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The BMEG is an expanding resource of interconnected data. Sources include:
| Resource | Description | Contains Resource | License | References |
|---|---|---|---|---|
| TCGA | The Cancer Genome Atlas (TCGA) profiles the DNA, RNA, protein, and epigenetic levels of over 10,000 individuals across 33 cancer types. | – | ||
| MC3 | The Cancer Genome Atlas (TCGA) cancer genomics dataset includes over 10,000 tumor-normal exome pairs across 33 different cancer types, in total >400 TB of raw data files requiring analysis. | – | https://www.ncbi.nlm.nih.gov/pubmed/29596782 | |
| GTEx | The Genotype-Tissue Expression (GTEx) project. | – | https://www.ncbi.nlm.nih.gov/pubmed/23715323 | |
| PharmacoDB | An integrative database for mining drug sensitivty data for over 650K experiemnts involving 1600 cancer cell lines and 750 compounds. | – | – | https://www.ncbi.nlm.nih.gov/pubmed/30053271 |
| CCLE | https://depmap.org/portal/ccle/terms_and_conditions | https://www.ncbi.nlm.nih.gov/pubmed/22460905 | ||
| CTRP | https://ocg.cancer.gov/programs/ctd2/using-ctd2-data | https://www.ncbi.nlm.nih.gov/pubmed/23993102 | ||
| GDSC | CC BY-NC-ND 2.5 | https://www.ncbi.nlm.nih.gov/pubmed/23180760 | ||
| CCLE | The Cancer Cell Line Encyclopedia(CCLE): gene expression, chromosomal copy number and massively parallel sequencing data from 947 human cancer cell lines. | – | https://depmap.org/portal/ccle/terms_and_conditions | https://www.ncbi.nlm.nih.gov/pubmed/22460905 |
| Cell Model Passports | The Cell Model Passports provides manual and programmatic access to a cancer cell model database containing curated patient, sample and model relationship information as well as genomic and functional datasets. | – | https://cellmodelpassports.sanger.ac.uk/documentation/cellmodelpassports/datasets | – |
| Ensembl | The Ensembl project has been aggregating, processing, integrating and redistributing genomic datasets since the initial release of the draft human genome, with the aim of accelerating genomics research through rapid open distribution of public data. | – | https://uswest.ensembl.org/info/about/legal/disclaimer.html | https://www.ncbi.nlm.nih.gov/pubmed/21045057 |
| GO | Gene Ontology Consortium is a controlled vocabulary describing knowledge of gene and protein roles in cells. | – | CC BY 4.0 | http://www.ncbi.nlm.nih.gov/pubmed/10802651 |
| MonDO | The Monarch Disease Ontology merges in multiple disease resources to yield a coherent ontology. | – | CC BY 3.0 | https://www.biorxiv.org/content/10.1101/048843v3 |
| MSigDB | The Molecular Signatures Database is a collection of annotated gene sets. | – | CC BY 4.0 | https://www.ncbi.nlm.nih.gov/pubmed/21546393 |
| PFAM | Pfam is a database of protein families and annotations. | – | CC0 | https://www.ncbi.nlm.nih.gov/pubmed/30357350 |
| PubChem | PubChem is a public repository containing information about chemical substances and their biological activities. | – | https://www.ncbi.nlm.nih.gov/pubmed/26400175 | |
| PubMed | PubMed is an archive of biomedical and life sciencesjournal literature. | – | https://www.nlm.nih.gov/databases/download/terms_and_conditions.html | |
| VICC G2P | The VICC G2P is a framework for aggregating and harmonizing variant interpretations to produce a meta-knowledgebase of 12,856 aggregate interpretations covering 3,437 unique variants in 415 genes, 357 diseases, and 791 drugs. | – | – | https://www.biorxiv.org/content/10.1101/366856v1 |
| CGI | CC0 | |||
| CIViC | CC0 | |||
| JaxCKB | CC BY-NC-SA 4.0 | |||
| MolecularMatch | https://www.molecularmatch.com/terms/ | |||
| OnkoKB | https://oncokb.org/terms | |||
| PMKB | CC BY 4.0 | |||
| Pathway Commons | Pathway Commons integrates public pathway and interaction databases. | – | – | https://www.ncbi.nlm.nih.gov/pubmed/21071392 |
| BIND | Open Access | https://www.ncbi.nlm.nih.gov/pubmed/12519993 | ||
| BioGRID | MIT | https://www.ncbi.nlm.nih.gov/pubmed/16381927 | ||
| CORUM | https://www.helmholtz-muenchen.de/en/data-protection-statement/index.html | https://www.ncbi.nlm.nih.gov/pubmed/30357367 | ||
| CTD | http://ctdbase.org/about/legal.jsp | https://www.ncbi.nlm.nih.gov/pubmed/27651457 | ||
| DIP | CC BY-ND 3.0 | https://www.ncbi.nlm.nih.gov/pubmed/14681454 | ||
| HPRD | http://hprd.org/download | https://www.ncbi.nlm.nih.gov/pubmed/18988627 | ||
| HumanCyc | SRI | https://www.ncbi.nlm.nih.gov/pubmed/15642094 | ||
| INOH | CC BY-SA | https://www.ncbi.nlm.nih.gov/pubmed/22120663 | ||
| IntAct | Open Access | https://www.ncbi.nlm.nih.gov/pubmed/24234451 | ||
| KEGG Pathway | https://www.ncbi.nlm.nih.gov/pubmed/23433509 | |||
| NetPath | CC0 | https://www.ncbi.nlm.nih.gov/pubmed/20067622 | ||
| Panther | GNU GPL V2 | https://www.ncbi.nlm.nih.gov/pubmed/27899595 | ||
| PhosphositePlus | CC BY-NC-SA 3.0 | https://www.ncbi.nlm.nih.gov/pubmed/25514926 | ||
| Protein Interaction Database | https://www.ncbi.nlm.nih.gov/pubmed/18832364 | |||
| Reactome | CC0 | https://www.ncbi.nlm.nih.gov/pubmed/29145629 | ||
| Recon X | CC BY-NC 2.0 | https://www.ncbi.nlm.nih.gov/pubmed/23455439 | ||
| WikiPathways | CC0 | https://www.ncbi.nlm.nih.gov/pubmed/18651794 | ||
| DGIDB | The Drug Gene Interaction Database integrates public interaction databases. | – | – | https://www.ncbi.nlm.nih.gov/pubmed/29156001 |
| CancerCommons | http://www.ncbi.nlm.nih.gov/pubmed/21307913 | |||
| ChEMBL Interactions | CC BY-SA 3.0 | https://www.ncbi.nlm.nih.gov/pubmed/24214965 | ||
| Clearity Foundation: Biomarkers | http://www.clearityfoundation.org/healthcare-pros/drugs-and-biomarkers.aspx | |||
| Clearity Foundation: Clinical Trials | https://www.clearityfoundation.org/form/findtrials.aspx | |||
| DoCM | CC BY 4.0 | http://www.ncbi.nlm.nih.gov/pubmed/27684579 | ||
| FDA Biomarkers | https://www.fda.gov/drugs/science-research-drugs/table-pharmacogenomic-biomarkers-drug-labeling | |||
| Guide to Pharmacology: Interactions | http://www.ncbi.nlm.nih.gov/pubmed/24234439 | |||
| My Cancer Genome | https://www.mycancergenome.org/content/page/legal-policies-licensing/ | https://www.mycancergenome.org/ | ||
| NCI Cancer Gene Index | https://wiki.nci.nih.gov/display/cageneindex | |||
| TALC | http://www.ncbi.nlm.nih.gov/pubmed/24377743 | |||
| TDG Clincal Trials | http://www.ncbi.nlm.nih.gov/pubmed/24016212 | |||
| TEND | http://www.ncbi.nlm.nih.gov/pubmed/21804595 | |||
| TTD | http://www.ncbi.nlm.nih.gov/pubmed/19933260 |