AmiGO 2: Cross References

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Information about Cross References

The data for this page is also available as a YAML file and as a derived plain text file. See the documentation here in the repository for more details.

AgBase

AgBase resource for functional analysis of agricultural plant and animal gene products

Site: http://www.agbase.msstate.edu/
Object: entity
Example ID: P02264
URL syntax: https://agbase.arizona.edu/cgi-bin/getEntry.pl?db_pick=all&database=Swiss-Prot&gb_acc=[example_id]

AGI_LocusCode

Arabidopsis Genome Initiative

Site: http://www.arabidopsis.org
Object: gene
Example ID: AGI_LocusCode:At2g17950
URL syntax: http://arabidopsis.org/servlets/TairObject?type=locus&name=[example_id]
URL example: https://www.arabidopsis.org/servlets/TairObject?type=locus&name=At2g17950

AGRICOLA_ID

AGRICultural OnLine Access

Site: http://agricola.nal.usda.gov/
Object: entity
Example ID: AGRICOLA_NAL:TP248.2 P76 v.14

AGRICOLA_IND

AGRICultural OnLine Access

Site: http://agricola.nal.usda.gov/
Object: entity
Example ID: AGRICOLA_IND:IND23252955

AlphaFold

AlphaFold Protein Structure Database

Site: https://alphafold.ebi.ac.uk/
Object: protein
Example ID: AlphaFold:Q5VSL9
URL syntax: https://alphafold.ebi.ac.uk/entry/[example_id]
URL example: https://alphafold.ebi.ac.uk/entry/Q5VSL9

Alzheimers_University_of_Toronto

Alzheimers Project at University of Toronto

Site: http://www.ims.utoronto.ca/
Object: entity

Animal_CorrDB

CorrDB

Site: https://www.animalgenome.org/CorrDB
Object: Correlation
Example ID: Animal_CorrDB:37232
URL syntax: https://www.animalgenome.org/CorrDB/q/?id=[example_id]
URL example: https://www.animalgenome.org/CorrDB/q/?id=37232

Animal_QTLdb

QTLdb

Site: https://www.animalgenome.org/QTLdb
Object: QTL
Example ID: Animal_QTLdb:23155
URL syntax: https://www.animalgenome.org/QTLdb/q?id=[example_id]
URL example: https://www.animalgenome.org/QTLdb/q?id=23155

APweb

Angiosperm Phylogeny Website

Site: http://www.mobot.org/mobot/research/apweb/
Object: entity
Example ID: APweb:Glossary
URL syntax: http://www.mobot.org/mobot/research/apweb/top/glossarya_h.html
URL example: http://www.mobot.org/mobot/research/apweb/top/glossarya_h.html

ARBA

ARBA machine learning models for automatic annotation of UniProtKB unreviewed entries

Site: https://www.uniprot.org/arba/
Object: entity
Example ID: ARBA:ARBA00000001
URL syntax: https://www.uniprot.org/arba/[example_id]
URL example: https://www.uniprot.org/arba/ARBA00000001

ARUK-UCL

Alzheimers Research Gene Ontology Initiative

Site: https://www.ucl.ac.uk/cardiovascular/research/pre-clinical-and-fundamental-science/functional-gene-annotation/neurological-gene-0
Object: entity

ASAP

A Systematic Annotation Package for Community Analysis of Genomes

Site: https://asap.genetics.wisc.edu/asap/ASAP1.htm
Object: gene
Example ID: ASAP:ABF-0014586
URL syntax: https://asap.genetics.wisc.edu/asap/feature_info.php?FeatureID=[example_id]
URL example: https://asap.genetics.wisc.edu/asap/feature_info.php?FeatureID=ABF-0014586

AspGDID

Aspergillus Genome Database

Site: http://www.aspergillusgenome.org/
Object: gene
Example ID: AspGD:ASPL0000067538
URL syntax: http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=[example_id]
URL example: http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=ASPL0000067538

ASPGD

Aspergillus Genome Database

Site: http://www.aspergillusgenome.org/
Object: gene
Example ID: AspGD:ASPL0000067538
URL syntax: http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=[example_id]
URL example: http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=ASPL0000067538

AspGD_LOCUS

Aspergillus Genome Database

Site: http://www.aspergillusgenome.org/
Object: entity
Example ID: AspGD_LOCUS:AN10942
URL syntax: http://www.aspergillusgenome.org/cgi-bin/locus.pl?locus=[example_id]
URL example: http://www.aspergillusgenome.org/cgi-bin/locus.pl?locus=AN10942

AspGD_REF

Aspergillus Genome Database

Site: http://www.aspergillusgenome.org/
Object: entity
Example ID: AspGD_REF:90
URL syntax: http://www.aspergillusgenome.org/cgi-bin/reference/reference.pl?dbid=[example_id]
URL example: http://www.aspergillusgenome.org/cgi-bin/reference/reference.pl?dbid=90

BFO

Basic Formal Ontology

Site: http://purl.obolibrary.org/obo/bfo
Object: entity
Example ID: BFO:0000066
URL syntax: http://purl.obolibrary.org/obo/BFO_[example_id]
URL example: http://purl.obolibrary.org/obo/BFO_0000066

BHF-UCL

Cardiovascular Gene Ontology Annotation Initiative

Site: https://www.ucl.ac.uk/cardiovascular/research/pre-clinical-and-fundamental-science/functional-gene-annotation/cardiovascular-gene
Object: entity

BioCyc

BioCyc collection of metabolic pathway databases

Site: http://biocyc.org/
Object: entity
Example ID: BioCyc:PWY-5271
URL syntax: http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=[example_id]
URL example: http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-5271

BIOMDID

BioModels Database

Site: https://www.ebi.ac.uk/biomodels/
Object: entity
Example ID: BIOMD:BIOMD0000000045
URL syntax: https://www.ebi.ac.uk/biomodels/[example_id]
URL example: https://www.ebi.ac.uk/biomodels/BIOMD0000000045

BIOMD

BioModels Database

Site: https://www.ebi.ac.uk/biomodels/
Object: entity
Example ID: BIOMD:BIOMD0000000045
URL syntax: https://www.ebi.ac.uk/biomodels/[example_id]
URL example: https://www.ebi.ac.uk/biomodels/BIOMD0000000045

BIORXIV

bioRxiv

Site: https://www.biorxiv.org/
Object: entity
Example ID: bioRxiv:10.1101/530881v2
URL syntax: https://www.biorxiv.org/content/[example_id]
URL example: https://www.biorxiv.org/content/10.1101/530881v2

BRENDA

BRENDA, The Comprehensive Enzyme Information System

Site: http://www.brenda-enzymes.info
Object: catalytic activity
Example ID: BRENDA:4.2.1.3
URL syntax: https://www.brenda-enzymes.info/enzyme.php?ecno=[example_id]
URL example: https://www.brenda-enzymes.info/enzyme.php?ecno=4.2.1.3

BTO

BRENDA tissue / enzyme ontology

Site: http://purl.obolibrary.org/obo/bto
Object: entity
Example ID: BTO_0002164
URL syntax: http://purl.obolibrary.org/obo/BTO_[example_id]
URL example: http://purl.obolibrary.org/obo/BTO_0002164

CACAO

Community Assessment of Community Annotation with Ontologies

Site: http://gowiki.tamu.edu/wiki/index.php/Category:CACAO
Object: entity
Example ID: MYCS2:A0QNF5
URL syntax: https://gowiki.tamu.edu/wiki/index.php/[example_id]
URL example: https://gowiki.tamu.edu/wiki/index.php/MYCS2:A0QNF5

CAFA

Critical Assessment of Protein Function Annotation

Site: http://biofunctionprediction.org/cafa/
Object: entity

CARO

Common Anatomy Reference Ontology

Site: http://purl.obolibrary.org/obo/caro
Object: entity
Example ID: CARO:0020003
URL syntax: http://purl.obolibrary.org/obo/CARO_[example_id]
URL example: http://purl.obolibrary.org/obo/CARO_0020003

CAS

CAS Chemical Registry

Site: http://www.cas.org/expertise/cascontent/registry/index.html
Object: entity
Example ID: CAS:58-08-2

CASGEN

Catalog of Fishes genus database

Site: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp
Object: entity
Example ID: CASGEN:1040
URL syntax: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?genid=[example_id]
URL example: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?genid=1040

CAS_GEN

Catalog of Fishes genus database

Site: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp
Object: entity
Example ID: CASGEN:1040
URL syntax: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?genid=[example_id]
URL example: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?genid=1040

CASREF

Catalog of Fishes publications database

Site: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp
Object: entity
Example ID: CASREF:2031
URL syntax: https://researcharchive.calacademy.org/research/ichthyology/catalog/getref.asp?id=[example_id]
URL example: https://researcharchive.calacademy.org/research/ichthyology/catalog/getref.asp?id=2031

CASSPC

Catalog of Fishes species database

Site: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp
Object: entity
URL syntax: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=[example_id]
URL example: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=1979

CAS_SPC

Catalog of Fishes species database

Site: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp
Object: entity
URL syntax: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=[example_id]
URL example: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=1979

CAZY

Carbohydrate Active EnZYmes

Site: http://www.cazy.org/
Object: entity
Example ID: CAZY:PL11
URL syntax: http://www.cazy.org/[example_id].html
URL example: http://www.cazy.org/PL11.html

CDD

Conserved Domain Database at NCBI

Site: https://www.ncbi.nlm.nih.gov/cdd
Object: entity
Example ID: CDD:34222
URL syntax: http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=[example_id]
URL example: http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=34222

CGDID

Candida Genome Database

Site: http://www.candidagenome.org/
Object: gene
Example ID: CGD:CAL0000179664
URL syntax: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=[example_id]
URL example: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=CAL0000179664

CGD

Candida Genome Database

Site: http://www.candidagenome.org/
Object: gene
Example ID: CGD:CAL0000179664
URL syntax: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=[example_id]
URL example: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=CAL0000179664

CGD_LOCUS

Candida Genome Database

Site: http://www.candidagenome.org/
Object: entity
Example ID: CGD_LOCUS:HWP1
URL syntax: http://www.candidagenome.org/cgi-bin/locus.pl?locus=[example_id]
URL example: http://www.candidagenome.org/cgi-bin/locus.pl?locus=HWP1

CGD_REF

Candida Genome Database

Site: http://www.candidagenome.org/
Object: entity
Example ID: CGD_REF:1490
URL syntax: http://www.candidagenome.org/cgi-bin/reference/reference.pl?dbid=[example_id]
URL example: http://www.candidagenome.org/cgi-bin/reference/reference.pl?dbid=1490

CGSC

Site: http://cgsc.biology.yale.edu/
Object: entity
Example ID: CGSC:rbsK
URL example: http://cgsc.biology.yale.edu/Site.php?ID=315

ChEBI

Chemical Entities of Biological Interest

Site: http://www.ebi.ac.uk/chebi/
Object: chemical entity
Example ID: CHEBI:17234
URL syntax: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:[example_id]
URL example: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17234

CL

Cell Type Ontology

Site: http://cellontology.org
Object: cell
Example ID: CL:0000041
URL syntax: http://purl.obolibrary.org/obo/CL_[example_id]
URL example: http://purl.obolibrary.org/obo/CL_0000041

CO_125

Crop Ontology CGIAR Musa Anatomy

Site: http://www.cropontology.org/ontology/CO_125:0000000/CGIAR_Musa_anatomy
Object: entity
Example ID: CO_125:0000002
URL example: http://www.cropontology.org/ontology/CO_125:0000000

COG

NCBI Clusters of Orthologous Groups

Site: http://www.ncbi.nlm.nih.gov/COG/
Object: entity

COG_Cluster

NCBI COG cluster

Site: http://www.ncbi.nlm.nih.gov/COG/
Object: entity
Example ID: COG_Cluster:COG0001
URL syntax: http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=[example_id]
URL example: http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=COG0001

COG_Function

NCBI COG function

Site: http://www.ncbi.nlm.nih.gov/COG/
Object: entity
Example ID: COG_Function:H
URL syntax: http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun=[example_id]
URL example: http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun=H

COG_Pathway

NCBI COG pathway

Site: http://www.ncbi.nlm.nih.gov/COG/
Object: entity
Example ID: COG_Pathway:14
URL syntax: http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=[example_id]
URL example: http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=14

CollecTF

Database of transcription factor binding sites (TFBS) in the Bacteria domain

Site: http://www.collectf.org/
Object: entity

ComplexPortal

Complex Portal database of macromolecular complexes

Site: https://www.ebi.ac.uk/complexportal
Object: macromolecular complex
Example ID: ComplexPortal:CPX-2158
URL syntax: https://www.ebi.ac.uk/complexportal/complex/[example_id]
URL example: https://www.ebi.ac.uk/complexportal/complex/CPX-2158

CORIELL

Coriell Institute for Medical Research

Site: http://ccr.coriell.org/
Object: entity
Example ID: GM07892
URL syntax: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=[example_id]
URL example: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07892

CORUM

CORUM - the Comprehensive Resource of Mammalian protein complexes

Site: https://mips.helmholtz-muenchen.de/corum/
Object: entity
Example ID: CORUM:837
URL syntax: https://mips.helmholtz-muenchen.de/corum/?id=[example_id]
URL example: https://mips.helmholtz-muenchen.de/corum/?id=837

cribi_vitis

Vitis CRIBI database

Site: http://genomes.cribi.unipd.it
Object: entity
Example ID: VIT_00s0173g00270
URL syntax: http://genomes.cribi.unipd.it/cgi-bin/pqs2/report.pl?gene_name=[example_id]&release=v1
URL example: http://genomes.cribi.unipd.it/cgi-bin/pqs2/report.pl?gene_name=VIT_00s0173g00270&release=v1

dbSNP

NCBI dbSNP

Site: http://www.ncbi.nlm.nih.gov/projects/SNP
Object: entity
Example ID: dbSNP:rs3131969
URL syntax: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=[example_id]
URL example: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=rs3131969

DDANAT

Dictyostelium discoideum anatomy

Site: http://dictybase.org/Dicty_Info/dicty_anatomy_ontology.html
Object: anatomical entity
Example ID: DDANAT:0000068

DDBJ

DNA Databank of Japan

Site: https://www.ddbj.nig.ac.jp
Object: entity
Example ID: DDBJ:AA816246
URL syntax: http://getentry.ddbj.nig.ac.jp/getentry/na/[example_id]
URL example: http://getentry.ddbj.nig.ac.jp/getentry/na/AA816246

DictyBase

dictyBase

Site: http://dictybase.org
Object: gene
Example ID: dictyBase:DDB_G0277859
URL syntax: http://dictybase.org/gene/[example_id]
URL example: http://dictybase.org/gene/DDB_G0277859

DDB

dictyBase

Site: http://dictybase.org
Object: gene
Example ID: dictyBase:DDB_G0277859
URL syntax: http://dictybase.org/gene/[example_id]
URL example: http://dictybase.org/gene/DDB_G0277859

dictyBase_gene_name

dictyBase

Site: http://dictybase.org
Object: entity
Example ID: dictyBase_gene_name:mlcE
URL syntax: http://dictybase.org/gene/[example_id]
URL example: http://dictybase.org/gene/mlcE

dictyBase_REF

dictyBase literature references

Site: http://dictybase.org
Object: entity
Example ID: dictyBase_REF:10157
URL syntax: http://dictybase.org/publication/[example_id]
URL example: http://dictybase.org/publication/10157

DDB_REF

dictyBase literature references

Site: http://dictybase.org
Object: entity
Example ID: dictyBase_REF:10157
URL syntax: http://dictybase.org/publication/[example_id]
URL example: http://dictybase.org/publication/10157

DisProt

Site: https://www.disprot.org
Object: entity
Example ID: DP00086
URL syntax: https://www.disprot.org/[example_id]
URL example: https://www.disprot.org/DP00086

DOI

Digital Object Identifier

Site: http://dx.doi.org/
Object: entity
Example ID: DOI:10.1016/S0963-9969(99)00021-6
URL syntax: http://dx.doi.org/[example_id]
URL example: http://dx.doi.org/10.1016/S0963-9969(99)00021-6

DTU

DTU Health Tech Services

Site: http://www.cbs.dtu.dk/services
Object: entity
Example ID: CBS:TMHMM
URL example: http://www.cbs.dtu.dk/services/TMHMM/

EC

Enzyme Commission

Site: http://enzyme.expasy.org/
Object: catalytic activity
Example ID: EC:1.1.1.1
URL syntax: https://enzyme.expasy.org/EC/[example_id]
URL example: https://enzyme.expasy.org/EC/1.1.1.1

EchoBASE

EchoBASE post-genomic database for Escherichia coli

Site: https://www.york.ac.uk/res/thomas/
Object: gene
Example ID: EchoBASE:EB0231
URL syntax: https://www.york.ac.uk/res/thomas/Gene.cfm?&recordID=[example_id]
URL example: https://www.york.ac.uk/res/thomas/Gene.cfm?&recordID=EB0231

ECO

Evidence Code Ontology

Site: http://www.evidenceontology.org/
Object: entity
Example ID: ECO:0000315
URL syntax: http://www.evidenceontology.org/browse/#ECO_[example_id]
URL example: http://www.evidenceontology.org/browse/#ECO_0000315

EcoCyc

Scientific database for the bacterium Escherichia coli K-12 MG1655

Site: https://ecocyc.org/
Object: biological_process
Example ID: EcoCyc:P2-PWY
URL syntax: https://ecocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=[example_id]
URL example: https://ecocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=P2-PWY

EcoCyc_GENE

Scientific database for the bacterium Escherichia coli K-12 MG1655

Site: https://ecocyc.org/
Object: protein-containing complex
Example ID: EcoCyc:ABC-28-CPLX
URL syntax: https://ecocyc.org/ECOLI/NEW-IMAGE?id=[example_id]
URL example: https://ecocyc.org/ECOLI/NEW-IMAGE?id=ABC-28-CPLX

ECOCYC_REF

Scientific database for the bacterium Escherichia coli K-12 MG1655

Site: https://ecocyc.org/
Object: entity
Example ID: EcoCyc_REF:COLISALII
URL syntax: https://ecocyc.org/ECOLI/reference.html?type=CITATION-FRAME&object=[example_id]
URL example: https://ecocyc.org/ECOLI/reference.html?type=CITATION-FRAME&object=COLISALII

EcoliWiki

EcoliWiki from EcoliHub

Site: http://ecoliwiki.net/
Object: gene

EMAPA

Mouse gross anatomy and development, abstract

Site: http://emouseatlas.org/
Object: anatomical entity
Example ID: EMAPA:16032
URL syntax: http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:[example_id]
URL example: http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:16894

EMBL

EMBL Nucleotide Sequence Database

Site: http://www.ebi.ac.uk/embl/
Object: gene
Example ID: EMBL:AA816246
URL syntax: http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&Submit=Go&id=[example_id]
URL example: http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&Submit=Go&id=AA816246

ENA

European Nucleotide Archive

Site: http://www.ebi.ac.uk/ena/
Object: entity
Example ID: ENA:AA816246
URL syntax: http://www.ebi.ac.uk/ena/data/view/[example_id]
URL example: http://www.ebi.ac.uk/ena/data/view/AA816246

ensembl

Ensembl database of automatically annotated genomic data

Site: http://www.ensembl.org/
Object: transcript
Example ID: ENSEMBL:ENSP00000265949
URL syntax: http://www.ensembl.org/id/[example_id]
URL example: http://www.ensembl.org/id/ENSP00000265949

ENSEMBL_GeneID

Ensembl database of automatically annotated genomic data

Site: http://www.ensembl.org/
Object: gene
Example ID: ENSEMBL_GeneID:ENSG00000126016
URL syntax: http://www.ensembl.org/id/[example_id]
URL example: http://www.ensembl.org/id/ENSG00000126016

ENSEMBL_ProteinID

Ensembl database of automatically annotated genomic data

Site: http://www.ensembl.org/
Object: protein
Example ID: ENSEMBL_ProteinID:ENSP00000361027
URL syntax: http://www.ensembl.org/id/[example_id]
URL example: http://www.ensembl.org/id/ENSP00000361027

ENSEMBL_TranscriptID

Ensembl database of automatically annotated genomic data

Site: http://www.ensembl.org/
Object: transcript
Example ID: ENSEMBL_TranscriptID:ENST00000371959
URL syntax: http://www.ensembl.org/id/[example_id]
URL example: http://www.ensembl.org/id/ENST00000371959

EnsemblFungi

Ensembl Fungi, the Ensembl database for accessing genome-scale data from fungi.

Site: http://fungi.ensembl.org/
Object: gene
Example ID: EnsemblFungi:YOR197W
URL syntax: http://www.ensemblgenomes.org/id/[example_id]
URL example: http://www.ensemblgenomes.org/id/YOR197W

EnsemblMetazoa

Ensembl Metazoa, the Ensembl database for accessing genome-scale data from non-vertebrate metazoa.

Site: http://metazoa.ensembl.org/
Object: gene
Example ID: EnsemblMetazoa:FBgn0052693
URL syntax: http://www.ensemblgenomes.org/id/[example_id]
URL example: http://www.ensemblgenomes.org/id/FBgn0052693

EnsemblPlants/Gramene

Ensembl Plants, the Ensembl database for accessing genome-scale data from plants.

Site: http://plants.ensembl.org/
Object: gene
Example ID: EnsemblPlants:LOC_Os01g22954
URL syntax: http://www.ensemblgenomes.org/id/[example_id]
URL example: http://www.ensemblgenomes.org/id/LOC_Os01g22954

EnsemblPlants

Ensembl Plants, the Ensembl database for accessing genome-scale data from plants.

Site: http://plants.ensembl.org/
Object: gene
Example ID: EnsemblPlants:LOC_Os01g22954
URL syntax: http://www.ensemblgenomes.org/id/[example_id]
URL example: http://www.ensemblgenomes.org/id/LOC_Os01g22954

EnsemblProtists

Ensembl Protists, the Ensembl database for accessing genome-scale data from protists.

Site: http://protists.ensembl.org/
Object: gene
Example ID: EnsemblProtists:PFL2550w
URL syntax: http://www.ensemblgenomes.org/id/[example_id]
URL example: http://www.ensemblgenomes.org/id/PFL2550w

ENZYME

Swiss Institute of Bioinformatics enzyme database

Site: https://enzyme.expasy.org/
Object: entity
Example ID: 1.1.1.1
URL syntax: https://enzyme.expasy.org/EC/[example_id]
URL example: https://enzyme.expasy.org/EC/1.1.1.1

EO_GIT

GitHub Issue Tracker for EO

Site: https://github.com/Planteome/plant-environment-ontology
Object: entity
Example ID: EO_GIT:76
URL syntax: https://github.com/Planteome/plant-environment-ontology/issues/[example_id]
URL example: https://github.com/Planteome/plant-environment-ontology/issues/76

EuPathDB

The Eukaryotic Pathogen Database

Site: http://eupathdb.org
Object: gene
Example ID: EuPathDB:LtaP17.1490
URL syntax: http://eupathdb.org/gene/[example_id]
URL example: http://eupathdb.org/gene/LtaP17.1490

Eurofung

Eurofungbase community annotation

Site: http://www.eurofung.net/option=com_content&task=section&id=3&Itemid=4
Object: entity

FLYBASE

FlyBase

Site: http://flybase.org/
Object: gene
Example ID: FB:FBgn0000024
URL syntax: http://flybase.org/reports/[example_id].html
URL example: http://flybase.org/reports/FBgn0000024.html

FB

FlyBase

Site: http://flybase.org/
Object: gene
Example ID: FB:FBgn0000024
URL syntax: http://flybase.org/reports/[example_id].html
URL example: http://flybase.org/reports/FBgn0000024.html

FBbt

Drosophila gross anatomy

Site: http://flybase.org/
Object: entity
Example ID: FBbt:00005177
URL syntax: http://flybase.org/cgi-bin/fbcvq.html?query=FBbt:[example_id]
URL example: http://flybase.org/cgi-bin/fbcvq.html?query=FBbt:00005177

FMA

Foundational Model of Anatomy

Site: http://sig.biostr.washington.edu/projects/fm/index.html
Object: entity
Example ID: FMA:61905

FYPO

Fission Yeast Phenotype Ontology

Site: http://www.pombase.org/
Object: entity
Example ID: FYPO:0000001

GenBank

Site: http://www.ncbi.nlm.nih.gov/Genbank/
Object: protein
Example ID: GB:AA816246
URL syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=[example_id]
URL example: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=AA816246

GB

GenBank

Site: http://www.ncbi.nlm.nih.gov/Genbank/
Object: protein
Example ID: GB:AA816246
URL syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=[example_id]
URL example: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=AA816246

Gene3D

Domain Architecture Classification

Site: http://gene3d.biochem.ucl.ac.uk/Gene3D/
Object: entity
Example ID: Gene3D:3.30.390.30
URL syntax: http://gene3d.biochem.ucl.ac.uk/search?mode=family&sterm=[example_id]
URL example: http://gene3d.biochem.ucl.ac.uk/search?mode=family&sterm=3.30.390.30

GeneDB

Site: http://www.genedb.org/gene/
Object: gene
Example ID: PF3D7_1467300
URL syntax: http://www.genedb.org/gene/[example_id]
URL example: http://www.genedb.org/gene/PF3D7_1467300

Genesys-pgr

Gene DB, Genesys

Site: https://www.genesys-pgr.org/
Object: entity
Example ID: Genesys-pgr:CM1015-16
URL syntax: https://www.genesys-pgr.org/acn/search?q=[example_id]
URL example: https://www.genesys-pgr.org/acn/search?q=CM1015-16

GEO

NCBI Gene Expression Omnibus

Site: http://www.ncbi.nlm.nih.gov/geo/
Object: entity
Example ID: GEO:GDS2223
URL syntax: http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=[example_id]
URL example: http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS2223

GO

Gene Ontology Database

Site: http://amigo.geneontology.org/
Object: macromolecular complex
Example ID: GO:0044776
URL syntax: http://amigo.geneontology.org/amigo/term/GO:[example_id]
URL example: http://amigo.geneontology.org/amigo/term/GO:0044776

GO_CENTRAL

GO Central

Site: http://www.geneontology.org/GO.refgenome.shtml
Object: entity

GO_Noctua

GO Noctua

Site: https://github.com/geneontology/noctua-models
Object: entity

GO_REF

Gene Ontology Database references

Site: http://current.geneontology.org/metadata/gorefs/index.html
Object: entity
Example ID: 0000001
URL syntax: http://purl.obolibrary.org/obo/go/references/[example_id]
URL example: http://purl.obolibrary.org/obo/go/references/0000001

GOC

Gene Ontology Consortium

Site: http://www.geneontology.org/
Object: entity

GOC-OWL

Gene Ontology Consortium - Logical inferences

Site: http://www.geneontology.org/
Object: entity

gomodel

Gene Ontology Causal Activity Model Database

Site: http://www.geneontology.org/gocam
Object: model
Example ID: gomodel:5ae3b0f600001522
URL syntax: http://www.geneontology.org/gocam/[example_id]
URL example: http://www.geneontology.org/gocam/gomodel:5ae3b0f600001522

GONUTS

Gene Ontology Normal Usage Tracking System (GONUTS)

Site: http://gowiki.tamu.edu
Object: entity
Example ID: GONUTS:MOUSE:CD28
URL syntax: https://gowiki.tamu.edu/wiki/index.php/[example_id]
URL example: https://gowiki.tamu.edu/wiki/index.php/MOUSE:CD28

GOREL

GO Extensions to OBO Relation Ontology Ontology

Site: http://purl.obolibrary.org/obo/ro
Object: entity

GR

Gramene

Site: http://www.gramene.org/
Object: protein
Example ID: GR:sd1
URL syntax: http://www.gramene.org/db/searches/browser?search_type=All&RGN=on&query=[example_id]
URL example: http://www.gramene.org/db/searches/browser?search_type=All&RGN=on&query=sd1

GR_Ensembl

Gramene

Site: http://www.gramene.org/
Object: entity
Example ID: GR_Ensembl:At1g10040
URL syntax: http://gramene.org/?idList=[example_id]
URL example: http://gramene.org/?idList=At1g10040

GR_gene

Gramene

Site: http://www.gramene.org/
Object: entity
Example ID: GR_GENE:GR:0060198
URL syntax: http://www.gramene.org/db/genes/search_gene?acc=[example_id]
URL example: http://www.gramene.org/db/genes/search_gene?acc=GR:0060198

GR_MUT

A Comparative Mapping Resource for Grains

Site: http://www.gramene.org/
Object: entity
Example ID: GR_MUT:GR:0060198
URL syntax: http://www.gramene.org/db/genes/search_gene?acc=[example_id]
URL example: http://www.gramene.org/db/genes/search_gene?acc=GR:0060198

GR_protein

Gramene

Site: http://www.gramene.org/
Object: protein
Example ID: GR_PROTEIN:Q6VSV0
URL syntax: http://www.gramene.org/db/protein/protein_search?acc=[example_id]
URL example: http://www.gramene.org/db/protein/protein_search?acc=Q6VSV0

GR_QTL

Gramene

Site: http://www.gramene.org/
Object: entity
Example ID: GR_QTL:CQU7
URL syntax: http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=[example_id]
URL example: http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=CQU7

GR_REF

Gramene

Site: http://www.gramene.org/
Object: entity
Example ID: GR_REF:659
URL syntax: http://www.gramene.org/db/literature/pub_search?ref_id=[example_id]
URL example: http://www.gramene.org/db/literature/pub_search?ref_id=659

grin

Germplasm Resources Information Network

Site: https://www.ars-grin.gov/
Object: germplasm
Example ID: GRIN:1882640
URL syntax: https://npgsweb.ars-grin.gov/gringlobal/accessiondetail.aspx?id=[example_id]
URL example: https://npgsweb.ars-grin.gov/gringlobal/accessiondetail.aspx?id=1882640

GRINDesc

Germplasm Resources Information Network

Site: https://www.ars-grin.gov/
Object: germplasm descriptors
Example ID: GRINdesc:89033
URL syntax: https://npgsweb.ars-grin.gov/gringlobal/descriptordetail.aspx?id=[example_id]
URL example: https://npgsweb.ars-grin.gov/gringlobal/descriptordetail.aspx?id=89033

H-invDB

H-invitational Database

Site: http://www.h-invitational.jp/
Object: entity

H-invDB_cDNA

H-invitational Database

Site: http://www.h-invitational.jp/
Object: entity
Example ID: H-invDB_cDNA:AK093148
URL syntax: http://www.h-invitational.jp/hinv/spsoup/transcript_view?acc_id=[example_id]
URL example: http://www.h-invitational.jp/hinv/spsoup/transcript_view?acc_id=AK093149

H-invDB_locus

H-invitational Database

Site: http://www.h-invitational.jp/
Object: entity
Example ID: H-invDB_locus:HIX0014446
URL syntax: http://www.h-invitational.jp/hinv/spsoup/locus_view?hix_id=[example_id]
URL example: http://www.h-invitational.jp/hinv/spsoup/locus_view?hix_id=HIX0014446

HAMAP

High-quality Automated and Manual Annotation of microbial Proteomes

Site: http://hamap.expasy.org/
Object: entity
Example ID: HAMAP:MF_00031
URL syntax: http://hamap.expasy.org/unirule/[example_id]
URL example: http://hamap.expasy.org/unirule/MF_00131

HGNC

HUGO Gene Nomenclature Committee

Site: http://www.genenames.org/
Object: gene
Example ID: HGNC:29
URL syntax: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:[example_id]
URL example: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:29

HGNC-UCL

UCL-based HGNC

Site: https://www.ucl.ac.uk/cardiovascular/hgnc-gene-annotation
Object: entity

HPA

Human Protein Atlas tissue profile information

Site: http://www.proteinatlas.org/
Object: entity
Example ID: HPA:HPA000237
URL syntax: http://www.proteinatlas.org/tissue_profile.php?antibody_id=[example_id]
URL example: http://www.proteinatlas.org/tissue_profile.php?antibody_id=HPA000237

HPA_antibody

Human Protein Atlas antibody information

Site: http://www.proteinatlas.org/
Object: entity
Example ID: HPA_antibody:HPA000237
URL syntax: http://www.proteinatlas.org/antibody_info.php?antibody_id=[example_id]
URL example: http://www.proteinatlas.org/antibody_info.php?antibody_id=HPA000237

HUGO

Human Genome Organisation

Site: http://www.hugo-international.org/
Object: entity

iBB

iBeetleBase

Site: https://ibeetle-base.uni-goettingen.de/
Object: entity
Example ID: TC006055
URL syntax: https://ibeetle-base.uni-goettingen.de/details|[example_id]
URL example: https://ibeetle-base.uni-goettingen.de/details/TC006055

IMG

Integrated Microbial Genomes; JGI web site for genome annotation

Site: http://img.jgi.doe.gov
Object: entity
Example ID: IMG:640008772
URL syntax: http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=[example_id]
URL example: http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=640008772

IMGT_HLA

IMGT/HLA human major histocompatibility complex sequence database

Site: http://www.ebi.ac.uk/imgt/hla
Object: entity
Example ID: IMGT_HLA:HLA00031

IMGT_LIGM

ImMunoGeneTics database covering immunoglobulins and T-cell receptors

Site: http://www.imgt.org/
Object: entity
Example ID: IMGT_LIGM:U03895

IntAct

IntAct protein interaction database

Site: https://www.ebi.ac.uk/intact/
Object: protein-containing complex
Example ID: IntAct:EBI-10205244
URL syntax: http://www.ebi.ac.uk/complexportal/complex/[example_id]
URL example: http://www.ebi.ac.uk/complexportal/complex/EBI-10205244

IPR

InterPro database of protein domains and motifs

Site: http://www.ebi.ac.uk/interpro/
Object: polypeptide region
Example ID: InterPro:IPR000001
URL syntax: http://www.ebi.ac.uk/interpro/entry/[example_id]
URL example: http://www.ebi.ac.uk/interpro/entry/IPR015421

INTERPRO

InterPro database of protein domains and motifs

Site: http://www.ebi.ac.uk/interpro/
Object: polypeptide region
Example ID: InterPro:IPR000001
URL syntax: http://www.ebi.ac.uk/interpro/entry/[example_id]
URL example: http://www.ebi.ac.uk/interpro/entry/IPR015421

iPTMnet

iPTMnet protein post-translational modification database

Site: https://research.bioinformatics.udel.edu/iptmnet/
Object: entity
Example ID: iPTM:P06493
URL syntax: https://research.bioinformatics.udel.edu/iptmnet/entry/[example_id]/
URL example: https://research.bioinformatics.udel.edu/iptmnet/entry/P06493/

IRGC

International Rice Genebank Collection

Site: https://www.genesys-pgr.org
Object: entity
Example ID: IRGC:10012
URL syntax: https://www.genesys-pgr.org/acn/search?q=IRGC+[example_id]
URL example: https://www.genesys-pgr.org/acn/search?q=IRGC+10013

IRIC

International Rice Research Institute

Site: https://oryzasnp.org
Object: entity
Example ID: IRIS_313-8922
URL syntax: https://oryzasnp.org/_variety.zul?irisid=[example_id]
URL example: https://oryzasnp.org/_variety.zul?irisid=IRIS_313-8922

ISBN

International Standard Book Number

Site: https://www.worldcat.org
Object: entity
Example ID: ISBN:0781702534
URL syntax: https://www.worldcat.org/search?q=bn%3A[example_id]
URL example: https://www.worldcat.org/search?q=bn%3A0781702534

ISSN

International Standard Serial Number

Site: http://www.issn.org/
Object: entity
Example ID: ISSN:1234-1231

IUPHAR/BPS

IUPHAR/BPS Guide to Pharmacology

Site: https://www.guidetopharmacology.org/
Object: entity

IUPHAR_GPCR

International Union of Pharmacology

Site: http://www.iuphar.org/
Object: entity
Example ID: IUPHAR_GPCR:13
URL syntax: https://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=[example_id]
URL example: https://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=13

IUPHAR_RECEPTOR

International Union of Pharmacology

Site: http://www.iuphar.org/
Object: entity
Example ID: IUPHAR_RECEPTOR:56
URL syntax: https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=[example_id]
URL example: https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=56

Jaiswal_Lab

Site: http://wiki.plantontology.org/index.php/PO_REF:00008
Object: entity
Example ID: Jaiswal_Lab:gene00002
URL syntax: http://wiki.plantontology.org/index.php/PO_REF:00008
URL example: http://wiki.plantontology.org/index.php/PO_REF:00008

JaponicusDB

Site: https://www.japonicusdb.org/
Object: gene
Example ID: JaponicusDB:SJAG_01143
URL syntax: https://www.japonicusdb.org/gene/[example_id]
URL example: https://www.japonicusdb.org/gene/SJAG_01143

JSTOR

Digital archive of scholarly articles

Site: https://www.jstor.org/
Object: entity
Example ID: JSTOR:3093870
URL syntax: https://www.jstor.org/stable/[example_id]
URL example: https://www.jstor.org/stable/3093870

KEGG

Kyoto Encyclopedia of Genes and Genomes

Site: http://www.genome.ad.jp/kegg/
Object: entity

KEGG_ENZYME

KEGG Enzyme Database

Site: http://www.genome.jp/dbget-bin/www_bfind?enzyme
Object: entity
Example ID: KEGG_ENZYME:2.1.1.4
URL syntax: http://www.genome.jp/dbget-bin/www_bget?ec:[example_id]
URL example: http://www.genome.jp/dbget-bin/www_bget?ec:2.1.1.4

KEGG_LIGAND

KEGG LIGAND Database

Site: http://www.genome.ad.jp/kegg/docs/upd_ligand.html
Object: chemical entity
Example ID: KEGG_LIGAND:C00577
URL syntax: http://www.genome.jp/dbget-bin/www_bget?cpd:[example_id]
URL example: http://www.genome.jp/dbget-bin/www_bget?cpd:C00577

KEGG_PATHWAY

KEGG Pathways Database

Site: http://www.genome.jp/kegg/pathway.html
Object: entity
Example ID: KEGG_PATHWAY:ot00020
URL syntax: http://www.genome.jp/dbget-bin/www_bget?path:[example_id]
URL example: http://www.genome.jp/dbget-bin/www_bget?path:ot00020

KEGG_REACTION

KEGG Reaction Database

Site: http://www.genome.jp/kegg/reaction/
Object: entity
Example ID: KEGG:R02328
URL syntax: http://www.genome.jp/dbget-bin/www_bget?rn:[example_id]
URL example: http://www.genome.jp/dbget-bin/www_bget?rn:R02328

LIFEdb

LifeDB

Site: http://www.lifedb.de/
Object: entity
Example ID: LIFEdb:DKFZp564O1716
URL syntax: https://www.dkfz.de/en/mga/Groups/LIFEdb-Database.html?ID=[example_id]
URL example: https://www.dkfz.de/en/mga/Groups/LIFEdb-Database.html?ID=DKFZp564O1716

MA

Adult Mouse Anatomical Dictionary

Site: http://www.informatics.jax.org/
Object: entity
Example ID: MA:0000003
URL syntax: http://www.informatics.jax.org/searches/AMA.cgi?id=MA:[example_id]
URL example: http://www.informatics.jax.org/searches/AMA.cgi?id=MA:0000003

MACSC_REF

Maize Genetics and Genomics Database

Site: http://www.maizegdb.org/
Object: entity
Example ID: MACSC_REF:78112
URL syntax: http://www.maizegdb.org/cgi-bin/displaytraitrecord.cgi?id=[example_id]
URL example: http://www.maizegdb.org/cgi-bin/displaytraitrecord.cgi?id=78112

MaizeGDB

Site: https://www.maizegdb.org/
Object: entity
Example ID: MaizeGDB:12098
URL syntax: https://maizegdb.org/gene_center/gene/[example_id]
URL example: https://maizegdb.org/gene_center/gene/12098

MaizeGDB_Locus

MaizeGDB

Site: https://www.maizegdb.org/
Object: gene
Example ID: MaizeGDB_Locus:25011
URL syntax: https://www.maizegdb.org/gene_center/gene/[example_id]
URL example: https://www.maizegdb.org/gene_center/gene/25011

MaizeGDB_QTL

Maize Genetics and Genomics Database

Site: https://www.maizegdb.org/
Object: entity
Example ID: MaizeGDB_QTL:78112
URL syntax: https://www.maizegdb.org/data_center/trait?id=[example_id]
URL example: https://www.maizegdb.org/data_center/trait?id=78112

MaizeGDB_REF

Maize Genetics and Genomics Database

Site: https://www.maizegdb.org/
Object: entity
Example ID: MaizeGDB_REF:9021423
URL syntax: http://maizegdb.org/data_center/reference?id=[example_id]
URL example: http://maizegdb.org/data_center/reference?id=9021423

MaizeGDB_stock

Maize Genetics and Genomics Database

Site: https://www.maizegdb.org/
Object: entity
Example ID: MaizeGDB_stock:282110
URL syntax: https://maizegdb.org/data_center/stock?id=[example_id]
URL example: https://maizegdb.org/data_center/stock?id=282110

MEDLINE

Medline literature database

Site: http://www.nlm.nih.gov/databases/databases_medline.html
Object: entity
Example ID: MEDLINE:20572430

MEROPS

MEROPS peptidase database

Site: https://www.ebi.ac.uk/merops/
Object: protein
Example ID: MEROPS:A08.001
URL syntax: https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=[example_id]
URL example: https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=A08.001

MEROPS_fam

MEROPS peptidase database

Site: https://www.ebi.ac.uk/merops
Object: protein family
Example ID: MEROPS_fam:M18
URL syntax: https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=[example_id]
URL example: https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=M18

MESH

Medical Subject Headings

Site: https://meshb.nlm.nih.gov
Object: entity
Example ID: MeSH:D017209
URL syntax: http://id.nlm.nih.gov/mesh/[example_id]
URL example: http://id.nlm.nih.gov/mesh/D017209

MSH

Medical Subject Headings

Site: https://meshb.nlm.nih.gov
Object: entity
Example ID: MeSH:D017209
URL syntax: http://id.nlm.nih.gov/mesh/[example_id]
URL example: http://id.nlm.nih.gov/mesh/D017209

METACYC

Metabolic Encyclopedia of metabolic and other pathways

Site: https://metacyc.org/
Object: entity
Example ID: MetaCyc:GLUTDEG-PWY
URL syntax: https://biocyc.org/META/NEW-IMAGE?type=NIL&object=[example_id]
URL example: https://biocyc.org/META/NEW-IMAGE?type=NIL&object=GLUTDEG-PWY

MGCSC_GENETIC_STOCKS

Maize Genetics and Genomics Database

Site: http://www.maizegdb.org
Object: entity
Example ID: MGCSC_GENETIC_STOCKS:78112
URL syntax: http://www.maizegdb.org/cgi-bin/displaystockrecord.cgi?id=[example_id]
URL example: http://www.maizegdb.org/cgi-bin/displaytraitrecord.cgi?id=78112

MGD

Mouse Genome Database

Site: http://www.informatics.jax.org/
Object: entity
Example ID: MGD:Adcy9

MGI

Mouse Genome Informatics

Site: http://www.informatics.jax.org/
Object: variation
Example ID: MGI:MGI:3590672
URL syntax: http://www.informatics.jax.org/accession/[example_id]
URL example: http://www.informatics.jax.org/accession/MGI:3590672

MIPS_funcat

MIPS Functional Catalogue

Site: http://mips.gsf.de/proj/funcatDB/
Object: entity
Example ID: MIPS_funcat:11.02
URL syntax: http://mips.gsf.de/cgi-bin/proj/funcatDB/search_advanced.pl?action=2&wert=[example_id]
URL example: http://mips.gsf.de/cgi-bin/proj/funcatDB/search_advanced.pl?action=2&wert=11.02

MITRE

The MITRE Corporation

Site: http://www.mitre.org/
Object: entity

ModBase

ModBase comprehensive Database of Comparative Protein Structure Models

Site: http://modbase.compbio.ucsf.edu/
Object: entity
Example ID: ModBase:P10815
URL syntax: http://salilab.org/modbase/searchbyid?databaseID=[example_id]
URL example: http://salilab.org/modbase/searchbyid?databaseID=P04848

NASC_code

Nottingham Arabidopsis Stock Centre Seeds Database

Site: http://arabidopsis.info
Object: entity
Example ID: NASC_code:N3371
URL syntax: http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code=[example_id]
URL example: http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code=N3371

NASC

Nottingham Arabidopsis Stock Centre Seeds Database

Site: http://arabidopsis.info
Object: entity
Example ID: NASC_code:N3371
URL syntax: http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code=[example_id]
URL example: http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code=N3371

NC-IUBMB

Nomenclature Committee of the International Union of Biochemistry and Molecular Biology

Site: http://www.chem.qmw.ac.uk/iubmb/
Object: entity

NCBI

National Center for Biotechnology Information

Site: http://www.ncbi.nlm.nih.gov/
Object: entity

NCBI_gi

NCBI databases

Site: http://www.ncbi.nlm.nih.gov/
Object: gene
Example ID: NCBI_gi:113194944
URL syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=[example_id]
URL example: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=113194944

NCBI_GP

NCBI GenPept

Site: http://www.ncbi.nlm.nih.gov/
Object: protein
Example ID: NCBI_GP:EAL72968
URL syntax: https://www.ncbi.nlm.nih.gov/protein/[example_id]
URL example: https://www.ncbi.nlm.nih.gov/protein/EAL72968

NCBI_locus_tag

NCBI locus tag

Site: http://www.ncbi.nlm.nih.gov/
Object: entity
Example ID: NCBI_locus_tag:CTN_0547

LocusID

NCBI Gene

Site: http://www.ncbi.nlm.nih.gov/
Object: gene
Example ID: NCBI_Gene:4771
URL syntax: https://www.ncbi.nlm.nih.gov/gene/[example_id]
URL example: https://www.ncbi.nlm.nih.gov/gene/4771

NCBI_Gene

NCBI Gene

Site: http://www.ncbi.nlm.nih.gov/
Object: gene
Example ID: NCBI_Gene:4771
URL syntax: https://www.ncbi.nlm.nih.gov/gene/[example_id]
URL example: https://www.ncbi.nlm.nih.gov/gene/4771

GeneID

NCBI Gene

Site: http://www.ncbi.nlm.nih.gov/
Object: gene
Example ID: NCBI_Gene:4771
URL syntax: https://www.ncbi.nlm.nih.gov/gene/[example_id]
URL example: https://www.ncbi.nlm.nih.gov/gene/4771

NCBIGene

NCBI Gene

Site: http://www.ncbi.nlm.nih.gov/
Object: gene
Example ID: NCBI_Gene:4771
URL syntax: https://www.ncbi.nlm.nih.gov/gene/[example_id]
URL example: https://www.ncbi.nlm.nih.gov/gene/4771

NIF_Subcellular

Neuroscience Information Framework standard ontology, subcellular hierarchy

Site: http://www.neurolex.org/wiki
Object: entity
Example ID: NIF_Subcellular:sao1186862860
URL syntax: http://www.neurolex.org/wiki/[example_id]
URL example: http://www.neurolex.org/wiki/sao1770195789

NTNU_SB

Norwegian University of Science and Technology, Systems Biology team

Site: http://www.ntnu.edu/nt/systemsbiology
Object: entity

OBI

Ontology for Biomedical Investigations

Site: http://obi-ontology.org/
Object: entity
Example ID: OBI:0000038
URL example: http://purl.obolibrary.org/obo/OBI_0000038

OBO_SF2_PECO

Source Forge OBO plant-experimental-conditions-ontology (PECO) term request tracker

Site: https://sourceforge.net/p/obo/plant-environment-ontology-eo/
Object: entity
Example ID: OBO_SF2_PECO:89
URL syntax: https://sourceforge.net/p/obo/plant-environment-ontology-eo/[example_id]
URL example: https://sourceforge.net/p/obo/plant-environment-ontology-eo/89/

OBO_SF2_PO

Source Forge OBO Plant Ontology (PO) term request tracker

Site: https://sourceforge.net/p/obo/plant-ontology-po-term-requests/
Object: entity
Example ID: OBO_SF2_PO:500
URL syntax: http://sourceforge.net/p/obo/plant-ontology-po-term-requests/[example_id]
URL example: http://sourceforge.net/p/obo/plant-ontology-po-term-requests/500

OBO_SF_PO

Source Forge OBO Plant Ontology (PO) term request tracker

Site: http://sourceforge.net/tracker/?func=browse&group_id=76834&atid=835555
Object: entity
Example ID: OBO_SF_PO:3184921
URL syntax: https://sourceforge.net/tracker/index.php?func=detail&aid=[example_id]&group_id=76834&atid=835555
URL example: https://sourceforge.net/tracker/index.php?func=detail&aid=3184921&group_id=76834&atid=835555

OMIM

Mendelian Inheritance in Man

Site: https://omim.org/
Object: entity
Example ID: OMIM:190198
URL syntax: https://omim.org/entry/[example_id]
URL example: https://omim.org/entry/190198

MIM

Mendelian Inheritance in Man

Site: https://omim.org/
Object: entity
Example ID: OMIM:190198
URL syntax: https://omim.org/entry/[example_id]
URL example: https://omim.org/entry/190198

OMSSA

Open Mass Spectrometry Search Algorithm

Site: http://pubchem.ncbi.nlm.nih.gov/omssa/
Object: entity

orcid

Open Researcher and Contributor

Site: https://orcid.org/
Object: entity
Example ID: orcid:0000-0003-4423-4370
URL syntax: https://orcid.org/[example_id]
URL example: https://orcid.org/0000-0003-4423-4370

PANTHER

Protein ANalysis THrough Evolutionary Relationships Classification System

Site: http://www.pantherdb.org/
Object: protein family
Example ID: PANTHER:PTHR11455
URL syntax: http://www.pantherdb.org/panther/lookupId.jsp?id=[example_id]
URL example: http://www.pantherdb.org/panther/lookupId.jsp?id=PTHR10000

ParkinsonsUK-UCL

Parkinsons Disease Gene Ontology Initiative

Site: https://www.ucl.ac.uk/cardiovascular/research/pre-clinical-and-fundamental-science/functional-gene-annotation/neurological-gene
Object: entity

PATO

Phenotypic quality ontology

Site: http://www.obofoundry.org/ontology/pato.html
Object: entity
Example ID: PATO:0001420
URL example: http://purl.obolibrary.org/obo/PATO_0001420

PATRIC

PathoSystems Resource Integration Center

Site: https://www.patricbrc.org
Object: entity
Example ID: PATRIC:fig%7C83332.12.peg.11
URL syntax: https://www.patricbrc.org/view/Feature/[example_id]
URL example: https://www.patricbrc.org/view/Feature/fig%7C83332.12.peg.1

PDB

Protein Data Bank

Site: https://www.rcsb.org/pdb/
Object: protein
Example ID: PDB:1A4U
URL syntax: https://www.rcsb.org/structure/[example_id]
URL example: https://www.rcsb.org/structure/1A4U

PECO_GIT

GitHub Issue Tracker for PECO

Site: https://github.com/Planteome/plant-experimental-conditions-ontology
Object: entity
Example ID: PECO_GIT:76
URL syntax: https://github.com/Planteome/plant-environment-ontology/issues/[example_id]
URL example: https://github.com/Planteome/plant-experimental-conditions-ontology/issues/76

Pfam

Pfam database of protein families

Site: https://www.ebi.ac.uk/interpro/entry/pfam
Object: polypeptide region
Example ID: Pfam:PF00046
URL syntax: https://www.ebi.ac.uk/interpro/entry/pfam/[example_id]
URL example: https://www.ebi.ac.uk/interpro/entry/pfam/PF00069

PharmGKB

Pharmacogenetics and Pharmacogenomics Knowledge Base

Site: https://www.pharmgkb.org
Object: entity
Example ID: PharmGKB:PA267
URL syntax: https://www.pharmgkb.org/do/serve?objId=[example_id]
URL example: https://www.pharmgkb.org/do/serve?objId=PA267

PhenoScape

PhenoScape Knowledgebase

Site: http://phenoscape.org/
Object: entity

PHI-base

Pathogen-Host Interactions Database

Site: http://www.phi-base.org/
Object: entity
Example ID: PHI:3
URL syntax: http://www.phi-base.org/searchFacet.htm?queryTerm=PHI:[example_id]
URL example: http://www.phi-base.org/searchFacet.htm?queryTerm=PHI:3

PIR

Protein Information Resource

Site: https://proteininformationresource.org/
Object: protein
Example ID: PIR:I49499
URL syntax: https://proteininformationresource.org/cgi-bin/nbrfget?uid=[example_id]
URL example: https://proteininformationresource.org/cgi-bin/nbrfget?uid=I49499

PIRSF

PIR Superfamily Classification System

Site: http://pir.georgetown.edu/pirsf/
Object: entity
Example ID: PIRSF:SF002327
URL syntax: http://pir.georgetown.edu/cgi-bin/ipcSF?id=[example_id]
URL example: http://pir.georgetown.edu/cgi-bin/ipcSF?id=SF002327

PlantSystematics_image_archive

PlantSystematics.org

Site: http://plantsystematics.org
Object: entity
Example ID: PlantSystematics_image_archivee:37658
URL syntax: http://www.plantsystematics.org/imagebyid_[example_id].html
URL example: http://www.plantsystematics.org/imagebyid_37658.html

PlasmoDB

Site: https://plasmodb.org
Object: gene
Example ID: PF3D7_1467300
URL syntax: https://plasmodb.org/plasmo/app/record/gene/[example_id]
URL example: https://plasmodb.org/plasmo/app/record/gene/PF3D7_1467300

PMC

Pubmed Central

Site: https://www.ncbi.nlm.nih.gov/pmc/
Object: entity
Example ID: PMCID:PMC201377
URL syntax: https://www.ncbi.nlm.nih.gov/pmc/articles/[example_id]
URL example: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC201377/

PMCID

Pubmed Central

Site: https://www.ncbi.nlm.nih.gov/pmc/
Object: entity
Example ID: PMCID:PMC201377
URL syntax: https://www.ncbi.nlm.nih.gov/pmc/articles/[example_id]
URL example: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC201377/

PUBMED

PubMed

Site: https://www.ncbi.nlm.nih.gov/pubmed
Object: entity
Example ID: PMID:31931324
URL syntax: http://www.ncbi.nlm.nih.gov/pubmed/[example_id]
URL example: https://www.ncbi.nlm.nih.gov/pubmed/31931324

PMID

PubMed

Site: https://www.ncbi.nlm.nih.gov/pubmed
Object: entity
Example ID: PMID:31931324
URL syntax: http://www.ncbi.nlm.nih.gov/pubmed/[example_id]
URL example: https://www.ncbi.nlm.nih.gov/pubmed/31931324

PO

Plant Ontology

Site: http://www.planteome.org/
Object: plant structure development stage
Example ID: PO:0025131
URL syntax: http://browser.planteome.org/amigo/term/PO:[example_id]
URL example: http://browser.planteome.org/amigo/term/PO:0025131

PO_GIT

GitHub Issue Tracker for PO

Site: https://github.com/Planteome/plant-ontology
Object: entity
Example ID: PO_GIT:626
URL syntax: https://github.com/Planteome/plant-ontology/issues/[example_id]
URL example: https://github.com/Planteome/plant-ontology/issues/626

PO_REF

Plant Ontology custom references

Site: http://planteome.org/po_ref
Object: entity
Example ID: PO_REF:00001
URL syntax: http://planteome.org/po_ref/[example_id]
URL example: http://planteome.org/po_ref/00001

POC

Plant Ontology Consortium

Site: http://www.plantontology.org/
Object: entity

PomBase

Site: https://www.pombase.org/
Object: gene
Example ID: PomBase:SPBC11B10.09
URL syntax: https://www.pombase.org/gene/[example_id]
URL example: https://www.pombase.org/gene/SPBC11B10.09

Pompep

Schizosaccharomyces pombe protein data

Site: https://www.pombase.org/downloads/protein-datasets
Object: entity
Example ID: Pompep:SPAC890.04C

PPI

Pseudomonas syringae community annotation project

Site: http://www.pseudomonas-syringae.org/
Object: entity

PR

Protein Ontology

Site: https://proconsortium.org/
Object: protein
Example ID: PR:Q64445
URL syntax: https://purl.obolibrary.org/obo/PR_[example_id]
URL example: https://purl.obolibrary.org/obo/PR_000060258

PRO

Protein Ontology

Site: https://proconsortium.org/
Object: protein
Example ID: PR:Q64445
URL syntax: https://purl.obolibrary.org/obo/PR_[example_id]
URL example: https://purl.obolibrary.org/obo/PR_000060258

PRINTS

PRINTS compendium of protein fingerprints

Site: http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/
Object: polypeptide region
Example ID: PRINTS:PR00025
URL syntax: http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false®expr=off&prints_accn=[example_id]
URL example: http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false®expr=off&prints_accn=PR00025

Prosite

Prosite database of protein families and domains

Site: https://prosite.expasy.org/
Object: polypeptide region
Example ID: PDOC00314
URL syntax: https://prosite.expasy.org/[example_id]
URL example: https://prosite.expasy.org/PDOC00314

protein_id

DDBJ / ENA / GenBank

Site: http://www.ddbj.nig.ac.jp/
Object: protein
Example ID: protein_id:CAA71991

PseudoCAP

Pseudomonas Genome Project

Site: http://www.pseudomonas.com
Object: entity
Example ID: PseudoCAP:PA4756
URL syntax: http://www.pseudomonas.com/feature/show?locus_tag=[example_id]
URL example: http://www.pseudomonas.com/feature/show?locus_tag=PA4756

PSI-MI

Proteomic Standard Initiative for Molecular Interaction

Site: http://www.psidev.info/
Object: entity
Example ID: MI_0018
URL syntax: http://purl.obolibrary.org/obo/
URL example: http://purl.obolibrary.org/obo/MI_0018

MI

Proteomic Standard Initiative for Molecular Interaction

Site: http://www.psidev.info/
Object: entity
Example ID: MI_0018
URL syntax: http://purl.obolibrary.org/obo/
URL example: http://purl.obolibrary.org/obo/MI_0018

MOD

Proteomics Standards Initiative protein modification ontology

Site: http://www.psidev.info/groups/protein-modifications
Object: entity
Example ID: MOD_00219
URL syntax: http://purl.obolibrary.org/obo/[example_id]
URL example: http://purl.obolibrary.org/obo/MOD_00219

PSI-MOD

Proteomics Standards Initiative protein modification ontology

Site: http://www.psidev.info/groups/protein-modifications
Object: entity
Example ID: MOD_00219
URL syntax: http://purl.obolibrary.org/obo/[example_id]
URL example: http://purl.obolibrary.org/obo/MOD_00219

PSO_GIT

GitHub Issue Tracker for PSO

Site: https://github.com/Planteome/plant-stress-ontology
Object: entity
Example ID: PSO_GIT:169
URL syntax: https://github.com/Planteome/plant-stress-ontology/issues/[example_id]
URL example: https://github.com/Planteome/plant-stress-ontology/issues/169

PSORT

PSORT protein subcellular localization databases and prediction tools for bacteria

Site: https://www.psort.org/
Object: entity

PubChem_BioAssay

NCBI PubChem database of bioassay records

Site: https://pubchem.ncbi.nlm.nih.gov
Object: entity
Example ID: PubChem_BioAssay:177
URL syntax: https://pubchem.ncbi.nlm.nih.gov/bioassay/[example_id]
URL example: https://pubchem.ncbi.nlm.nih.gov/bioassay/177

PubChem_Compound

NCBI PubChem database of chemical structures

Site: https://pubchem.ncbi.nlm.nih.gov
Object: chemical entity
Example ID: PubChem_Compound:159296
URL syntax: https://pubchem.ncbi.nlm.nih.gov/compound/[example_id]
URL example: https://pubchem.ncbi.nlm.nih.gov/compound/159296

PubChem_Substance

NCBI PubChem database of chemical substances

Site: https://pubchem.ncbi.nlm.nih.gov
Object: chemical entity
Example ID: PubChem_Substance:4594
URL syntax: https://pubchem.ncbi.nlm.nih.gov/substance/[example_id]
URL example: https://pubchem.ncbi.nlm.nih.gov/substance/4594

RAP-DB

Rice annotation Project database

Site: https://rapdb.dna.affrc.go.jp
Object: entity
Example ID: RAP-DB:Os01t0100600-01
URL syntax: https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=[example_id]
URL example: https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=Os01t0100600-01

REAC

Reactome - a curated knowledgebase of biological pathways

Site: https://www.reactome.org/
Object: entity
Example ID: Reactome:R-HSA-109582
URL syntax: https://www.reactome.org/content/detail/[example_id]
URL example: https://www.reactome.org/content/detail/R-HSA-109582

REACTOME

Reactome - a curated knowledgebase of biological pathways

Site: https://www.reactome.org/
Object: entity
Example ID: Reactome:R-HSA-109582
URL syntax: https://www.reactome.org/content/detail/[example_id]
URL example: https://www.reactome.org/content/detail/R-HSA-109582

REBASE

REBASE restriction enzyme database

Site: http://rebase.neb.com/rebase/rebase.html
Object: entity
Example ID: REBASE:EcoRI
URL syntax: http://rebase.neb.com/rebase/enz/[example_id].html
URL example: http://rebase.neb.com/rebase/enz/EcoRI.html

REFGENOME

GO Reference Genomes

Site: http://www.geneontology.org/GO.refgenome.shtml
Object: entity

RefSeq

Site: http://www.ncbi.nlm.nih.gov/RefSeq/
Object: protein
Example ID: RefSeq:XP_001068954
URL syntax: https://www.ncbi.nlm.nih.gov/protein/[example_id]
URL example: https://www.ncbi.nlm.nih.gov/protein/NP_001121125

RESID

RESID Database of Protein Modifications

Site: https://proteininformationresource.org/resid/resid.shtml
Object: entity
Example ID: RESID:AA0062
URL syntax: https://proteininformationresource.org/cgi-bin/resid?id=[example_id]
URL example: https://proteininformationresource.org/cgi-bin/resid?id=AA0062

Rfam

Rfam database of RNA families

Site: https://rfam.org
Object: entity
Example ID: Rfam:RF00012
URL syntax: https://rfam.org/family/[example_id]
URL example: https://rfam.org/family/RF00012

RAD

Rat Genome Database

Site: https://rgd.mcw.edu/
Object: gene
Example ID: RGD:2004
URL syntax: https://rgd.mcw.edu/rgdweb/search/search.html?term=[example_id]
URL example: https://rgd.mcw.edu/rgdweb/search/search.html?term=2004

RGD

Rat Genome Database

Site: https://rgd.mcw.edu/
Object: gene
Example ID: RGD:2004
URL syntax: https://rgd.mcw.edu/rgdweb/search/search.html?term=[example_id]
URL example: https://rgd.mcw.edu/rgdweb/search/search.html?term=2004

RGDID

Rat Genome Database

Site: https://rgd.mcw.edu/
Object: gene
Example ID: RGD:2004
URL syntax: https://rgd.mcw.edu/rgdweb/search/search.html?term=[example_id]
URL example: https://rgd.mcw.edu/rgdweb/search/search.html?term=2004

RHEA

Rhea, the Annotated Reactions Database

Site: https://www.rhea-db.org
Object: entity
Example ID: RHEA:25811
URL syntax: https://www.rhea-db.org/rhea/[example_id]
URL example: https://www.rhea-db.org/rhea/25811

RiceSES

Rice Knowledge Bank

Site: http://www.ncbi.nlm.nih.gov/PubMed/
Object: entity
Example ID: RiceSES:bakanae-diseases-bak
URL syntax: http://www.knowledgebank.irri.org/extension/crop-damage-diseases/[example_id].html
URL example: http://www.knowledgebank.irri.org/extension/crop-damage-diseases/bakanae-diseases-bak.html

RNAcentral

Site: https://rnacentral.org
Object: ribonucleic acid
Example ID: RNAcentral:URS000047C79B_9606
URL syntax: https://rnacentral.org/rna/[example_id]
URL example: https://rnacentral.org/rna/URS000047C79B_9606

RNAMDB

RNA Modification Database

Site: https://mods.rna.albany.edu/
Object: entity
Example ID: RNAmods:20
URL syntax: https://mods.rna.albany.edu/mods/modifications/view/[example_id]
URL example: https://mods.rna.albany.edu/mods/modifications/view/20

RNAmods

RNA Modification Database

Site: https://mods.rna.albany.edu/
Object: entity
Example ID: RNAmods:20
URL syntax: https://mods.rna.albany.edu/mods/modifications/view/[example_id]
URL example: https://mods.rna.albany.edu/mods/modifications/view/20

RO

OBO Relation Ontology Ontology

Site: http://purl.obolibrary.org/obo/ro
Object: entity
Example ID: RO:0002211
URL syntax: http://purl.obolibrary.org/obo/RO_[example_id]
URL example: http://purl.obolibrary.org/obo/RO_0002211

SABIO-RK

SABIO Reaction Kinetics

Site: http://sabio.villa-bosch.de/
Object: entity
Example ID: SABIO-RK:1858
URL syntax: http://sabio.villa-bosch.de/reacdetails.jsp?reactid=[example_id]
URL example: http://sabio.villa-bosch.de/reacdetails.jsp?reactid=1858

Sanger

Wellcome Trust Sanger Institute

Site: http://www.sanger.ac.uk/
Object: entity

SEED

The SEED;

Site: http://www.theseed.org
Object: entity
Example ID: SEED:fig|83331.1.peg.1
URL syntax: http://www.theseed.org/linkin.cgi?id=[example_id]
URL example: http://www.theseed.org/linkin.cgi?id=fig|83331.1.peg.1

SGDID

Saccharomyces Genome Database

Site: http://www.yeastgenome.org/
Object: gene
Example ID: SGD:S000006169
URL syntax: https://www.yeastgenome.org/search?q=[example_id]&is_quick=true
URL example: https://www.yeastgenome.org/search?q=S000006169&is_quick=true

SGD

Saccharomyces Genome Database

Site: http://www.yeastgenome.org/
Object: gene
Example ID: SGD:S000006169
URL syntax: https://www.yeastgenome.org/search?q=[example_id]&is_quick=true
URL example: https://www.yeastgenome.org/search?q=S000006169&is_quick=true

SGD_LOCUS

Saccharomyces Genome Database

Site: http://www.yeastgenome.org/
Object: entity
Example ID: SGD_LOCUS:GAL4
URL syntax: https://www.yeastgenome.org/search?q=[example_id]&is_quick=true
URL example: https://www.yeastgenome.org/search?q=S000006169&is_quick=true

SGD_PWY

Saccharomyces Genome Database YeastPathways

Site: https://pathway.yeastgenome.org/
Object: entity
Example ID: SGD_PWY:CYSTEINE-SYN2-PWY
URL syntax: https://www.yeastgenome.org/locus/[example_id]
URL example: https://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=NIL&object=SERSYN-PWY

SGD_REF

Saccharomyces Genome Database

Site: http://www.yeastgenome.org/
Object: entity
Example ID: SGD_REF:S000049602
URL syntax: http://www.yeastgenome.org/reference/[example_id]/overview
URL example: http://www.yeastgenome.org/reference/S000049602/overview

SGN

Sol Genomics Network

Site: https://www.sgn.cornell.edu/
Object: gene
Example ID: SGN_gene:7740
URL syntax: http://solgenomics.net/phenome/locus_display.pl?locus_id=[example_id]
URL example: http://solgenomics.net/phenome/locus_display.pl?locus_id=7740

SGN_gene

Sol Genomics Network

Site: https://www.sgn.cornell.edu/
Object: gene
Example ID: SGN_gene:7740
URL syntax: http://solgenomics.net/phenome/locus_display.pl?locus_id=[example_id]
URL example: http://solgenomics.net/phenome/locus_display.pl?locus_id=7740

SGN_germplasm

Sol Genomics Network

Site: https://solgenomics.net/
Object: entity
Example ID: SGN_germplasm:6583
URL syntax: http://solgenomics.net/stock/[example_id]/view/
URL example: http://solgenomics.net/stock/6583/view/

SGN_ref

Sol Genomics Network

Site: https://www.sgn.cornell.edu/
Object: entity
Example ID: SGN_ref:861
URL syntax: https://sgn.cornell.edu/chado/publication.pl?pub_id=[example_id]
URL example: https://sgn.cornell.edu/chado/publication.pl?pub_id=861

SMART

Simple Modular Architecture Research Tool

Site: http://smart.embl-heidelberg.de/
Object: polypeptide region
Example ID: SMART:SM00005
URL syntax: http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=[example_id]
URL example: http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=SM00005

SO

Sequence Ontology

Site: http://www.sequenceontology.org/
Object: sequence motif
Example ID: SO:0001166
URL syntax: http://www.sequenceontology.org/browser/current_svn/term/SO:[example_id]
URL example: http://www.sequenceontology.org/browser/current_svn/term/SO:0001166

Soy_gene

SoyBase

Site: https://soybase.org/
Object: gene
Example ID: Glyma18g02210
URL syntax: https://www.soybase.org/sbt/search/search_results.php?category=FeatureName&search_term=[example_id]
URL example: https://www.soybase.org/sbt/search/search_results.php?category=FeatureName&search_term=Glyma18g02210

SOY_QTL

SoyBase

Site: https://soybase.org/
Object: entity
Example ID: Seedling, abnormal+1-1
URL syntax: https://www.soybase.org/sbt/search/search_results.php?category=QTLName&search_term=[example_id]
URL example: https://www.soybase.org/sbt/search/search_results.php?category=QTLName&search_term=Seedling,+abnormal+1-1

SOY_ref

SoyBase

Site: https://soybase.org/
Object: entity
Example ID: SOY ref:SoyBase6597900
URL syntax: https://www.soybase.org/sbt/search/search_results.php?category=Soybase_ID&search_term=[example_id]
URL example: https://www.soybase.org/sbt/search/search_results.php?category=Soybase_ID&search_term=SoyBase3142000126

SUPERFAMILY

SUPERFAMILY protein annotation database

Site: http://supfam.org/
Object: entity
Example ID: SUPERFAMILY:56994
URL syntax: http://supfam.org/scop/[example_id]
URL example: http://supfam.org/scop/56994

SynGO

The Synapse Gene Ontology and Annotation Initiative

Site: https://www.syngoportal.org/
Object: entity

SynGO-UCL

The Synapse Gene Ontology and Annotation Initiative at UCL

Site: https://www.ucl.ac.uk/cardiovascular/research/pre-clinical-and-fundamental-science/functional-gene-annotation/neurological-gene-2
Object: entity

SYSCILIA_CCNET

Syscilia

Site: http://syscilia.org/
Object: entity

TAIR

The Arabidopsis Information Resource

Site: http://www.arabidopsis.org/
Object: primary transcript
Example ID: TAIR:locus:2146653
URL syntax: http://arabidopsis.org/servlets/TairObject?accession=[example_id]
URL example: http://arabidopsis.org/servlets/TairObject?accession=locus:2146653

taxon

NCBI Taxonomy

Site: http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/
Object: entity
Example ID: taxon:7227
URL syntax: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=[example_id]
URL example: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=3702

ncbi_taxid

NCBI Taxonomy

Site: http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/
Object: entity
Example ID: taxon:7227
URL syntax: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=[example_id]
URL example: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=3702

NCBITaxon

NCBI Taxonomy

Site: http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/
Object: entity
Example ID: taxon:7227
URL syntax: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=[example_id]
URL example: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=3702

TC

Transport Protein Database

Site: http://www.tcdb.org/
Object: protein
Example ID: TC:9.A.4.1.1
URL syntax: http://www.tcdb.org/tcdb/index.php?tc=[example_id]
URL example: http://www.tcdb.org/tcdb/index.php?tc=9.A.4.1.1

tfclass

TFClass is a resource for the classification of eukaryotic transcription factors based on the characteristics of their DNA-binding domains

Site: http://tfclass.bioinf.med.uni-goettingen.de/
Object: protein
Example ID: TFCLASS_FAMILY:2.1.1
URL syntax: http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=[example_id]
URL example: http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=2.1.1

TFCLASS_FAMILY

TFClass is a resource for the classification of eukaryotic transcription factors based on the characteristics of their DNA-binding domains

Site: http://tfclass.bioinf.med.uni-goettingen.de/
Object: protein
Example ID: TFCLASS_FAMILY:2.1.1
URL syntax: http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=[example_id]
URL example: http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=2.1.1

TGD

Tetrahymena Genome Database

Site: http://www.ciliate.org/
Object: entity

TGD_LOCUS

Tetrahymena Genome Database

Site: http://www.ciliate.org/
Object: entity
Example ID: TGD_LOCUS:PDD1
URL syntax: http://db.ciliate.org/cgi-bin/locus.pl?locus=[example_id]
URL example: http://db.ciliate.org/cgi-bin/locus.pl?locus=PDD1

TGD_REF

Tetrahymena Genome Database

Site: http://www.ciliate.org/
Object: entity
Example ID: TGD_REF:T000005818
URL syntax: http://db.ciliate.org/cgi-bin/reference/reference.pl?dbid=[example_id]
URL example: http://db.ciliate.org/cgi-bin/reference/reference.pl?dbid=T000005818

TIGRFAMS

TIGRFAMs HMM collection at the J. Craig Venter Institute

Site: http://tigrfams.jcvi.org/cgi-bin/index.cgi
Object: polypeptide region
Example ID: TIGRFAMS:TIGR00254
URL syntax: http://tigrfams.jcvi.org/cgi-bin/HmmReportPage.cgi?acc=[example_id]
URL example: http://tigrfams.jcvi.org/cgi-bin/HmmReportPage.cgi?acc=TIGR00254

TIGR_TIGRFAMS

TIGRFAMs HMM collection at the J. Craig Venter Institute

Site: http://tigrfams.jcvi.org/cgi-bin/index.cgi
Object: polypeptide region
Example ID: TIGRFAMS:TIGR00254
URL syntax: http://tigrfams.jcvi.org/cgi-bin/HmmReportPage.cgi?acc=[example_id]
URL example: http://tigrfams.jcvi.org/cgi-bin/HmmReportPage.cgi?acc=TIGR00254

TO_GIT

GitHub Issue Tracker for TO

Site: https://github.com/Planteome/plant-trait-ontology
Object: entity
Example ID: TO_GIT:381
URL syntax: https://github.com/Planteome/plant-trait-ontology/issues/[example_id]
URL example: https://github.com/Planteome/plant-trait-ontology/issues/381

TRANSFAC

TRANSFAC database of eukaryotic transcription factors

Site: http://www.gene-regulation.com/pub/databases.html#transfac
Object: entity

TreeGenes

Forest Tree Genome Database

Site: http://dendrome.ucdavis.edu/treegenes/
Object: entity
Example ID: TreeGenes:254
URL syntax: http://dendrome.ucdavis.edu/treegenes/protein/view_protein.php?id=[example_id]
URL example: http://dendrome.ucdavis.edu/treegenes/protein/view_protein.php?id=254

TriTrypDB

Site: https://tritrypdb.org/
Object: gene
Example ID: Tb927.1.630
URL syntax: https://tritrypdb.org/tritrypdb/app/record/gene/[example_id]
URL example: https://tritrypdb.org/tritrypdb/app/record/gene/Tb927.1.630

UBERON

Uber-anatomy ontology

Site: http://uberon.org
Object: life cycle stage
Example ID: UBERON:0000069
URL syntax: http://purl.obolibrary.org/obo/UBERON_[example_id]

UM-BBD

EAWAG Biocatalysis/Biodegradation Database

Site: http://eawag-bbd.ethz.ch/
Object: entity

UM-BBD_enzymeID

EAWAG Biocatalysis/Biodegradation Database

Site: http://eawag-bbd.ethz.ch/
Object: entity
Example ID: UM-BBD_enzymeID:e0413
URL syntax: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=[example_id]
URL example: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=e0230

UM-BBD_pathwayID

EAWAG Biocatalysis/Biodegradation Database

Site: http://eawag-bbd.ethz.ch/
Object: entity
Example ID: UM-BBD_pathwayID:acr
URL syntax: http://eawag-bbd.ethz.ch/[example_id]/[example_id]_map.html
URL example: http://eawag-bbd.ethz.ch/acr/acr_map.html

UM-BBD_reactionID

EAWAG Biocatalysis/Biodegradation Database

Site: http://eawag-bbd.ethz.ch/
Object: entity
Example ID: UM-BBD_reactionID:r0129
URL syntax: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=[example_id]
URL example: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=r0129

UM-BBD_ruleID

EAWAG Biocatalysis/Biodegradation Database

Site: http://eawag-bbd.ethz.ch/
Object: entity
Example ID: UM-BBD_ruleID:bt0330
URL syntax: http://eawag-bbd.ethz.ch/servlets/rule.jsp?rule=[example_id]
URL example: http://eawag-bbd.ethz.ch/servlets/rule.jsp?rule=bt0330

UniParc

UniProt Archive

Site: https://www.uniprot.org/uniparc/
Object: entity
Example ID: UniParc:UPI000000000A
URL syntax: https://www.uniprot.org/uniparc/[example_id]
URL example: https://www.uniprot.org/uniparc/UPI000000000A

UniPathway

Site: http://www.grenoble.prabi.fr/obiwarehouse/unipathway
Object: biological_process
Example ID: UniPathway:UPA00155
URL syntax: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=[example_id]
URL example: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=UPA00155

UniProtKB

Universal Protein Knowledgebase

Site: http://www.uniprot.org
Object: protein
Example ID: UniProtKB:P51587
URL syntax: https://www.uniprot.org/uniprot/[example_id]
URL example: https://www.uniprot.org/uniprot/

SP_KW

UniProt Knowledgebase keywords

Site: http://www.uniprot.org/keywords/
Object: entity
Example ID: UniProtKB-KW:KW-0812
URL syntax: https://www.uniprot.org/keywords/[example_id]
URL example: https://www.uniprot.org/keywords/KW-0812

UniProtKB-KW

UniProt Knowledgebase keywords

Site: http://www.uniprot.org/keywords/
Object: entity
Example ID: UniProtKB-KW:KW-0812
URL syntax: https://www.uniprot.org/keywords/[example_id]
URL example: https://www.uniprot.org/keywords/KW-0812

UniProtKB-SubCell

UniProt Knowledgebase Subcellular Location vocabulary

Site: https://www.uniprot.org/locations/
Object: entity
Example ID: UniProtKB-SubCell:SL-0012
URL syntax: http://www.uniprot.org/locations/[example_id]
URL example: http://www.uniprot.org/locations/SL-0012

SP_SL

UniProt Knowledgebase Subcellular Location vocabulary

Site: https://www.uniprot.org/locations/
Object: entity
Example ID: UniProtKB-SubCell:SL-0012
URL syntax: http://www.uniprot.org/locations/[example_id]
URL example: http://www.uniprot.org/locations/SL-0012

UniRule

Manually curated rules for automatic annotation of UniProtKB unreviewed entries

Site: https://www.uniprot.org/unirule/
Object: entity
Example ID: UniRule:UR000107224
URL syntax: https://www.uniprot.org/unirule/[example_id]
URL example: https://www.uniprot.org/unirule/UR000107224

VZ

ViralZone

Site: http://viralzone.expasy.org/
Object: entity
Example ID: VZ:957
URL syntax: http://viralzone.expasy.org/all_by_protein/[example_id].html
URL example: http://viralzone.expasy.org/all_by_protein/957.html

WormBase

WormBase database of nematode biology

Site: http://www.wormbase.org/
Object: protein
Example ID: WB:CE00274
URL syntax: http://www.wormbase.org/get?name=[example_id]
URL example: http://www.wormbase.org/get?name=CE00274

WB

WormBase database of nematode biology

Site: http://www.wormbase.org/
Object: protein
Example ID: WB:CE00274
URL syntax: http://www.wormbase.org/get?name=[example_id]
URL example: http://www.wormbase.org/get?name=CE00274

WB_REF

WormBase database of nematode biology

Site: http://www.wormbase.org/
Object: entity
Example ID: WB_REF:WBPaper00004823
URL syntax: http://www.wormbase.org/get?name=[example_id]
URL example: http://www.wormbase.org/get?name=WBPaper00004823

WBbt

C. elegans gross anatomy

Site: http://www.wormbase.org/
Object: metazoan anatomical entity
Example ID: WBbt:0005733
URL syntax: http://www.wormbase.org/get?name=[example_id]
URL example: http://www.wormbase.org/get?name=WBbt:0005733

WBls

C. elegans development

Site: http://www.wormbase.org/
Object: nematoda life stage
Example ID: WBls:0000010
URL syntax: http://www.wormbase.org/get?name=[example_id]
URL example: http://www.wormbase.org/get?name=WBls:0000010

WBPhenotype

WormBase phenotype ontology

Site: http://www.wormbase.org/
Object: quality
Example ID: WBPhenotype:0002117
URL syntax: http://www.wormbase.org/get?name=[example_id]
URL example: http://www.wormbase.org/get?name=WBPhenotype:0002117

Wikipedia

Site: http://en.wikipedia.org/
Object: entity
Example ID: Wikipedia:Endoplasmic_reticulum
URL syntax: http://en.wikipedia.org/wiki/[example_id]
URL example: http://en.wikipedia.org/wiki/Endoplasmic_reticulum

WikipediaVersioned

Site: http://en.wikipedia.org/
Object: entity
Example ID: WikipediaVersioned:Fallopian_tube&oldid=998395727
URL syntax: https://en.wikipedia.org/w/index.php?title=[example_id]
URL example: https://en.wikipedia.org/w/index.php?title=Fallopian_tube&oldid=998395727

Xenbase

Site: http://www.xenbase.org/
Object: strain
Example ID: Xenbase:XB-LINE-1248
URL syntax: http://www.xenbase.org/entry/[example_id]
URL example: http://www.xenbase.org/entry/XB-LINE-1248

YeastFunc

Yeast Function

Site: http://func.med.harvard.edu/yeast/
Object: entity

ZFIN

Zebrafish Information Network

Site: http://zfin.org/
Object: variation
Example ID: ZDB-GENE-990415-103
URL syntax: http://zfin.org/[example_id]
URL example: http://zfin.org/ZDB-GENE-990415-103