- dbGap : https://www.ncbi.nlm.nih.gov/gap
- SRA : https://www.ncbi.nlm.nih.gov/sra
- Epigenomics: http://www.roadmapepigenomics.org/
- Rat Genome Database: http://rgd.mcw.edu/
- ClinVar : https://www.ncbi.nlm.nih.gov/clinvar/
- ENA: http://www.ebi.ac.uk/ena
- Ensembl: http://www.ensembl.org/index.html
- Ensembl Genomes: http://ensemblgenomes.org/
- EGA: https://www.ebi.ac.uk/ega/home
- GeneCards http://www.genecards.org/
- Gemma: http://www.chibi.ubc.ca/Gemma/home.html
- GEO http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS4356
- BioGPS http://biogps.org/#goto=welcome
- Expression Atlas - https://www.ebi.ac.uk/gxa/home
- Brain Map Project http://brain-map.org/
- ArrayExpress: https://www.ebi.ac.uk/arrayexpress/
- Mouse Expression Atlas http://www.emouseatlas.org/
- Bgee https://bgee.org/
- GWAS Central: http://help.gwascentral.org/info/web-services/search/
- Intact: Protein http://www.ebi.ac.uk/intact/
- STRING-db: http://string-db.org/
- MINT: http://mint.bio.uniroma2.it/mint
- BioModel. (BioModels/System Biology)
- Reactome www.reactome.org
- Wikipathways http://www.wikipathways.org/index.php/Help:WikiPathways_Webservice/API, API http://webservice.wikipathways.org/listPathways
- KEEG (http://www.kegg.jp/kegg/rest/keggapi.html)
- Yed Med Database: https://yped.med.yale.edu:8443/repository/
- ProteomeForms : http://repository.topdownproteomics.org/proteoforms/?DataSetId=1
- ProteomicsDB : https://www.proteomicsdb.org/
- PaxDB. https://pax-db.org/
- Chorus https://chorusproject.org/pages/index.html
- PRIDE: https://www.ebi.ac.uk/pride/archive/
- PeptideAtlas: www.peptideatlas.org
- HPA : http://www.proteinatlas.org
- Biological Magnetic Resonance Data Bank http://www.bmrb.wisc.edu/
- PDB : www.rcsb.org/pdb/
## Metabolomics & Small molecules
- ChEBI: https://www.ebi.ac.uk/chebi/
- ChEMBL: https://www.ebi.ac.uk/chembl/
- MetaboLights: http://www.ebi.ac.uk/metabolights/
- UniProt: http://www.uniprot.org/
- InterPro: https://www.ebi.ac.uk/interpro/
- Pfam: http://pfam.xfam.org/
- CATH/Gene3D: http://www.cathdb.info/
- GlycoSuiteDB http://www.unicarbkb.org/
- MobiDB - http://mobidb.bio.unipd.it/
- Cazy: http://www.cazy.org/
- Enzyme Portal: www.ebi.ac.uk/enzymeportal
## Other Databases
-
SILVA: https://www.arb-silva.de/
-
BRENDA: www.brenda-enzymes.org
-
CATH-Gene3D: http://www.cathdb.info/
-
IUPHAR/BPS: http://www.guidetopharmacology.org/
-
Pathogen-Host Interaction Database: http://www.phi-base.org/
-
Biomedical Atlas Centre:
-
NGS-Logistics: https://ngsl.esat.kuleuven.be
-
BBMRI.fi: http://www.bbmri.fi
-
IS Finder: https://www-is.biotoul.fr
-
CRISPRdb: http://crispr.u-psud.fr/crispr/
-
MetExplore: http://www.metexplore.fr
-
GiantVirus: http://www.giantvirus.org
-
RNAspace: http://www.rnaspace.org
-
Orphanet: http://www.orpha.net
-
RaDICO: http://www.radico.fr/fr/
-
ACSN: https://acsn.curie.fr
-
IMGT: http://www.imgt.org
-
HOGENOM: http://doua.prabi.fr/databases/hogenom/home.php?contents=query
-
ASPicDB
-
DIGIT
-
CoarkOakDB
-
TreePortal
-
GOMapMan: http://www.gomapman.org
-
BASE: http://base.thep.lu.se
-
FireDB
-
MoDEL
-
CellBase
-
CentrosomeDB
-
ABS
-
HCAD
-
EPD
-
Progenetix
-
OrthoDB
-
ImmunoDB
-
miROrtho
-
PROSITE