Biomedical knowledge graph-optimized prompt generation for large language models.

John Scotter Morris John H. Morris Scotter Morris http://www.cgl.ucsf.edu/home/scooter/ https://orcid.org/0000-0003-0290-7979 https://www.wikidata.org/entity/Q64854675 University of California, San Francisco, USA

Karthik Soman Peter W. Rose John H. Morris Rabia E. Akbas Brett Smith Braian Peetoom Catalina Villouta-Reyes Gabriel Cerono Yongmei Shi Angela Rizk-Jackson Sharat Israni Charlotte A. Nelson Sui Huang Sergio E. Baranzini Biomedical knowledge graph-optimized prompt generation for large language models. 2024 40 Bioinform. 9 https://doi.org/10.1093/bioinformatics/btae560 db/journals/bioinformatics/bioinformatics40.html#SomanRMASPVCSRI24

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

Maija Utriainen John H. Morris clusterMaker2: a major update to clusterMaker, a multi-algorithm clustering app for Cytoscape. 134 2023 December 24 BMC Bioinform. 1 https://doi.org/10.1186/s12859-023-05225-z db/journals/bmcbi/bmcbi24.html#UtriainenM23

Dexter Pratt Rudolf T. Pillich John H. Morris Translating desktop success to the web in the cytoscape project. 2023 May 3 Frontiers Bioinform. https://doi.org/10.3389/fbinf.2023.1125949 db/journals/fbinf/fbinf3.html#PrattPM23

Karthik Soman Peter W. Rose John H. Morris Rabia E. Akbas Brett Smith Braian Peetoom Catalina Villouta-Reyes Gabriel Cerono Yongmei Shi Angela Rizk-Jackson Sharat Israni Charlotte A. Nelson Sui Huang Sergio E. Baranzini Biomedical knowledge graph-enhanced prompt generation for large language models. 2023 abs/2311.17330 CoRR https://doi.org/10.48550/arXiv.2311.17330 db/journals/corr/corr2311.html#abs-2311-17330

Sergio E. Baranzini Katy Börner John H. Morris Charlotte A. Nelson Karthik Soman Erica Schleimer Michael J. Keiser Mark A. Musen Roger Pearce Tahsin Reza Brett Smith Bruce William Herr II Boris Oskotsky Angela Rizk-Jackson Katherine P. Rankin Stephan J. Sanders Riley Bove Peter W. Rose Sharat Israni Sui Huang A Biomedical Open Knowledge Network Harnesses the Power of AI to Understand Deep Human Biology. 46-58 2022 43 AI Mag. 1 https://doi.org/10.1609/aimag.v43i1.19125 db/journals/aim/aim43.html#BaranziniBMNSSK22

Eliot Ragueneau Anjali Shrivastava John H. Morris Noemi del-Toro Henning Hermjakob Pablo Porras IntAct App: a Cytoscape application for molecular interaction network visualization and analysis. 3684-3685 2021 37 Bioinform. 20 https://doi.org/10.1093/bioinformatics/btab319 db/journals/bioinformatics/bioinformatics37.html#RagueneauSMdHP21

Marc Legeay Nadezhda T. Doncheva John H. Morris Lars Juhl Jensen Visualize omics data on networks with Omics Visualizer, a Cytoscape App. 157 2020 9 F1000Research https://doi.org/10.12688/f1000research.22280.1 https://www.wikidata.org/entity/Q94602451 db/journals/f1000research/f1000research9.html#LegeayDMJ20

Damian Szklarczyk Annika L. Gable David Lyon Alexander Junge Stefan Wyder Jaime Huerta-Cepas Milan Simonovic Nadezhda T. Doncheva John H. Morris Peer Bork Lars Juhl Jensen Christian von Mering STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. D607-D613 2019 47 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gky1131 https://www.wikidata.org/entity/Q60469724 db/journals/nar/nar47.html#SzklarczykGLJWH19

G. Elisabeta Marai Bruno Pinaud Katja Bühler Alexander Lex John H. Morris Ten simple rules to create biological network figures for communication. 2019 15 PLoS Comput. Biol. 9 https://doi.org/10.1371/journal.pcbi.1007244 https://www.wikidata.org/entity/Q90305620 db/journals/ploscb/ploscb15.html#MaraiPBLM19

Barry Demchak David Otasek Alexander R. Pico Gary D. Bader Keiichiro Ono Brett Settle Eric Sage John H. Morris William J. R. Longabaugh Christian Tannus Lopes Michael Kucera Adam Treister Benno Schwikowski Piet Molenaar Trey Ideker The Cytoscape Automation app article collection. 800 2018 7 F1000Research https://doi.org/10.12688/f1000research.15355.1 https://www.wikidata.org/entity/Q55439024 db/journals/f1000research/f1000research7.html#DemchakOPBOSSMLLKTSMI18

Brett Settle David Otasek John H. Morris Barry Demchak Copycat Layout: Network layout alignment via Cytoscape Automation. 822 2018 7 F1000Research https://doi.org/10.12688/f1000research.15144.1 https://www.wikidata.org/entity/Q56396501 db/journals/f1000research/f1000research7.html#SettleOMD18

Brett Settle David Otasek John H. Morris Barry Demchak aMatReader: Importing adjacency matrices via Cytoscape Automation. 823 2018 7 F1000Research https://doi.org/10.12688/f1000research.15146.1 https://www.wikidata.org/entity/Q55692909 db/journals/f1000research/f1000research7.html#SettleOMD18a

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

Damian Szklarczyk John H. Morris Helen Cook Michael Kuhn 0004 Stefan Wyder Milan Simonovic Alberto Santos Nadezhda T. Doncheva Alexander Roth 0001 Peer Bork Lars Juhl Jensen Christian von Mering The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. D362-D368 2017 45 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkw937 https://www.wikidata.org/entity/Q39125771 db/journals/nar/nar45.html#SzklarczykMC0WS17

Angela F. Harper Janelle B. Leuthaeuser Patricia C. Babbitt John H. Morris Thomas E. Ferrin Leslie B. Poole Jacquelyn S. Fetrow An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins. 2017 13 PLoS Comput. Biol. 2 https://doi.org/10.1371/journal.pcbi.1005284 https://www.wikidata.org/entity/Q36276889 db/journals/ploscb/ploscb13.html#HarperLBMFPF17

Janelle B. Leuthaeuser John H. Morris Angela F. Harper Thomas E. Ferrin Patricia C. Babbitt Jacquelyn S. Fetrow DASP3: identification of protein sequences belonging to functionally relevant groups. 458:1-458:13 2016 17 BMC Bioinform. https://doi.org/10.1186/s12859-016-1295-z https://www.wikidata.org/entity/Q36190134 db/journals/bmcbi/bmcbi17.html#LeuthaeuserMHFB16

John H. Morris Allan Wu Roxanne A. Yamashita Aron Marchler-Bauer Thomas E. Ferrin cddApp: a Cytoscape app for accessing the NCBI conserved domain database. 134-136 2015 31 Bioinform. 1 https://doi.org/10.1093/bioinformatics/btu605 https://www.wikidata.org/entity/Q34737302 db/journals/bioinformatics/bioinformatics31.html#MorrisWYMF15

John H. Morris Vijay Dhameliya Steven Federowicz Alexander R. Pico Thomas E. Ferrin CyAnimator: Simple Animations of Cytoscape Networks. 482 2015 4 F1000Research https://doi.org/10.12688/f1000research.6852.1 db/journals/f1000research/f1000research4.html#MorrisDFPF15

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

Alexander R. Pico Gary D. Bader Barry Demchak Oriol Guitart Pla Timothy Hull William J. R. Longabaugh Christian Tannus Lopes Samad Lotia Piet Molenaar Jason Montojo John H. Morris Keiichiro Ono Benno Schwikowski David Welker Trey Ideker The Cytoscape app article collection. 138 2014 3 F1000Research https://doi.org/10.12688/f1000research.4642.1 https://www.wikidata.org/entity/Q41967577 db/journals/f1000research/f1000research3.html#PicoBDPHLLLMMMOSWI14

John H. Morris Allan Kuchinsky Thomas E. Ferrin Alexander R. Pico enhancedGraphics: a Cytoscape app for enhanced node graphics. 147 2014 3 F1000Research https://doi.org/10.12688/f1000research.4460.1 https://www.wikidata.org/entity/Q41991813 db/journals/f1000research/f1000research3.html#MorrisKFP14

John H. Morris Allan Wu Nadezhda T. Doncheva Mario Albrecht Thomas E. Ferrin setsApp: Set operations for Cytoscape Nodes and Edges. 149 2014 3 F1000Research https://doi.org/10.12688/f1000research.4392.1 db/journals/f1000research/f1000research3.html#MorrisWDAF14

Stefanie Jäger Peter Cimermancic Natali Gulbahce Jeffrey R. Johnson Kathryn E. McGovern Starlynn C. Clarke Michael Shales Gaelle Mercenne Lars Pache Kathy Li Hilda Hernandez Gwendolyn M. Jang Shoshannah L. Roth Eyal Akiva John Marlett Melanie Stephens Iván D'Orso Jason Fernandes Marie E. Fahey Cathal Mahon Anthony J. O'Donoghue Aleksandar Todorovic John H. Morris David A. Maltby Tom Alber Gerard Cagney Frederic D. Bushman John A. Young Sumit K. Chanda Wesley I. Sundquist Tanja Kortemme Ryan D. Hernandez Charles S. Craik Alma Burlingame Andrej Sali Alan D. Frankel Nevan J. Krogan Global landscape of HIV-human protein complexes. 365-370 2012 481 Nat. 7381 https://doi.org/10.1038/nature10719 https://www.wikidata.org/entity/Q24300336 db/journals/nature/nature481.html#JagerCGJMCSMPLH12

Leonard Apeltsin John H. Morris Patricia C. Babbitt Thomas E. Ferrin Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution. 326-333 2011 27 Bioinform. 3 https://doi.org/10.1093/bioinformatics/btq655 https://www.wikidata.org/entity/Q33759251 db/journals/bioinformatics/bioinformatics27.html#ApeltsinMBF11

John H. Morris Leonard Apeltsin Aaron M. Newman Jan Baumbach Tobias Wittkop Gang Su Gary D. Bader Thomas E. Ferrin clusterMaker: a multi-algorithm clustering plugin for Cytoscape. 436 2011 12 BMC Bioinform. https://doi.org/10.1186/1471-2105-12-436 https://www.wikidata.org/entity/Q34070756 db/journals/bmcbi/bmcbi12.html#MorrisANBWSBF11

Gang Su Allan Kuchinsky John H. Morris David J. States Fan Meng GLay: community structure analysis of biological networks. 3135-3137 2010 26 Bioinform. 24 https://doi.org/10.1093/bioinformatics/btq596 https://www.wikidata.org/entity/Q33760198 db/journals/bioinformatics/bioinformatics26.html#SuKMSM10

Andrés F. Flórez Daeui Park Jong Bhak Byoung-Chul Kim Allan Kuchinsky John H. Morris Jairo Espinosa Carlos Muskus Protein network prediction and topological analysis in <i>Leishmania major </i>as a tool for drug target selection. 484 2010 11 BMC Bioinform. https://doi.org/10.1186/1471-2105-11-484 https://www.wikidata.org/entity/Q33704536 db/journals/bmcbi/bmcbi11.html#FlorezPBKKMEM10

John H. Morris Conrad C. Huang Patricia C. Babbitt Thomas E. Ferrin structureViz: linking Cytoscape and UCSF Chimera. 2345-2347 2007 23 Bioinform. 17 https://doi.org/10.1093/bioinformatics/btm329 https://www.wikidata.org/entity/Q45962594 db/journals/bioinformatics/bioinformatics23.html#MorrisHBF07

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

Thomas E. Ferrin Conrad C. Huang Daniel M. Greenblatt Doug Stryke Kathleen M. Giacomini John H. Morris Enhancing Data Sharing in Collaborative Research Projects with DASH. 2005 conf/psb/2005 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb05/ferrin.pdf db/conf/psb/psb2005.html#FerrinHGSGM05 Rabia E. Akbas Eyal Akiva Tom Alber Mario Albrecht Daniel E. Almonacid Leonard Apeltsin Patricia C. Babbitt Gary D. Bader Sergio BaranziniSergio E. Baranzini Alan E. Barber II Jan Baumbach Jong Bhak Krish Bharat Peer Bork Katy Börner Riley Bove Shoshana D. Brown Katja Bühler Alma Burlingame Frederic D. Bushman Gerard Cagney Gabriel Cerono Arjun Chakraborty Sumit K. Chanda Patricia J. Chang Peter Cimermancic Starlynn C. Clarke Bruce R. Conklin Helen Cook Sylvain V. Costes Antony V. Cox Charles S. Craik Ashley F. Custer Noemi del-Toro Barry Demchak Vijay Dhameliya Nadezhda T. Doncheva Iván D'Orso Jairo Espinosa Marie E. Fahey Steven Federowicz Jason Fernandes Thomas E. Ferrin Jacquelyn S. Fetrow Andrés F. Flórez Alan D. Frankel Annika L. Gable Kathleen M. Giacomini Daniel M. Greenblatt Oriol GuitartOriol Guitart Pla Natali Gulbahce Josef Hardi Angela F. Harper Courtney A. Harper Adil Harroud Henning Hermjakob Hilda Hernandez Ryan D. Hernandez Bruce W. HerrBruce William Herr II Geoffrey G. Hicks Michael A. Hicks 0002 Gemma L. Holliday Conrad C. Huang Sui Huang Jaime Huerta-Cepas Timothy Hull Trey Ideker Sharat Israni Stefanie Jäger Gwendolyn M. Jang Lars Juhl Jensen Susan J. Johns Jeffrey R. Johnson Alexander Junge Michiko Kawamoto Michael J. Keiser Byoung-Chul Kim Tanja Kortemme Nevan J. Krogan Michael Kucera Allan Kuchinsky Michael Kuhn 0004 Florian Lauck Marc Legeay Janelle B. Leuthaeuser Alexander Lex Kathy Li Songyan Liu William J. R. Longabaugh Christian Tannus Lopes Samad Lotia David Lyon Cathal Mahon David A. Maltby G. Elisabeta Marai Aron Marchler-Bauer Taline Mardirossian John Marlett Susan T. Mashiyama Kathryn E. McGovern Harald von Melchner Elaine C. Meng Fan Meng Gaelle Mercenne Christian von Mering David Mischel Piet Molenaar Jason Montojo Mark A. Musen Carlos Muskus Charlotte A. Nelson Aaron M. Newman Alex S. Nord Anthony J. O'Donoghue Sunil Ojha Keiichiro Ono Boris Oskotsky David Otasek Lars Pache Daeui Park Roger A. PearceRoger Pearce Braian Peetoom Scott C.-H. Pegg Eric F. Pettersen Alexander R. Pico Rudolf T. Pillich Bruno Pinaud Leslie B. Poole Pablo Porras Dexter Pratt Eliot Ragueneau Katherine P. Rankin Tahsin Reza Angela Rizk-Jackson Peter W. Rose Janet Rossant Alexander Roth 0001 Shoshannah L. Roth Patricia Ruiz Eric Sage Andrej Sali Lauren M. Sanders Stephan J. Sanders Alberto Santos Gundolf Schenk Erica Schleimer Alexandra M. Schnoes Benno Schwikowski Brett Settle Michael Shales Yongmei Shi Anjali Shrivastava Milan Simonovic William C. Skarnes Brett Smith Karthik Soman Philippe Soriano William L. Stanford David J. States Melanie Stephens Doug Stryke Gang Su Wesley I. Sundquist Damian Szklarczyk Alice Tang Aleksandar Todorovic Adam Treister Maija Utriainen Catalina Villouta-Reyes David Welker Tobias Wittkop Allan Wu Wolfgang Wurst Stefan Wyder Ken-ichi Yamamura Roxanne A. Yamashita John A. Young Stephen G. Young Jeffrey M. Yunes Xiaoyuan Zhou