Welcome to the Help Wanted section of the Bioregistry đź‘‹, a place where both first-time contributors or veteran Bioregistras can find small, meaningful ways to contribute novel curations.

It’s one of the core values of the Bioregistry project to provide attribution and appreciation to curation contributors, here’s how that works:

  1. We associate your ORCID identifier with records that you submitted or helped improve. These are displayed proudly on our site’s contributions page.
  2. We associate your GitHub handle with the commits to the repository (even if one of the Bioregistry team members or an automated workflow on GitHub makes it on your behalf) to get GitHub cred.
  3. We will consider all curation contributors as co-authors on Bioregistry papers.

Table of Contents:

Each of the following sections has its own instructions on how to get started making your own curations. If there’s something unclear, please let us know via the GitHub issue tracker, and we can improve this page.

  1. Improving the Metaregistry
  2. Aligning Wikidata database records
  3. Curating regular expression patterns
  4. Curating URI format strings
  5. Curating example local unique identifiers

Improving the Metaregistry

The Bioregistry processes and semi-automatically aligns metadata from external registries such as Identifiers.org, the OBO Foundry, FAIRsharing, and others. These alignments constitute the Bioregistry’s metaregistry. Some resources (e.g., Identifiers.org) have similar scope, minimum metadata standards, and curation standards to the Bioregistry and are imported in full. Others are aligned only when prefixes can be matched based on an algorithm.

This means that there are potentially many records in external registries that are relevant for the Bioregistry, but either were not able to be mapped to an existing prefix, or do not have a mapping but would be valuable to import.

The following table links to curation sheets for each external registry that show relevant metadata to help curate each record as one of the following:

  1. Record corresponds to a prefix in the Bioregistry. Tutorial TBD.
  2. Record is relevant but does not have a corresponding prefix in the Bioregistry. See the tutorial on importing external prefixes.
  3. Record is irrelevant for the bioregistry. See the tutorial on curating explicit prefix blacklists.
Prefix Name
aberowl AberOWL
agroportal AgroPortal
bartoc BARTOC
biocontext BioContext
biolink Biolink
bioportal BioPortal
cellosaurus Cellosaurus
cropoct CropOCT
ecoportal EcoPortal
edam EDAM
fairsharing FAIRSharing
go GO
hl7 HL7
ncbi NCBI
ontobee OntoBee
prefixcommons Prefix Commons
re3data re3data
uniprot UniProt
wikidata Wikidata

Aligning Wikidata Database Records

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. Make sure an item doesn’t exist already by doing a cursory search of Wikidata.
  2. Create a new item.
  3. Create the first relationship instance of (P31) and target biological database (Q4117139).
  4. Add second relationship official website (P856)
  5. 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 (1458)
Prefix Name
aaindex AAindex
aao Amphibian gross anatomy
abcd AntiBodies Chemically Defined database
abm Applied Biological Materials cell line products
ac Activity Streams
aceview.worm Aceview Worm
addexbio AddexBio cell line products
addgene Addgene Plasmid Repository
ado Alzheimer's Disease Ontology
adw Animal natural history and life history
aeo Anatomical Entity Ontology
aeon Academic Event Ontology
aero Adverse Event Reporting Ontology
affy.probeset Affymetrix Probeset
afo Allotrope Merged Ontology Suite
aftol.taxonomy Assembling the Fungal Tree of Life - Taxonomy
agilent.probe Agilent Probe
agricola Agricultural Online Access
agrkb Alliance of Genome Resources Knowledge Base
agro Agronomy Ontology
agsd Animal Genome Size Database
aism Ontology for the Anatomy of the Insect SkeletoMuscular system
alfred The ALlele FREquency Database
allergome Allergome
alzforum.mutation Alzforum Mutations
alzgene Alzheimer Gene Database
amoebadb AmoebaDB
amphx The Amphioxus Development and Anatomy Ontology
antibodyregistry Antibody Registry
aop AOPWiki
aop.events AOPWiki (Key Event)
aop.relationships AOPWiki (Key Event Relationship)
aop.stressor AOPWiki (Stressor)
apaonto Psychology Ontology
apd Antimicrobial Peptide Database
aphidbase.transcript AphidBase Transcript
apid.interactions APID Interactomes
apo Ascomycete phenotype ontology
apollosv Apollo Structured Vocabulary
arachnoserver ArachnoServer
araport Arabidopsis Information Portal
archdb ArchDB
ardb Antibiotic Resistance Genes Database
ark Archival Resource Key
aro Antibiotic Resistance Ontology
arrayexpress ArrayExpress
arrayexpress.platform ArrayExpress Platform
arraymap ArrayMap
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
astd ASTD
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
bacmap.biog BacMap Biography
bacmap.map BacMap Map
bactibase Bactibase
bams Brain Architecture Knowledge Management System Neuroanatomical Ontology
bao BioAssay Ontology
bartoc Basic Register of Thesauri, Ontologies & Classifications
bbkg Blue Brain Project Knowledge Graph
bbtp Blue Brain Project Topological sampling Knowledge Graph
bcgo Beta Cell Genomics Ontology
bcio The Behaviour Change Intervention Ontology
bco Biological Collections Ontology
bcrc BCRC Strain Collection Catalog
bcrj Banco de Celulas do Rio de Janeiro
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
beiresources BEI Resources
bel Biological Expression Language
bfo Basic Formal Ontology
bgee.family Bgee family
bgee.gene Bgee gene
bgee.organ Bgee organ
bgee.stage Bgee stage
bibo The Bibliographic Ontology
bido Bibliometric Data Ontology
bigg.compartment BiGG Compartment
bigg.metabolite BiGG Metabolite
bigg.model BiGG Model
bigg.reaction BiGG Reaction
bila Bilateria anatomy
bind BIND accession number
bindingdb BindingDB
biocarta.pathway BioCarta Pathway
biocatalogue.service BioCatalogue Service
biocyc BioCyc collection of metabolic pathway databases
biofactoid Biofactoid
biogrid BioGRID
biogrid.interaction BioGRID Interactions
biolegend BioLegend
biolink Biolink Model
biomagresbank BioMagResBank
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
biopixie biological Process Inference from eXperimental Interaction Evidence/Microarray Experiment Functional Integration Technology
bioportal BioPortal
bioproject BioProject
bioregistry Bioregistry
bioregistry.collection Bioregistry Collections
bioregistry.registry Bioregistry Metaregistry
bioregistry.schema Bioregistry Schema
biosample BioSample
bioschemas BioSchemas
biosimulations biosimulations
biosimulators BioSimulators
biostudies BioStudies database
biosystems BioSystems
biotools BioTools
biozil BIOZIL
birnlex Biomedical Informatics Research Network Lexicon
biro Bibliographic Reference Ontology
bitbucket Bitbucket
bitterdb.cpd BitterDB Compound
bitterdb.rec BitterDB Receptor
bko SBGN Bricks data and ontology
bmrb Biological Magnetic Resonance Data Bank
bmrb.restraint NMR Restraints Grid
bootstrep Gene Regulation Ontology
bpdb Bio-Pesticides DataBase
brenda BRENDA Enzyme
brenda.ligand BRENDA Ligand
brenda.ligandgroup BRENDA Ligand Group
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
c4o Citation Counting and Context Characterisation Ontology
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
casspc Eschmeyer's Catalog of Fishes
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 Cells
cco Cell Cycle Ontology
ccrid National Experimental Cell Resource Sharing Platform
cdao Comparative Data Analysis Ontology
cdd Conserved Domain Database at NCBI
cdno Compositional Dietary Nutrition Ontology
cdpd Canadian Drug Product Database
cdt Current Dental Terminology
cell_biolabs Cell Biolabs cell line products
cell_model_passport Sanger Cell Model Passports
cellbank.australia CellBank Australia
cellimage Cell Image Library
cellopub Cellosaurus Publication
cellosaurus.resource Cellosaurus Registry
cellrepo Cell Version Control Repository
cemo The COVID-19 epidemiology and monitoring ontology
ceph Cephalopod Ontology
cgd Candida Genome Database
cghdb CGH Data Base
cgnc Chicken Gene Nomenclature Consortium
cgsc Coli Genetic Stock Center
charprot CharProt
chembank ChemBank
chembl ChEMBL
chembl.cell ChEMBL database of bioactive drug-like small molecules - Cell lines section
chembl.target ChEMBL target
chemdb ChemDB
chemidplus ChemIDplus
cheminf Chemical Information Ontology
chemrof Chemical Entity Materials and Reactions Ontological Framework
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
cito Citation Typing Ontology
civic.aid CIViC Assertion
civic.did CIViC Disease
civic.eid CIViC Evidence
civic.sid CIViC Source
civic.tid CIViC Therapy
clao Collembola Anatomy Ontology
classyfire ClassyFire
clb ChecklistBank
cldb Cell Line Database
clingene ClinGen Allele Registry
clinvar.record ClinVar Record
clinvar.submission ClinVar Submission
clinvar.submitter ClinVar Submitter
cls Cell Lines Service
clyh Clytia hemisphaerica Development and Anatomy Ontology
cmecs Costal and Marine Ecological Classification Standard
cmf CranioMaxilloFacial ontology
cmo Clinical measurement ontology
cmpo Cellular Microscopy Phenotype Ontology
cnrs French National Center for Scientific Research - Research Group Identifier
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
co_367 Quinoa Ontology ontology
co_370 Apple Ontology
cob Core Ontology for Biology and Biomedicine
coconut COlleCtion of Open Natural ProdUcTs
codelink GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray
cog Cluster of orthologous genes
cog.category COG Categories
cog.pathway COG Pathways
cohd MIMIC III Database
col Catalogue of Life
colao Coleoptera Anatomy Ontology
collagenmutdb Collagen Mutation Database
colonatlas Colorectal Cancer Atlas
combine.specifications COMBINE specifications
come The Bioinorganic Motif Database
commoncoreontology Common Core Ontologies
compulyeast Compluyeast-2D-DB
confident.event ConfIDent Event
confident.series ConfIDent Event Series
conoserver ConoServer
conso Curation of Neurodegeneration Supporting Ontology
cordis.article CORDIS Article
cordis.project CORDIS Project
coriell Coriell Institute for Medical Research
corrdb CorrDB
corum Comprehensive Resource of Mammalian protein complexes
cosmic COSMIC Gene
cosmic.cell COSMIC Cell Lines
covid19 COVID-19 Surveillance Ontology
covoc CoVoc Coronavirus Vocabulary
cp Cellular Phenotypes
cpc Cooperative Patent Classification
cpt Current Procedural Terminology
credit CASRAI Contributor Roles Taxonomy
crisprdb CRISPRdb
cro Contributor Role Ontology
crop2ml CropMRepository
cryoem Cryo Electron Microscopy ontology
cryptodb CryptoDB
csa Catalytic Site Atlas
csd Cambridge Structural Database
csp Computer Retrieval of Information on Science Projects Thesaurus
cst Cell Signaling Technology Pathways
cst.ab Cell Signaling Technology Antibody
ctcae Common Terminology Criteria for Adverse Events
ctd.chemical CTD Chemical
ctd.disease CTD Disease
ctd.gene CTD Gene
cteno Ctenophore Ontology
cto Clinical Trials Ontology
cubedb Cube db
cutg Codon Usage Tabulated from GenBank
cvdo Cardiovascular Disease Ontology
cvx Vaccine administered code set
d1id DataONE
dailymed DailyMed
dandi Distributed Archives for Neurophysiology Data Integration
darc Database of Aligned Ribosomal Complexes
dashr Database of small human noncoding RNAs
dashr.expression DASHR expression
datacite DataCite Ontology
datacommons Data Commons
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
dbo DBPedia Ontology
dbprobe NCBI Probe database Public registry of nucleic acid reagents
dbvar.study Database of Genomic Structural Variation - Study
dbvar.variant Database of Genomic Structural Variation - Variant
dc Dublin Core Elements (1.1)
dc_cl Dendritic cell
dcat Data Catalog
dcterms Dublin Core Metadata Initiative Terms
dctypes Dublin Core Types
ddanat Dictyostelium discoideum anatomy
ddinter.drug Curated Drug-Drug Interactions Database - Drug
ddinter.interaction Curated Drug-Drug Interactions Database - Interaction
ddpheno Dictyostelium discoideum phenotype ontology
debio Decentralized Biomedical Ontology
decipher DECIPHER CNV Syndromes
degradome Degradome Database
deo Discourse Elements Ontology
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
dg5b0d BloodPAC
dgrc Drosophila Genomics Resource Center
dhba Developing Human Brain Atlas
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
discoverx DiscoverX cell line products
disdriv Disease Drivers Ontology
diseaseclass Disease Class
disprot DisProt
disprot.region DisProt region
dlxb Linear double stranded DNA sequences
dlxc Circular double stranded DNA sequences composed
dmba Developing Mouse Brain Atlas
doap Description of a Project
doco Document Components Ontology
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.category DrugBank Drug Category
drugbank.salt DrugBank Salts
drugbankv4.target DrugBank Target v4
dsmz Deutsche Sammlung von Mikroorganismen und Zellkulturen
dso Data Science Ontology
dto Drug Target Ontology
duo Data Use Ontology
eaglei eagle-i
easychair.cfp EasyChair Call for Paper
easychair.topic EasyChair Topic
ebisc European Bank for induced pluripotent Stem Cells
ecacc European Collection of Authenticated Cell Culture
ecao The Echinoderm Anatomy and Development Ontology
ecg Electrocardiogram Ontology
echobase EchoBASE post-genomic database for Escherichia coli
ecocore An ontology of core ecological entities
ecocyc EcoCyc
ecogene Database of Escherichia coli Sequence and Function
ecolexicon EcoLexicon
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
edam.data EDAM Data
edam.format EDAM Format
edam.operation EDAM Operation
edam.topic EDAM Topic
edda EDDA Study Designs Taxonomy
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
emaps Mouse Developmental Anatomy Ontology with Theiler Stage
emdb Electron Microscopy Data Bank
emolecules Reaxys eMolecules
empiar Electron Microscopy Public Image Archive
ena.embl European Nucleotide Archive
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
eo Plant Environment Ontology
eol Environment Ontology for Livestock
epcc European Paediatric Cardiac Codes
epd Eukaryotic Promoter Database
epio Epilepsy Ontology
epo Epidemiology Ontology
epso Epilepsy and Seizure Ontology
erm European Registry of Materials
ero eagle-i resource ontology
eropmoscow Endogenous Regulatory OligoPeptide knowledgebase-Moscow
erv Human Endogenous Retrovirus Database
esldb eukaryotic Subcellular Localization database
estdab European Searchable Tumour Line Database
eu89h JRC Data Catalogue
euclinicaltrials EU Clinical Trials
eugenes Eukaryotic Genes
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
fabio FaBiO, the FRBR-aligned Bibliographic Ontology
facebase FaceBase Data Repository
fairsharing FAIRsharing
fairsharing.organization FAIRsharing Organization
fairsharing.user FAIRsharing User
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.
fbql FlyBase Qualifiers
fbrf FlyBase Reference Report
fbsp Fly taxonomy
fbtc Flybase Cell Line
fcb the FAIR Cookbook
fcsfree Fetal Calf Serum-Free Database
fhir.implementation FHIR United States Implementation Guides
fideo Food Interactions with Drugs Evidence Ontology
fivestars Five Stars of Online Research Articles Ontology
fix Physico-chemical methods and properties
flopo Flora Phenotype Ontology
flowrepository FlowRepository
flu Influenza Ontology
flybrain.ndb FlyBrain Neuron Database
flymine.chromosome FlyMine Chromosome Band
foaf Friend of a Friend
fobi Food-Biomarker Ontology
foodb.food FooDB Food
foodex2 Food classification and description system
foodon The Food Ontology
fovt FuTRES Ontology of Vertebrate Traits
fplx FamPlex
fr FAIR* Reviews Ontology
frapo Funding, Research Administration and Projects Ontology
frbr Functional Requirements for Bibliographic Records
fsnp F-SNP
ftt Feature Type Thesaurus
funcbase.fly FuncBase Fly
funcbase.human FuncBase Human
funcbase.mouse FuncBase Mouse
funcbase.yeast FuncBase Yeast
funderregistry FunderRegistry
fungidb FungiDB
fyeco Fission Yeast Experimental Conditions Ontology
fyler Fyler
fypo Fission Yeast Phenotype Ontology
ga4ghdos Data Object Service
gabi Network of Different Plant Genomic Research Projects
galen GALEN
gateway Health Data Research Innovation Gateway
gaz Gazetteer
gc Genetic Code
gcst GWAS Catalog
gdc Genomic Data Commons Data Portal
gdsc Genomics of Drug Sensitivity in Cancer
gear Gene Expression Analysis Resource
gecko Genomics Cohorts Knowledge Ontology
gemet General Multilingual Environmental Thesaurus
genatlas Genatlas
genbank GenBank
gendis Genomic Distribution of structural Superfamilies
genecards GeneCards
genecards.geneannot GeneAnnot: Microarray Gene Annotation
genecards.geneloc Gene Location
genecards.genenote Gene Normal Tissue Expression
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
geonames GeoNames
geonames.feature GeoNames Feature Code
gexo Gene Expression Ontology
gfo General Formal Ontology
ghr Genetics Home Reference
giardiadb GiardiaDB
github github
github.issue GitHub Issue
github.pull GitHub Pull Request
gitlab GitLab
glida.gpcr GLIDA GPCR
glida.ligand GLIDA Ligand
glycoepitope GlycoEpitope
glycomapsdb GlycoMapsDB
glycomedb GlycomeDB
glyconavi GlycoNAVI
glycopost GlycoPOST
glycosciencesdb Glycosciences.DB
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
gno Glycan Naming and Subsumption Ontology
gnomad Genome Aggregation Database
gnpis GnpIS
go Gene Ontology
go.gpi Gene Product Information Schema
go.model Gene Ontology Causal Assembly Model
go.ref Gene Ontology Database references
go.resource Gene Ontology Registry
go.rule Gene Ontology Rules
goa Gene Ontology Annotation Database
goche GO Chemicals
goeco GO Evidence Code
gold Genomes Online Database
gold.genome GOLD genome
gold.meta GOLD metadata
google.book Google Books
google.patent Google Patents
google.scholar Google Scholar Researcher
gorel GO Relations
gpcrdb G protein-coupled receptor database
gpmdb Global Proteome Machine Database
graingenes.reference GrainGenes
graingenes.symbol GrainGenes
gramene.gene Gramene Gene
gramene.growthstage Gramene Growth Stage Ontology
gramene.protein Gramene protein
gramene.qtl Gramene QTL
gramene.reference Gramene Reference
gramene.taxonomy Gramene Taxonomy
greengenes 16S rRNA gene database
grid Global Research Identifier Database
grin Germplasm Resources Information Network
gro Gene Regulation Ontology
grsdb G-Rich Sequences Database
gsfa General Standard for Food Additives 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
hagr.genage The Ageing Gene Database
hagr.gendr The Dietary Restriction Gene Database
hamap High-quality Automated and Manual Annotation of microbial Proteomes
hancestro Human Ancestry Ontology
hao Hymenoptera Anatomy Ontology
hathitrust Hathi Trust Digital Library
hba Human Brain Atlas
hbvar A Database of Human Hemoglobin Variants and Thalassemias
hc.din Health Canada Drug Identification Number
hc.npn Health Canada Natural Product Number
hcao Human Cell Atlas Ontology
hcpcs Healthcare Common Procedure Coding System
hcvdb Hepatitis C Virus Database Project
hdr Homeodomain Research
hesa UK Higher Education Statistics Agency
hgmd Human Gene Mutation Database
hgnc.genefamily HGNC gene family
hgnc.genegroup HGNC Gene Group
hinv.locus H-InvDb Locus
hinv.protein H-InvDb Protein
hinv.transcript H-InvDb Transcript
hipsci Human Induced Pluripotent Stem Cells Initiative
hivreagentprogram NIH HIV Reagent Program
hl7.v2codesystem HL7 V2 Code Systems
hl7.v3codesystem HL7 V2 Code Systems
hms.lincs.antibody HMS Library of Integrated Network-based Cellular Signatures Antibodies
hms.lincs.cell HMS LINCS Cell
hms.lincs.compound HMS LINCS Compound
hms.lincs.dataset HMS Library of Integrated Network-based Cellular Signatures Datasets
hog Homologous Organ Groups
hogenom Database of Complete Genome Homologous Genes Families
hoip Homeostasis imbalance process ontology
hom Homology Ontology
homd.seq HOMD Sequence Metainformation
homd.taxon Human Oral Microbiome Database
horizon_discovery Horizon Discovery cell line collection
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
hprd Human Protein Reference Database
hpscreg Human Pluripotent Stem Cell Registry
hsapdv Human Developmental Stages
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
icdc Integrated Canine Data Commons
iceberg.cime ICEberg cis-integrative and mobilizable element
iceberg.element ICEberg integrative and conjugative element
iceberg.family ICEberg family
iceberg.ime ICEberg integrative and mobilizable element
iceo Integrative and Conjugative Element Ontology
icepo Ion Channel Electrophysiology Ontology
icf International Classification of Functioning, Disability and Health
iclc Interlab Cell Line Collection
ico Informed Consent Ontology
ideal Intrinsically Disordered proteins with Extensive Annotations and Literature
ido Infectious Disease Ontology
idocovid19 The COVID-19 Infectious Disease Ontology
idoden Dengue Fever Ontology
idog Integrated Resource for Domestic Dog
idomal Malaria Ontology
idoo Identifiers.org Ontology
idot Identifiers.org Terms
idpo Intrinsically Disordered Proteins Ontology
idr Image Data Resource
iedb Immune Epitope Database
ietf.language Internet Engineering Task Force Language Tag
iev Event (INOH pathway ontology)
igrhcellid Integrated Genomic Resources of human Cell Lines for Identification
igsn International Geo Sample Number
igsr International Genome Sample Resource
ihw International Histocompatibility Workshop cell lines
illumina.probe Illumina Probe Identifier
imanis Imanis Life Sciences cell line products
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
imgt.primerdb IMGT/PRIMER-DB
imotdb Database of Spatially Interacting Motifs in Proteins
imr Molecule role (INOH Protein name/family name ontology)
inaturalist.place iNaturalist Place
inaturalist.user iNaturalist User
inhand The International Harmonization of Nomenclature and Diagnostic criteria
innatedb A Knowledge Resource for Innate Immunity Interactions and Pathways
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
interfil Human Intermediate Filament Database
interpro InterPro
iobc Interlinking Ontology for Biological Concepts
ipi International Protein Index
ird.segment IRD Segment Sequence
irefweb iRefWeb
iresite Database of experimentally verified IRES structures
iro Insect Resistance Ontology
isbn International Standard Book Number
ised Influenza Sequence and Epitope Database
isfinder Insertion sequence elements database
isni International Standard Name Identifier
iso.3166 ISO 3166-1 Country Code
issn International Standard Serial Number
ito Intelligence Task Ontology
iuphar.family IUPHAR family
ivdb Influenza Virus Database
jax Jackson Laboratories Strain
jaxmice JAX Mice
jcggdb Japan Consortium for Glycobiology and Glycotechnology Database
jcm Japan Collection of Microorganisms
jcrb JRBC Cell Bank
jcsd Japan Chemical Substance Dictionary
jstor Digital archive of scholarly articles
jws JWS Online
kaggle Kaggle
kclb Korean Cell Line Bank
kegg Kyoto Encyclopedia of Genes and Genomes
kegg.brite KEGG BRITE
kegg.compound KEGG Compound
kegg.dgroup KEGG Drug Group
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
kegg.rclass KEGG Reaction Class
kerafast Kerafast cell lines
kupo Kidney and Urinary Pathway Ontology
kyinno KYinno cell lines
labo clinical LABoratory Ontology
langual Langua aLimentaria Thesaurus
lbo Livestock Breed Ontology
lei Global LEI Index
lepao Lepidoptera Anatomy Ontology
lgai.cede LG Chemical Entity Detection Dataset (LGCEDe)
lgic Ligand-Gated Ion Channel database
licebase LiceBase
ligandbook LigandBook
ligandbox LigandBox
ligandexpo Ligand Expo
ligea Cancer cell LInes GEne fusions portAl
limore Liver Cancer Model Repository
lincs.cell LINCS Cell
lincs.data LINCS Data
lincs.protein LINCS Protein
lincs.smallmolecule LINCS Small Molecule
linguist Linguist
linkml LinkML
lipidbank LipidBank
lipro Lipid Ontology
lncipedia LNCipedia
loggerhead Loggerhead nesting
lonza Lonza
loqate The localization and quantitation atlas of the yeast proteome
lpt Livestock Product Trait Ontology
lrg Locus Reference Genomic
lspci Laboratory of Systems Pharmacology Compound
lter Long Term Ecological Research Controlled Vocabulary
ma Mouse adult gross anatomy
macie Mechanism, Annotation and Classification in Enzymes
maizegdb.locus MaizeGDB Locus
mamo Mathematical modeling ontology
mampol Mammalia Polymorphism Database
mao Multiple alignment
massive MassIVE
mat Minimal Anatomical Terminology
matrixdb MatrixDB
matrixdb.association MatrixDB Association
maxo Medical Action Ontology
mba Mouse Brain Atlas
mcc Cell Line Ontology [derivative]
mco Microbial Conditions Ontology
mdm Medical Data Models
medgen Human Medical Genetics
medlineplus MedlinePlus Health Topics
merops.clan MEROPS Clan
merops.entry MEROPS Entry
merops.family MEROPS Family
mesh.2012 MeSH 2012
mesh.2013 MeSH 2013
mesh.vocab Medical Subject Headings Vocabulary
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
metatlas Metabolic Atlas
metatlas.metabolite Metabolic Atlas Metabolite
metatlas.reaction Metabolic Atlas Reaction
metlin Metabolite and Tandem Mass Spectrometry Database
metnetdb Metabolic Network Exchange 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 Minimum Anformation About a Phylogenetic Analysis Ontology
micro Ontology of Prokaryotic Phenotypic and Metabolic Characters
microscope MicroScope
microsporidia MicrosporidiaDB
millipore Merck Millipore (EMD Millipore)
mimodb MimoDB
minid Minimal Viable Identifier
minid.test MINID Test
mint Molecular Interaction Database
mipmod MIPModDB
mir Identifiers.org Registry
mirex mirEX
miriam Identifiers.org namespace
miriam.collection MIRIAM Registry collection
miriam.resource MIRIAM Legacy Registry Identifier
mirnao microRNA Ontology
mirnest miRNEST
miro Mosquito insecticide resistance
mirte miRNA Target Prediction at EMBL
mixs Minimal Information about any Sequence
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
mmsinc MMsINC
mmsl Multum MediSource Lexicon
mmusdv Mouse Developmental Stages
mo Microarray experimental conditions
mobidb MobiDB
mod Protein modification
modeldb ModelDB
modeldb.concept ModelDB concept
molbase Molbase
molbase.sheffield MolBase
molmedb MolMeDB
molmovdb Database of Macromolecular Movements
mop Molecular Process Ontology
morpheus Morpheus model repository
mosaic MOSAiC Ontology
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
mtbd Mouse Tumor Biology Database
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 TubercuList knowledge base
mycobank Fungal Nomenclature and Species Bank
mzspec Universal Spectrum Identifier
n2t Name-to-Thing
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.bioplanet National Center for Advancing Translation Sciences BioPlanet
ncats.drug NCATS Drugs
ncbi.assembly Assembly
ncbi.genome NCBI Genome
ncbi.resource NCBI Registry
ncbibook NCBI Bookshelf
ncbigi GenInfo Identifier
ncbiprotein NCBI Protein
ncim NCI Metathesaurus
ncro Non-Coding RNA Ontology
nddf National Drug Data File
ndex Network Data Exchange
nembase Nematode & Neglected Genomics
nemo Neuroscience Multi-Omic BRAIN Initiative Data
nemo2 Neural ElectroMagnetic Ontology
neurolex NIF Standard Ontology: Neurolex
neuromorpho NeuroMorpho
neurondb NeuronDB
neurovault.collection NeuroVault Collection
neurovault.image NeuroVault Image
nextdb Nematode Expression Pattern DataBase
nextprot.family neXtProt family
ngl NASA GeneLab
nhcdr NINDS Human Cell and Data Repository
niaest NIA Mouse cDNA Project
nif.cell NIF Cell
nif.dysfunction NIF Dysfunction
nif.ext NIF Standard Ontology: External
nif.grossanatomy NIF Gross Anatomy
nif.std NIF Standard Ontology
nihreporter.project NIH RePORTER
nist NIST Chemistry WebBook
nlm National Library of Medicine Catalog
nlx.anat NeuroLex Anatomy
nlx.br NIF Standard Ontology: Brain Regions
nlx.cell NIF Standard Ontology: Cell Types
nlx.chem NIF Standard Ontology: Chemical
nlx.dys NeuroLex Dysfunction
nlx.func NIF Standard Ontology: Cognitive Function
nlx.inv NIF Standard Ontology: Investigations
nlx.mol NIF Standard Ontology: Molecules
nlx.oen NIF Standard Ontology: OEN Terms in Neurolex
nlx.org NIF Standard Ontology: Organisms
nlx.qual NIF Standard Ontology: Qualities
nlx.res NIF Standard Ontology: Digital Resources
nlx.sub NIF Standard Ontology: Subcellular Entities
nmpdr National Microbial Pathogen Data Resource
nmr NMR-instrument specific component of metabolomics investigations
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
npo NanoParticle Ontology
nsc USA National Service Center Number
nsf.award National Science Foundation Award
nucc.characteristic National Uniform Claim Committee Characteristic
nucc.taxonomy National Uniform Claim Committee Taxonomy
nucleardb NucleaRDB
nucleotide Nucleotide
oa Web Annotation Ontology
oae Ontology of Adverse Events
oarcs Ontology of Arthropod Circulatory Systems
oba Ontology of Biological Attributes
oban Open Biomedical Annotations
obcs Ontology of Biological and Clinical Statistics
obi Ontology for Biomedical Investigations
obib Ontology for Biobanking
obo Open Biological and Biomedical Ontologies
oboinowl OBO in OWL
occ OpenCitations Corpus
oci Open Citation Identifier
ocid Ontology Concept Identifiers
oclc Online Computer Library Center 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 Oral Health and Disease Ontology
ohmi Ontology of Host-Microbiome Interactions
ohpi Ontology of Host Pathogen Interactions
oid ISO Object Identifier
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
omim.ps OMIM Phenotypic Series
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
ontoavida Ontology for Avida digital evolution platform
ontoneo Obstetric and Neonatal Ontology
oostt Ontology of Organizational Structures of Trauma centers and Trauma systems
opb Ontology of Physics for Biology
openalex OpenAlex
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
oslc OASIS Open Services for Lifecycle Collaboration Core Vocabulary
otl Oryza Tag Line
ovae Ontology of Vaccine Adverse Events
owl Web Ontology Language
owlstar Ontological Interpretations for Web Property Graphs
p3db.protein P3DB Protein
p3db.site P3DB Site
paleodb Paleobiology Database
pandit Protein and Associated NucleotideDomains with Inferred Trees
panorama Panorama Public
panther.family PANTHER Family
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
pathguide Pathguide
pathoplant PathoPlant®
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
pba Primate Brain Atlas
pcl Provisional Cell Ontology
pco Population and Community Ontology
pd_st Platynereis stage ontology
pdb-ccd Chemical Component Dictionary
pdbsum PDBsum; at-a-glance overview of macromolecular structures
pdc.study Proteomic Data Commons
pdro The Prescription of Drugs Ontology
pdumdv Platynereis Developmental Stages
peco Plant Experimental Conditions Ontology
ped Protein Ensemble Database
ped.ensemble Protein Ensemble Database ensemble
peff PSI Extended File Format
pennsieve Pennsieve
pepbank PepBank Peptide Database
peptideatlas PeptideAtlas
peptideatlas.dataset PeptideAtlas Dataset
perkinelmer PerkinElmer cell line collection
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 PharmGKB Gene
pharmvar Pharmacogene Variation Consortium
phenolexplorer Phenol-Explorer
phenx PhenX Toolkit
phipo Pathogen Host Interaction Phenotype Ontology
phosphopoint.kinase PhosphoPoint Kinase
phosphopoint.protein PhosphoPoint Phosphoprotein
phosphosite.protein PhosphoSite Protein
phosphosite.residue PhosphoSite Residue
phosphosite.sitegroup PhosphoSite Site Group
phylomedb PhylomeDB
phytozome.locus Plant Genome Network
pibase Database of structurally defined protein interfaces
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 Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology
planp Planarian Phenotype Ontology
planttfdb Plant Transcription Factor Database
plasmodb PlasmoDB
plo Plasmodium Life Cycle
pmap.cutdb CutDB
pmap.substratedb SubstrateDB
pmdb Protein Model Database
pmp Protein Model Portal
pmr Physical Medicine and Rehabilitation
pmr.workspace Physiome Model Repository workspace
po Plant Ontology
pocketome Pocketome
polbase PolBase
poro Porifera Ontology
ppdb Pesticide Properties DataBase
ppo Plant Phenology Ontology
ppr Europe PMC Preprints
prefixcommons Prefix Commons
pride PRIDE Controlled Vocabulary
pride.project PRIDE Project
prints PRINTS compendium of protein fingerprints
probonto Probability Distribution Ontology
proco Process Chemistry Ontology
prodom ProDom
proglyc ProGlycProt
propreo Proteomics data and process provenance
protclustdb ProtClustDB
protcom Database of protein-protein complexes
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
pubchem.cell PubChem Cell Line
pubchem.classification PubChem Classification
pubchem.element PubChem Element
publons.researcher Publons Researcher
puro Publishing Roles Ontology
pwo Publishing Workflow Ontology
px ProteomeXchange
pypi PyPI
qb The data cube vocabulary
qtldb Animal Genome QTL
qudt Quantities, Units, Dimensions, and Types Ontology
radiomics Radiomics Ontology
radlex RSNA Informatics RadLex
rapdb.locus RAP-DB Locus
rapdb.transcript Rice annotation Project database
ratmap Rat Genome Database
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
receptome.family Human Plasma Membrane Receptome Families
redfly Regulatory Elements Database for Drosophila
refseq Reference Sequence Collection
reo Reagent Ontology
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
rfc Internet Standard -- IETF Request for Comments
rgap Rice Genome Annotation Project
rgd.qtl Rat Genome Database qTL
rgd.strain Rat Genome Database strain
ribocentre Ribocentre
ricecyc Rice Metabolic Pathways
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
rism RISM Online
rna_sstrand RNA SSTRAND
rnajunction Database of RNA Junctions and Kissing loop Structures
rnaloops RNAloops
rnamod The RNA Modification Database
rnamods RNA Modification Database
rnao RNA ontology
rnavdb RNA Virus Database
ro Relation Ontology
roleo Role Ontology
ror Research Organization Registry
rouge Rodent Unidentified Gene-Encoded Large Proteins
rrid Research Resource Identification
rs Rat Strain Ontology
rtecs Registry of Toxic Effects of Chemical Substances
runbiosimulations runBioSimulations
rxno Name Reaction Ontology
s_mart_db The S/MAR transaction DataBase
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
sao Subcellular Anatomy Ontology
sasbdb Small Angle Scattering Biological Data Bank
sbo Systems Biology Ontology
scdo Sickle Cell Disease Ontology
schem Selventa Chemicals
schema Schema.org
scholia.resource Scholia Registry
sciflection Sciflection
scomp Selventa Complexes
scop Structural Classification of Proteins - Unique Identifier
scop.sccs SCOP(e) concise classification string
scop.sid Structural Classification of Protein - Stable Domain Identifier
scopus Scopus Researcher
scoro Scholarly Contributions and Roles Ontology
scpd Saccharomyces cerevisiae promoter database
scr SciCrunch Registry
scretf ScerTF
sdap Structural Database of Allergenic Proteins
sdbs Spectral Database for Organic Compounds
sdgio Sustainable Development Goals Interface Ontology
sdis Selventa Diseases
sedml.format SED-ML data format
sedml.language SED-ML model format
seed The SEED;
seed.compound SEED Compound
seed.reaction SEED Reactions
semapv Semantic Mapping Vocabulary
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
sh Shapes Constraint Language
shareloc ShareLoc
sheepqtldb Animal Genome Sheep QTL
shex Shape Expression Vocabulary
shibase ShiBASE
sibo Social Insect Behavior Ontology
sider.drug SIDER Drug
sider.effect SIDER Side Effect
sigmaaldrich Sigma Aldrich
signaling-gateway Signaling Gateway
signor Signaling Network Open Resource
signor.relation SIGNOR Relation
sio Semanticscience Integrated Ontology
siren Scientific Information Retrieval and Exchange Network
sisu Sequencing Initiative Suomi
sitex SitEx
skip Stemcell Knowledge and Information Portal
skm Stress Knowledge Map
skos Simple Knowledge Organization System
skosxl Simple Knowledge Organization System eXtension for Labels
slkbase SUM Breast Cancer Cell Line Knowledge Base
smart Simple Modular Architecture Research Tool
smid C. elegans Small Molecule Identifier Database
smpdb Small Molecule Pathway Database
snap Snapshot
snornabase snoRNABase
snp2tfbs SNP to Transcription Factor Binding Sites
snp500cancer SNP500Cancer
so Sequence types and features ontology
sopharm Suggested Ontology for Pharmacogenomics
soybase SoyBase
span Span
spbase SpBase
spdx Software Package Data Exchange License
sphn Swiss Personalized Health Network Schema
spike.map SPIKE Map
splash Spectra Hash Code
splicenest SpliceNest
spp Signaling Pathways Project
srao FAIRsharing Subject Ontology
ssbd.dataset System Science of Biological Dynamics dataset
ssbd.project System Science of Biological Dynamics project
sssom Simple Standard for Sharing Ontological Mappings
sstoss Sequence-Structural Templates of Single-member Superfamilies
stap Statistical Torsional Angles Potentials
stato The Statistical Methods Ontology
stitch Search Tool for Interactions of Chemicals
storedb Store DB
storedb.dataset STOREDB at University of Cambridge
storedb.file STOREDB at University of Cambridge
storedb.study STOREDB at University of Cambridge
string Search Tool for Retrieval of Interacting Genes/Proteins
sty UMLS Semantic Types Ontology
subtilist Bacillus subtilis genome sequencing project
subtiwiki SubtiWiki
sugarbind SugarBind
supfam SUPERFAMILY
sweetrealm Semantic Web for Earth and Environment Technology Ontology
swh Software Heritage
swiss-model SWISS-MODEL Repository
swissregulon SwissRegulon
swo Software ontology
swrl A Semantic Web Rule Language Combining OWL and RuleML
syoid Gemina Symptom Ontology
t3db Toxin and Toxin Target Database
t4fs terms4FAIRskills
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
tcb Tick Cell Biobank
tccd The Cell Cycle DB
tfclass Classification of Transcription Factors in Mammalia
tgd Tetrahymena Genome Database
tgma Mosquito gross anatomy ontology
tgn Getty Thesaurus of Geographic Names
th Terminologia Histologica
thermofisher Thermo Fisher Scientific
tigrfam TIGR protein families
time Time Ontology in OWL
tkg Tohoku University cell line catalog
tngb Telethon Network of Genetic Biobanks
to Plant Trait Ontology
tokue TOKU-E Cell-culture Database
tol Tree of Life Web Project
topdb Topology Data Bank of Transmembrane Proteins
topfind TopFind
toxoplasma ToxoDB
trans Pathogen Transmission Ontology
transportdb TransportDB
transyt Transport Systems Tracker
tred Transcriptional Regulatory Element Database
treebase TreeBASE
treefam TreeFam
trichdb TrichDB
tritrypdb TriTrypDB
trnadbce tRNA Gene Database
ttd.drug TTD Drug
ttd.target TTD Target
txpo Toxic Process Ontology
ubio.namebank uBio NameBank
ubprop Uberon Property
ucas UK Universities and Colleges Admissions Service
ucum Unified Code for Units of Measure
ukprn UK Provider Reference Number
umbbd.compound UM-BBD compound
umbbd.enzyme EAWAG Biocatalysis/Biodegradation Database
umbbd.pathway EAWAG Biocatalysis/Biodegradation Database
umbbd.rule EAWAG Biocatalysis/Biodegradation Database
umls.aui Unified Medical Language System Atomic Unique Identifier
unigene UniGene
unimod Unimod protein modification database for mass spectrometry
uniparc UniProt Archive
unipathway.compound UniPathway Compound
unipathway.reaction UniPathway Reaction
uniprot.arba Association-Rule-Based Annotator
uniprot.chain UniProt Chain
uniprot.isoform UniProt Isoform
uniprot.keyword UniProt Keywords
uniprot.location UniProt Subcellular Locations
uniprot.proteome UniProt Proteomes
uniprot.ptm UniProt Post-Translational Modification
uniprot.resource UniProt Resource
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
vac Vaccine Adjuvant Compendium
validatordb ValidatorDB
vandf Veterans Administration National Drug File
vann A vocabulary for annotating vocabulary descriptions
vario Variation Ontology
vbase2 Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse
vbo Vertebrate Breed Ontology
vbrc Viral Bioinformatics Resource Center
vcell VCell Published Models
vectorbase Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens
vega Vertebrate Genome Annotation Database
vegbank VegBank
venom Veterinary Nomenclature
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
violinnet ViolinNet
viperdb VIPERdb
vipr Virus Pathogen Resource
virgen VirGen
virmirdb Vir-Mir db
viroligo VirOligo
virsirna VIRsiRNA
virushostdb Virus-HostDB
vita Virus' miRNA target
vmc Variation Modelling Collaboration
vmhgene VMH Gene
vmhmetabolite VMH metabolite
vmhreaction VMH reaction
void Vocabulary of Interlinked Datasets
vsao Vertebrate Skeletal Anatomy Ontology
vsdb Veterinary Substances DataBase
vsmo Ontology for vector surveillance and management
vso Vital Sign Ontology
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
wicell WiCell Research Institute Cell Collection
wikidata Wikidata
wikidata.property Wikidata Property
wikigenes WikiGenes
wikipedia.en Wikipedia
worfdb C. elegans ORFeome cloning project
world2dpage The World-2DPAGE database
wormpep Wormpep
xco Experimental condition ontology
xenbase Xenbase
ximbio Ximbio
xl Cross-linker reagents ontology
xlmod HUPO-PSI cross-linking and derivatization reagents controlled vocabulary
xmetdb Xenobiotics Metabolism Database
xml Extensible Markup Language
xpo Xenopus Phenotype Ontology
xsd XML Schema Definition
xuo XUO
ydpm Yeast Deletion and the Mitochondrial Proteomics Project
yeastintron Yeast Intron Database v4.3
yeastract Yeast Searching for Transcriptional Regulators and Consensus Tracking
yetfasco YeTFasCo
ygob Yeast Genome Order Browser
yid Yeast Intron Database v3
ymdb Yeast Metabolome Database
ypo Yeast Phenotype Ontology
yrcpdr YRC PDR
zea Maize gross anatomy
zeco Zebrafish Experimental Conditions Ontology
zfa Zebrafish anatomy and development ontology
zfs Zebrafish developmental stages ontology
zp Zebrafish Phenotype Ontology

Adding a Regular Expression Pattern for Each Resource’s Local Unique Identifiers

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

Entries (319)
Prefix Name
4dn.replicate 4D Nucleome Data Portal Experiment Replicate
aaindex AAindex
abcd AntiBodies Chemically Defined database
abm Applied Biological Materials cell line products
ac Activity Streams
addexbio AddexBio cell line products
afo Allotrope Merged Ontology Suite
agsd Animal Genome Size Database
alfred The ALlele FREquency Database
alzforum.mutation Alzforum Mutations
alzgene Alzheimer Gene Database
apaonto Psychology Ontology
archdb ArchDB
asrp Arabidopsis Small RNA Project
astd ASTD
bactibase Bactibase
bams Brain Architecture Knowledge Management System Neuroanatomical Ontology
beiresources BEI Resources
bel Biological Expression Language
bibo The Bibliographic Ontology
bido Bibliometric Data Ontology
bind BIND accession number
biomagresbank BioMagResBank
biopixie biological Process Inference from eXperimental Interaction Evidence/Microarray Experiment Functional Integration Technology
bioregistry Bioregistry
bioregistry.registry Bioregistry Metaregistry
bioschemas BioSchemas
biozil BIOZIL
biro Bibliographic Reference Ontology
bootstrep Gene Regulation Ontology
c4o Citation Counting and Context Characterisation Ontology
ccle Cancer Cell Line Encyclopedia Cells
ccrid National Experimental Cell Resource Sharing Platform
cell_biolabs Cell Biolabs cell line products
cell_model_passport Sanger Cell Model Passports
cellbank.australia CellBank Australia
cellosaurus.resource Cellosaurus Registry
cghdb CGH Data Base
chembank ChemBank
chembl.cell ChEMBL database of bioactive drug-like small molecules - Cell lines section
chemrof Chemical Entity Materials and Reactions Ontological Framework
chiro ChEBI Integrated Role Ontology
citexplore CiteXplore
cito Citation Typing Ontology
cls Cell Lines Service
cmf CranioMaxilloFacial ontology
cog.category COG Categories
cog.pathway COG Pathways
cohd MIMIC III Database
collagenmutdb Collagen Mutation Database
colonatlas Colorectal Cancer Atlas
come The Bioinorganic Motif Database
commoncoreontology Common Core Ontologies
confident.series ConfIDent Event Series
cp Cellular Phenotypes
credit CASRAI Contributor Roles Taxonomy
csp Computer Retrieval of Information on Science Projects Thesaurus
cutg Codon Usage Tabulated from GenBank
datacite DataCite Ontology
datacommons Data Commons
dbo DBPedia Ontology
dbvar.study Database of Genomic Structural Variation - Study
dbvar.variant Database of Genomic Structural Variation - Variant
dc Dublin Core Elements (1.1)
dcat Data Catalog
dcterms Dublin Core Metadata Initiative Terms
dctypes Dublin Core Types
deo Discourse Elements Ontology
dictybase dictyBase
dinto The Drug-Drug Interactions Ontology
discoverx DiscoverX cell line products
doap Description of a Project
doco Document Components Ontology
dpo Drosophila Phenotype Ontology
drduke Dr. Duke's Phytochemical and Ethnobotanical Databases chemical
dsmz Deutsche Sammlung von Mikroorganismen und Zellkulturen
dso Data Science Ontology
eaglei eagle-i
easychair.cfp EasyChair Call for Paper
ebisc European Bank for induced pluripotent Stem Cells
ecocyc EcoCyc
ecolexicon EcoLexicon
edda EDDA Study Designs Taxonomy
enzo Enzo Life Sciences
epcc European Paediatric Cardiac Codes
epo Epidemiology Ontology
eropmoscow Endogenous Regulatory OligoPeptide knowledgebase-Moscow
esldb eukaryotic Subcellular Localization database
eugenes Eukaryotic Genes
eurofir European Food Information Resource Network
ev eVOC (Expressed Sequence Annotation for Humans)
evm eVOC mouse development stage
fabio FaBiO, the FRBR-aligned Bibliographic Ontology
faldo Feature Annotation Location Description Ontology
fcsfree Fetal Calf Serum-Free Database
fhir.implementation FHIR United States Implementation Guides
fivestars Five Stars of Online Research Articles Ontology
flymine.chromosome FlyMine Chromosome Band
foaf Friend of a Friend
foodex2 Food classification and description system
fr FAIR* Reviews Ontology
frapo Funding, Research Administration and Projects Ontology
frbr Functional Requirements for Bibliographic Records
galen GALEN
genbank GenBank
gendis Genomic Distribution of structural Superfamilies
genecards.geneannot GeneAnnot: Microarray Gene Annotation
genecards.geneloc Gene Location
genecards.genenote Gene Normal Tissue Expression
geonames.feature GeoNames Feature Code
gexo Gene Expression Ontology
gfo General Formal Ontology
ghr Genetics Home Reference
github.issue GitHub Issue
github.pull GitHub Pull Request
glycomapsdb GlycoMapsDB
glygen Computational and Informatics Resources for Glycoscience
gnomad Genome Aggregation Database
go.gpi Gene Product Information Schema
go.model Gene Ontology Causal Assembly Model
go.resource Gene Ontology Registry
goeco GO Evidence Code
google.book Google Books
google.scholar Google Scholar Researcher
graingenes.reference GrainGenes
graingenes.symbol GrainGenes
grin Germplasm Resources Information Network
gro Gene Regulation Ontology
gtr Genetic Testing Registry
habronattus Habronattus courtship
hagr.genage The Ageing Gene Database
hagr.gendr The Dietary Restriction Gene Database
hbvar A Database of Human Hemoglobin Variants and Thalassemias
hcao Human Cell Atlas Ontology
hcpcs Healthcare Common Procedure Coding System
hipsci Human Induced Pluripotent Stem Cells Initiative
hivreagentprogram NIH HIV Reagent Program
horizon_discovery Horizon Discovery cell line collection
icd10pcs International Classification of Diseases, 10th Revision, Procedure Coding System
iclc Interlab Cell Line Collection
igrhcellid Integrated Genomic Resources of human Cell Lines for Identification
igsr International Genome Sample Resource
imanis Imanis Life Sciences cell line products
imdrf International Medical Device Regulators Forum
imgt.primerdb IMGT/PRIMER-DB
imotdb Database of Spatially Interacting Motifs in Proteins
inhand The International Harmonization of Nomenclature and Diagnostic criteria
inn International Nonproprietary Names
innatedb A Knowledge Resource for Innate Immunity Interactions and Pathways
interfil Human Intermediate Filament Database
iobc Interlinking Ontology for Biological Concepts
ipi International Protein Index
iresite Database of experimentally verified IRES structures
ised Influenza Sequence and Epitope Database
ivdb Influenza Virus Database
jcrb JRBC Cell Bank
kclb Korean Cell Line Bank
kegg.brite KEGG BRITE
kegg.enzyme KEGG Enzyme
kegg.ligand KEGG LIGAND
kerafast Kerafast cell lines
kyinno KYinno cell lines
leafsnap Leafsnap
ligea Cancer cell LInes GEne fusions portAl
limore Liver Cancer Model Repository
linkml LinkML
lipro Lipid Ontology
lncipedia LNCipedia
loggerhead Loggerhead nesting
loqate The localization and quantitation atlas of the yeast proteome
mampol Mammalia Polymorphism Database
mao Multiple alignment
matrixdb MatrixDB
mcc Cell Line Ontology [derivative]
merops.clan MEROPS Clan
mesh.vocab Medical Subject Headings Vocabulary
metnetdb Metabolic Network Exchange Database
mfo Medaka fish anatomy and development
miaa Minimal Information About Anatomy ontology
millipore Merck Millipore (EMD Millipore)
mirbase.family miRBase Families
mirnao microRNA Ontology
mirte miRNA Target Prediction at EMBL
mmsinc MMsINC
molmovdb Database of Macromolecular Movements
mtbd Mouse Tumor Biology Database
multicellds MultiCellDS
n2t Name-to-Thing
namerxn NameRXN
ncats.drug NCATS Drugs
ncbi.resource NCBI Registry
ndex Network Data Exchange
nembase Nematode & Neglected Genomics
nemo2 Neural ElectroMagnetic Ontology
nhcdr NINDS Human Cell and Data Repository
nif.cell NIF Cell
nif.dysfunction NIF Dysfunction
nif.grossanatomy NIF Gross Anatomy
nist NIST Chemistry WebBook
nmpdr National Microbial Pathogen Data Resource
novus Novus Biologicals
oa Web Annotation Ontology
obo Open Biological and Biomedical Ontologies
oboinowl OBO in OWL
om Ontology of units of Measure
omo OBO Metadata Ontology
oncotree OncoTree
orth Orthology Ontology
oslc OASIS Open Services for Lifecycle Collaboration Core Vocabulary
owl Web Ontology Language
pandit Protein and Associated NucleotideDomains with Inferred Trees
panorama Panorama Public
pao Plant Anatomy Ontology
pathguide Pathguide
pathoplant PathoPlant®
pd_st Platynereis stage ontology
pdbsum PDBsum; at-a-glance overview of macromolecular structures
pepbank PepBank Peptide Database
perkinelmer PerkinElmer cell line collection
pesticides Alan Wood's Pesticides
pgdso Plant Growth and Development Stage
pharmacodb.cell PharmacoDB Cells
pharmvar Pharmacogene Variation Consortium
pibase Database of structurally defined protein interfaces
pictar PicTar
plo Plasmodium Life Cycle
ppr Europe PMC Preprints
prefixcommons Prefix Commons
propreo Proteomics data and process provenance
protcom Database of protein-protein complexes
prov PROV Namespace
pseudogene PseudoGene
pspub Phenoscape Publication
publons.publication Publons publication
puro Publishing Roles Ontology
pwo Publishing Workflow Ontology
qudt Quantities, Units, Dimensions, and Types Ontology
radiomics Radiomics Ontology
ratmap Rat Genome Database
rdf Resource Description Framework
rdfs RDF Schema
receptome.family Human Plasma Membrane Receptome Families
redfly Regulatory Elements Database for Drosophila
reproduceme REPRODUCE-ME Ontology
reto Regulation of Transcription Ontology
rexo Regulation of Gene Expression Ontology
rgap Rice Genome Annotation Project
ricecyc Rice Metabolic Pathways
rna_sstrand RNA SSTRAND
rnajunction Database of RNA Junctions and Kissing loop Structures
rnavdb RNA Virus Database
s_mart_db The S/MAR transaction DataBase
sael Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List
schema Schema.org
scholia.resource Scholia Registry
scop.sccs SCOP(e) concise classification string
scop.sid Structural Classification of Protein - Stable Domain Identifier
scoro Scholarly Contributions and Roles Ontology
scpd Saccharomyces cerevisiae promoter database
sdap Structural Database of Allergenic Proteins
semapv Semantic Mapping Vocabulary
sh Shapes Constraint Language
shex Shape Expression Vocabulary
shibase ShiBASE
sigmaaldrich Sigma Aldrich
skos Simple Knowledge Organization System
skosxl Simple Knowledge Organization System eXtension for Labels
snap Snapshot
snornabase snoRNABase
snp500cancer SNP500Cancer
sopharm Suggested Ontology for Pharmacogenomics
span Span
spbase SpBase
splicenest SpliceNest
sstoss Sequence-Structural Templates of Single-member Superfamilies
sweetrealm Semantic Web for Earth and Environment Technology Ontology
swrl A Semantic Web Rule Language Combining OWL and RuleML
syoid Gemina Symptom Ontology
tahe Terminology of Anatomy of Human Embryology
tahh Terminology of Anatomy of Human Histology
tccd The Cell Cycle DB
te Terminologia Embryologica
tfclass Classification of Transcription Factors in Mammalia
th Terminologia Histologica
thermofisher Thermo Fisher Scientific
time Time Ontology in OWL
tokue TOKU-E Cell-culture Database
transportdb TransportDB
tred Transcriptional Regulatory Element Database
trnadbce tRNA Gene Database
ubprop Uberon Property
ucsc UCSC Genome Browser
ucum Unified Code for Units of Measure
unirule UniRule
unpd Universal Natural Products Database
upheno Unified Phenotype Ontology
vann A vocabulary for annotating vocabulary descriptions
vega Vertebrate Genome Annotation Database
viperdb VIPERdb
virgen VirGen
virmirdb Vir-Mir db
viroligo VirOligo
virushostdb Virus-HostDB
vita Virus' miRNA target
vmc Variation Modelling Collaboration
void Vocabulary of Interlinked Datasets
vsao Vertebrate Skeletal Anatomy Ontology
vsmo Ontology for vector surveillance and management
wgs84 WGS84 Geo Positioning
wicell WiCell Research Institute Cell Collection
world2dpage The World-2DPAGE database
xl Cross-linker reagents ontology
xml Extensible Markup Language
xsd XML Schema Definition
xuo XUO
yeastract Yeast Searching for Transcriptional Regulators and Consensus Tracking
ygob Yeast Genome Order Browser
ypo Yeast Phenotype Ontology
zea Maize gross anatomy

Curating URI Format Strings

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

{
  ...
  "jax": {
    "example": "004435",
    "name": "Jackson Laboratories Strain",
    "uri_format": "https://www.jax.org/strain/$1"
    // <-- this one here
  },
  ...
}
Entries (77)
Prefix Name
afo Allotrope Merged Ontology Suite
agilent.probe Agilent Probe
bams Brain Architecture Knowledge Management System Neuroanatomical Ontology
bel Biological Expression Language
cdt Current Dental Terminology
codelink GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray
cohd MIMIC III Database
cp Cellular Phenotypes
credit CASRAI Contributor Roles Taxonomy
ctcae Common Terminology Criteria for Adverse Events
cvx Vaccine administered code set
dbmhc Database of human Major Histocompatibility Complex
dsm4 Diagnostic and Statistical Manual of Mental Disorders (4th Edition)
dsm5 Diagnostic and Statistical Manual of Mental Disorders (5th Edition)
ecn EC number
ecolexicon EcoLexicon
epcc European Paediatric Cardiac Codes
eurofir European Food Information Resource Network
evm eVOC mouse development stage
fbql FlyBase Qualifiers
fivestars Five Stars of Online Research Articles Ontology
fr FAIR* Reviews Ontology
fyeco Fission Yeast Experimental Conditions Ontology
fyler Fyler
genecards.geneannot GeneAnnot: Microarray Gene Annotation
gexo Gene Expression Ontology
gmelin Gmelins Handbuch der anorganischen Chemie
goeco GO Evidence Code
google.scholar Google Scholar Researcher
gorel GO Relations
hc.din Health Canada Drug Identification Number
hcao Human Cell Atlas Ontology
hesa UK Higher Education Statistics Agency
ietf.language Internet Engineering Task Force Language Tag
ihw International Histocompatibility Workshop cell lines
illumina.probe Illumina Probe Identifier
imdrf International Medical Device Regulators Forum
inhand The International Harmonization of Nomenclature and Diagnostic criteria
ised Influenza Sequence and Epitope Database
iso.3166 ISO 3166-1 Country Code
kegg.dgroup KEGG Drug Group
kegg.rclass KEGG Reaction Class
kupo Kidney and Urinary Pathway Ontology
lncipedia LNCipedia
miaa Minimal Information About Anatomy ontology
mirte miRNA Target Prediction at EMBL
mmsl Multum MediSource Lexicon
molbase.sheffield MolBase
namerxn NameRXN
nist NIST Chemistry WebBook
npass Natural Product Activity and Species Source Database
nucc.characteristic National Uniform Claim Committee Characteristic
nucc.taxonomy National Uniform Claim Committee Taxonomy
phosphosite.sitegroup PhosphoSite Site Group
pictar PicTar
pspub Phenoscape Publication
reaxys Reaxys
reto Regulation of Transcription Ontology
rexo Regulation of Gene Expression Ontology
rtecs Registry of Toxic Effects of Chemical Substances
sael Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List
scopus Scopus Researcher
signor.relation SIGNOR Relation
siren Scientific Information Retrieval and Exchange Network
span Span
syoid Gemina Symptom Ontology
te Terminologia Embryologica
th Terminologia Histologica
ubprop Uberon Property
ucas UK Universities and Colleges Admissions Service
umls.aui Unified Medical Language System Atomic Unique Identifier
unpd Universal Natural Products Database
venom Veterinary Nomenclature
virgen VirGen
vmc Variation Modelling Collaboration
vuid Veterans Health Administration (VHA) unique identifier
xuo XUO

Example Local Unique Identifier

As a courtesy to newcomers, it’s nice to show an example local unique 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 (38)
Prefix Name
bams Brain Architecture Knowledge Management System Neuroanatomical Ontology
bootstrep Gene Regulation Ontology
cmf CranioMaxilloFacial ontology
cp Cellular Phenotypes
dinto The Drug-Drug Interactions Ontology
epcc European Paediatric Cardiac Codes
epo Epidemiology Ontology
eurofir European Food Information Resource Network
evm eVOC mouse development stage
habronattus Habronattus courtship
inhand The International Harmonization of Nomenclature and Diagnostic criteria
kegg.ligand KEGG LIGAND
lipro Lipid Ontology
loggerhead Loggerhead nesting
miaa Minimal Information About Anatomy ontology
mirnao microRNA Ontology
nif.cell NIF Cell
nif.dysfunction NIF Dysfunction
nif.grossanatomy NIF Gross Anatomy
obo Open Biological and Biomedical Ontologies
pao Plant Anatomy Ontology
pd_st Platynereis stage ontology
pgdso Plant Growth and Development Stage
plo Plasmodium Life Cycle
pspub Phenoscape Publication
sael Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List
sopharm Suggested Ontology for Pharmacogenomics
span Span
syoid Gemina Symptom Ontology
tahe Terminology of Anatomy of Human Embryology
tahh Terminology of Anatomy of Human Histology
tokue TOKU-E Cell-culture Database
ubprop Uberon Property
unpd Universal Natural Products Database
vmc Variation Modelling Collaboration
xl Cross-linker reagents ontology
xuo XUO
ypo Yeast Phenotype Ontology