| 1 | AACR Project GENIE | Cancer Genomics | global cancer registry sharing real-world data from top cancer centers | GENIE |
| 2 | BioGRID | Interaction | Protein, Genetic and Chemical Interactions | BioGRID |
| 3 | Biomart | Gene | mappings of gene ids from biomart using pybiomart | BioMart |
| 4 | Borealis - list2 | Gene | conservation scores from canadian research data repository data | Borealis: The Canadian Dataverse Repository |
| 5 | cBioPortal | Cancer Genomics | Open-source resource for interactive exploration of multidimensional cancer genomics data sets | cBioPortal |
| 6 | Cell Ontology | Terminology | an ontology of cell types | Cell Ontology |
| 7 | Cellosaurus | Terminology | a knowledge resource on cell lines | Cellosaurus |
| 8 | ChEBI | Drug/Compound | IDs and accession numbers only | Chemical Entities of Biological Interest (ChEBI) |
| 9 | ChEMBL | Drug/Compound | a manually curated database of bioactive molecules with drug-like properties | ChEMBL Database |
| 10 | ClinVar | Genetics | aggregated information about genomic variation and its relationship to human health | ClinVar |
| 11 | Compartments | Gene | protein subcellular localization from manually curated literature, high-throughput screens, automatic text mining, and sequence-based prediction methods | COMPARTMENTS |
| 12 | Complex Portal | Interaction | a manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms (only human data is included) | Complex Portal |
| 13 | dbSNP | Genetics | contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations | dbSNP |
| 14 | depmap | Expression | Cancer Dependency Map data | The Cancer Dependency Map Project at Broad Institute |
| 15 | Drugbank | Drug/Compound | drug information | DrugBank |
| 16 | Drugcentral | Drug/Compound | drug information | Drug Central |
| 17 | EBI – GWAS Catalog | Gene | catalog of human genome-wide association studies | GWAS Catalog |
| 18 | EBI – HGNC | Gene | resource for approved human gene nomenclature | HGNC |
| 19 | EFO | Terminology | systematic description of experimental variables available in EBI databases | EFO - The Experimental Factor Ontology < EMBL-EBI |
| 20 | Ensembl – Gene | Gene | gene information from ensemble | Ensembl |
| 21 | Expasy - Enzyme | Protein | the nomenclature of enzymes | Expasy - ENZYME |
| 22 | FDA - Adverse Event Reporting System | Drug/Compound | The FDA Adverse Event Reporting System (FAERS) is a database that contains information on adverse event and medication error reports submitted to FDA. | FAERS |
| 23 | FDA - UNII | Clinical | FDA’s global Substance Registration System enables an efficient and accurate exchange of information on substances through their Unique Ingredient Identifiers (UNIIs) which can be generated at any time in the regulatory life cycle | FDA's Global Substance Registration System |
| 24 | Gencode | Gene | genecode for mouse | GENCODE - Mouse Release M32 |
| 25 | Geneontology | Pathway | information on the functions of genes | Gene Ontology |
| 26 | GeneRIF | Gene | functional annotation of genes | About Gene RIF - Gene - NCBI |
| 27 | GSEA - MSigDB | Pathway | curated gene sets (C2) from msigdb | Human MSigDB Collections |
| 28 | GTExPortal | Expression | gene expression data from samples collected from 54 non-diseased tissue sites across nearly 1000 individuals | GTEx Portal |
| 29 | HomoloGene | Gene | an automated system for constructing putative homology groups from the complete gene sets of a wide range of eukaryotic species | Home - HomoloGene - NCBI |
| 30 | Human protein atlas | Protein | Transcript expression values across normal and cancer tissue | Protein atlas |
| 31 | IGV Tracks | Gene | Human tracks for integrative genomics viewer, containing NCBI reference sequences, clinVar Variants, nested Repeats and Cis-Regulatory Elements | IGV |
| 32 | IntAct | Interaction | molecular interaction data | IntAct |
| 33 | InterPro | Protein | the classification of protein families, predicting domains and important sites | InterPro |
| 34 | JASPAR | Genetics | database of manually curated, non-redundant transcription factor binding profiles | JASPAR |
| 35 | KEGG | Genetics/Pathway | resource for understanding high-level functions of biological systems. Includes KEGG data for drugs, variants, diseases, pathways, ligands and genes | KEGG |
| 36 | MeSH | Terminology | medical subject headings | Home - MeSH - NCBI |
| 37 | miRWalk | Chemical Biology | miRNA-target interactions | miRWalk |
| 38 | Monarch | Interaction | Gene – disease – phenotype relationships retrieved from the monarch knowledge graph | Monarch |
| 39 | Mondo | Terminology | disease ontology aimed at harmonizing disease definitions across the world | Mondo |
| 40 | MyGene | Gene | gene annotation data | MyGene.info |
| 41 | NA (Paper) | Chemical Biology | data from paper: 'Reimagining high-throughput profiling of reactive cysteines for cell-based screening of large electrophile libraries' | Reimagining high-throughput profiling of reactive cysteines for cell-based screening of large electrophile libraries | Nature Biotechnology |
| 42 | NA (Paper) | Chemical Biology | data from paper: 'hUbiquitome: a database of experimentally verified ubiquitination cascades in humans' | hUbiquitome: a database of experimentally verified ubiquitination cascades in humans |
| 43 | NA (Paper) | Chemical Biology | data from The PROTACtable genome paper | The PROTACtable genome | Nature Reviews Drug Discovery |
| 44 | NA (Paper) | Protein | data from paper: ‘Proteome-wide mapping of short-lived proteins in human cells’ | Proteome-wide mapping of short-lived proteins in human cells |
| 45 | NCBI - Gene | Gene | human gene id, name, symbol and synonyms from NCBI gene | Home - Gene - NCBI |
| 46 | NCBI - Orthologs | Gene | gene_orthologs table from NCBI gene | How are orthologs calculated? - NCBI |
| 47 | NCBI - Taxonomy | Gene | a curated classification and nomenclature for all of the organisms in the public sequence databases | Home - Taxonomy - NCBI |
| 48 | OMIM | Genetics | catalog of human genes and genetic disorders | OMIM |
| 49 | OpenTargets – Target/Disease evidence | Genetics | evidence between targets and diseases from OpenTargets | OpenTargets |
| 50 | PDB - Ligand expo | Protein | chemical and structural information about small molecules within the structure entries of the Protein Data Bank | Ligand Expo |
| 51 | PDBbind-CN | Protein | a comprehensive collection of experimentally measured binding affinity data for all biomolecular complexes deposited in the Protein Data Bank | PDBbind |
| 52 | Pig RNA atlas | Gene | Gene expression for protein-coding genes in 98 pig tissues and their human orthologs | Pig-Atlas |
| 53 | Protac-DB | Drug/Compound | Database of proteolysis targeting chimeras | Protac-DB |
| 54 | Reactome | Pathway | Chebi to reactome mapping | Reactome |
| 55 | Reactome | Pathway | signaling and metabolic molecules and their relations organized into biological pathways and processes | Reactome |
| 56 | SAbDab | Protein | all the antibody structures available in the PDB, annotated and presented in a consistent fashion | SAbDab: The Structural Antibody Database |
| 57 | Scannet | NA | NA | NA |
| 58 | Selleckchem | Drug/Compound | compound data (smiles ...) | Selleck Chemicals |
| 59 | SIFTS | Protein | Structure Integration with Function, Taxonomy and Sequence (SIFTS) is a project in the PDBe-KB resource for residue-level mapping between UniProt and PDB entries | SIFTS < PDBe < EMBL-EBI |
| 60 | STRING | Genetics | protein interactions | STRING |
| 61 | Swiss-Model | Protein | annotated 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline | SWISS-MODEL Repository |
| 62 | TCGA - The cancer genome atlas program | Expression | data from molecularly characterized over 20,000 primary cancer and matched normal samples spanning 33 cancer types | The Cancer Genome Atlas Program (TCGA) - NCI |
| 63 | The Human Protein Atlas | Expression | expression profiles in human tissues of genes both on the mRNA and protein level | The Human Protein Atlas |
| 64 | Uberon | Terminology | cross-species ontology | Uber-anatomy ontology |
| 65 | UbiNet | Drug/Compound | updated, validated, and abundant E3-substrate interactions, detailed classification of human E3 ligases | UbiNet 2.0 |
| 66 | UMLS | Terminology | medical and biomedical vocabularies and standards | UMLS Knowledge Sources: File Downloads |
| 67 | Uniprot | Protein/Gene | orthologous protein data | UniProt |
| 68 | Uniprot | Protein | protein to protein family mapping | UniProt |
| 69 | Uniprot - OrthoDB | Protein | database of orthologous groups | OrthoDB | Cross-referenced databases | UniProt |
| 70 | Uniprot - Subcellular location | Protein | Location of proteins within cells | Subcellular location | UniProt help |
| 71 | Uniprot - Swiss-Prot | Protein/Gene | curated protein data | UniProt |
| 72 | Uniprot - Trembl | Protein | non curated computationally analyzed records | UniProt |