The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information.

Elaine C. Meng

John H. Morris Karthik Soman Rabia E. Akbas Xiaoyuan Zhou Brett Smith Elaine C. Meng Conrad C. Huang Gabriel Cerono Gundolf Schenk Angela Rizk-Jackson Adil Harroud Lauren M. Sanders Sylvain V. Costes Krish Bharat Arjun Chakraborty Alexander R. Pico Taline Mardirossian Michael J. Keiser Alice Tang Josef Hardi Yongmei Shi Mark A. Musen Sharat Israni Sui Huang Peter W. Rose Charlotte A. Nelson Sergio E. Baranzini The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information. 2023 February 39 Bioinform. 2 https://doi.org/10.1093/bioinformatics/btad080 https://www.wikidata.org/entity/Q123023119 db/journals/bioinformatics/bioinformatics39.html#MorrisSAZSMHCSRHSCBCPMKT23

Gemma L. Holliday Shoshana D. Brown Eyal Akiva David Mischel Michael A. Hicks 0002 John H. Morris Conrad C. Huang Elaine C. Meng Scott C.-H. Pegg Thomas E. Ferrin Patricia C. Babbitt Biocuration in the structure-function linkage database: the anatomy of a superfamily. bax006 2017 2017 Database J. Biol. Databases Curation https://doi.org/10.1093/database/bax006 https://www.wikidata.org/entity/Q33787500 db/journals/biodb/biodb2017.html#HollidayBAMH17

Gemma L. Holliday Shoshana D. Brown Eyal Akiva David Mischel Michael A. Hicks 0002 John H. Morris Conrad C. Huang Elaine C. Meng Scott C.-H. Pegg Thomas E. Ferrin Patricia C. Babbitt Biocuration in the structure-function linkage database: the anatomy of a superfamily. bax045 2017 2017 Database J. Biol. Databases Curation https://doi.org/10.1093/database/bax045 https://www.wikidata.org/entity/Q54898134 db/journals/biodb/biodb2017.html#HollidayBAMHMHM17

Eyal Akiva Shoshana D. Brown Daniel E. Almonacid Alan E. Barber II Ashley F. Custer Michael A. Hicks 0002 Conrad C. Huang Florian Lauck Susan T. Mashiyama Elaine C. Meng David Mischel John H. Morris Sunil Ojha Alexandra M. Schnoes Doug Stryke Jeffrey M. Yunes Thomas E. Ferrin Gemma L. Holliday Patricia C. Babbitt The Structure-Function Linkage Database. 521-530 2014 42 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkt1130 https://www.wikidata.org/entity/Q37661971 db/journals/nar/nar42.html#AkivaBABCHHLMMMMOSSYFHB14

Conrad C. Huang Elaine C. Meng John H. Morris Eric F. Pettersen Thomas E. Ferrin Enhancing UCSF Chimera through web services. 478-484 2014 42 Nucleic Acids Res. Webserver-Issue https://doi.org/10.1093/nar/gku377 https://www.wikidata.org/entity/Q33860839 db/journals/nar/nar42.html#HuangMMPF14

Ursula Pieper 0001 Benjamin M. Webb David T. Barkan Dina Schneidman-Duhovny Avner Schlessinger Hannes Braberg Zheng Yang Elaine C. Meng Eric F. Pettersen Conrad C. Huang Ruchira S. Datta Parthasarathy Sampathkumar Mallur S. Madhusudhan Kimmen Sjölander Thomas E. Ferrin Stephen K. Burley Andrej Sali ModBase, a database of annotated comparative protein structure models, and associated resources. 465-474 2011 39 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkq1091 https://www.wikidata.org/entity/Q24613729 db/journals/nar/nar39.html#PieperWBSSBYMPHDSMSFBS11

Sunil Ojha Elaine C. Meng Patricia C. Babbitt Evolution of Function in the "Two Dinucleotide Binding Domains" Flavoproteins. 2007 3 PLoS Comput. Biol. 7 https://doi.org/10.1371/journal.pcbi.0030121 https://www.wikidata.org/entity/Q28469259 db/journals/ploscb/ploscb3.html#OjhaMB07

Elaine C. Meng Eric F. Pettersen Gregory S. Couch Conrad C. Huang Thomas E. Ferrin Tools for integrated sequence-structure analysis with UCSF Chimera. 339 2006 7 BMC Bioinform. https://doi.org/10.1186/1471-2105-7-339 https://www.wikidata.org/entity/Q21284249 db/journals/bmcbi/bmcbi7.html#MengPCHF06

Alex S. Nord Patricia J. Chang Bruce R. Conklin Antony V. Cox Courtney A. Harper Geoffrey G. Hicks Conrad C. Huang Susan J. Johns Michiko Kawamoto Songyan Liu Elaine C. Meng John H. Morris Janet Rossant Patricia Ruiz William C. Skarnes Philippe Soriano William L. Stanford Doug Stryke Harald von Melchner Wolfgang Wurst Ken-ichi Yamamura Stephen G. Young Patricia C. Babbitt Thomas E. Ferrin The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. 642-648 2006 34 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkj097 https://www.wikidata.org/entity/Q25255719 db/journals/nar/nar34.html#NordCCCHHHJKLMMRRSSSSMWYYBF06

Eric F. Pettersen Thomas D. Goddard Conrad C. Huang Gregory S. Couch Daniel M. Greenblatt Elaine C. Meng Thomas E. Ferrin UCSF Chimera - A visualization system for exploratory research and analysis. 1605-1612 2004 25 J. Comput. Chem. 13 https://doi.org/10.1002/jcc.20084 https://www.wikidata.org/entity/Q27860666 db/journals/jcc/jcc25.html#PettersenGHCGMF04

Doug Stryke Michiko Kawamoto Conrad C. Huang Susan J. Johns Leslie A. King Courtney A. Harper Elaine C. Meng Roy E. Lee Alice Yee Larry L'Italien Pao-Tien Chuang Stephen G. Young William C. Skarnes Patricia C. Babbitt Thomas E. Ferrin BayGenomics: a resource of insertional mutations in mouse embryonic stem cells. 278-281 2003 31 Nucleic Acids Res. 1 db/journals/nar/nar31.html#StrykeKHJKHMLYLCYSBF03 https://doi.org/10.1093/nar/gkg064 https://www.wikidata.org/entity/Q39790431

Ranyee A. Chiang Elaine C. Meng Conrad C. Huang Thomas E. Ferrin Patricia C. Babbitt The Structure Superposition Database. 505-510 2003 31 Nucleic Acids Res. 1 db/journals/nar/nar31.html#ChiangMHFB03 https://doi.org/10.1093/nar/gkg127 https://www.wikidata.org/entity/Q39790717

Elaine C. Meng Irwin D. Kuntz Donald J. Abraham Glen Eugene Kellogg Evaluating docked complexes with the HINT exponential function and empirical atomic hydrophobicities. 299-306 1994 8 J. Comput. Aided Mol. Des. 3 db/journals/jcamd/jcamd8.html#MengKAK94 https://doi.org/10.1007/BF00126747 https://www.wikidata.org/entity/Q46148600

Donald J. Abraham Rabia E. Akbas Eyal Akiva Daniel E. Almonacid Patricia C. Babbitt Sergio BaranziniSergio E. Baranzini Alan E. Barber II David T. Barkan Krish Bharat Hannes Braberg Shoshana D. Brown Stephen K. Burley Gabriel Cerono Arjun Chakraborty Patricia J. Chang Ranyee A. Chiang Pao-Tien Chuang Bruce R. Conklin Sylvain V. Costes Gregory S. Couch Antony V. Cox Ashley F. Custer Ruchira S. Datta Thomas E. Ferrin Thomas D. Goddard Daniel M. Greenblatt Josef Hardi Courtney A. Harper Adil Harroud Geoffrey G. Hicks Michael A. Hicks 0002 Gemma L. Holliday Conrad C. Huang Sui Huang Sharat Israni Susan J. Johns Michiko Kawamoto Michael J. Keiser Glen Eugene Kellogg Leslie A. King Irwin D. Kuntz Florian Lauck Roy E. Lee Larry L'Italien Songyan Liu M. S. Madhusudhan 0001Mallur S. Madhusudhan Taline Mardirossian Susan T. Mashiyama Harald von Melchner David Mischel John Scotter MorrisJohn H. Morris Mark A. Musen Charlotte A. Nelson Alex S. Nord Sunil Ojha Scott C.-H. Pegg Eric F. Pettersen Alexander R. Pico Ursula Pieper 0001 Angela Rizk-Jackson Peter W. Rose Janet Rossant Patricia Ruiz Andrej Sali Parthasarathy Sampathkumar Lauren M. Sanders Gundolf Schenk Avner Schlessinger Dina SchneidmanDina Schneidman-Duhovny Alexandra M. Schnoes Yongmei Shi Kimmen Sjölander William C. Skarnes Brett Smith Karthik Soman Philippe Soriano William L. Stanford Doug Stryke Alice Tang Ben M. WebbBenjamin M. Webb Wolfgang Wurst Ken-ichi Yamamura Zheng Yang Alice Yee Stephen G. Young Jeffrey M. Yunes Xiaoyuan Zhou