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Knowledge graphs are powerful tools for representing and organising complex biomedical data.
Dbpedia: A nucleus for a web of open data
Sören Auer, Christian Bizer, Georgi Kobilarov, Jens Lehmann, Richard Cyganiak, and Zachary G. Ives · 2007
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Drugbank: a knowledgebase for drugs, drug actions and drug targets
David S. Wishart, Craig Knox, Anchi Guo, Dean Cheng, Savita Shrivastava, Dan Tzur, Bijaya Gautam, and Murtaza Hassanali · 2008
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Prediction of drug-target interaction networks from the integration of chemical and genomic spaces
Yoshihiro Yamanishi, Michihiro Araki, Alex Gutteridge, Wataru Honda, and Minoru Kanehisa · 2008
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Reactome: a database of reactions, pathways and biological processes
David Croft, Gavin O’Kelly, Guanming Wu, Robin Haw, Marc Gillespie, Lisa Matthews, Michael Caudy, Phani V. Garapati, Gopal Gopinath, Bijay Jassal, Steven Jupe, Irina Kalatskaya, Shahana Mahajan, Bruce May, Nelson Ndegwa, Esther Schmidt, Veronica Shamovsky, Christina K. Yung, Ewan Birney, Henning Hermjakob, Peter D’Eustachio, and Lincoln Stein · 2011
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The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
Damian Szklarczyk, Andrea Franceschini, Michael Kuhn, Milan Simonovic, Alexander Roth, Pablo Minguez, Tobias Doerks, Manuel Stark, Jean Muller, Peer Bork, Lars J. Jensen, and Christian von Mering · 2011
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Data-Driven Prediction of Drug Effects and Interactions
Nicholas P. Tatonetti, Patrick P. Ye, Roxana Daneshjou, and Russ B. Altman · 2012
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Translating Embeddings for Modeling Multi-relational Data
Antoine Bordes, Nicolas Usunier, Alberto Garcia-Duran, Jason Weston, and Oksana Yakhnenko · 2013
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A community computational challenge to predict the activity of pairs of compounds
Mukesh Bansal, Jichen Yang, Charles Karan, Michael P Menden, James C Costello, Hao Tang, Guanghua Xiao, Yajuan Li, Jeffrey Allen, Rui Zhong, et al · 2014
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Knowledge Graph Embedding by Translating on Hyperplanes
Zhen Wang, Jianwen Zhang, Jianlin Feng, and Zheng Chen · 2014
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Embedding entities and relations for learning and inference in knowledge bases
Bishan Yang, Wen-tau Yih, Xiaodong He, Jianfeng Gao, and Li Deng · 2015
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KEGG as a reference resource for gene and protein annotation
Minoru Kanehisa, Yoko Sato, Masayuki Kawashima, Miho Furumichi, and Mao Tanabe · 2016
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Complex embeddings for simple link prediction
Théo Trouillon, Johannes Welbl, Sebastian Riedel, Éric Gaussier, and Guillaume Bouchard · 2016
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The Amyloid Cascade Hypothesis in Alzheimer’s Disease: It’s Time to Change Our Mind
Roberta Ricciarelli and Ernesto Fedele · 2017
Cited alongside, same era.
Knowledge Graph Embedding: A Survey of Approaches and Applications
Quan Wang, Zhendong Mao, Bin Wang, and Li Guo · 2017
Cited alongside, same era.
Convolutional 2d knowledge graph embeddings
Tim Dettmers, Pasquale Minervini, Pontus Stenetorp, and Sebastian Riedel · 2018
Cited alongside, same era.
Canonical tensor decomposition for knowledge base completion
Timothée Lacroix, Nicolas Usunier, and Guillaume Obozinski · 2018
Cited alongside, same era.
Modeling polypharmacy side effects with graph convolutional networks
Marinka Zitnik, Monica Agrawal, and Jure Leskovec · 2018
Predicting polypharmacy side effects through a relation-wise graph attention network
Vincenzo Carletti, Pasquale Foggia, Antonio Greco, Antonio Roberto, and Mario Vento · 2020
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You CAN teach an old dog new tricks! on training knowledge graph embeddings
Daniel Ruffinelli, Samuel Broscheit, and Rainer Gemulla · 2020
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BioKG: A Knowledge Graph for Relational Learning On Biological Data
Brian Walsh, Sameh K. Mohamed, and Vít Nováček · 2020
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Graph neural networks: A review of methods and applications
Jie Zhou, Ganqu Cui, Shengding Hu, Zhengyan Zhang, Cheng Yang, Zhiyuan Liu, Lifeng Wang, Changcheng Li, and Maosong Sun · 2020
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SAFRAN: an interpretable, rule-based link prediction method outperforming embedding models
Simon Ott, Christian Meilicke, and Matthias Samwald · 2021
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Cited alongside, same era.
Anytime bottom-up rule learning for knowledge graph completion
Christian Meilicke, Melisachew Wudage Chekol, Daniel Ruffinelli, and Heiner Stuckenschmidt · 2019
Cited alongside, same era.
Rotate: Knowledge graph embedding by relational rotation in complex space
Zhiqing Sun, Zhi-Hong Deng, Jian-Yun Nie, and Jian Tang · 2019
Cited alongside, same era.
Iteratively learning embeddings and rules for knowledge graph reasoning
Wen Zhang, Bibek Paudel, Liang Wang, Jiaoyan Chen, Hai Zhu, Wei Zhang, Abraham Bernstein, and Huajun Chen · 2019
Cited alongside, same era.
LibKGE - a knowledge graph embedding library for reproducible research
Samuel Broscheit, Daniel Ruffinelli, Adrian Kochsiek, Patrick Betz, and Rainer Gemulla · 2020
Cited alongside, same era.
A method for the rational selection of drug repurposing candidates from multimodal knowledge harmonization
Bruce Schultz, Andrea Zaliani, Christian Ebeling, Jeanette Reinshagen, Denisa Bojkova, Vanessa Lage-Rupprecht, Reagon Karki, Sören Lukassen, Yojana Gadiya, Neal G. Ravindra, Sayoni Das, Shounak Baksi, Daniel Domingo-Fernández, Manuel Lentzen, Mark Strivens, Tamara Raschka, Jindrich Cinatl, Lauren Nicole DeLong, Phil Gribbon, Gerd Geisslinger, Sandra Ciesek, David van Dijk, Steve Gardner, Alpha Tom Kodamullil, Holger Fröhlich, Manuel Peitsch, Marc Jacobs, Julia Hoeng, Roland Eils, Carsten Claussen, and Martin Hofmann-Apitius · 2021
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Understanding the performance of knowledge graph embeddings in drug discovery
Stephen Bonner, Ian P. Barrett, Cheng Ye, Rowan Swiers, Ola Engkvist, Charles Tapley Hoyt, and William L. Hamilton · 2022
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Comprehensive Analysis of Knowledge Graph Embedding Techniques Benchmarked on Link Prediction
Ilaria Ferrari, Giacomo Frisoni, Paolo Italiani, Gianluca Moro, and Claudio Sartori · 2022
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Knowledge graphs
Aidan Hogan, Eva Blomqvist, Michael Cochez, Claudia d’Amato, Gerard de Melo, Claudio Gutierrez, Sabrina Kirrane, José Emilio Labra Gayo, Roberto Navigli, Sebastian Neumaier, Axel-Cyrille Ngonga Ngomo, Axel Polleres, Sabbir M. Rashid, Anisa Rula, Lukas Schmelzeisen, Juan F. Sequeda, Steffen Staab, and Antoine Zimmermann · 2022
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Mining on Alzheimer’s diseases related knowledge graph to identity potential AD-related semantic triples for drug repurposing
Yi Nian, Xinyue Hu, Rui Zhang, Jingna Feng, Jingcheng Du, Fang Li, Larry Bu, Yuji Zhang, Yong Chen, and Cui Tao · 2022
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