subset of unigene sequence accessions which are expressed
Name: Tissue (expressed in)
Details: Tissues of origin for ESTs in the unigene cluster
  
Name: UniProt*
Description: Universal Protein Resource, a central repository of protein information from Swiss-Prot, TrEMBL and PIR
Main Database: Yes - Uniprot
   Complete: Yes
   Species specific: No
URL: http://www.pir.uniprot.org/
Name: UniProt Accession
Details: the conserved identifier for uniprot sequences assigned at the time of inclusion (covers both primary and secondary accessions) Ex: P00044, Q61990
Name: UniProt Entry Name
Details: the unique identifier for uniprot, often containing biologically relevant information Ex: SUHW3_MOUSE, CP8B1_HUMAN
Name: UniProt Protein Name
Details: the recommended protein name as defined in UniProt Ex: Alpha-1B-glycoprotein, Acetylglutamate kinase
Name: UniProt Info
Details: Information on the length, molecular weight, PI, organism and definition of the UniProt identifiers
  
Name: UniSTS ID
Description: sequence tagged sites (STSs) database identifier
Main Database: Yes - Unists
   Complete: Yes
   Species specific: No
Examples: 65536, 3, 196608
URL: http://www.ncbi.nlm.nih.gov/sites/entrez?db=unists
Name: UniSTS Info
Details: information on the primers, PCR product size, organism etc. for a UniSTS ID
  
Name: VectorBase*
Description: Identifier for the VectorBase, the NIAID Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens
Main Database: No - information obtained from cross references in Gene
URL: http://www.vectorbase.org/
Name: VectorBase Gene ID
Details: VectorBase gene identifier Ex: AAEL000096, ISCW012994, CPIJ009919
  
Name: VEGA*
Description: identifiers for VEGA, the Vertebrate Genome Annotation Database
Main Database: No - information obtained from cross references in Ensembl
URL: http://vega.sanger.ac.uk/
Name: VEGA Gene ID
Details: VEGA gene identifier Ex: OTTMUSG00000000057, OTTMUSG00000000030
Name: VEGA Transcript ID
Details: VEGA transcript identifier Ex: OTTHUMT00000002842, OTTMUST00000059950
Name: VEGA Protein ID
Details: VEGA transcript identifier Ex: OTTMUSP00000031249, OTTHUMP00000001143
  
Name: WormBase*
Description: identifiers for wormbase, databases on the Caenorhabditis elegans and related nematodes
Main Database: No - information obtained from cross references in Ensembl, Gene and UniProt
URL: http://www.wormbase.org/
Name: WormBase Gene ID
Details: WormBase gene identifier Ex: WBGene00012357, WBGene00011300
Name: WormPep Protein ID
Details: protein identifier for the C elegans protein database Ex: CE35027, CE39182
  
Name: XenBase*
Description: identifier for XenBase, the Xenopus laevis and Xenopus tropicalis biology and genomics resource
Main Database: No - information obtained from cross references in Gene and UniProt
URL: http://www.xenbase.org
Name: XenBase Gene ID
Details: XenBase gene identifier Ex: XB-GENE-487001, XB-GENE-494124
  
Name: ZFIN ID
Description: identifier for ZFIN, the Zebrafish Model Organism Database
Main Database: No - information obtained from cross references in Ensembl, UniProt and Gene
Examples: ZDB-GENE-000210-17, ZDB-GENE-980526-104
URL: http://zfin.org/