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A curated list by Sage Bionetworks of external resources that are automatically linked on Synapse.org and affiliated data portals

Identifier
0000016
Contributors
Robert Allaway
Size
203
Prefix Name
ado Alzheimer's Disease Ontology
agrkb Alliance of Genome Resources Knowledge Base
anzctr Australian New Zealand Clinical Trials Registry
arrayexpress ArrayExpress
arxiv arXiv
atc Anatomical Therapeutic Chemical Classification System
atcc American Type Culture Collection
bacdive BacDive
bfo Basic Formal Ontology
bgee.gene Bgee gene
biocyc BioCyc collection of metabolic pathway databases
biogrid BioGRID
bioportal BioPortal
bioproject BioProject
biorxiv bioRxiv
biosample BioSample
biostudies BioStudies database
bmrb.entry Biological Magnetic Resonance Data Bank
brenda BRENDA Enzyme Provider
brenda.ligand BRENDA Ligand
brenda.ligandgroup BRENDA Ligand Group
bto BRENDA Tissue Ontology
cath CATH Protein Structural Domain Superfamily
cbioportal The cBioPortal for Cancer Genomics
cdd Conserved Domain Database at NCBI
cellimage Cell Image Library
cellxgene.collection Chan Zuckerberg CELLxGENE Collection
chebi Chemical Entities of Biological Interest
chembl ChEMBL
chembl.compound ChEMBL Compound
chemspider ChemSpider
civic.aid CIViC Assertion
civic.did CIViC Disease
civic.eid CIViC Evidence
civic.gid CIViC gene
civic.sid CIViC Source
civic.tid CIViC Therapy
civic.vid CIViC variant
clinicaltrials ClinicalTrials.gov
clinvar.record ClinVar Record
clinvar.variation ClinVar Variation
complexportal Complex Portal
cosmic.cell COSMIC Cell Lines
cosmic.gene COSMIC Gene Provider
cpt Current Procedural Terminology
ctd.chemical CTD Chemical Provider
ctri India Clinical Trials Registry
cvx Vaccine administered code set
dbgap Database of Genotypes and Phenotypes
dbsnp dbSNP Reference SNP number
decipher DECIPHER CNV Syndromes
depmap DepMap Cell Lines
dhba Developing Human Brain Atlas
disprot DisProt
dmba Developing Mouse Brain Atlas
doi Digital Object Identifier
doid Human Disease Ontology
drks German Clinical Trials Register
drugbank DrugBank
drugcentral Drug Central
duo Data Use Ontology
ec Enzyme Nomenclature
ecacc European Collection of Authenticated Cell Culture
edam EDAM Ontology
ega.dataset European Genome-phenome Archive Dataset
ega.study European Genome-phenome Archive Study
emdb Electron Microscopy Data Bank
empiar Electron Microscopy Public Image Archive
ena.embl European Nucleotide Archive
ensembl Ensembl Gene
ensembl.metazoa Ensembl Metazoa, the Ensembl database for accessing genome-scale data from non-vertebrate metazoa.
ensembl.plant Ensembl Plants
euclinicaltrials EU Clinical Trials
eupath VEuPathDB ontology
exac.variant ExAC Variant
fairsharing FAIRsharing
flybase FlyBase Gene
fma Foundational Model of Anatomy
funderregistry FunderRegistry
gard Genetic and Rare Diseases Information Center
gbif Global Biodiversity Information Facility
gdc Genomic Data Commons Data Portal
genecards.gene GeneCards Gene
geo NCBI Gene Expression Omnibus
go Gene Ontology
gramene.gene Gramene Gene
gramene.growthstage Gramene Growth Stage Ontology
gramene.protein Gramene protein
gtdb Genome Taxonomy Database
hba Human Brain Atlas
hc.trial Health Canada Clinical Trials Database
hgnc HUGO Gene Nomenclature Committee
hl7.v2codesystem HL7 V2 Code System
hmdb Human Metabolome Database
icd10 International Classification of Diseases, 10th Revision
icd9 International Classification of Diseases, 9th Revision
icdc Integrated Canine Data Commons
icf International Classification of Functioning, Disability and Health
idr Image Data Resource
imgt.hla IMGT/HLA human major histocompatibility complex sequence database
inchi InChI
inchikey InChIKey
insdc Nucleotide Sequence Database
insdc.sra Sequence Read Archive
intact IntAct protein interaction
interpro InterPro
iso.3166 ISO 3166-1 Country Code
isrctn International Clinical Trials Registry Platform
itis Integrated Taxonomic Information System
jaxmice Jackson Laboratories Mouse Strain
kegg KEGG ID Deprecated
kegg.compound KEGG Compound
kegg.disease KEGG Disease
kegg.drug KEGG Drug
kegg.glycan KEGG Glycan
kegg.pathway KEGG pathway
kegg.reaction KEGG Reaction
loinc Logical Observation Identifiers Names and Codes
massive MassIVE
mba Mouse Brain Atlas
mesh Medical Subject Headings
metabolights MetaboLights Compound
metacyc.compound Metabolic Encyclopedia of metabolic and other pathways
mgi Mouse Genome Informatics
mir Identifiers.org Registry
mirbase miRBase pre-miRNA
mondo Mondo Disease Ontology
ncbigene NCBI Gene
ncbiprotein NCBI Protein
ncbitaxon NCBI Taxonomy
ncit NCI Thesaurus
ndc National Drug Code
ndfrt National Drug File - Reference Terminology
nextprot nextProt
nihreporter.project NIH RePORTER
nord National Organization for Rare Disorders
omim Online Mendelian Inheritance in Man
omop Observational Medical Outcomes Partnership
orcid Open Researcher and Contributor
orpha Orphanet
orphanet.ordo Orphanet Rare Disease Ontology
osf Open Science Framework ID
panther.family PANTHER Family
panther.pathway PANTHER Pathway
panther.pthcmp PANTHER Pathway Component
pba Primate Brain Atlas
pdb PDB Structure
pdb-ccd Chemical Component Dictionary
pdb.ligand PDB ligand
pdc.study Proteomic Data Commons
peco Plant Experimental Conditions Ontology
peptideatlas.dataset PeptideAtlas Dataset
pfam Pfam protein family
pfam.clan Pfam protein clan
pharmgkb.disease PharmGKB Disease
pharmgkb.drug PharmGKB Drug
pharmgkb.gene PharmGKB Gene
pharmgkb.pathways PharmGKB pathway
pmc PubMed Central
pombase PomBase
pride.project PRIDE Project
pubchem.compound PubChem compound
pubmed PubMed
px ProteomeXchange
radlex RSNA Informatics RadLex
reactome Reactome
rebec Brazilian Registry of Clinical Trials
refseq Reference Sequence Collection
rfam Rfam database of RNA families
rfc Internet Standard -- IETF Request for Comments
rgd Rat Genome Database
rhea Rhea reaction
rnacentral RNACentral
ror Research Organization Registry
rrid Research Resource Identification
rrrc Rat Resource and Research Center
rxnorm RxNorm
scop Structural Classification of Proteins - Unique Identifier
sgd Saccharomyces Genome Database
signor Signaling Network Open Resource
snomedct SNOMED CT (International Edition)
so Sequence types and features ontology
ssbd.dataset System Science of Biological Dynamics dataset
ssbd.project System Science of Biological Dynamics project
stitch Search Tool for Interactions of Chemicals
string Search Tool for Retrieval of Interacting Genes/Proteins Provider
tao Teleost Anatomy Ontology
tcdb Transporter Classification Database
uberon Uber Anatomy Ontology
unii Unique Ingredient Identifier
uniparc UniProt Archive
uniprot UniProt Protein
uniprot.isoform UniProt Isoform
uniprot.proteome UniProt Proteomes
uniref UniRef
wikidata Wikidata
wikigenes WikiGenes Provider
wikipathways WikiPathways
wormbase WormBase
xenbase Xenbase
zenodo.record Zenodo
zfin Zebrafish Information Network Gene
zinc ZINC is not Commercial
Indirect Dependencies
Prefix Name
ro Relation Ontology
xsd XML Schema Definition
xml Extensible Markup Language
owl Web Ontology Language
rdfs RDF Schema
rdf Resource Description Framework
foaf Friend of a Friend
dcterms Dublin Core Metadata Initiative Terms
iao Information Artifact Ontology