This page has the curation todo list. Anybody who makes a significant amount of curation will be included as co-authors on the (in preparation) Bioregistry manuscript.

Wikidata

The following entries in the Bioregistry have not been annotated with the ["wikidata"]["database"] entry because it either exists in Wikidata and it needs to be annotated, or it does not exist in Wikidata and needs to be created, then annotated.

Creating a Wikidata item

  1. Create a new item.
  2. Create the first relationship instance of (P31) and target biological database (Q4117139).
  3. Add second relationship official website (P856)
  4. Fill in any other information you want! country, main subject, maintained by, etc.

Editing the Bioregistry

  1. Follow this link to edit directly on GitHub.
  2. Here’s an example of 3dmet, which has the wikidata database annotated properly.
    {
       "3dmet": {
          "miriam": {
             "deprecated": false,
             "description": "3DMET is a database collecting three-dimensional structures of natural metabolites.",
             "id": "00000066",
             "name": "3DMET",
             "namespaceEmbeddedInLui": false,
             "pattern": "^B\\d{5}$",
             "prefix": "3dmet"
          },
          "n2t": {
             "prefix": "3dmet"
          },
          "wikidata": {
             "database": "Q23948774",  // <-- this is it!!
             "property": "P2796"
          }
       },
       ...
    }
    
Entries (1163)
Prefix Name
4dn.biosource 4D Nucleome Data Portal Biosource
4dn.replicate 4D Nucleome Data Portal Experiment Replicate
aao Amphibian gross anatomy
abcd AntiBodies Chemically Defined database
abs Annotated Regulatory Binding Sites
ac Activity Streams
aceview.worm Aceview Worm
addgene Addgene Plasmid Repository
adw Animal natural history and life history
aeo Anatomical Entity Ontology
aero Adverse Event Reporting Ontology
affy.probeset Affymetrix Probeset
afo Allotrope Merged Ontology Suite
aftol.taxonomy Assembling the Fungal Tree of Life - Taxonomy
agricola Agricultural Online Access
agro Agronomy Ontology
aism Ontology for the Anatomy of the Insect SkeletoMuscular system
allergome Allergome
alzforum.mutation Alzforum Mutations
amoebadb AmoebaDB
amphx The Amphioxus Development and Anatomy Ontology
antibodyregistry Antibody Registry
antweb Ant Database
aop AOPWiki
aop.events AOPWiki (Key Event)
aop.relationships AOPWiki (Key Event Relationship)
aop.stressor AOPWiki (Stressor)
apd Antimicrobial Peptide Database
aphidbase.transcript AphidBase Transcript
apid.interactions APID Interactomes
apo Yeast phenotypes
apollosv Apollo Structured Vocabulary
arachnoserver ArachnoServer
araport Arabidopsis Information Portal
ardb Antibiotic Resistance Genes Database
ark Archival Resource Key
aro Antibiotic Resistance Ontology
arrayexpress ArrayExpress
arrayexpress.platform ArrayExpress Platform
arraymap ArrayMap
arxiv arXiv
asap A Systematic Annotation Package for Community Analysis of Genomes
ascl Astrophysics Source Code Library
asin Amazon Standard Identification Number
aspgd.locus Aspergillus Genome Database
aspgd.protein AspGD Protein
asrp Arabidopsis Small RNA Project
assembly Assembly
atc Anatomical Therapeutic Chemical Classification System
atcc American Type Culture Collection
atcvet Anatomical Therapeutic Chemical Vetinary
atfdb.family Animal TFDB Family
ato Amphibian taxonomy
atol Animal Trait Ontology for Livestock
autdb AutDB
bacdive Bacterial Diversity Metadatabase
bacmap.biog BacMap Biography
bacmap.map BacMap Map
bactibase Bactibase: a database dedicated to bacteriocins
bams Brain Architecture Knowledge Management System Neuroanatomical Ontology
bao BioAssay Ontology
bcgo Beta Cell Genomics Ontology
bcio The Behaviour Change Intervention Ontology
bco Biological Collections Ontology
bdgp.est Berkeley Drosophila Genome Project EST database
bdgp.insertion BDGP insertion DB
bdsc Bloomington Drosophila Stock Center
beetlebase Tribolium Genome Database -- Insertion
begdb Benchmark Energy & Geometry Database
bel Biological Expression Language
bfo Basic Formal Ontology
bgee.family Bgee family
bgee.gene Bgee gene
bgee.organ Bgee organ
bgee.stage Bgee stage
bigg.compartment BiGG Compartment
bigg.metabolite BiGG Metabolite
bigg.model BiGG Model
bigg.reaction BiGG Reaction
bila Bilateria anatomy
bindingdb BindingDB
biocarta.pathway BioCarta Pathway
biocatalogue.service BioCatalogue Service
biocyc BioCyc collection of metabolic pathway databases
biogrid BioGRID
biogrid.interaction BioGRID Interactions
biolegend BioLegend
biolink BioLink Model
biominder Bio-MINDER Tissue Database
biomodels.db BioModels Database
biomodels.kisao Kinetic Simulation Algorithm Ontology
biomodels.teddy Terminology for Description of Dynamics
biomodels.vocabulary SBML RDF Vocabulary
bionumbers BioNumbers
bioportal BioPortal
bioproject BioProject
bioregistry Bioregistry
bioregistry.collection Bioregistry Collections
bioregistry.schema Bioregistry Schema
biorxiv bioRxiv
biosample BioSample
biosimulations biosimulations
biosimulators BioSimulators
biostudies BioStudies database
biosystems BioSystems
biotools BioTools
biozil BIOZIL
birnlex Biomedical Informatics Research Network Lexicon
bitterdb.cpd BitterDB Compound
bitterdb.rec BitterDB Receptor
bmrb Biological Magnetic Resonance Data Bank
bmrb.restraint NMR Restraints Grid
bold.taxonomy Barcode of Life database
bootstrep Gene Regulation Ontology
bpdb Bio-Pesticides DataBase
brenda BRENDA, The Comprehensive Enzyme Information System
broad Broad Fungal Genome Initiative
bs Biosapiens Protein Feature Ontology
bspo Biological Spatial Ontology
bugbase.expt BugBase Expt
bugbase.protocol BugBase Protocol
bykdb Bacterial Tyrosine Kinase Database
cabri Common Access to Biological Resources and Information Project
cadsr Cancer Data Standards Registry and Repository
caloha CALIPHO Group Ontology of Human Anatomy
cameo Continuous Automated Model Evaluation
caps CAPS-DB
caro Common Anatomy Reference Ontology
cas CAS Chemical Registry
cath CATH Protein Structural Domain Superfamily
cath.domain CATH domain
cath.superfamily CATH superfamily
cattleqtldb Animal Genome Cattle QTL
cazy Carbohydrate Active EnZYmes
cba Chinese Biological Abstracts
cbioportal The cBioPortal for Cancer Genomics
ccdc CCDC Number
ccds Consensus CDS
ccle Cancer Cell Line Encyclopedia (CCLE) Cells
cco Cell Cycle Ontology
cdao Comparative Data Analysis Ontology
cdd Conserved Domain Database at NCBI
cdno Compositional Dietary Nutrition Ontology
cdpd Canadian Drug Product Database
cellbank.australia CellBank Australia
cellimage Cell Image Library
cellrepo Cell Version Control Repository
ceph Cephalopod Ontology
cgd Candida Genome Database
cgnc Chicken Gene Nomenclature Consortium
cgsc Coli Genetic Stock Center
charprot CharProt
chembl ChEMBL
chembl.target ChEMBL target
chemdb ChemDB
chemidplus ChemIDplus
cheminf Chemical Information Ontology
chickenqtldb Animal Genome Chicken QTL
chiro ChEBI Integrated Role Ontology
chmo Chemical Methods Ontology
cido Coronavirus Infectious Disease Ontology
cio Confidence Information Ontology
citexplore CiteXplore
civic.aid CIViC Assertion
civic.eid CIViC Evidence
clao Collembola Anatomy Ontology
classyfire ClassyFire
cldb Cell Line Database
clingene ClinGen Allele Registry
clinicaltrials ClinicalTrials.gov
clinvar.record ClinVar Record
clinvar.submission ClinVar Submission
clinvar.submitter ClinVar Submitter
clo Cell Line Ontology
clyh Clytia hemisphaerica Development and Anatomy Ontology
cmf CranioMaxilloFacial ontology
cmo Clinical measurement ontology
cmpo Cellular Microscopy Phenotype Ontology
co_320 Rice ontology
co_321 Wheat ontology
co_322 Maize ontology
co_323 Barley ontology
co_324 Sorghum ontology
co_325 Banana ontology
co_326 Coconut ontology
co_327 Pearl millet ontology
co_330 Potato ontology
co_331 Sweet Potato ontology
co_333 Beet Ontology ontology
co_334 Cassava ontology
co_335 Common Bean ontology
co_336 Soybean ontology
co_337 Groundnut ontology
co_338 Chickpea ontology
co_339 Lentil ontology
co_340 Cowpea ontology
co_341 Pigeonpea ontology
co_343 Yam ontology
co_345 Brachiaria ontology
co_346 Mungbean ontology
co_347 Castor bean ontology
co_348 Brassica ontology
co_350 Oat ontology
co_356 Vitis ontology
co_357 Woody Plant Ontology ontology
co_358 Cotton ontology
co_359 Sunflower ontology
co_360 Sugar Kelp trait ontology
co_365 Fababean ontology
co_366 Bambara groundnut ontology
cob Core Ontology for Biology and Biomedicine
coconut COlleCtion of Open Natural ProdUcTs
cog Cluster of orthologous genes
cog.category COG Categories
cog.pathway COG Pathways
cohd MIMIC III Database
combine.specifications COMBINE specifications
come The Bioinorganic Motif Database
comptox CompTox Chemistry Dashboard
compulyeast Compluyeast-2D-DB
conoserver ConoServer
conso Curation of Neurodegeneration Supporting Ontology
coriell Coriell Institute for Medical Research
corrdb CorrDB
corum CORUM - the Comprehensive Resource of Mammalian protein complexes
cosmic COSMIC Gene
cosmic.cell COSMIC Cell Lines
covid19 COVID-19 Ontology
covoc CoVoc Coronavirus Vocabulary
cp Cellular Phenotypes
cpc Cooperative Patent Classification
cpga Cereal Plant Gross Anatomy
crisprdb CRISPRdb
cro Contributor Role Ontology
cryoem Cryo Electron Microscopy ontology
cryptodb CryptoDB
csa Catalytic Site Atlas
csd Cambridge Structural Database
csp Computer Retrieval of Information on Science Projects (CRISP) Thesaurus
cst Cancer Staging Terms
cst.ab Cell Signaling Technology Antibody
ctd.chemical CTD Chemical
ctd.disease CTD Disease
ctd.gene CTD Gene
cteno Ctenophore Ontology
cto CTO: Core Ontology of Clinical Trials
cubedb Cube db
cvdo Cardiovascular Disease Ontology
d1id DataONE
dailymed DailyMed
dandi DANDI: Distributed Archives for Neurophysiology Data Integration
darc Database of Aligned Ribosomal Complexes
dashr Database of small human noncoding RNAs
dashr.expression DASHR expression
datanator.gene Datanator Gene
datanator.metabolite Datanator Metabolite
datanator.reaction Datanator Reaction
datf Database of Arabidopsis Transcription Factors
dbd Transcription Factor Database
dbest EST database maintained at the NCBI.
dbg2introns DBG2 Introns
dbgap Database of Genotypes and Phenotypes
dbmhc Database of human Major Histocompatibility Complex
dbprobe NCBI Probe database Public registry of nucleic acid reagents
dbsnp NCBI dbSNP
dc Disease Class
dc_cl Dendritic cell
dcat Data Catalog
dcterms Dublin Core Metadata Vocabulary
dctypes Dublin Core Types
ddanat Dictyostelium discoideum anatomy
ddpheno Dictyostelium discoideum phenotype ontology
degradome Degradome Database
depmap DepMap Cell Lines
depod Human Dephosphorylation Database
dermo Human Dermatological Disease Ontology
dev.ga4ghdos Development Data Object Service
dg.4503 BioData Catalyst
dg.4dfc NCI Data Commons Framework Services
dg.6vts JCOIN
dg.anv0 Anvil
dg.f82a1a Kids First
dicom DICOM Controlled Terminology
dictybase dictyBase
dictybase.est dictyBase Expressed Sequence Tag
dictybase.gene Dictybase Gene
did Decentralized Identifier
dideo Drug-drug Interaction and Drug-drug Interaction Evidence Ontology
dinto The Drug-Drug Interactions Ontology
dip Database of Interacting Proteins
disdriv Disease Drivers Ontology
disprot DisProt
disprot.region DisProt region
dlxb Linear double stranded DNA sequences
dlxc Circular double stranded DNA sequences composed
doi Digital Object Identifier
dommino Database of Macromolecular Interactions
door Database for Prokaryotic Operons
doqcs.model Database of Quantitative Cellular Signaling: Model
doqcs.pathway Database of Quantitative Cellular Signaling: Pathway
dpo Drosophila Phenotype Ontology
dpv Description of Plant Viruses
dragondb.allele DragonDB Allele
dragondb.dna DragonDB DNA
dragondb.locus DragonDB Locus
dragondb.protein DragonDB Protein
dron The Drug Ontology
drsc Drosophila RNAi Screening Center
drugbank DrugBank
drugbank.salt DrugBank Salts
drugbankv4.target DrugBank Target v4
drugcentral Drug Central
dsmz Deutsche Sammlung von Mikroorganismen und Zellkulturen
dto Drug Target Ontology
duo Data Use Ontology
eaglei eagle-i
ecacc European Collection of Authenticated Cell Culture
ecao The Echinoderm Anatomy and Development Ontology
eccode Enzyme Nomenclature
ecg Electrocardiogram Ontology
echobase EchoBASE post-genomic database for Escherichia coli
eco Evidence ontology
ecocore An ontology of core ecological entities
ecocyc EcoCyc
ecogene Database of Escherichia coli Sequence and Function
ecoliwiki EcoliWiki from EcoliHub
ecto Environmental conditions, treatments and exposures ontology
ecyano.entity E-cyanobacterium entity
ecyano.experiment E-cyanobacterium Experimental Data
ecyano.model E-cyanobacterium model
ecyano.rule E-cyanobacterium rule
edam Bioinformatics operations, data types, formats, identifiers and topics
efo Experimental Factor Ontology
ega.dataset European Genome-phenome Archive Dataset
ega.study European Genome-phenome Archive Study
eggnog eggNOG
ehda Human developmental anatomy, timed version
ehdaa Human developmental anatomy, abstract version
ehdaa2 Human developmental anatomy, abstract
elm Eukaryotic Linear Motif Resource
emap Mouse gross anatomy and development, timed
emapa Mouse Developmental Anatomy Ontology
emdb Electron Microscopy Data Bank
emolecules Reaxys eMolecules
empiar Electron Microscopy Public Image Archive
ena.embl European Nucleotide Archive
encode ENCODE: Encyclopedia of DNA Elements
enm eNanoMapper Ontology
ensembl.bacteria Ensembl Bacteria
ensembl.fungi Ensembl Fungi, the Ensembl database for accessing genome-scale data from fungi.
ensembl.metazoa Ensembl Metazoa, the Ensembl database for accessing genome-scale data from non-vertebrate metazoa.
ensembl.plant Ensembl Plants
ensembl.protist Ensembl Protists
ensemblglossary Ensembl Glossary
envipath enviPath
envo Environment Ontology
enzo Enzo Life Sciences
eol Environment Ontology for Livestock
epcc European Paediatric Cardiac Codes
epd Eukaryotic Promoter Database
epo Epidemiology Ontology
epso Epilepsy Ontology
erm European Registry of Materials
ero eagle-i resource ontology
erv Human Endogenous Retrovirus Database
eu89h JRC Data Catalogue
euclinicaltrials EU Clinical Trials
eupath VEuPathDB ontology
eurofir European Food Information Resource Network
ev eVOC (Expressed Sequence Annotation for Humans)
evm eVOC mouse development stage
exac.gene ExAC Gene
exac.transcript ExAC Transcript
exac.variant ExAC Variant
exo Exposure ontology
facebase FaceBase Data Repository
fairsharing FAIRsharing
faldo Feature Annotation Location Description Ontology
fao Fungal gross anatomy
fbbi Biological Imaging Methods Ontology
fbbt Drosophila gross anatomy
fbcv FlyBase Controlled Vocabulary
fbdv Drosophila development
fbol International Fungal Working Group Fungal Barcoding.
fbrf FlyBase Reference Report
fbsp Fly taxonomy
fbtc Flybase Cell Line
fideo Food Interactions with Drugs Evidence Ontology
fix Physico-chemical methods and properties
flopo Flora Phenotype Ontology
flowrepository FlowRepository
flu Influenza Ontology
fma Foundational Model of Anatomy
foaf Friend of a Friend
fobi Food-Biomarker Ontology
foodb.compound FooDB Compound
foodon The Food Ontology
fovt FuTRES Ontology of Vertebrate Traits
fplx FamPlex
fsnp F-SNP
funcbase.fly FuncBase Fly
funcbase.human FuncBase Human
funcbase.mouse FuncBase Mouse
funcbase.yeast FuncBase Yeast
funderregistry FunderRegistry
fungidb FungiDB
fyler Fyler
fypo Fission Yeast Phenotype Ontology
ga4ghdos Data Object Service
gabi Network of Different Plant Genomic Research Projects
galen Galen Ontology
gard Genetic and Rare Diseases Information Center
gateway Health Data Research Innovation Gateway
gaz Gazetteer
gbif Global Biodiversity Information Facility
gc Genetic Code
gcst GWAS Catalog
gdc Genomic Data Commons Data Portal
gdsc Genomics of Drug Sensitivity in Cancer
gecko Genomics Cohorts Knowledge Ontology
genatlas Genatlas
genbank GenBank
genecards GeneCards
genefarm GeneFarm
genepio Genomic Epidemiology Ontology
genetree GeneTree
genewiki Gene Wiki
geno Genotype Ontology
genpept GenPept
genprop Genome Properties
geo NCBI Gene Expression Omnibus
geogeo Geographical Entity Ontology
gexo Gene Expression Ontology
ghr Genetics Home Reference
giardiadb GiardiaDB
github github
glida.gpcr GLIDA GPCR
glida.ligand GLIDA Ligand
glycoepitope GlycoEpitope
glycomedb GlycomeDB
glyconavi GlycoNAVI
glycopost GlycoPOST
glygen GlyGen: Computational and Informatics Resources for Glycoscience
glytoucan GlyTouCan
gmd Golm Metabolome Database
gmd.analyte Golm Metabolome Database Analyte
gmd.gcms Golm Metabolome Database GC-MS spectra
gmd.profile Golm Metabolome Database Profile
gmd.ref Golm Metabolome Database Reference Substance
gmelin Gmelins Handbuch der anorganischen Chemie
gno Glycan Naming and Subsumption Ontology
gnpis GnpIS
go Gene Ontology
go.model Gene Ontology Causal Assembly Model
go.ref Gene Ontology Database references
goa Gene Ontology Annotation Database Identifier
goeco GO Evidence Code
gold Genomes Online Database
gold.genome GOLD genome
gold.meta GOLD metadata
google.patent Google Patents
google.scholar Google Scholar Researcher ID
gorel GO Relations
gpcrdb G protein-coupled receptor database
gpmdb Global Proteome Machine Database
gramene.gene Gramene Gene
gramene.growthstage Gramene Growth Stage Ontology
gramene.protein Gramene protein
gramene.qtl Gramene QTL
gramene.taxonomy Gramene Taxonomy
grassbase GrassBase
greengenes 16S rRNA gene database
grid Global Research Identifier Database
grin.taxonomy Germplasm Resources Information Network
gro Gene Regulation Ontology
grsdb G-Rich Sequences Database
gsfa General Standard for Food Additives (GSFA) Online Database
gsso Gender, Sex, and Sexual Orientation Ontology
gtex Genotype-Tissue Expression
gtr Genetic Testing Registry
gudmap Genitourinary Development Molecular Anatomy Project
gwascentral.marker GWAS Central Marker
gwascentral.phenotype GWAS Central Phenotype
gwascentral.study GWAS Central Study
gxa.expt GXA Expt
gxa.gene GXA Gene
habronattus Habronattus courtship
hamap High-quality Automated and Manual Annotation of microbial Proteomes
hancestro Human Ancestry Ontology
hao Hymenoptera Anatomy Ontology
hcao Human Cell Atlas Ontology
hcpcs Healthcare Common Procedure Coding System
hcvdb Hepatitis C Virus Database
hdr Homeodomain Research
hgmd Human Gene Mutation Database
hgnc HUGO Gene Nomenclature Committee
hgnc.genefamily HGNC Family
hgnc.genegroup HGNC Gene Group
hgnc.symbol HGNC Symbol
hinv.locus H-InvDb Locus
hinv.protein H-InvDb Protein
hinv.transcript H-InvDb Transcript
hms.lincs.compound HMS LINCS Compound
hog Homologous Organ Groups
hogenom Database of Complete Genome Homologous Genes Families
hom Homology Ontology
homd.seq HOMD Sequence Metainformation
homd.taxon HOMD Taxonomy
hovergen Homologous Vertebrate Genes Database
hpa Human Protein Atlas tissue profile information
hpath Histopathology Ontology
hpm.peptide Human Proteome Map Peptide
hpm.protein Human Proteome Map Protein
hprd Human Protein Reference Database
hpscreg Human Pluripotent Stem Cell Registry
hsapdv Human Developmental Stages
hsdb Hazardous Substances Data Bank
hso Health Surveillance Ontology
hssp Database of homology-derived secondary structure of proteins
htn Hypertension Ontology
huge Human Unidentified Gene-Encoded
iao Information Artifact Ontology
icd10 International Classification of Diseases
icd11 International Classification of Diseases 11th Revision
icd9 International Classification of Diseases 9th Revision
icdc Integrated Canine Data Commons
icdo The International Classification of Diseases for Oncology
iceberg.element ICEberg element
iceberg.family ICEberg family
iceo Integrative and Conjugative Element Ontology
ico Informed Consent Ontology
ideal Intrinsically Disordered proteins with Extensive Annotations and Literature
identifiers.namespace Identifiers.org namespace
ido Infectious Disease Ontology
idocovid19 The COVID-19 Infectious Disease Ontology
idoden Dengue Fever Ontology
idomal Malaria Ontology
idoo Identifiers.org Ontology
idot Identifiers.org Terms
idr Image Data Resource
iedb Immune Epitope Database
iev Event (INOH pathway ontology)
igsn International Geo Sample Number
ihw International Histocompatibility Workshop cell lines
imdrf International Medical Device Regulators Forum
imex International Molecular Exchange
img.gene Integrated Microbial Genomes Gene
img.taxon Integrated Microbial Genomes Taxon
imgt.hla IMGT/HLA human major histocompatibility complex sequence database
imgt.ligm ImMunoGeneTics database covering immunoglobulins and T-cell receptors
imr Molecule role (INOH Protein name/family name ontology)
inchi InChI
inchikey InChIKey
inn International Nonproprietary Names
ino Interaction Network Ontology
insdc Nucleotide Sequence Database
insdc.cds INSDC CDS
insdc.gca Genome assembly database
insdc.run International Nucleotide Sequence Database Collaboration (INSDC) Run
insdc.sra Sequence Read Archive
intact IntAct protein interaction database
intact.molecule IntAct Molecule
interlex InterLex
interpro InterPro
ird.segment IRD Segment Sequence
irefweb iRefWeb
iro Insect Resistance Ontology
isbn International Standard Book Number
isfinder Insertion sequence elements database
isni International Standard Name Identifier
issn International Standard Serial Number
itis Integrated Taxonomic Information System
ito Intelligence Task Ontology
iuphar.family IUPHAR family
jax Jackson Laboratories Strain
jaxmice JAX Mice
jcggdb Japan Consortium for Glycobiology and Glycotechnology Database
jcm Japan Collection of Microorganisms
jcsd Japan Chemical Substance Dictionary
jstor Digital archive of scholarly articles
jws JWS Online
kaggle Kaggle
kegg Kyoto Encyclopedia of Genes and Genomes
kegg.compound KEGG Compound
kegg.disease KEGG Disease
kegg.drug KEGG Drug
kegg.environ KEGG Environ
kegg.enzyme KEGG Enzyme
kegg.genes KEGG Genes
kegg.genome KEGG Genome
kegg.glycan KEGG Glycan
kegg.ligand KEGG LIGAND
kegg.metagenome KEGG Metagenome
kegg.module KEGG Module
kegg.orthology KEGG Orthology
kegg.pathway KEGG Pathways Database
kupo Kidney and Urinary Pathway Ontology
labo clinical LABoratory Ontology
lbo Livestock Breed Ontology
lei Global LEI Index
lgai.cede LG Chemical Entity Detection Dataset (LGCEDe)
lgic Ligand-Gated Ion Channel database
licebase LiceBase
ligandbook LigandBook
ligandbox LigandBox
ligandexpo Ligand Expo
lincs.cell LINCS Cell
lincs.data LINCS Data
lincs.protein LINCS Protein
lincs.smallmolecule LINCS Small Molecule
linguist Linguist
lipidbank LipidBank
lipidmaps LIPID MAPS
lipro Lipid Ontology
lncipedia LNCipedia
loggerhead Loggerhead nesting
loinc Logical Observation Identifiers Names and Codes
lrg Locus Reference Genomic
lspci Laboratory of Systems Pharmacology Compound ID
ma Mouse adult gross anatomy
macie Mechanism, Annotation and Classification in Enzymes
maizegdb.locus MaizeGDB Locus
mamo Mathematical modeling ontology
mao Multiple alignment
massive MassIVE
mat Minimal Anatomical Terminology
matrixdb MatrixDB
matrixdb.association MatrixDB Association
maxo Medical Action Ontology
mcc Cell Line Ontology [derivative]
mco Microbial Conditions Ontology
mdm Medical Data Models
meddra Medical Dictionary for Regulatory Activities Terminology
medgen Human Medical Genetics
medlineplus MedlinePlus Health Topics
merops MEROPS peptidase database
merops.family MEROPS Family
merops.inhibitor MEROPS Inhibitor
mesh.2012 MeSH 2012
mesh.2013 MeSH 2013
metacyc.compound Metabolic Encyclopedia of metabolic and other pathways
metacyc.reaction MetaCyc Reaction
metanetx.chemical MetaNetX chemical
metanetx.compartment MetaNetX compartment
metanetx.reaction MetaNetX reaction
metlin Metabolite and Tandem Mass Spectrometry Database
mex Metabolome Express
mf Mental Functioning Ontology
mfmo Mammalian Feeding Muscle Ontology
mfo Medaka fish anatomy and development
mfoem Emotion Ontology
mfomd Mental Disease Ontology
mge Aclame
mgnify.analysis MGnify Analysis
mgnify.proj MGnify Project
mgnify.samp MGnify Sample
mi Molecular Interactions Controlled Vocabulary
miaa Minimal Information About Anatomy ontology
miapa MIAPA Ontology
micro Ontology of Prokaryotic Phenotypic and Metabolic Characters
microscope MicroScope
microsporidia MicrosporidiaDB
mim.ps OMIM Phenotypic Series
mimodb MimoDB
minid Minimal Viable Identifier
minid.test MINID Test
mint Molecular Interaction Database
mipmod MIPModDB
mir Identifiers.org Registry
mirex mirEX
miriam.collection MIRIAM Registry collection
miriam.resource MIRIAM Registry resource
mirnao microRNA Ontology
mirnest miRNEST
miro Mosquito insecticide resistance
mirtarbase miRTarBase
mirte miRNA Target Prediction at EMBL
mlc MLCommons Association
mmdb Molecular Modeling Database
mmmp.biomaps Melanoma Molecular Map Project Biomaps
mmo Measurement method ontology
mmp.cat MarCat
mmp.db MarDB
mmp.fun MarFun
mmp.ref MarRef
mmrrc Mutant Mouse Resource and Research Centers
mmsl Multum MediSource Lexicon
mmusdv Mouse Developmental Stages
mo Microarray experimental conditions
mobidb MobiDB
mod Protein modification
modeldb ModelDB
molbase Molbase
molbase.sheffield MolBase
molmedb MolMeDB
mondo Monarch Disease Ontology
mop Molecular Process Ontology
morpheus Morpheus model repository
mp Mammalian Phenotype Ontology
mpath Mouse pathology ontology
mpid Microbial Protein Interaction Database
mpio Minimum PDDI Information Ontology
mro MHC Restriction Ontology
ms Mass spectrometry ontology
msigdb Molecular Signatures Database
msio Metabolomics Standards Initiative Ontology
multicellds MultiCellDS
multicellds.cell_line MultiCellDS Digital Cell Line
multicellds.collection MultiCellDS collection
multicellds.snapshot MultiCellDS Digital snapshot
mw.project Metabolomics Workbench Project
mw.study Metabolomics Workbench Study
myco.lepra MycoBrowser leprae
myco.marinum MycoBrowser marinum
myco.smeg MycoBrowser smegmatis
myco.tuber MycoBrowser tuberculosis
mycobank Fungal Nomenclature and Species Bank
mzspec Universal Spectrum Identifier
namerxn NameRXN
napdi Natural Product-Drug Interaction Research Data Repository
napp Nucleic Acids Phylogenetic Profiling
narcis National Academic Research and Collaborations Information System
nasc NASC code
nbn National Bibliography Number
nbo Neuro Behavior Ontology
nbrc NITE Biological Resource Center
ncats.drug NCATS Drugs
ncbiprotein NCBI Protein
ncim NCI Metathesaurus
ncro Non-Coding RNA Ontology
ndc National Drug Code
nddf National Drug Data File
ndex Network Data Exchange
nemo Neural ElectroMagnetic Ontology
neurolex NeuroLex
neuromorpho NeuroMorpho
neuronames NeuroNames
neurondb NeuronDB
neurovault.collection NeuroVault Collection
neurovault.image NeuroVault Image
nextdb Nematode Expression Pattern DataBase
nextprot.family neXtProt family
ngl NASA GeneLab
niaest NIA Mouse cDNA Project
nif_cell NIF Cell
nif_dysfunction NIF Dysfunction
nif_grossanatomy NIF Gross Anatomy
nist NIST Chemistry WebBook
nlm National Library of Medicine (NLM) Catalog
nlxanat NeuroLex Anatomy
nlxdys NeuroLex Dysfunction
nmr NMR-instrument specific component of metabolomics investigations
nmrshiftdb2 NMR Shift Database
nomen NOMEN - A nomenclatural ontology for biological names
noncodev3 NONCODE v3
noncodev4.gene NONCODE v4 Gene
noncodev4.rna NONCODE v4 Transcript
norine Nonribosomal Peptides Database
novus Novus Biologicals
npass Natural Product Activity and Species Source Database
nuclearbd NucleaRDB
nucleotide Nucleotide
oa Web Annotation Ontology
oae Ontology of Adverse Events
oarcs Ontology of Arthropod Circulatory Systems
oba Ontology of Biological Attributes
obcs Ontology of Biological and Clinical Statistics
obi Ontology for Biomedical Investigations
obib Ontology for Biobanking
obo Internal OBO and PyOBO Relations
oboinowl OBO in OWL
occ OpenCitations Corpus
oci Open Citation Identifier
ocid Ontology Concept Identifiers
oclc Online Computer Library Center (OCLC) WorldCat
odam Open Data for Access and Mining
odc.sci Open Data Commons for Spinal Cord Injury
odc.tbi Open Data Commons for Traumatic Brain Injury
odor Odor Molecules DataBase
ogg The Ontology of Genes and Genomes
ogi Ontology for genetic interval
ogsf Ontology of Genetic Susceptibility Factor
ohd The Oral Health and Disease Ontology
ohmi Ontology of Host-Microbiome Interactions
ohpi Ontology of Host Pathogen Interactions
oid OID Repository
olatdv Medaka Developmental Stages
om Ontology of units of Measure
oma.grp OMA Group
oma.hog OMA HOGs
oma.protein OMA Protein
omia Online Mendelian Inheritance in Animals
omiabis Ontologized MIABIS
omit Ontology for MicroRNA Target
omo OBO Metadata Ontology
omop Observational Medical Outcomes Partnership
omrse Ontology of Medically Related Social Entities
oncotree OncoTree
one Ontology for Nutritional Epidemiology
ons Ontology for Nutritional Studies
ontoneo Obstetric and Neonatal Ontology
oostt Ontology of Organizational Structures of Trauma centers and Trauma systems
opb Ontology of Physics for Biology
opl Ontology for Parasite LifeCycle
opm Orientations of Proteins in Membranes Database
opmi Ontology of Precision Medicine and Investigation
ordb Olfactory Receptor Database
oridb.sacch OriDB Saccharomyces
oridb.schizo OriDB Schizosaccharomyces
ornaseq Ontology of RNA Sequencing
orphanet.ordo Orphanet Rare Disease Ontology
orth Orthology Ontology
orthodb OrthoDB
oryzabase.gene Oryzabase Gene
oryzabase.mutant Oryzabase Mutant
oryzabase.reference Oryzabase Reference
oryzabase.stage Oryzabase Stage
oryzabase.strain Oryzabase Strain
otl Oryza Tag Line
ovae Ontology of Vaccine Adverse Events
owl OWL Ontology
p3db.protein P3DB Protein
p3db.site P3DB Site
paleodb Paleobiology Database
panorama Panorama Public
panther.family Protein ANalysis THrough Evolutionary Relationships Classification System
panther.node PANTHER Node
panther.pathway PANTHER Pathway
panther.pthcmp PANTHER Pathway Component
pao Plant Anatomy Ontology
pass2 Protein Alignment organised as Structural Superfamily
pathbank PathBank
pathwaycommons Pathway Commons
pato Phenotype And Trait Ontology
pav Provenance, Authoring, and Versioning Vocabulary
paxdb.organism PaxDb Organism
paxdb.protein PaxDb Protein
pazar Pazar Transcription Factor
pco Population and Community Ontology
pd_st Platynereis stage ontology
pdb-ccd Chemical Component Dictionary
pdb.ligand Protein Data Bank Ligand
pdro The Prescription of Drugs Ontology
pdumdv Platynereis Developmental Stages
peco Plant Environment Ontology
ped Protein Ensemble Database
ped.ensemble Protein Ensemble Database ensemble
peff PSI Extended File Format
peptideatlas PeptideAtlas
peptideatlas.dataset PeptideAtlas Dataset
peroxibase Peroxibase
pesticides Alan Wood's Pesticides
pfam.clan Pfam Clans
pfr Proteoform Atlas
pgdso Plant Growth and Development Stage
pgs Polygenic Score Catalog
pgx Progenetix
pharmacodb.cell PharmacoDB Cells
pharmacodb.dataset PharmacoDB Datasets
pharmacodb.tissue PharmacoDB Tissues
pharmgkb.disease PharmGKB Disease
pharmgkb.drug PharmGKB Drug
pharmgkb.gene Pharmacogenetics and Pharmacogenomics Knowledge Base
pharmgkb.pathways PharmGKB Pathways
phenolexplorer Phenol-Explorer
phipo Pathogen Host Interaction Phenotype Ontology
phosphopoint.kinase PhosphoPoint Kinase
phosphopoint.protein PhosphoPoint Phosphoprotein
phosphosite.protein PhosphoSite Protein
phosphosite.residue PhosphoSite Residue
phylomedb PhylomeDB
phytozome.locus Plant Genome Network
pictar PicTar
pid.pathway NCI Pathway Interaction Database: Pathway
pigqtldb Animal Genome Pig QTL
pina Protein Interaction Network Analysis
piroplasma PiroplasmaDB
pirsf PIR Superfamily Classification System
pkdb PK-DB
plana planaria-ontology
planp Planarian Phenotype Ontology
planttfdb Plant Transcription Factor Database
plasmodb PlasmoDB Plasmodium Genome Resource
plo Plasmodium Life Cycle
pmap.cutdb CutDB
pmap.substratedb SubstrateDB
pmc Pubmed Central
pmdb Protein Model Database
pmp Protein Model Portal
pmr Physical Medicine and Rehabilitation
po Plant Ontology
pocketome Pocketome
polbase PolBase
poro Porifera Ontology
ppdb Pesticide Properties DataBase
ppo Plant Phenology Ontology
ppr Europe PMC Preprints
pride PRIDE Controlled Vocabulary
pride.project PRIDE Project
prints PRINTS compendium of protein fingerprints
probonto Probability Distribution Ontology
prodom ProDom
proglyc ProGlycProt
propreo Proteomics data and process provenance
protclustdb ProtClustDB
proteomicsdb.peptide ProteomicsDB Peptide
proteomicsdb.protein ProteomicsDB Protein
protonet.cluster ProtoNet Cluster
protonet.proteincard ProtoNet ProteinCard
prov PROV Namespace
pscdb Protein Structural Change Database
psdo Performance Summary Display Ontology
pseudomonas Pseudomonas Genome Database
psipar Protein Affinity Reagents
pso Plant Stress Ontology
pspub Phenoscape Publication
pubchem.bioassay NCBI PubChem database of bioassay records
publons.researcher Publons Researcher ID
pubmed PubMed
px ProteomeXchange
pypi PyPI
qtldb Animal Genome QTL
qudt Quantities, Units, Dimensions, and Types Ontology
radiomics Radiomics Ontology
rapdb.locus RAP-DB Locus
rapdb.transcript RAP-DB Transcript
rbk Rebuilding a Kidney
rbo Radiation Biology Ontology
rcb RIKEN Bioresource Center Cell Bank
rdf Resource Description Framework
rdfs RDF Schema
rdo RGD Disease_Ontology
re3data re3data
reaxys Reaxys
rebase REBASE restriction enzyme database
receptome.family Human Plasma Membrane Receptome Families
refseq Reference Sequence Collection
repeatsdb.protein RepeatsDB Protein
repeatsdb.structure RepeatsDB Structure
reproduceme REPRODUCE-ME Ontology
resid Protein covalent bond
reto Regulation of Transcription Ontology
rex Physico-chemical process
rexo Regulation of Gene Expression Ontology
rfam Rfam database of RNA families
rgd.qtl Rat Genome Database qTL
rgd.strain Rat Genome Database strain
ricegap Rice Genome Annotation Project
ricenetdb.compound RiceNetDB Compound
ricenetdb.gene RiceNetDB Gene
ricenetdb.mirna RiceNetDB miRNA
ricenetdb.protein RiceNetDB Protein
ricenetdb.reaction RiceNetDB Reaction
rnacentral RNAcentral
rnamod The RNA Modification Database
rnamods RNA Modification Database
rnao RNA ontology
ro Relation Ontology
rouge Rodent Unidentified Gene-Encoded Large Proteins
rrid Research Resource Identification
rs Rat Strain Ontology
runbiosimulations runBioSimulations
rxno Name Reaction Ontology
sabiork.compound SABIO-RK Compound
sabiork.ec SABIO-RK EC Record
sabiork.kineticrecord SABIO Reaction Kinetics
sabiork.reaction SABIO-RK Reaction
sael Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List
salk Salk Institute for Biological Studies Accession
sao Subcellular Anatomy Ontology
sasbdb Small Angle Scattering Biological Data Bank
sbo Systems Biology Ontology
scdo Sickle Cell Disease Ontology
schem Selventa Chemicals
scomp Selventa Complexes
scop Structural Classification of Protein
scopus Scopus Researcher Identifier
scretf ScerTF
sdbs Spectral Database for Organic Compounds
sdgio Sustainable Development Goals Interface Ontology
sdis Selventa iseasess
sedml.format SED-ML data format
sedml.language SED-ML model format
seed The SEED;
seed.compound SEED Compound
seed.reaction SEED Reactions
sep Sample processing and separation techniques
sepio Scientific Evidence and Provenance Information Ontology
sfam Selventa Families
sgd.pathways Saccharomyces genome database pathways
sgn Sol Genomics Network
sheepqtldb Animal Genome Sheep QTL
sibo Social Insect Behavior Ontology
sider.drug SIDER Drug
sider.effect SIDER Side Effect
sigmaaldirch Sigma Aldrich
signaling-gateway Signaling Gateway
signor Signaling Network Open Resource
signor.relation SIGNOR Relation
sio Semanticscience Integrated Ontology
sisu Sequencing Initiative Suomi
sitex SitEx
skip Stemcell Knowledge and Information Portal
skos Simple Knowledge Organization System
smart Simple Modular Architecture Research Tool
smid C. elegans Small Molecule Identifier Database
smiles Simplified molecular-input line-entry system
smpdb Small Molecule Pathway Database
snap Snapshot
snornabase snoRNABase
snp2tfbs SNP to Transcription Factor Binding Sites
so Sequence types and features ontology
sopharm Suggested Ontology for Pharmacogenomics
soybase Glycine max Genome Database
span Span
spd Spider Ontology
spdx Software Package Data Exchange License
spike.map SPIKE Map
splash Spectra Hash Code
spp Signaling Pathways Project
srao FAIRsharing Subject Ontology
ssbd.dataset System Science of Biological Dynamics dataset
ssbd.project System Science of Biological Dynamics project
stap Statistical Torsional Angles Potentials
stato The Statistical Methods Ontology
stitch Search Tool for Interactions of Chemicals
storedb Store DB
string Search Tool for Retrieval of Interacting Genes/Proteins
sty Semantic Types Ontology
subtilist Bacillus subtilis genome sequencing project
subtiwiki SubtiWiki
sugarbind SugarBind
supfam SUPERFAMILY
swh Software Heritage
swiss-model SWISS-MODEL Repository
swissregulon SwissRegulon
swo Software ontology
symp Symptom Ontology
syoid Gemina Symptom Ontology Identifier
t3db Toxin and Toxin Target Database
tads Tick Anatomy Ontology
tahe Terminology of Anatomy of Human Embryology
tahh Terminology of Anatomy of Human Histology
tair.gene TAIR Gene
tair.locus The Arabidopsis Information Resource
tair.protein TAIR Protein
tao Teleost Anatomy Ontology
tarbase TarBase
taxrank Taxonomic rank vocabulary
te Terminologia Embryologica
tfclass Classification of Transcription Factors in Mammalia
tgd Tetrahymena Genome Database
tgma Mosquito gross anatomy ontology
th Terminologia Histologica
thermofisher Thermo Fisher Scientific
tigrfam TIGR protein families
tkg Tohoku University cell line catalog
to Plant Trait Ontology
tol Tree of Life
topdb Topology Data Bank of Transmembrane Proteins
topfind TopFind
toxoplasma ToxoDB
trans Pathogen Transmission Ontology
transyt Transport Systems Tracker
treebase TreeBASE
treefam TreeFam
trichdb TrichDB
tritrypdb TriTrypDB
ttd.drug TTD Drug
ttd.target TTD Target
txpo Toxic Process Ontology
uberon Uber Anatomy Ontology
ubio.namebank uBio NameBank
ubprop Uberon Property
ucsc UCSC Genome Browser
umbbd.compound UM-BBD Compound
umbbd.enzyme EAWAG Biocatalysis/Biodegradation Database
umbbd.pathway EAWAG Biocatalysis/Biodegradation Database
umbbd.rule EAWAG Biocatalysis/Biodegradation Database
umls Unified Medical Language System
unigene UniGene
unii Unique Ingredient Identifier
unimod Unimod protein modification database for mass spectrometry
uniparc UniProt Archive
unipathway.compound UniPathway Compound
unipathway.reaction UniPathway Reaction
uniprot.chain UniProt Chain
uniprot.disease UniProt Diseases
uniprot.isoform UniProt Isoform
uniprot.keyword UniProt Keywords
uniprot.location UniProt Subcellular Locations
uniprot.tissue Tissue List
uniprot.var UniProt Variants
uniref UniRef
unirule UniRule
unists Database of Sequence Tagged Sites
unite Molecular database for the identification of fungi
unpd Universal Natural Products Database
uo Units of measurement ontology
upheno Unified Phenotype Ontology
uspto United States Patent and Trademark Office
validatordb ValidatorDB
vandf Veterans Administration National Drug File
vario Variation Ontology
vbase2 Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse
vbrc Viral Bioinformatics Resource Center
vectorbase Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens
vega Vertebrate Genome Annotation Database
vegbank VegBank
vfb Virtual Fly Brain
vfdb.gene VFDB Gene
vfdb.genus VFDB Genus
vgnc Vertebrate Gene Nomenclature Committee
vhog Vertebrate Homologous Organ Group Ontology
viaf Virtual International Authority File
vido The Virus Infectious Disease Ontology
vipr Virus Pathogen Resource
viralzone ViralZone
virsirna VIRsiRNA
vmc Variation Modelling Collaboration
vmhgene VMH Gene
vmhmetabolite VMH metabolite
vmhreaction VMH reaction
vo Vaccine Ontology
void Vocabulary of Interlinked Datasets
vsao Vertebrate Skeletal Anatomy Ontology
vsdb Veterinary Substances DataBase
vt Vertebrate trait ontology
vto Vertebrate Taxonomy Ontology
vuid Veterans Health Administration (VHA) unique identifier
wb.rnai WormBase RNAi
wbbt C. elegans Gross Anatomy Ontology
wbls C. elegans development ontology
wbphenotype C. elegans phenotype
webelements Web Elements
wgs84 WGS84 Geo Positioning
wikidata Wikidata
wikidata.property Wikidata Property
wikigenes WikiGenes
wikipedia.en Wikipedia
worfdb C. elegans ORFeome cloning project
wormpep Wormpep
worms World Register of Marine Species
xao Xenopus Anatomy Ontology
xco Experimental condition ontology
xenbase Xenbase
xl Cross-linker reagents ontology
xlmod HUPO-PSI cross-linking and derivatization reagents controlled vocabulary
xpo Xenopus Phenotype Ontology
xsd XML Schema Definition
xuo XUO
ydpm Yeast Deletion and the Mitochondrial Proteomics Project
yeastintron Yeast Intron Database v4.3
yetfasco YeTFasCo
yid Yeast Intron Database v3
ymdb Yeast Metabolome Database
yrcpdr YRC PDR
zea Maize gross anatomy
zeco Zebrafish Experimental Conditions Ontology
zfa Zebrafish anatomy and development ontology
zfs Zebrafish developmental stages ontology
zinc ZINC is not Commercial
zp Zebrafish Phenotype Ontology

Pattern

Same drill for patterns - these entries need a ["pattern"] entry that includes a regular expression describing the local identifiers for this namespace.

Entries (348)
Prefix Name
4dn.replicate 4D Nucleome Data Portal Experiment Replicate
aao Amphibian gross anatomy
abcd AntiBodies Chemically Defined database
ac Activity Streams
aero Adverse Event Reporting Ontology
afo Allotrope Merged Ontology Suite
agro Agronomy Ontology
aism Ontology for the Anatomy of the Insect SkeletoMuscular system
alzforum.mutation Alzforum Mutations
amphx The Amphioxus Development and Anatomy Ontology
apollosv Apollo Structured Vocabulary
araport Arabidopsis Information Portal
asrp Arabidopsis Small RNA Project
ato Amphibian taxonomy
atol Animal Trait Ontology for Livestock
bactibase Bactibase: a database dedicated to bacteriocins
bams Brain Architecture Knowledge Management System Neuroanatomical Ontology
bcgo Beta Cell Genomics Ontology
bcio The Behaviour Change Intervention Ontology
bco Biological Collections Ontology
bel Biological Expression Language
bila Bilateria anatomy
biolegend BioLegend
bioregistry Bioregistry
biorxiv bioRxiv
biozil BIOZIL
birnlex Biomedical Informatics Research Network Lexicon
bmrb.restraint NMR Restraints Grid
bootstrep Gene Regulation Ontology
bpdb Bio-Pesticides DataBase
caro Common Anatomy Reference Ontology
cba Chinese Biological Abstracts
ccle Cancer Cell Line Encyclopedia (CCLE) Cells
cdao Comparative Data Analysis Ontology
cdno Compositional Dietary Nutrition Ontology
cellbank.australia CellBank Australia
cgnc Chicken Gene Nomenclature Consortium
cheminf Chemical Information Ontology
chiro ChEBI Integrated Role Ontology
cido Coronavirus Infectious Disease Ontology
citexplore CiteXplore
clao Collembola Anatomy Ontology
clingene ClinGen Allele Registry
clo Cell Line Ontology
clyh Clytia hemisphaerica Development and Anatomy Ontology
cmf CranioMaxilloFacial ontology
cmpo Cellular Microscopy Phenotype Ontology
co_320 Rice ontology
co_321 Wheat ontology
co_322 Maize ontology
co_323 Barley ontology
co_324 Sorghum ontology
co_325 Banana ontology
co_326 Coconut ontology
co_327 Pearl millet ontology
co_330 Potato ontology
co_331 Sweet Potato ontology
co_333 Beet Ontology ontology
co_334 Cassava ontology
co_335 Common Bean ontology
co_336 Soybean ontology
co_337 Groundnut ontology
co_338 Chickpea ontology
co_339 Lentil ontology
co_340 Cowpea ontology
co_341 Pigeonpea ontology
co_343 Yam ontology
co_345 Brachiaria ontology
co_346 Mungbean ontology
co_347 Castor bean ontology
co_348 Brassica ontology
co_350 Oat ontology
co_356 Vitis ontology
co_357 Woody Plant Ontology ontology
co_358 Cotton ontology
co_359 Sunflower ontology
co_360 Sugar Kelp trait ontology
co_365 Fababean ontology
co_366 Bambara groundnut ontology
cob Core Ontology for Biology and Biomedicine
cog.category COG Categories
cog.pathway COG Pathways
cohd MIMIC III Database
come The Bioinorganic Motif Database
cosmic.cell COSMIC Cell Lines
covoc CoVoc Coronavirus Vocabulary
cp Cellular Phenotypes
cpga Cereal Plant Gross Anatomy
cryoem Cryo Electron Microscopy ontology
csp Computer Retrieval of Information on Science Projects (CRISP) Thesaurus
cto CTO: Core Ontology of Clinical Trials
cvdo Cardiovascular Disease Ontology
dbmhc Database of human Major Histocompatibility Complex
dc Disease Class
dc_cl Dendritic cell
dcat Data Catalog
dcterms Dublin Core Metadata Vocabulary
dctypes Dublin Core Types
dermo Human Dermatological Disease Ontology
dicom DICOM Controlled Terminology
dictybase dictyBase
dideo Drug-drug Interaction and Drug-drug Interaction Evidence Ontology
dinto The Drug-Drug Interactions Ontology
diseasesdb Diseases Database
dpo Drosophila Phenotype Ontology
dron The Drug Ontology
drugcentral Drug Central
dsmz Deutsche Sammlung von Mikroorganismen und Zellkulturen
dto Drug Target Ontology
duo Data Use Ontology
eaglei eagle-i
ecacc European Collection of Authenticated Cell Culture
ecao The Echinoderm Anatomy and Development Ontology
ecocyc EcoCyc
ehda Human developmental anatomy, timed version
ehdaa Human developmental anatomy, abstract version
emap Mouse gross anatomy and development, timed
empiar Electron Microscopy Public Image Archive
enm eNanoMapper Ontology
ensemblglossary Ensembl Glossary
enzo Enzo Life Sciences
eol Environment Ontology for Livestock
epcc European Paediatric Cardiac Codes
epo Epidemiology Ontology
epso Epilepsy Ontology
ero eagle-i resource ontology
eupath VEuPathDB ontology
eurofir European Food Information Resource Network
ev eVOC (Expressed Sequence Annotation for Humans)
evm eVOC mouse development stage
faldo Feature Annotation Location Description Ontology
fbbt Drosophila gross anatomy
fbrf FlyBase Reference Report
fbsp Fly taxonomy
fbtc Flybase Cell Line
fideo Food Interactions with Drugs Evidence Ontology
fishbase.species FishBase
flopo Flora Phenotype Ontology
flu Influenza Ontology
foaf Friend of a Friend
fobi Food-Biomarker Ontology
fovt FuTRES Ontology of Vertebrate Traits
galen Galen Ontology
gard Genetic and Rare Diseases Information Center
gbif Global Biodiversity Information Facility
gecko Genomics Cohorts Knowledge Ontology
genbank GenBank
genepio Genomic Epidemiology Ontology
gexo Gene Expression Ontology
ghr Genetics Home Reference
glygen GlyGen: Computational and Informatics Resources for Glycoscience
go.model Gene Ontology Causal Assembly Model
goeco GO Evidence Code
google.scholar Google Scholar Researcher ID
gorel GO Relations
gro Gene Regulation Ontology
gsfa General Standard for Food Additives (GSFA) Online Database
gtr Genetic Testing Registry
habronattus Habronattus courtship
hancestro Human Ancestry Ontology
hcao Human Cell Atlas Ontology
hcpcs Healthcare Common Procedure Coding System
hms.lincs.compound HMS LINCS Compound
hog Homologous Organ Groups
hom Homology Ontology
hpath Histopathology Ontology
hsdb Hazardous Substances Data Bank
hso Health Surveillance Ontology
htn Hypertension Ontology
icd11 International Classification of Diseases 11th Revision
icd9 International Classification of Diseases 9th Revision
icdo The International Classification of Diseases for Oncology
iceo Integrative and Conjugative Element Ontology
ico Informed Consent Ontology
idocovid19 The COVID-19 Infectious Disease Ontology
idoden Dengue Fever Ontology
iev Event (INOH pathway ontology)
imdrf International Medical Device Regulators Forum
imr Molecule role (INOH Protein name/family name ontology)
inn International Nonproprietary Names
ino Interaction Network Ontology
iro Insect Resistance Ontology
jax Jackson Laboratories Strain
kegg.enzyme KEGG Enzyme
kegg.ligand KEGG LIGAND
kupo Kidney and Urinary Pathway Ontology
labo clinical LABoratory Ontology
lbo Livestock Breed Ontology
lipro Lipid Ontology
lncipedia LNCipedia
loggerhead Loggerhead nesting
loinc Logical Observation Identifiers Names and Codes
mao Multiple alignment
mat Minimal Anatomical Terminology
matrixdb MatrixDB
maxo Medical Action Ontology
mcc Cell Line Ontology [derivative]
mf Mental Functioning Ontology
mfmo Mammalian Feeding Muscle Ontology
mfo Medaka fish anatomy and development
mfoem Emotion Ontology
mfomd Mental Disease Ontology
miaa Minimal Information About Anatomy ontology
miapa MIAPA Ontology
micro Ontology of Prokaryotic Phenotypic and Metabolic Characters
mim.ps OMIM Phenotypic Series
mirbase.family miRBase Families
mirnao microRNA Ontology
mirte miRNA Target Prediction at EMBL
mmsl Multum MediSource Lexicon
mpio Minimum PDDI Information Ontology
mro MHC Restriction Ontology
msigdb Molecular Signatures Database
msio Metabolomics Standards Initiative Ontology
multicellds MultiCellDS
namerxn NameRXN
ncats.drug NCATS Drugs
ncro Non-Coding RNA Ontology
nddf National Drug Data File
ndex Network Data Exchange
ndfrt National Drug File - Reference Terminology
neuronames NeuroNames
nif_cell NIF Cell
nif_dysfunction NIF Dysfunction
nif_grossanatomy NIF Gross Anatomy
nist NIST Chemistry WebBook
nlm National Library of Medicine (NLM) Catalog
nlxanat NeuroLex Anatomy
nlxdys NeuroLex Dysfunction
nomen NOMEN - A nomenclatural ontology for biological names
novus Novus Biologicals
oa Web Annotation Ontology
oae Ontology of Adverse Events
oarcs Ontology of Arthropod Circulatory Systems
obcs Ontology of Biological and Clinical Statistics
obib Ontology for Biobanking
obo Internal OBO and PyOBO Relations
oboinowl OBO in OWL
ogg The Ontology of Genes and Genomes
ogi Ontology for genetic interval
ogms Ontology for General Medical Science
ogsf Ontology of Genetic Susceptibility Factor
ohd The Oral Health and Disease Ontology
ohmi Ontology of Host-Microbiome Interactions
ohpi Ontology of Host Pathogen Interactions
om Ontology of units of Measure
omiabis Ontologized MIABIS
omo OBO Metadata Ontology
omop Observational Medical Outcomes Partnership
omrse Ontology of Medically Related Social Entities
oncotree OncoTree
one Ontology for Nutritional Epidemiology
ons Ontology for Nutritional Studies
ontoneo Obstetric and Neonatal Ontology
oostt Ontology of Organizational Structures of Trauma centers and Trauma systems
opl Ontology for Parasite LifeCycle
opmi Ontology of Precision Medicine and Investigation
ornaseq Ontology of RNA Sequencing
orth Orthology Ontology
ovae Ontology of Vaccine Adverse Events
owl OWL Ontology
panorama Panorama Public
pao Plant Anatomy Ontology
pd_st Platynereis stage ontology
pdro The Prescription of Drugs Ontology
peff PSI Extended File Format
pesticides Alan Wood's Pesticides
pgdso Plant Growth and Development Stage
pharmacodb.cell PharmacoDB Cells
pharmacodb.dataset PharmacoDB Datasets
pharmacodb.tissue PharmacoDB Tissues
pictar PicTar
plo Plasmodium Life Cycle
ppdb Pesticide Properties DataBase
ppo Plant Phenology Ontology
ppr Europe PMC Preprints
propreo Proteomics data and process provenance
prov PROV Namespace
psdo Performance Summary Display Ontology
pseudogene PseudoGene
pso Plant Stress Ontology
pspub Phenoscape Publication
publons.researcher Publons Researcher ID
qudt Quantities, Units, Dimensions, and Types Ontology
radiomics Radiomics Ontology
rbo Radiation Biology Ontology
rdf Resource Description Framework
rdfs RDF Schema
reaxys Reaxys
receptome.family Human Plasma Membrane Receptome Families
reproduceme REPRODUCE-ME Ontology
reto Regulation of Transcription Ontology
rex Physico-chemical process
rexo Regulation of Gene Expression Ontology
rnamod The RNA Modification Database
sael Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List
salk Salk Institute for Biological Studies Accession
sao Subcellular Anatomy Ontology
scdo Sickle Cell Disease Ontology
sdgio Sustainable Development Goals Interface Ontology
sep Sample processing and separation techniques
sepio Scientific Evidence and Provenance Information Ontology
sigmaaldirch Sigma Aldrich
skip Stemcell Knowledge and Information Portal
skos Simple Knowledge Organization System
smid C. elegans Small Molecule Identifier Database
smiles Simplified molecular-input line-entry system
snap Snapshot
snornabase snoRNABase
sopharm Suggested Ontology for Pharmacogenomics
span Span
srao FAIRsharing Subject Ontology
ssbd.dataset System Science of Biological Dynamics dataset
ssbd.project System Science of Biological Dynamics project
stato The Statistical Methods Ontology
syoid Gemina Symptom Ontology Identifier
tahe Terminology of Anatomy of Human Embryology
tahh Terminology of Anatomy of Human Histology
tao Teleost Anatomy Ontology
te Terminologia Embryologica
tfclass Classification of Transcription Factors in Mammalia
th Terminologia Histologica
thermofisher Thermo Fisher Scientific
txpo Toxic Process Ontology
ubprop Uberon Property
ucsc UCSC Genome Browser
uniprot.disease UniProt Diseases
uniprot.keyword UniProt Keywords
unirule UniRule
unpd Universal Natural Products Database
upheno Unified Phenotype Ontology
vandf Veterans Administration National Drug File
vega Vertebrate Genome Annotation Database
vhog Vertebrate Homologous Organ Group Ontology
vido The Virus Infectious Disease Ontology
vmc Variation Modelling Collaboration
vo Vaccine Ontology
void Vocabulary of Interlinked Datasets
vsao Vertebrate Skeletal Anatomy Ontology
vsdb Veterinary Substances DataBase
vuid Veterans Health Administration (VHA) unique identifier
vz ViralZone
wgs84 WGS84 Geo Positioning
wikidata.property Wikidata Property
xl Cross-linker reagents ontology
xsd XML Schema Definition
xuo XUO
zea Maize gross anatomy

URL Formatter

Same drill for URL Formatters - these entries need a ["url"] entry. This is a URL with a $1 character where the local identifier gets put.

{
   ...
   "jax": {
      "example": "004435",
      "name": "Jackson Laboratories Strain",
      "url": "https://www.jax.org/strain/$1"  // <-- this one here
   },
   ...
}
Entries (102)
Prefix Name
afo Allotrope Merged Ontology Suite
asrp Arabidopsis Small RNA Project
atol Animal Trait Ontology for Livestock
bams Brain Architecture Knowledge Management System Neuroanatomical Ontology
bcio The Behaviour Change Intervention Ontology
bel Biological Expression Language
birnlex Biomedical Informatics Research Network Lexicon
bs Biosapiens Protein Feature Ontology
caloha CALIPHO Group Ontology of Human Anatomy
cmpo Cellular Microscopy Phenotype Ontology
co_326 Coconut ontology
cohd MIMIC III Database
covoc CoVoc Coronavirus Vocabulary
cp Cellular Phenotypes
cryoem Cryo Electron Microscopy ontology
csp Computer Retrieval of Information on Science Projects (CRISP) Thesaurus
dbmhc Database of human Major Histocompatibility Complex
dermo Human Dermatological Disease Ontology
dicom DICOM Controlled Terminology
diseasesdb Diseases Database
dto Drug Target Ontology
ecg Electrocardiogram Ontology
enm eNanoMapper Ontology
ensemblglossary Ensembl Glossary
eol Environment Ontology for Livestock
epcc European Paediatric Cardiac Codes
eurofir European Food Information Resource Network
evm eVOC mouse development stage
fishbase.species FishBase
fyler Fyler
galen Galen Ontology
gard Genetic and Rare Diseases Information Center
gexo Gene Expression Ontology
gmelin Gmelins Handbuch der anorganischen Chemie
goeco GO Evidence Code
google.scholar Google Scholar Researcher ID
gorel GO Relations
gro Gene Regulation Ontology
gtr Genetic Testing Registry
hcao Human Cell Atlas Ontology
hcpcs Healthcare Common Procedure Coding System
hog Homologous Organ Groups
hpath Histopathology Ontology
icd11 International Classification of Diseases 11th Revision
icd9 International Classification of Diseases 9th Revision
icdo The International Classification of Diseases for Oncology
idocovid19 The COVID-19 Infectious Disease Ontology
idoden Dengue Fever Ontology
ihw International Histocompatibility Workshop cell lines
imdrf International Medical Device Regulators Forum
kupo Kidney and Urinary Pathway Ontology
lbo Livestock Breed Ontology
lncipedia LNCipedia
mcc Cell Line Ontology [derivative]
miaa Minimal Information About Anatomy ontology
mirte miRNA Target Prediction at EMBL
mmsl Multum MediSource Lexicon
molbase.sheffield MolBase
msigdb Molecular Signatures Database
msio Metabolomics Standards Initiative Ontology
namerxn NameRXN
nddf National Drug Data File
ndfrt National Drug File - Reference Terminology
nist NIST Chemistry WebBook
npass Natural Product Activity and Species Source Database
om Ontology of units of Measure
omop Observational Medical Outcomes Partnership
orth Orthology Ontology
peff PSI Extended File Format
pictar PicTar
pseudogene PseudoGene
pspub Phenoscape Publication
radiomics Radiomics Ontology
rdo RGD Disease_Ontology
reaxys Reaxys
reproduceme REPRODUCE-ME Ontology
reto Regulation of Transcription Ontology
rexo Regulation of Gene Expression Ontology
sael Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List
schem Selventa Chemicals
scomp Selventa Complexes
scopus Scopus Researcher Identifier
sdgio Sustainable Development Goals Interface Ontology
sdis Selventa iseasess
sfam Selventa Families
signor.relation SIGNOR Relation
smiles Simplified molecular-input line-entry system
snap Snapshot
snornabase snoRNABase
span Span
srao FAIRsharing Subject Ontology
syoid Gemina Symptom Ontology Identifier
te Terminologia Embryologica
th Terminologia Histologica
ubprop Uberon Property
unpd Universal Natural Products Database
vandf Veterans Administration National Drug File
vega Vertebrate Genome Annotation Database
vido The Virus Infectious Disease Ontology
vmc Variation Modelling Collaboration
vuid Veterans Health Administration (VHA) unique identifier
xuo XUO

Example Identifier

As a courtesy to newcomers, it’s nice to show an example local identifier. These entries need a ["example"] entry.

{
   ...
   "jax": {
      "example": "004435",  // <-- this one here
      "name": "Jackson Laboratories Strain",
      "url": "https://www.jax.org/strain/$1"
   },
   ...
}
Entries (73)
Prefix Name
aao Amphibian gross anatomy
afo Allotrope Merged Ontology Suite
ato Amphibian taxonomy
bams Brain Architecture Knowledge Management System Neuroanatomical Ontology
bcgo Beta Cell Genomics Ontology
bila Bilateria anatomy
bootstrep Gene Regulation Ontology
chiro ChEBI Integrated Role Ontology
cmf CranioMaxilloFacial ontology
cohd MIMIC III Database
cp Cellular Phenotypes
cpga Cereal Plant Gross Anatomy
dc_cl Dendritic cell
dinto The Drug-Drug Interactions Ontology
dpo Drosophila Phenotype Ontology
ehda Human developmental anatomy, timed version
ehdaa Human developmental anatomy, abstract version
emap Mouse gross anatomy and development, timed
epcc European Paediatric Cardiac Codes
epo Epidemiology Ontology
eurofir European Food Information Resource Network
ev eVOC (Expressed Sequence Annotation for Humans)
evm eVOC mouse development stage
fbsp Fly taxonomy
flu Influenza Ontology
gexo Gene Expression Ontology
gro Gene Regulation Ontology
habronattus Habronattus courtship
hcao Human Cell Atlas Ontology
iev Event (INOH pathway ontology)
imdrf International Medical Device Regulators Forum
imr Molecule role (INOH Protein name/family name ontology)
kegg.enzyme KEGG Enzyme
kegg.ligand KEGG LIGAND
lipro Lipid Ontology
loggerhead Loggerhead nesting
mao Multiple alignment
mat Minimal Anatomical Terminology
mcc Cell Line Ontology [derivative]
mfo Medaka fish anatomy and development
miaa Minimal Information About Anatomy ontology
mirnao microRNA Ontology
nif_cell NIF Cell
nif_dysfunction NIF Dysfunction
nif_grossanatomy NIF Gross Anatomy
nist NIST Chemistry WebBook
obo Internal OBO and PyOBO Relations
omo OBO Metadata Ontology
omop Observational Medical Outcomes Partnership
pao Plant Anatomy Ontology
pd_st Platynereis stage ontology
pgdso Plant Growth and Development Stage
plo Plasmodium Life Cycle
propreo Proteomics data and process provenance
pspub Phenoscape Publication
reto Regulation of Transcription Ontology
rexo Regulation of Gene Expression Ontology
sael Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List
sao Subcellular Anatomy Ontology
sep Sample processing and separation techniques
sopharm Suggested Ontology for Pharmacogenomics
span Span
syoid Gemina Symptom Ontology Identifier
tahe Terminology of Anatomy of Human Embryology
tahh Terminology of Anatomy of Human Histology
ubprop Uberon Property
unpd Universal Natural Products Database
upheno Unified Phenotype Ontology
vmc Variation Modelling Collaboration
vsao Vertebrate Skeletal Anatomy Ontology
xl Cross-linker reagents ontology
xuo XUO
zea Maize gross anatomy