├── AUTHORS.MD ├── CITATION.bib ├── CONTRIBUTING.MD ├── LICENSE ├── README.md ├── chapters ├── applications.md ├── drug_discovery_kgs.md ├── ontologies.md ├── other_resources.md └── source_datasets.md └── kg-drug-discovery.png /AUTHORS.MD: -------------------------------------------------------------------------------- 1 | Authors and contributors to awesome-drug-discovery-knowledge-graphs: 2 | 3 | - Stephen Bonner -------------------------------------------------------------------------------- /CITATION.bib: -------------------------------------------------------------------------------- 1 | @article{bonner2022review, 2 | title={A review of biomedical datasets relating to drug discovery: A knowledge graph perspective}, 3 | author={Bonner, Stephen and Barrett, Ian P and Ye, Cheng and Swiers, Rowan and Engkvist, Ola and Bender, Andreas and Hoyt, Charles Tapley and Hamilton, William L}, 4 | journal={Briefings in Bioinformatics}, 5 | volume={23}, 6 | number={6}, 7 | year={2022}, 8 | publisher={Oxford Academic} 9 | } 10 | -------------------------------------------------------------------------------- /CONTRIBUTING.MD: -------------------------------------------------------------------------------- 1 | # How to contribute 2 | 3 | Thank you for considering contributing to our resource. Before adding a new dataset, please ensure that the dataset is easily available for download by the public and that the data could be used for some form of drug discovery. 4 | 5 | Additionally, here are some important things to check when you contribute: 6 | 7 | * Update the appropriate chapter. 8 | * Add the new paper to the markdown file 9 | * If your contribution has an implementation please add the link to the implementation. 10 | * Do not forget to update the AUTHORS.MD. -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | Apache License 2 | Version 2.0, January 2004 3 | http://www.apache.org/licenses/ 4 | 5 | TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 6 | 7 | 1. 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12 | 13 |

14 | 15 | ## Overview 16 | 17 | Drug discovery and development is a complex and costly process. Machine learning approaches are being investigated to help improve the effectiveness and speed of multiple stages of the drug discovery pipeline. Of these, those that use Knowledge Graphs (KG) have promise in many tasks, including drug repurposing, drug toxicity prediction and target gene-disease prioritisation. In a drug discovery KG, crucial elements including genes, diseases and drugs are represented as entities, whilst relationships between them indicate an interaction. However, to construct high-quality KGs, suitable data is required. In this review, we detail publicly available sources suitable for use in constructing drug discovery focused KGs. We aim to help guide machine learning and KG practitioners who are interested in applying new techniques to the drug discovery field, but who may be unfamiliar with the relevant data sources. The datasets are selected via strict criteria, categorised according to the primary type of information contained within and are considered based upon what information could be extracted to build a KG. We then present a comparative analysis of existing public drug discovery KGs and a evaluation of selected motivating case studies from the literature. Additionally, we raise numerous and unique challenges and issues associated with the domain and its datasets, whilst also highlighting key future research directions. We hope this review will motivate KGs use in solving key and emerging questions in the drug discovery domain. 18 | 19 | ## The Survey Paper 20 | 21 | This repository accompanies our survey paper [A Review of Biomedical Datasets Relating to Drug Discovery: A Knowledge Graph Perspective](https://arxiv.org/abs/2102.10062). 22 | 23 | Please consider citing the associated paper for this resource if you find it useful: 24 | 25 | ``` 26 | @article{bonner2022review, 27 | title={A review of biomedical datasets relating to drug discovery: A knowledge graph perspective}, 28 | author={Bonner, Stephen and Barrett, Ian P and Ye, Cheng and Swiers, Rowan and Engkvist, Ola and Bender, Andreas and Hoyt, Charles Tapley and Hamilton, William L}, 29 | journal={Briefings in Bioinformatics}, 30 | volume={23}, 31 | number={6}, 32 | year={2022}, 33 | publisher={Oxford Academic} 34 | } 35 | ``` 36 | 37 | ----------------------------------------------------------------- 38 | 39 | ## Contents 40 | 41 | This repository primarily collects together public knowledge graph which could be used for drug discovery. We provide a list of such resources with links to the associated manuscripts, download locations and, wherever possible, the code used to create or update the resources. The list can be found using the link below: 42 | 43 | [Drug Discovery Knowledge Graphs](https://github.com/AstraZeneca/awesome-drug-discovery-knowledge-graphs/blob/master/chapters/drug_discovery_kgs.md) 44 | 45 | 46 | Additionally, we provide separate lists of key biomedical resources which are often used to compose these graphs, as well as some notable applications of KG use within drug discovery: 47 | 48 | 1. [Source Datasets](https://github.com/AstraZeneca/awesome-drug-discovery-knowledge-graphs/blob/master/chapters/source_datasets.md) 49 | 2. [Biomedical Ontologies](https://github.com/AstraZeneca/awesome-drug-discovery-knowledge-graphs/blob/master/chapters/ontologies.md) 50 | 3. [Applications](https://github.com/AstraZeneca/awesome-drug-discovery-knowledge-graphs/blob/master/chapters/applications.md) 51 | 4. [Other Resources](https://github.com/AstraZeneca/awesome-drug-discovery-knowledge-graphs/blob/master/chapters/other_resources.md) 52 | 53 | ----------------------------------------------------------------- 54 | 55 | ## Contributing 56 | 57 | We welcome the addition of new resources, please see our [contributing guide](https://github.com/AstraZeneca/awesome-drug-discovery-knowledge-graphs/blob/master/CONTRIBUTING.MD) for information on how to do this. 58 | 59 | ----------------------------------------------------------------- 60 | 61 | ## Note On Publication Version 62 | 63 | This list will continue to evolve as new resources are made available. If you want to view the list which matches the version of the published manuscript, please use this [link.](https://github.com/AstraZeneca/awesome-drug-discovery-knowledge-graphs/releases/tag/v1.0.0) 64 | 65 | -------------------------------------------------------------------------------- 66 | 67 | **License** 68 | 69 | - [Apache 2.0](https://github.com/AstraZeneca/awesome-drug-discovery-knowledge-graphs/blob/master/LICENSE) 70 | -------------------------------------------------------------------------------- 71 | -------------------------------------------------------------------------------- /chapters/applications.md: -------------------------------------------------------------------------------- 1 | ## Applications 2 | 3 | ### Polypharmacy 4 | 5 | - **Preclinical validation of therapeutic targets predicted by tensor factorization on heterogeneous graphs (Bioinformatics 2018)** 6 | - Zitnik, Marinka, Monica Agrawal, and Jure Leskovec. 7 | - [[Paper]](https://academic.oup.com/bioinformatics/article/34/13/i457/5045770) 8 | 9 | ### Drug-Target Interaction 10 | 11 | - **Discovering protein drug targets using knowledge graph embeddings (Bioinformatics 2020)** 12 | - Mohamed, Sameh K., Vít Nováček, and Aayah Nounu. 13 | - [[Paper]](https://academic.oup.com/bioinformatics/article/36/2/603/5542390) 14 | 15 | ### Gene-Disease Prioritization 16 | 17 | - **Preclinical validation of therapeutic targets predicted by tensor factorization on heterogeneous graphs (Scientific reports 2020)** 18 | - Paliwal, Saee, Alex de Giorgio, Daniel Neil, Jean-Baptiste Michel, and Alix MB Lacoste. 19 | - [[Paper]](https://www.nature.com/articles/s41598-020-74922-z) -------------------------------------------------------------------------------- /chapters/drug_discovery_kgs.md: -------------------------------------------------------------------------------- 1 | ## Drug Discovery Knowledge Graphs 2 | 3 | ### Public Resources 4 | 5 | #### 2025 6 | 7 | - **VitaGraph (arXiv 2025)** 8 | - Francesco Madeddu, Lucia Testa, Gianluca De Carlo, Michele Pieroni, Andrea Mastropietro, Aris Anagnostopoulos, Paolo Tieri & Sergio Barbarossa 9 | - [[Paper]](https://arxiv.org/abs/2505.11185) 10 | - [[Dataset Download]](https://www.kaggle.com/datasets/gianlucadecarlods/vitagraph) 11 | - [[Construction Code]](https://github.com/GiDeCarlo/VitaGraph) 12 | 13 | #### 2024 14 | 15 | - **HealX KG - Open Source Version (Nature Communications 2024)** 16 | - Saatviga Sudhahar, Bugra Ozer, Jiakang Chang, Wayne Chadwick, Daniel O’Donovan, Aoife Campbell, Emma Tulip, Neil Thompson & Ian Roberts 17 | - [[Paper]](https://www.nature.com/articles/s41467-024-50024-6) 18 | - [[Dataset Download]](https://github.com/healx/automated-biological-evidence-generation-in-drug-discovery/tree/main/data) 19 | 20 | #### 2023 21 | 22 | - **PrimeKG (Scientific Data 2023)** 23 | - Payal Chandak, Kexin Huang & Marinka Zitnik. 24 | - [[Paper]](https://www.nature.com/articles/s41597-023-01960-3) 25 | - [[Dataset Download]](https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/IXA7BM) 26 | - [[Website]](https://zitniklab.hms.harvard.edu/projects/PrimeKG/) 27 | - [[Construction Code]](https://github.com/mims-harvard/PrimeKG) 28 | 29 | #### 2022 30 | 31 | - **PharMeBINet (Scientific Data 2022)** 32 | - Cassandra Königs, Marcel Friedrichs & Theresa Dietrich. 33 | - [[Paper]](https://www.nature.com/articles/s41597-022-01510-3) 34 | - [[Dataset Download]](https://zenodo.org/record/6578218) 35 | - [[Website]](https://pharmebi.net/#/) 36 | - [[Construction Code]](https://github.com/ckoenigs/PharMeBINet) 37 | 38 | - **Clinical Knowledge Graph (CKG) (Nature Biotech 2022)** 39 | - Santos, Alberto, Ana R. Colaço, Annelaura B. Nielsen, Lili Niu, Philipp E. Geyer, Fabian Coscia, Nicolai J. Wewer Albrechtsen, Filip Mundt, Lars Juhl Jensen, and Matthias Mann. 40 | - [[Paper]](https://www.nature.com/articles/s41587-021-01145-6) 41 | - [[Dataset Download]](https://data.mendeley.com/datasets/mrcf7f4tc2/1) 42 | - [[Website]](https://ckg.readthedocs.io/en/latest/) 43 | - [[Construction Code]](https://github.com/MannLabs/CKG) 44 | 45 | #### 2020 46 | 47 | - **Drug Repurposing Knowledge Graph (DRKG) (arXiv 2020)** 48 | - Ioannidis, Vassilis N., Xiang Song, Saurav Manchanda, Mufei Li, Xiaoqin Pan, Da Zheng, Xia Ning, Xiangxiang Zeng, and George Karypis. 49 | - [[Paper]](https://github.com/gnn4dr/DRKG/blob/master/DRKG%20Drug%20Repurposing%20Knowledge%20Graph.pdf) 50 | - [[Dataset Download]](https://github.com/gnn4dr/DRKG) 51 | 52 | - **BioKG (CIKM 2020)** 53 | - Walsh, Brian, Sameh K. Mohamed, and Vít Nováček. 54 | - [[Paper]](https://dl.acm.org/doi/10.1145/3340531.3412776) 55 | - [[Dataset Download]](https://github.com/dsi-bdi/biokg/releases/tag/v1.0.0) 56 | - [[Construction Code]](https://github.com/dsi-bdi/biokg) 57 | 58 | - **OpenBioLink (Bioinformatics 2020)** 59 | - Breit, Anna, Simon Ott, Asan Agibetov, and Matthias Samwald. 60 | - [[Paper]](https://arxiv.org/abs/1912.04616) 61 | - [[Dataset Download]](https://zenodo.org/record/3834052) 62 | - [[Construction Code]](https://github.com/OpenBioLink/OpenBioLink) 63 | - [[Website]](https://openbiolink.github.io/) 64 | 65 | - **PharmKG (Briefings in Bioinformatics 2020)** 66 | - Zheng, Shuangjia, Jiahua Rao, Ying Song, Jixian Zhang, Xianglu Xiao, Evandro Fei Fang, Yuedong Yang, and Zhangming Niu. 67 | - [[Paper]](https://doi.org/10.1093/bib/bbaa344) 68 | - [[Dataset Download]](https://zenodo.org/record/4077338) 69 | - [[Website]](https://github.com/MindRank-Biotech/PharmKG) 70 | 71 | #### 2017 72 | 73 | - **Hetionet (eLife 2017)** 74 | - Himmelstein, Daniel Scott, Antoine Lizee, Christine Hessler, Leo Brueggeman, Sabrina L. Chen, Dexter Hadley, Ari Green, Pouya Khankhanian, and Sergio E. Baranzini. 75 | - [[Paper]](https://elifesciences.org/articles/26726) 76 | - [[Dataset Download]](https://github.com/hetio/hetionet) 77 | - [[Construction Code]](https://github.com/dhimmel/integrate) 78 | - [[Website]](https://het.io/) -------------------------------------------------------------------------------- /chapters/ontologies.md: -------------------------------------------------------------------------------- 1 | ## Biomedical Ontologies 2 | 3 | ### Disease 4 | 5 | - **Medical Subject Headings (MeSH) (BMAA 2000)** 6 | - Lipscomb, Carolyn E. 7 | - [[Paper]](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC35238/) 8 | - [[Website]](https://bioportal.bioontology.org/ontologies/MESH) 9 | 10 | - **Human Phenotype Ontology (HPO) (AJHG 2010)** 11 | - Robinson, Peter N., and S. Mundlos. 12 | - [[Paper]](https://www.sciencedirect.com/science/article/pii/S0002929708005351) 13 | - [[Website]](https://hpo.jax.org/app/) 14 | 15 | - **Experimental Factor Ontology (EFO) (Bioinformatics 2010)** 16 | - Malone, James, Ele Holloway, Tomasz Adamusiak, Misha Kapushesky, Jie Zheng, Nikolay Kolesnikov, Anna Zhukova, Alvis Brazma, and Helen Parkinson. 17 | - [[Paper]](https://academic.oup.com/bioinformatics/article/26/8/1112/208992?login=true) 18 | - [[Website]](https://www.ebi.ac.uk/efo/) 19 | 20 | - **Disease Ontology (DO) (Nucleic Acids Research 2012)** 21 | - Schriml, Lynn Marie, Cesar Arze, Suvarna Nadendla, Yu-Wei Wayne Chang, Mark Mazaitis, Victor Felix, Gang Feng, and Warren Alden Kibbe. 22 | - [[Paper]](https://academic.oup.com/nar/article/40/D1/D940/2903651?login=true) 23 | - [[Website]](https://disease-ontology.org/) 24 | 25 | - **Mondo Disease Ontology (MonDO) (Nucleic Acids Research 2017)** 26 | - Mungall, Christopher J., Julie A. McMurry, Sebastian Köhler, James P. Balhoff, Charles Borromeo, Matthew Brush, Seth Carbon et al. 27 | - [[Paper]](https://academic.oup.com/nar/article/45/D1/D712/2605791?login=true) 28 | - [[Website]](https://www.ebi.ac.uk/ols/ontologies/mondo) 29 | 30 | ### Gene 31 | 32 | - **Gene Ontology (GO) (Nature Genetics 2000)** 33 | - Ashburner, Michael, Catherine A. Ball, Judith A. Blake, David Botstein, Heather Butler, J. Michael Cherry, Allan P. Davis et al. 34 | - [[Paper]](https://www.nature.com/articles/ng0500_25) 35 | - [[Website]](http://geneontology.org/) 36 | 37 | ### Drug Discovery 38 | 39 | - **Drug Target Ontology Ontology (DTO) (Biomedical Semantics 2017)** 40 | - Lin, Yu, Saurabh Mehta, Hande Küçük-McGinty, John Paul Turner, Dusica Vidovic, Michele Forlin, Amar Koleti et al. 41 | - [[Paper]](https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0161-x) 42 | - [[Website]](http://drugtargetontology.org/) 43 | 44 | ### A Number of Ontologies and other KGs in the Biological and Biomedical Space 45 | 46 | - **Knowledge Graph Hub (KG Hub) is to provide a platform for building knowledge graphs (KGs) by adopting a set of guidelines and design principles** 47 | - J Harry Caufield, Tim Putman, Kevin Schaper, Deepak R Unni, Harshad Hegde, Tiffany J Callahan, Luca Cappelletti, Sierra A T Moxon, Vida Ravanmehr, et al. 48 | - [[Paper]](https://academic.oup.com/bioinformatics/article/39/7/btad418/7211646) 49 | - [[Website]](https://kghub.org) 50 | -------------------------------------------------------------------------------- /chapters/other_resources.md: -------------------------------------------------------------------------------- 1 | ### Other Biomedical Graphs and Interesting Projects 2 | 3 | - **Knowledge Graph Hub (KG Hub) is to provide a platform for building knowledge graphs (KGs) by adopting a set of guidelines and design principles** 4 | - J Harry Caufield, Tim Putman, Kevin Schaper, Deepak R Unni, Harshad Hegde, Tiffany J Callahan, Luca Cappelletti, Sierra A T Moxon, Vida Ravanmehr, et al. 5 | - [[Paper]](https://academic.oup.com/bioinformatics/article/39/7/btad418/7211646) 6 | - [[Website]](https://kghub.org) 7 | 8 | - **Stanford Biomedical Network Dataset Collection (BioSNAP) (2018)** 9 | - Santos, Alberto, Ana R. Colaço, Annelaura B. Nielsen, Lili Niu, Philipp E. Geyer, Fabian Coscia, Nicolai J. Wewer Albrechtsen, Filip Mundt, Lars Juhl Jensen, and Matthias Mann. 10 | - [[Dataset Download]](https://snap.stanford.edu/biodata/index.html) 11 | - [[Construction Code]](https://snap.stanford.edu/mambo/) 12 | 13 | - **Bio2RDF (Biomedical Informatics 2014)** 14 | - Dumontier, Michel, Alison Callahan, Jose Cruz-Toledo, Peter Ansell, Vincent Emonet, François Belleau, and Arnaud Droit. 15 | - [[Paper]](https://www.researchgate.net/profile/Francois-Belleau/publication/287066655_Bio2RDF_release_3_A_larger_connected_network_of_linked_data_for_the_life_sciences/links/6033cb0b299bf1cc26e43cf5/Bio2RDF-release-3-A-larger-connected-network-of-linked-data-for-the-life-sciences.pdf) 16 | - [[Dataset Download]](https://download.bio2rdf.org/#/) 17 | - [[Website]](https://bio2rdf.org/) 18 | -------------------------------------------------------------------------------- /chapters/source_datasets.md: -------------------------------------------------------------------------------- 1 | ## Source Datasets 2 | 3 | ### Gene and Gene Products 4 | 5 | - **UniProt (Nucleic Acids Research 2004)** 6 | - Apweiler, Rolf, Amos Bairoch, Cathy H. Wu, Winona C. Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger et al. 7 | - [[Paper]](https://academic.oup.com/nar/article/32/suppl_1/D115/2505378?login=true) 8 | - [[Website]](https://www.uniprot.org/) 9 | 10 | - **Ensembl (Nucleic Acids Research 2021)** 11 | - Howe, Kevin L., Premanand Achuthan, James Allen, Jamie Allen, Jorge Alvarez-Jarreta, M. Ridwan Amode, Irina M. Armean et al. 12 | - [[Paper]](https://academic.oup.com/nar/article/49/D1/D884/5952199?login=true) 13 | - [[Website]](https://www.ensembl.org/index.html) 14 | 15 | - **RNAcentral (Nucleic Acids Research 2021)** 16 | - RNAcentral Consortium. 17 | - [[Paper]](https://academic.oup.com/nar/article/49/D1/D212/5940500?login=true) 18 | - [[Website]](https://rnacentral.org/) 19 | 20 | - **Entrez (Nucleic Acids Research 2021)** 21 | - Brown, Garth R., Vichet Hem, Kenneth S. Katz, Michael Ovetsky, Craig Wallin, Olga Ermolaeva, Igor Tolstoy et al. 22 | - [[Paper]](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013746/) 23 | - [[Website]](https://www.ncbi.nlm.nih.gov/gene) 24 | 25 | 26 | ### Interactions, Pathways and Biological Processes 27 | 28 | - **STRING (Nucleic Acids Research 2019)** 29 | - Szklarczyk, Damian, Annika L. Gable, David Lyon, Alexander Junge, Stefan Wyder, Jaime Huerta-Cepas, Milan Simonovic et al. 30 | - [[Paper]](https://academic.oup.com/nar/article/47/D1/D607/5198476?login=true) 31 | - [[Website]](https://string-db.org/) 32 | 33 | - **BioGRID (Nucleic Acids Research 2006)** 34 | - Stark, Chris, Bobby-Joe Breitkreutz, Teresa Reguly, Lorrie Boucher, Ashton Breitkreutz, and Mike Tyers. 35 | - [[Paper]](https://academic.oup.com/nar/article/34/suppl_1/D535/1133554?login=true) 36 | - [[Website]](https://thebiogrid.org/) 37 | 38 | - **IntAct (Nucleic Acids Research 2004)** 39 | - Hermjakob, Henning, Luisa Montecchi‐Palazzi, Chris Lewington, Sugath Mudali, Samuel Kerrien, Sandra Orchard, Martin Vingron et al. 40 | - [[Paper]](https://academic.oup.com/nar/article/32/suppl_1/D452/2505218?login=true) 41 | - [[Website]](https://www.ebi.ac.uk/intact/home) 42 | 43 | - **OmniPath (Nature Methods 2016)** 44 | - Türei, Dénes, Tamás Korcsmáros, and Julio Saez-Rodriguez. 45 | - [[Paper]](https://www.nature.com/articles/nmeth.4077) 46 | - [[Website]](https://omnipathdb.org/) 47 | 48 | - **Reactome (Nucleic Acids Research 2005)** 49 | - Joshi-Tope, G., Marc Gillespie, Imre Vastrik, Peter D'Eustachio, Esther Schmidt, Bernard de Bono, Bijay Jassal et al. 50 | - [[Paper]](https://academic.oup.com/nar/article/33/suppl_1/D428/2505340?login=true) 51 | - [[Website]](https://reactome.org/) 52 | 53 | - **WikiPathways (Nucleic Acids Research 2016)** 54 | - Slenter, Denise N., Martina Kutmon, Kristina Hanspers, Anders Riutta, Jacob Windsor, Nuno Nunes, Jonathan Mélius et al. 55 | - [[Paper]](https://academic.oup.com/nar/article/46/D1/D661/4612963?login=true) 56 | - [[Website]](https://www.wikipathways.org/index.php/WikiPathways) 57 | 58 | - **KEGG Pathways (Nucleic Acids Research 1999)** 59 | - Ogata, Hiroyuki, Susumu Goto, Kazushige Sato, Wataru Fujibuchi, Hidemasa Bono, and Minoru Kanehisa. 60 | - [[Paper]](https://academic.oup.com/nar/article/27/1/29/1238108) 61 | - [[Website]](https://www.genome.jp/kegg/pathway.html) 62 | 63 | ### Disease 64 | 65 | - **KEGG Disease (Nucleic Acids Research 2007)** 66 | - Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T. and Yamanishi, Y 67 | - [[Paper]](https://academic.oup.com/nar/article-abstract/36/suppl_1/D480/2507484) 68 | - [[Website]](https://www.genome.jp/kegg/disease/) 69 | 70 | - **DISEASES (Methods 2015)** 71 | - Pletscher-Frankild, Sune, Albert Pallejà, Kalliopi Tsafou, Janos X. Binder, and Lars Juhl Jensen. 72 | - [[Paper]](https://www.sciencedirect.com/science/article/pii/S1046202314003831) 73 | - [[Website]](https://diseases.jensenlab.org/Search) 74 | 75 | - **DisGeNET (Nucleic Acids Research 2016)** 76 | - Piñero, Janet, Àlex Bravo, Núria Queralt-Rosinach, Alba Gutiérrez-Sacristán, Jordi Deu-Pons, Emilio Centeno, Javier García-García, Ferran Sanz, and Laura I. Furlong. 77 | - [[Paper]](https://pubmed.ncbi.nlm.nih.gov/27924018/) 78 | - [[Website]](https://www.disgenet.org/home/) 79 | 80 | - **OMIM (Nucleic Acids Research 2005)** 81 | - Hamosh, Ada, Alan F. Scott, Joanna S. Amberger, Carol A. Bocchini, and Victor A. McKusick. 82 | - [[Paper]](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC539987/) 83 | - [[Website]](https://www.omim.org/) 84 | 85 | - **GWAS Catalog (Nucleic Acids Research 2019)** 86 | - Buniello, Annalisa, Jacqueline A. L. MacArthur, Maria Cerezo, Laura W. Harris, James Hayhurst, Cinzia Malangone, Aoife McMahon et al. 87 | - [[Paper]](https://academic.oup.com/nar/article/47/D1/D1005/5184712?login=true) 88 | - [[Website]](https://www.ebi.ac.uk/gwas/) 89 | 90 | ### Drugs & Compounds 91 | 92 | - **ChEMBL (Nucleic Acids Research 2012)** 93 | - Gaulton, Anna, Louisa J. Bellis, A. Patricia Bento, Jon Chambers, Mark Davies, Anne Hersey, Yvonne Light et al. 94 | - [[Paper]](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245175/) 95 | - [[Website]](https://www.ebi.ac.uk/chembl/) 96 | 97 | - **PubChem (Nucleic Acids Research 2016)** 98 | - Kim, Sunghwan, Paul A. Thiessen, Evan E. Bolton, Jie Chen, Gang Fu, Asta Gindulyte, Lianyi Han et al. 99 | - [[Paper]](https://pubmed.ncbi.nlm.nih.gov/26400175/) 100 | - [[Website]](https://pubchem.ncbi.nlm.nih.gov/) 101 | 102 | - **DrugBank (Nucleic Acids Research 2008)** 103 | - Wishart, David S., Craig Knox, An Chi Guo, Dean Cheng, Savita Shrivastava, Dan Tzur, Bijaya Gautam, and Murtaza Hassanali. 104 | - [[Paper]](https://pubmed.ncbi.nlm.nih.gov/26400175/) 105 | - [[Website]](https://go.drugbank.com/) 106 | 107 | - **DrugCentral(Nucleic Acids Research 2017)** 108 | - Ursu, Oleg, Jayme Holmes, Jeffrey Knockel, Cristian G. Bologa, Jeremy J. Yang, Stephen L. Mathias, Stuart J. Nelson, and Tudor I. Oprea. 109 | - [[Paper]](https://pubmed.ncbi.nlm.nih.gov/27789690/) 110 | - [[Website]](https://drugcentral.org/) 111 | 112 | - **Binding DB (Combinatorial Chemistry & High Throughput Screening 2001)** 113 | - Chen, Xi, Ming Liu, and Michael K. Gilson. 114 | - [[Paper]](https://pubmed.ncbi.nlm.nih.gov/11812264/) 115 | - [[Website]](https://www.bindingdb.org/bind/index.jsp) 116 | 117 | - **RepoDB (Scientific Data 2017)** 118 | - Brown, Adam S., and Chirag J. Patel. 119 | - [[Paper]](https://www.nature.com/articles/sdata201729) 120 | - [[Website]](http://apps.chiragjpgroup.org/repoDB/) -------------------------------------------------------------------------------- /kg-drug-discovery.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstraZeneca/awesome-drug-discovery-knowledge-graphs/00e6826f7ad823cba73f4b133dd685feb2886d63/kg-drug-discovery.png --------------------------------------------------------------------------------