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• 2025
• 
  [j84]
  Harshad Hegde,Jennifer Vendetti,Damien Goutte-Gattat,J. Harry Caufield,John B. Graybeal,Nomi L. Harris,Naouel Karam,Christian Kindermann,Nicolas Matentzoglu,James A. Overton,Mark A. Musen,Christopher J. Mungall:
  A change language for ontologies and knowledge graphs.Database J. Biol. Databases Curation2025 (2025)
• 
  [j83]
  Yasemin Bridges,Vinicius de Souza,Katherina G. Cortes,Melissa Haendel,Nomi L. Harris,Daniel R. Korn,Nikolaos M. Marinakis,Nicolas Matentzoglu,James A. McLaughlin,Christopher J. Mungall,Aaron Odell,David Osumi-Sutherland,Peter N. Robinson,Damian Smedley,Julius O. B. Jacobsen:
  Towards a standard benchmark for phenotype-driven variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework.BMC Bioinform.26(1):87 (2025)
• 2024
• 
  [j82]
  Adam Wright,Mark D. Wilkinson,Christopher J. Mungall,Scott Cain,Stephen Richards,Paul W. Sternberg,Ellen Provin,Jonathan L. Jacobs,Scott Geib,Daniela Raciti,Karen Yook,Lincoln Stein,David C. Molik:
  FAIR Header Reference genome: a TRUSTworthy standard.Briefings Bioinform.25(3) (2024)
• 
  [j81]
  Oluwamayowa O. Amusat,Harshad Hegde,Christopher J. Mungall,Anna Giannakou,Neil P. Byers,Dan Gunter,Kjiersten Fagnan,Lavanya Ramakrishnan:
  Automated annotation of scientific texts for ML-based keyphrase extraction and validation.Database J. Biol. Databases Curation2024 (2024)
• 
  [j80]
  J. Harry Caufield,Harshad Hegde,Vincent Emonet,Nomi L. Harris,Marcin P. Joachimiak,Nicolas Matentzoglu,Hyeongsik Kim,Sierra A. T. Moxon,Justin T. Reese,Melissa A. Haendel,Peter N. Robinson,Christopher J. Mungall:
  Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning.Bioinform.40(3) (2024)
• 
  [j79]
  Sabrina Toro,Anna V. Anagnostopoulos,Susan M. Bello,Kai Lewis Blumberg,Rhiannon Cameron,Leigh Carmody,Alexander D. Diehl,Damion M. Dooley,William D. Duncan,Petra Fey,Pascale Gaudet,Nomi L. Harris,Marcin P. Joachimiak,Leila Kiani,Tiago Lubiana,Monica C. Munoz-Torres,Shawn T. O'Neil,David Osumi-Sutherland,Aleix Puig-Barbe,Justin T. Reese,Leonore Reiser,Sofia M. C. Robb,Troy Ruemping,James Seager,Eric Sid,Raymund Stefancsik,Magalie Weber,Valerie Wood,Melissa A. Haendel,Christopher J. Mungall:
  Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI).J. Biomed. Semant.15(1):19 (2024)
• 
  [j78]
  Lauren E. Chan,Elena Casiraghi,Justin T. Reese,Quaker E. Harmon,Kevin Schaper,Harshad Hegde,Giorgio Valentini,Charles Schmitt,Alison A. Motsinger-Reif,Janet E. Hall,Christopher J. Mungall,Peter N. Robinson,Melissa A. Haendel:
  Predicting nutrition and environmental factors associated with female reproductive disorders using a knowledge graph and random forests.Int. J. Medical Informatics187:105461 (2024)
• 
  [j77]
  Tudor Groza,J. Harry Caufield,Dylan Gration,Gareth Baynam,Melissa A. Haendel,Peter N. Robinson,Christopher J. Mungall,Justin T. Reese:
  An evaluation of GPT models for phenotype concept recognition.BMC Medical Informatics Decis. Mak.24(1):30 (2024)
• 
  [j76]
  James P. Balhoff,Christopher J. Mungall:
  Whelk: An OWL EL+RL Reasoner Enabling New Use Cases.TGDK2(2):7:1-7:17 (2024)
• 
  [c46]
  Emanuele Cavalleri,Mauricio Soto Gomez,Ali Pashaeibarough,Dario Malchiodi,J. Harry Caufield,Justin T. Reese,Christopher J. Mungall,Peter N. Robinson,Elena Casiraghi,Giorgio Valentini,Marco Mesiti:
  Initial achievements in relation extraction from RNA-focused scientific papers.SEBD2024:61-69
• 
  [c45]
  Emanuele Cavalleri,Mauricio Soto Gomez,Ali Pashaeibarough,Dario Malchiodi,J. Harry Caufield,Justin T. Reese,Chris Mungall,Peter N. Robinson,Elena Casiraghi,Giorgio Valentini,Marco Mesiti:
  SPIREX: Improving LLM-based relation extraction from RNA-focused scientific literature using graph machine learning.VLDB Workshops2024
• 
  [d1]
  James P. Balhoff,Christopher J. Mungall:
  Whelk reasoner.DROPS Artifacts,2024 
• 
  [i19]
  Marcin P. Joachimiak,Mark A. Miller,J. Harry Caufield,Ryan Ly,Nomi L. Harris,Andrew J. Tritt,Christopher J. Mungall,Kristofer E. Bouchard:
  The Artificial Intelligence Ontology: LLM-assisted construction of AI concept hierarchies.CoRRabs/2404.03044 (2024)
• 
  [i18]
  Matthew Avaylon,Ryan Ly,Andrew J. Tritt,Benjamin K. Dichter,Kristofer E. Bouchard,Christopher J. Mungall,Oliver Rübel:
  Methods for Linking Data to Online Resources and Ontologies with Applications to Neurophysiology.CoRRabs/2406.00063 (2024)
• 
  [i17]
  Kathleen R. Mullen,Imke Tammen,Nicolas A. Matentzoglu,Marius Mather,Christopher J. Mungall,Melissa A. Haendel,Frank W. Nicholas,Sabrina Toro,the Vertebrate Breed Ontology Consortium:
  The Vertebrate Breed Ontology: Towards Effective Breed Data Standardization.CoRRabs/2406.02623 (2024)
• 
  [i16]
  Harshad Hegde,Jennifer Vendetti,Damien Goutte-Gattat,J. Harry Caufield,John B. Graybeal,Nomi L. Harris,Naouel Karam,Christian Kindermann,Nicolas Matentzoglu,James A. Overton,Mark A. Musen,Christopher J. Mungall:
  A Change Language for Ontologies and Knowledge Graphs.CoRRabs/2409.13906 (2024)
• 
  [i15]
  J. Harry Caufield,Carlo Kroll,Shawn T. O'Neil,Justin T. Reese,Marcin P. Joachimiak,Harshad Hegde,Nomi L. Harris,Madan Krishnamurthy,James A. McLaughlin,Damian Smedley,Melissa A. Haendel,Peter N. Robinson,Christopher J. Mungall:
  CurateGPT: A flexible language-model assisted biocuration tool.CoRRabs/2411.00046 (2024)
• 2023
• 
  [j75]
  Guy Karlebach,Leigh Carmody,Jagadish Chandrabose Sundaramurthi,Elena Casiraghi,Peter Hansen,Justin T. Reese,Christopher J. Mungall,Giorgio Valentini,Peter N. Robinson:
  An expectation-maximization framework for comprehensive prediction of isoform-specific functions.Bioinform.39(4) (2023)
• 
  [j74]
  Lauren E. Chan,Anne E. Thessen,William D. Duncan,Nicolas Matentzoglu,Charles Schmitt,Cynthia J. Grondin,Nicole A. Vasilevsky,Julie A. McMurry,Peter N. Robinson,Christopher J. Mungall,Melissa A. Haendel:
  The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): connecting toxicology and exposure to human health and beyond.J. Biomed. Semant.14(1):3 (2023)
• 
  [j73]
  Luca Cappelletti,Tommaso Fontana,Elena Casiraghi,Vida Ravanmehr,Tiffany J. Callahan,Carlos Cano,Marcin P. Joachimiak,Christopher J. Mungall,Peter N. Robinson,Justin T. Reese,Giorgio Valentini:
  GRAPE for fast and scalable graph processing and random-walk-based embedding.Nat. Comput. Sci.3(6):552-568 (2023)
• 
  [c44]
  Nicolas Matentzoglu,Ian Braun,Anita R. Caron,Damien Goutte-Gattat,Benjamin M. Gyori,Nomi L. Harris,Emily Hartley,Harshad B. Hegde,Sven Hertling,Charles Tapley Hoyt,Hyeongsik Kim,Huanyu Li,James A. McLaughlin,Cássia Trojahn,Nicole A. Vasilevsky,Christopher J. Mungall:
  A simple standard for ontological mappings 2023: updates on data model, collaborations and tooling.OM@ISWC2023:73-78
• 
  [i14]
  J. Harry Caufield,Tim E. Putman,Kevin Schaper,Deepak R. Unni,Harshad Hegde,Tiffany J. Callahan,Luca Cappelletti,Sierra A. T. Moxon,Vida Ravanmehr,Seth Carbon,Lauren E. Chan,Katherina Cortes,Kent A. Shefchek,Glass Elsarboukh,James P. Balhoff,Tommaso Fontana,Nicolas Matentzoglu,Richard M. Bruskiewich,Anne E. Thessen,Nomi L. Harris,Monica C. Munoz-Torres,Melissa A. Haendel,Peter N. Robinson,Marcin P. Joachimiak,Christopher J. Mungall,Justin T. Reese:
  KG-Hub - Building and Exchanging Biological Knowledge Graphs.CoRRabs/2302.10800 (2023)
• 
  [i13]
  J. Harry Caufield,Harshad Hegde,Vincent Emonet,Nomi L. Harris,Marcin P. Joachimiak,Nicolas Matentzoglu,HyeongSik Kim,Sierra A. T. Moxon,Justin T. Reese,Melissa A. Haendel,Peter N. Robinson,Christopher J. Mungall:
  Structured prompt interrogation and recursive extraction of semantics (SPIRES): A method for populating knowledge bases using zero-shot learning.CoRRabs/2304.02711 (2023)
• 
  [i12]
  Marcin P. Joachimiak,J. Harry Caufield,Nomi L. Harris,Hyeongsik Kim,Christopher J. Mungall:
  Gene Set Summarization using Large Language Models.CoRRabs/2305.13338 (2023)
• 
  [i11]
  Tiffany J. Callahan,Ignacio J. Tripodi,Adrianne L. Stefanski,Luca Cappelletti,Sanya Bathla Taneja,Jordan M. Wyrwa,Elena Casiraghi,Nicolas A. Matentzoglu,Justin T. Reese,Jonathan C. Silverstein,Charles Tapley Hoyt,Richard D. Boyce,Scott A. Malec,Deepak R. Unni,Marcin P. Joachimiak,Peter N. Robinson,Christopher J. Mungall,Emanuele Cavalleri,Tommaso Fontana,Giorgio Valentini,Marco Mesiti,Lucas A. Gillenwater,Brook E. Santangelo,Nicole A. Vasilevsky,Robert Hoehndorf,Tellen D. Bennett,Patrick B. Ryan,George Hripcsak,Michael G. Kahn,Michael Bada,William A. Baumgartner Jr.,Lawrence E. Hunter:
  An Open-Source Knowledge Graph Ecosystem for the Life Sciences.CoRRabs/2307.05727 (2023)
• 
  [i10]
  Tudor Groza,J. Harry Caufield,Dylan Gration,Gareth Baynam,Melissa A. Haendel,Peter N. Robinson,Chris Mungall,Justin T. Reese:
  An evaluation of GPT models for phenotype concept recognition.CoRRabs/2309.17169 (2023)
• 
  [i9]
  Nicolas Matentzoglu,J. Harry Caufield,Harshad B. Hegde,Justin T. Reese,Sierra A. T. Moxon,Hyeongsik Kim,Nomi L. Harris,Melissa A. Haendel,Christopher J. Mungall:
  MapperGPT: Large Language Models for Linking and Mapping Entities.CoRRabs/2310.03666 (2023)
• 
  [i8]
  Oluwamayowa O. Amusat,Harshad Hegde,Christopher J. Mungall,Anna Giannakou,Neil P. Byers,Dan Gunter,Kjiersten Fagnan,Lavanya Ramakrishnan:
  Automated Annotation of Scientific Texts for ML-based Keyphrase Extraction and Validation.CoRRabs/2311.05042 (2023)
• 
  [i7]
  Sabrina Toro,Anna V. Anagnostopoulos,Sue Bello,Kai Lewis Blumberg,Rhiannon Cameron,Leigh Carmody,Alexander D. Diehl,Damion M. Dooley,William D. Duncan,Petra Fey,Pascale Gaudet,Nomi L. Harris,Marcin P. Joachimiak,Leila Kiani,Tiago Lubiana,Monica C. Munoz-Torres,Shawn T. O'Neil,David Osumi-Sutherland,Aleix Puig,Justin P. Reese,Leonore Reiser,Sofia M. C. Robb,Troy Ruemping,James Seager,Eric Sid,Raymund Stefancsik,Magalie Weber,Valerie Wood,Melissa A. Haendel,Christopher J. Mungall:
  Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI).CoRRabs/2312.10904 (2023)
• 2022
• 
  [j72]
  Valérie de Crécy-Lagard,Rocio Amorin de Hegedus,Cecilia N. Arighi,Jill Babor,Alex Bateman,Ian Blaby,Crysten Blaby-Haas,Alan J. Bridge,Stephen K. Burley,Stacey Cleveland,Lucy J. Colwell,Ana Conesa,Christian Dallago,Antoine Danchin,Anita de Waard,Adam Deutschbauer,Raquel Dias,Yousong Ding,Gang Fang,Iddo Friedberg,John Gerlt,Joshua Goldford,Mark Gorelik,Benjamin M. Gyori,Christopher S. Henry,Geoffrey Hutinet,Marshall Jaroch,Peter D. Karp,Liudmyla Kondratova,Zhiyong Lu,Aron Marchler-Bauer,Maria Jesus Martin,Claire D. McWhite,Gaurav D. Moghe,Paul Monaghan,Anne Morgat,Christopher J. Mungall,Darren A. Natale,William C. Nelson,Seán I. O'Donoghue,Christine A. Orengo,Katherine H. O'Toole,Predrag Radivojac,Colbie Reed,Richard J. Roberts,Dmitri Rodionov,Irina A. Rodionova,Jeffrey DePons,Lana Saleh,Gloria M. Sheynkman,Françoise Thibaud-Nissen,Paul D. Thomas,Peter Uetz,David Vallenet,Erica Watson Carter,Peter Weigele,Valerie Wood,Elisha M. Wood-Charlson,Jin Xu:
  A roadmap for the functional annotation of protein families: a community perspective.Database J. Biol. Databases Curation2022(2022) (2022)
• 
  [j71]
  Nicolas Matentzoglu,James P. Balhoff,Susan M. Bello,Chris Bizon,Matthew H. Brush,Tiffany J. Callahan,Christopher G. Chute,William D. Duncan,Chris T. A. Evelo,Davera Gabriel,John B. Graybeal,Alasdair J. G. Gray,Benjamin M. Gyori,Melissa A. Haendel,Henriette Harmse,Nomi L. Harris,Ian Harrow,Harshad Hegde,Amelia L. Hoyt,Charles Tapley Hoyt,Dazhi Jiao,Ernesto Jiménez-Ruiz,Simon Jupp,Hyeongsik Kim,Sebastian Köhler,Thomas Liener,Qinqin Long,James Malone,James A. McLaughlin,Julie A. McMurry,Sierra A. T. Moxon,Monica C. Munoz-Torres,David Osumi-Sutherland,James A. Overton,Bjoern Peters,Tim E. Putman,Núria Queralt-Rosinach,Kent A. Shefchek,Harold Solbrig,Anne E. Thessen,Tania Tudorache,Nicole A. Vasilevsky,Alex H. Wagner,Christopher J. Mungall:
  A Simple Standard for Sharing Ontological Mappings (SSSOM).Database J. Biol. Databases Curation2022(2022) (2022)
• 
  [j70]
  Nicolas Matentzoglu,Damien Goutte-Gattat,Shawn Zheng Kai Tan,James P. Balhoff,Seth Carbon,Anita R. Caron,William D. Duncan,Joe E. Flack,Melissa A. Haendel,Nomi L. Harris,William R. Hogan,Charles Tapley Hoyt,Rebecca C. Jackson,Hyeongsik Kim,Hüseyin Kir,Martin Larralde,Julie A. McMurry,James A. Overton,Bjoern Peters,Clare Pilgrim,Raymund Stefancsik,Sofia M. C. Robb,Sabrina Toro,Nicole A. Vasilevsky,Ramona L. Walls,Christopher J. Mungall,David Osumi-Sutherland:
  Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies.Database J. Biol. Databases Curation2022(2022) (2022)
• 
  [j69]
  Suvarna Nadendla,Rebecca C. Jackson,James B. Munro,Federica Quaglia,Bálint Mészáros,Dustin Olley,Elizabeth T. Hobbs,Stephen M. Goralski,Marcus C. Chibucos,Christopher J. Mungall,Silvio C. E. Tosatto,Ivan Erill,Michelle G. Giglio:
  ECO: the Evidence and Conclusion Ontology, an update for 2022.Nucleic Acids Res.50(D1):1515-1521 (2022)
• 
  [c43]
  James P. Balhoff,Ugur Bayindir,Anita R. Caron,Nicolas Matentzoglu,David Osumi-Sutherland,Christopher J. Mungall:
  Ubergraph: Integrating OBO Ontologies into a Unified Semantic Graph.ICBO2022:1-9
• 
  [c42]
  James A. Overton,Rebecca C. Jackson,Nicolas Matentzoglu,William D. Duncan,Randi Vita,Nomi L. Harris,Christopher J. Mungall,Bjoern Peters:
  COB: A Core Ontology for Biology and Biomedicine.ICBO2022:1
• 
  [c41]
  Sabrina Toro,Nicolas Matentzoglu,Kathleen R. Mullen,Nicole A. Vasilevsky,Halie Rando,Melissa A. Haendel,Christopher J. Mungall,Zhi-Liang Hu,Gregoire Leroy,Imke Tammen,Frank W. Nicholas:
  Classifying Animal Breeds with the Vertebrate Breed Ontology (VBO).ICBO2022:1-7
• 
  [c40]
  Nicolas Matentzoglu,Joe E. Flack,John B. Graybeal,Nomi L. Harris,Harshad B. Hegde,Charles Tapley Hoyt,Hyeongsik Kim,Sabrina Toro,Nicole A. Vasilevsky,Christopher J. Mungall:
  A simple standard for ontological mappings 2022: updates of data model and outlook.OM@ISWC2022:61-66
• 
  [i6]
  Deepak R. Unni,Sierra A. T. Moxon,Michael Bada,Matthew H. Brush,Richard M. Bruskiewich,Paul A. Clemons,Vlado Dancík,Michel Dumontier,Karamarie Fecho,Gustavo Glusman,Jennifer J. Hadlock,Nomi L. Harris,Arpita Joshi,Tim E. Putman,Guangrong Qin,Stephen A. Ramsey,Kent A. Shefchek,Harold Solbrig,Karthik Soman,Anne E. Thessen,Melissa A. Haendel,Chris Bizon,Christopher J. Mungall:
  Biolink Model: A Universal Schema for Knowledge Graphs in Clinical, Biomedical, and Translational Science.CoRRabs/2203.13906 (2022)
• 
  [i5]
  Nicolas Matentzoglu,Damien Goutte-Gattat,Shawn Zheng Kai Tan,James P. Balhoff,Seth Carbon,Anita R. Caron,William D. Duncan,Joe E. Flack,Melissa A. Haendel,Nomi L. Harris,William R. Hogan,Charles Tapley Hoyt,Rebecca C. Jackson,Hyeongsik Kim,Hüseyin Kir,Martin Larralde,Julie A. McMurry,James A. Overton,Bjoern Peters,Clare Pilgrim,Raymund Stefancsik,Sofia M. C. Robb,Sabrina Toro,Nicole A. Vasilevsky,Ramona L. Walls,Christopher J. Mungall,David Osumi-Sutherland:
  Ontology Development Kit: a toolkit for building, maintaining, and standardising biomedical ontologies.CoRRabs/2207.02056 (2022)
• 2021
• 
  [j68]
  Rebecca C. Jackson,Nicolas Matentzoglu,James A. Overton,Randi Vita,James P. Balhoff,Pier Luigi Buttigieg,Seth Carbon,Mélanie Courtot,Alexander D. Diehl,Damion M. Dooley,William D. Duncan,Nomi L. Harris,Melissa A. Haendel,Suzanna E. Lewis,Darren A. Natale,David Osumi-Sutherland,Alan Ruttenberg,Lynn M. Schriml,Barry Smith,Christian J. Stoeckert Jr.,Nicole A. Vasilevsky,Ramona L. Walls,Jie Zheng,Christopher J. Mungall,Bjoern Peters:
  OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies.Database J. Biol. Databases Curation2021 (2021)
• 
  [j67]
  Vasundra Touré,Steven Vercruysse,Marcio Luis Acencio,Ruth C. Lovering,Sandra E. Orchard,Glyn Bradley,Cristina Casals-Casas,Claudine Chaouiya,Noemi del-Toro,Åsmund Flobak,Pascale Gaudet,Henning Hermjakob,Charles Tapley Hoyt,Luana Licata,Astrid Lægreid,Christopher J. Mungall,Anne Niknejad,Simona Panni,Livia Perfetto,Pablo Porras,Dexter Pratt,Julio Saez-Rodriguez,Denis Thieffry,Paul D. Thomas,Dénes Türei,Martin Kuiper:
  The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST).Bioinform.36(24):5712-5718 (2021)
• 
  [j66]
  Benjamin M. Good,Kimberly Van Auken,David P. Hill,Huaiyu Mi,Seth Carbon,James P. Balhoff,Laurent-Philippe Albou,Paul D. Thomas,Christopher J. Mungall,Judith A. Blake,Peter D'Eustachio:
  Reactome and the Gene Ontology: digital convergence of data resources.Bioinform.37(19):3343-3348 (2021)
• 
  [j65]
  Bin Hu,Shane Canon,Emiley A. Eloe-Fadrosh,Fnu Anubhav,Michal Babinski,Yuri Corilo,Karen Davenport,William D. Duncan,Kjiersten Fagnan,Mark Flynn,Brian Foster,David Hays,Marcel Huntemann,Elais Player Jackson,Julia Kelliher,Po-E Li,Chien-Chi Lo,Douglas Mans,Lee Ann McCue,Nigel Mouncey,Christopher J. Mungall,Paul D. Piehowski,Samuel O. Purvine,Montana Smith,Neha Jacob Varghese,Donald Winston,Yan Xu,Patrick S. G. Chain:
  Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale.Frontiers Bioinform.1 (2021)
• 
  [j64]
  Sebastian Köhler,Michael A. Gargano,Nicolas Matentzoglu,Leigh Carmody,David Lewis-Smith,Nicole A. Vasilevsky,Daniel Danis,Ganna Balagura,Gareth Baynam,Amy M. Brower,Tiffany J. Callahan,Christopher G. Chute,Johanna L. Est,Peter D. Galer,Shiva Ganesan,Matthias Griese,Matthias Haimel,Julia Pazmandi,Marc Hanauer,Nomi L. Harris,Michael Hartnett,Maximilian Hastreiter,Fabian Hauck,Yongqun He,Tim Jeske,Hugh Kearney,Gerhard Kindle,Christoph Klein,Katrin Knoflach,Roland Krause,David Lagorce,Julie A. McMurry,Jillian A. Miller,Monica C. Munoz-Torres,Rebecca L. Peters,Christina K. Rapp,Ana Rath,Shahmir A. Rind,Avi Z. Rosenberg,Michael M. Segal,Markus G. Seidel,Damian Smedley,Tomer Talmy,Yarlalu Thomas,Samuel A. Wiafe,Julie Xian,Zafer Yüksel,Ingo Helbig,Christopher J. Mungall,Melissa A. Haendel,Peter N. Robinson:
  The Human Phenotype Ontology in 2021.Nucleic Acids Res.49(Database-Issue):D1207-D1217 (2021)
• 
  [j63]
  Seth Carbon,Eric Douglass,Benjamin M. Good,Deepak R. Unni,Nomi L. Harris,Christopher J. Mungall,Siddartha Basu,Rex L. Chisholm,Robert J. Dodson,Eric Hartline,Petra Fey,Paul D. Thomas,Laurent-Philippe Albou,Dustin Ebert,Michael J. Kesling,Huaiyu Mi,Anushya Muruganujan,Xiaosong Huang,Tremayne Mushayahama,Sandra A. LaBonte,Deborah A. Siegele,Giulia Antonazzo,Helen Attrill,Nick H. Brown,Phani V. Garapati,Steven J. Marygold,Vitor Trovisco,Gilberto dos Santos,Kathleen Falls,Christopher J. Tabone,Pinglei Zhou,Joshua L. Goodman,Victor B. Strelets,Jim Thurmond,Penelope Garmiri,Rizwan Ishtiaq,Milagros Rodríguez-López,Marcio Luis Acencio,Martin Kuiper,Astrid Lægreid,Colin Logie,Ruth C. Lovering,Barbara Kramarz,Shirin C. C. Saverimuttu,Sandra M. Pinheiro,Heather Gunn,Renzhi Su,Katherine E. Thurlow,Marcus C. Chibucos,Michelle G. Giglio,Suvarna Nadendla,James B. Munro,Rebecca C. Jackson,Margaret J. Duesbury,Noemi del-Toro,Birgit H. M. Meldal,Kalpana Paneerselvam,Livia Perfetto,Pablo Porras,Sandra E. Orchard,Anjali Shrivastava,Hsin-Yu Chang,Robert D. Finn,Alex L. Mitchell,Neil D. Rawlings,Lorna J. Richardson,Amaia Sangrador-Vegas,Judith A. Blake,Karen R. Christie,Mary E. Dolan,Harold J. Drabkin,David P. Hill,Li Ni,Dmitry M. Sitnikov,Midori A. Harris,Stephen G. Oliver,Kim Rutherford,Valerie Wood,Jaqueline Hayles,Jürg Bähler,Elizabeth R. Bolton,Jeffrey DePons,Melinda R. Dwinell,G. Thomas Hayman,Mary L. Kaldunski,Anne E. Kwitek,Stanley J. F. Laulederkind,Cody Plasterer,Marek Tutaj,Mahima Vedi,Shur-Jen Wang,Peter D'Eustachio,Lisa Matthews,James P. Balhoff,Suzi A. Aleksander,Michael J. Alexander,J. Michael Cherry,Stacia R. Engel,Felix Gondwe,Kalpana Karra,Stuart R. Miyasato,Robert S. Nash,Matt Simison,Marek S. Skrzypek,Shuai Weng,Edith D. Wong,Marc Feuermann,Pascale Gaudet,Anne Morgat,Erica Bakker,Tanya Z. Berardini,Leonore Reiser,Shabari Subramaniam,Eva Huala,Cecilia N. Arighi,Andrea H. Auchincloss,Kristian B. Axelsen,Ghislaine Argoud-Puy,Alex Bateman,Marie-Claude Blatter,Emmanuel Boutet,Emily Bowler,Lionel Breuza,Alan J. Bridge,Ramona Britto,Hema Bye-A-Jee,Cristina Casals-Casas,Elisabeth Coudert,Paul Denny,Anne Estreicher,Maria Livia Famiglietti,George E. Georghiou,Arnaud Gos,Nadine Gruaz-Gumowski,Emma Hatton-Ellis,Chantal Hulo,Alexandr Ignatchenko,Florence Jungo,Kati Laiho,Philippe Le Mercier,Damien Lieberherr,Antonia Lock,Yvonne Lussi,Alistair MacDougall,Michele Magrane,Maria Jesus Martin,Patrick Masson,Darren A. Natale,Nevila Hyka-Nouspikel,Ivo Pedruzzi,Lucille Pourcel,Sylvain Poux,Sangya Pundir,Catherine Rivoire,Elena Speretta,Shyamala Sundaram,Nidhi Tyagi,Kate Warner,Rossana Zaru,Cathy H. Wu,Alexander D. Diehl,Juancarlos Chan,Christian A. Grove,Raymond Y. N. Lee,Hans-Michael Müller,Daniela Raciti,Kimberly Van Auken,Paul W. Sternberg,Matthew Berriman,Michael Paulini,Kevin L. Howe,Sibyl Gao,Adam Wright,Lincoln Stein,Douglas G. Howe,Sabrina Toro,Monte Westerfield,Pankaj Jaiswal,Laurel Cooper,Justin Elser:
  The Gene Ontology resource: enriching a GOld mine.Nucleic Acids Res.49(Database-Issue):D325-D334 (2021)
• 
  [j62]
  Justin T. Reese,Deepak R. Unni,Tiffany J. Callahan,Luca Cappelletti,Vida Ravanmehr,Seth Carbon,Kent A. Shefchek,Benjamin M. Good,James P. Balhoff,Tommaso Fontana,Hannah Blau,Nicolas Matentzoglu,Nomi L. Harris,Monica C. Munoz-Torres,Melissa A. Haendel,Peter N. Robinson,Marcin P. Joachimiak,Christopher J. Mungall:
  KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response.Patterns2(1):100155 (2021)
• 
  [c39]
  Lauren E. Chan,Nicole A. Vasilevsky,Anne E. Thessen,Nicolas Matentzoglu,William D. Duncan,Christopher J. Mungall,Melissa A. Haendel:
  A Semantic Model Leveraging Pattern-based Ontology Terms to Bridge Environmental Exposures and Health Outcomes.ICBO2021:48-55
• 
  [c38]
  Nicole A. Vasilevsky,Sabrina Toro,Nicolas Matentzoglu,Dazhi Jiao,Melissa A. Haendel,Peter N. Robinson,Christopher J. Mungall:
  Reclassification of Infectious Disease in the Mondo Disease Ontology.ICBO2021:104-109
• 
  [c37]
  Marcin P. Joachimiak,Harshad Hegde,William D. Duncan,Justin T. Reese,Luca Cappelletti,Anne E. Thessen,Christopher J. Mungall:
  KG-Microbe: A Reference Knowledge-Graph and Platform for Harmonized Microbial Information.ICBO2021:131-133
• 
  [c36]
  William D. Duncan,Faiza Ahmed,Fnu Anubhav,Jeffrey Baumes,Jonathan Beezley,Mark Borkum,Lisa M. Bramer,Shane Canon,Patrick S. G. Chain,Danielle Christianson,Yuri Corilo,Karen Davenport,Brandon Davis,Meghan Drake,Kjiersten Fagnan,Mark Flynn,David Hays,Bin Hu,Marcel Huntemann,Julia Kelliher,Sofya Lebedeva,Po-E Li,Mary Lipton,Chien-Chi Lo,Douglas Mans,Stanton Martin,Lee Ann McCue,David Millard,Kayd Miller,Nigel Mouncey,Paul D. Piehowski,Elais Player Jackson,Anastasiya Prymolenna,Samuel O. Purvine,T. B. K. Reddy,Rachel Richardson,Migun Shakya,Montana Smith,Jagadish Chandrabose Sundaramurthi,Mark A. Miller,Deepak R. Unni,Pajau Vangay,Bruce Wilson,Donald Winston,Elisha M. Wood-Charlson,Yan Xu,Emiley A. Eloe-Fadrosh,Christopher J. Mungall:
  Leveraging Ontologies within the National Microbiome Data Collaborative.ICBO2021:141-143
• 
  [c35]
  Mark A. Miller,Rebecca C. Jackson,Christopher J. Mungall:
  Bringing Schemas to the Schemaless.ICBO2021:144-147
• 
  [c34]
  Sierra A. T. Moxon,Harold Solbrig,Deepak R. Unni,Dazhi Jiao,Richard M. Bruskiewich,James P. Balhoff,Gaurav Vaidya,William D. Duncan,Harshad Hegde,Mark Miller,Matthew H. Brush,Nomi L. Harris,Melissa A. Haendel,Christopher J. Mungall:
  The Linked Data Modeling Language (LinkML): A General-Purpose Data Modeling Framework Grounded in Machine-Readable Semantics.ICBO2021:148-151
• 
  [i4]
  Luca Cappelletti,Tommaso Fontana,Elena Casiraghi,Vida Ravanmehr,Tiffany J. Callahan,Marcin P. Joachimiak,Christopher J. Mungall,Peter N. Robinson,Justin T. Reese,Giorgio Valentini:
  GraPE: fast and scalable Graph Processing and Embedding.CoRRabs/2110.06196 (2021)
• 
  [i3]
  Nicolas Matentzoglu,James P. Balhoff,Susan M. Bello,Chris Bizon,Matthew H. Brush,Tiffany J. Callahan,Christopher G. Chute,William D. Duncan,Chris T. A. Evelo,Davera Gabriel,John B. Graybeal,Alasdair J. G. Gray,Benjamin M. Gyori,Melissa A. Haendel,Henriette Harmse,Nomi L. Harris,Ian Harrow,Harshad Hegde,Amelia L. Hoyt,Charles Tapley Hoyt,Dazhi Jiao,Ernesto Jiménez-Ruiz,Simon Jupp,Hyeongsik Kim,Sebastian Köhler,Thomas Liener,Qinqin Long,James Malone,James A. McLaughlin,Julie A. McMurry,Sierra A. T. Moxon,Monica C. Munoz-Torres,David Osumi-Sutherland,James A. Overton,Bjoern Peters,Tim E. Putman,Núria Queralt-Rosinach,Kent A. Shefchek,Harold Solbrig,Anne E. Thessen,Tania Tudorache,Nicole A. Vasilevsky,Alex H. Wagner,Christopher J. Mungall:
  A Simple Standard for Sharing Ontological Mappings (SSSOM).CoRRabs/2112.07051 (2021)
• 2020
• 
  [j61]
  James A. Overton,Michael Cuffaro,Christopher J. Mungall:
  String of PURLs - frugal migration and maintenance of persistent identifiers.Data Sci.3(1):3-13 (2020)
• 
  [j60]
  Julie Agapite,Laurent-Philippe Albou,Suzi A. Aleksander,Joanna Argasinska,Valerio Arnaboldi,Helen Attrill,Susan M. Bello,Judith A. Blake,Olin Blodgett,Yvonne M. Bradford,Carol J. Bult,Scott Cain,Brian R. Calvi,Seth Carbon,Juancarlos Chan,Wen J. Chen,J. Michael Cherry,Jae-Hyoung Cho,Karen R. Christie,Madeline A. Crosby,Jeff de Pons,Mary E. Dolan,Gilberto dos Santos,Barbara Dunn,Nathan A. Dunn,Anne E. Eagle,Dustin Ebert,Stacia R. Engel,David Fashena,Ken Frazer,Sibyl Gao,Felix Gondwe,Joshua L. Goodman,L. Sian Gramates,Christian A. Grove,Todd W. Harris,Marie-Claire Harrison,Douglas G. Howe,Kevin L. Howe,Sagar Jha,James A. Kadin,Thomas C. Kaufman,Patrick Kalita,Kalpana Karra,Ranjana Kishore,Stanley J. F. Laulederkind,Raymond Y. N. Lee,Kevin A. MacPherson,Steven J. Marygold,Beverley Matthews,Gillian H. Millburn,Stuart R. Miyasato,Sierra A. T. Moxon,Hans-Michael Müller,Christopher J. Mungall,Anushya Muruganujan,Tremayne Mushayahama,Robert S. Nash,Patrick Ng,Michael Paulini,Norbert Perrimon,Christian Pich,Daniela Raciti,Joel E. Richardson,Matthew Russell,Susan Russo Gelbart,Leyla Ruzicka,Kevin Schaper,Mary Shimoyama,Matt Simison,Cynthia L. Smith,David R. Shaw,Ajay Shrivatsav,Marek S. Skrzypek,Jennifer R. Smith,Paul W. Sternberg,Christopher J. Tabone,Paul D. Thomas,Jyothi Thota,Sabrina Toro,Monika Tomczuk,Marek Tutaj,Monika Tutaj,Jose-Maria Urbano,Kimberly Van Auken,Ceri E. Van Slyke,Shur-Jen Wang,Shuai Weng,Monte Westerfield,Gary Williams,Edith D. Wong,Adam Wright,Karen Yook:
  Alliance of Genome Resources Portal: unified model organism research platform.Nucleic Acids Res.48(Database-Issue):D650-D658 (2020)
• 
  [j59]
  Kent A. Shefchek,Nomi L. Harris,Michael A. Gargano,Nicolas Matentzoglu,Deepak R. Unni,Matthew H. Brush,Dan Keith,Tom Conlin,Nicole A. Vasilevsky,Xingmin Aaron Zhang,James P. Balhoff,Larry Babb,Susan M. Bello,Hannah Blau,Yvonne M. Bradford,Seth Carbon,Leigh Carmody,Lauren E. Chan,Valentina Cipriani,Alayne Cuzick,Maria G. Della Rocca,Nathan A. Dunn,Shahim Essaid,Petra Fey,Christian A. Grove,Jean-Philippe F. Gourdine,Ada Hamosh,Midori A. Harris,Ingo Helbig,Maureen E. Hoatlin,Marcin P. Joachimiak,Simon Jupp,Kenneth B. Lett,Suzanna E. Lewis,Craig McNamara,Zoë May Pendlington,Clare Pilgrim,Tim E. Putman,Vida Ravanmehr,Justin T. Reese,Erin Rooney Riggs,Sofia M. C. Robb,Paola Roncaglia,James Seager,Erik Segerdell,Morgan Similuk,Andrea L. Storm,Courtney Thaxon,Anne E. Thessen,Julius O. B. Jacobsen,Julie A. McMurry,Tudor Groza,Sebastian Köhler,Damian Smedley,Peter N. Robinson,Christopher J. Mungall,Melissa A. Haendel,Monica C. Munoz-Torres,David Osumi-Sutherland:
  The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.Nucleic Acids Res.48(Database-Issue):D704-D715 (2020)
• 
  [j58]
  Elizabeth Arnaud,Marie-Angélique Laporte,Soonho Kim,Céline Aubert,Sabina Leonelli,Berta Miro,Laurel Cooper,Pankaj Jaiswal,Gideon Kruseman,Rosemary Shrestha,Pier Luigi Buttigieg,Christopher J. Mungall,Julian Pietragalla,Afolabi Agbona,Jacqueline Muliro,Jeffrey Detras,Vilma Hualla,Abhishek Rathore,Roma Rani Das,Ibnou Dieng,Guillaume Bauchet,Naama Menda,Cyril Pommier,Felix Shaw,David Lyon,Leroy Mwanzia,Henry Juarez,Enrico Bonaiuti,Brian Chiputwa,Oluremi Olatunbosun,Sandrine Auzoux,Esther Dzalé Yeumo,Lukas A. Mueller,Kevin A. T. Silverstein,Alexandra Lafargue,Erick Antezana,Medha Devare,Brian King:
  The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems.Patterns1(7):100105 (2020)
• 
  [j57]
  Anne E. Thessen,Ramona L. Walls,Lars Vogt,Jessica Singer,Robert Warren,Pier Luigi Buttigieg,James P. Balhoff,Christopher J. Mungall,Deborah L. McGuinness,Brian J. Stucky,Matthew J. Yoder,Melissa A. Haendel:
  Transforming the study of organisms: Phenomic data models and knowledge bases.PLoS Comput. Biol.16(11) (2020)
• 
  [c33]
  Laurel Cooper,Marie-Angélique Laporte,Justin Elser,Victoria Carollo Blake,Taner Z. Sen,Chris Mungall,Elizabeth Arnaud,Pankaj Jaiswal:
  The Plant Trait Ontology Links Wheat Traits for Crop Improvement and Genomics (short paper).ICBO/ODLS2020:1-2
• 
  [c32]
  Nicole A. Vasilevsky,Shahim Essaid,Nicolas Matentzoglu,Nomi L. Harris,Melissa A. Haendel,Peter N. Robinson,Christopher J. Mungall:
  Mondo Disease Ontology: Harmonizing Disease Concepts Across the World (short paper).ICBO/ODLS2020:1-2

• 2019
• 
  [j56]
  Rebecca C. Jackson,James P. Balhoff,Eric Douglass,Nomi L. Harris,Christopher J. Mungall,James A. Overton:
  ROBOT: A Tool for Automating Ontology Workflows.BMC Bioinform.20(1):407:1-407:10 (2019)
• 
  [j55]
  Sebastian Köhler,Leigh Carmody,Nicole A. Vasilevsky,Julius O. B. Jacobsen,Daniel Danis,Jean-Philippe F. Gourdine,Michael A. Gargano,Nomi L. Harris,Nicolas Matentzoglu,Julie A. McMurry,David Osumi-Sutherland,Valentina Cipriani,James P. Balhoff,Tom Conlin,Hannah Blau,Gareth Baynam,Richard Palmer,Dylan Gratian,Hugh J. S. Dawkins,Michael Segal,Anna C. Jansen,Ahmed Muaz,Willie H. Chang,Jenna Bergerson,Stanley J. F. Laulederkind,Zafer Yüksel,Sergi Beltran,Alexandra F. Freeman,Panagiotis I. Sergouniotis,Daniel Durkin,Andrea L. Storm,Marc Hanauer,Michael Brudno,Susan M. Bello,Murat Sincan,Kayli Rageth,Matthew T. Wheeler,Renske Oegema,Halima Lourghi,Maria G. Della Rocca,Rachel Thompson,Francisco Castellanos,James Priest,Charlotte Cunningham-Rundles,Ayushi Hegde,Ruth C. Lovering,Catherine Hajek,Annie Olry,Luigi Notarangelo,Morgan Similuk,Xingmin Aaron Zhang,David Gómez-Andrés,Hanns Lochmüller,Hélène Dollfus,Sergio Rosenzweig,Shruti Marwaha,Ana Rath,Kathleen Sullivan,Cynthia L. Smith,Joshua D. Milner,Dorothée Leroux,Cornelius F. Boerkoel,Amy Klion,Melody C. Carter,Tudor Groza,Damian Smedley,Melissa A. Haendel,Chris Mungall,Peter N. Robinson:
  Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.Nucleic Acids Res.47(Database-Issue):D1018-D1027 (2019)
• 
  [j54]
  Michelle G. Giglio,Rebecca Tauber,Suvarna Nadendla,James B. Munro,Dustin Olley,Shoshannah Ball,Elvira Mitraka,Lynn M. Schriml,Pascale Gaudet,Elizabeth T. Hobbs,Ivan Erill,Deborah A. Siegele,James C. Hu,Chris Mungall,Marcus C. Chibucos:
  ECO, the Evidence & Conclusion Ontology: community standard for evidence information.Nucleic Acids Res.47(Database-Issue):D1186-D1194 (2019)
• 
  [j53]
  Xingmin Aaron Zhang,Amy Yates,Nicole A. Vasilevsky,Jean-Philippe F. Gourdine,Tiffany J. Callahan,Leigh C. Carmody,Daniel Danis,Marcin P. Joachimiak,Vida Ravanmehr,Emily R. Pfaff,James Champion,Kimberly Robasky,Hao Xu,Karamarie Fecho,Nephi A. Walton,Richard L. Zhu,Justin Ramsdill,Christopher J. Mungall,Sebastian Köhler,Melissa A. Haendel,Clement J. McDonald,Daniel J. Vreeman,David B. Peden,Tellen D. Bennett,James A. Feinstein,Blake Martin,Adrianne L. Stefanski,Lawrence E. Hunter,Christopher G. Chute,Peter N. Robinson:
  Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery.npj Digit. Medicine2 (2019)
• 
  [c31]
  Leigh C. Carmody,Xingmin Aaron Zhang,Nicole A. Vasilevsky,Christopher J. Mungall,Nicolas Matentzoglu,Peter N. Robinson:
  Medical Action Ontology (MAxO).ICBO2019:1
• 2018
• 
  [j52]
  Randi Vita,James A. Overton,Christopher J. Mungall,Alessandro Sette,Bjoern Peters:
  FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability.Database J. Biol. Databases Curation2018:bax105 (2018)
• 
  [j51]
  Lisa C. Harper,Jacqueline D. Campbell,Ethalinda K. S. Cannon,Sook Jung,Monica Poelchau,Ramona L. Walls,Carson M. Andorf,Elizabeth Arnaud,Tanya Z. Berardini,Clayton L. Birkett,Steven B. Cannon,James D. Carson,Bradford Condon,Laurel Cooper,Nathan A. Dunn,Christine G. Elsik,Andrew D. Farmer,Stephen P. Ficklin,David M. Grant,Emily S. Grau,Nic Herndon,Zhi-Liang Hu,Jodi L. Humann,Pankaj Jaiswal,Clément Jonquet,Marie-Angélique Laporte,Pierre Larmande,Gerard R. Lazo,Fiona McCarthy,Naama Menda,Christopher J. Mungall,Monica C. Munoz-Torres,Sushma Naithani,Rex T. Nelson,Daureen Nesdill,Carissa A. Park,James M. Reecy,Leonore Reiser,Lacey-Anne Sanderson,Taner Z. Sen,Margaret Staton,Sabarinath Subramaniam,Marcela Karey Tello-Ruiz,Victor Unda,Deepak R. Unni,Liya Wang,Doreen Ware,Jill L. Wegrzyn,Jason Williams,Margaret Woodhouse,Jing Yu,Doreen Main:
  AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture.Database J. Biol. Databases Curation2018:bay088 (2018)
• 
  [j50]
  Nicolas Matentzoglu,James Malone,Chris Mungall,Robert Stevens:
  MIRO: guidelines for minimum information for the reporting of an ontology.J. Biomed. Semant.9(1):6:1-6:13 (2018)
• 
  [j49]
  Laurel Cooper,Austin Meier,Marie-Angélique Laporte,Justin Elser,Chris Mungall,Brandon T. Sinn,Dario Cavaliere,Seth Carbon,Nathan A. Dunn,Barry Smith,Botong Qu,Justin Preece,Eugene Zhang,Sinisa Todorovic,Georgios V. Gkoutos,John H. Doonan,Dennis W. Stevenson,Elizabeth Arnaud,Pankaj Jaiswal:
  The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.Nucleic Acids Res.46(Database-Issue):D1168-D1180 (2018)
• 
  [c30]
  Paula M. Mabee,James P. Balhoff,Wasila M. Dahdul,Hilmar Lapp,Christopher J. Mungall,Todd J. Vision:
  Reasoning over Anatomical Homology in the Phenoscape KB.ICBO2018
• 
  [c29]
  Rebecca Tauber,James P. Balhoff,Eric Douglass,Chris Mungall,James A. Overton:
  Standardizing Ontology Workflows Using ROBOT.ICBO2018
• 
  [c28]
  James P. Balhoff,Benjamin M. Good,Seth Carbon,Chris Mungall:
  Arachne: an OWL RL Reasoner Applied to Gene Ontology Causal Activity Models (and Beyond).ISWC (P&D/Industry/BlueSky)2018
• 
  [e1]
  Pankaj Jaiswal,Laurel Cooper,Melissa A. Haendel,Christopher J. Mungall:
  Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), Corvallis, Oregon, USA, August 7-10, 2018.CEUR Workshop Proceedings 2285,CEUR-WS.org2018[contents]
• 2017
• 
  [j48]
  Gai Elhanan,Christopher Ochs,José L. V. Mejino Jr.,Hao Liu,Christopher J. Mungall,Yehoshua Perl:
  From SNOMED CT to Uberon: Transferability of evaluation methodology between similarly structured ontologies.Artif. Intell. Medicine79:9-14 (2017)
• 
  [j47]
  Ian H. Holmes,Christopher J. Mungall:
  BioMake: a GNU make-compatible utility for declarative workflow management.Bioinform.33(21):3502-3504 (2017)
• 
  [j46]
  David Osumi-Sutherland,Mélanie Courtot,James P. Balhoff,Christopher J. Mungall:
  Dead simple OWL design patterns.J. Biomed. Semant.8(1):18:1-18:7 (2017)
• 
  [j45]
  Edison Ong,Zuoshuang Xiang,Bin Zhao,Yue Liu,Yu Lin,Jie Zheng,Chris Mungall,Mélanie Courtot,Alan Ruttenberg,Yongqun He:
  Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration.Nucleic Acids Res.45(Database-Issue):D347-D352 (2017)
• 
  [j44]
  Christopher J. Mungall,Julie A. McMurry,Sebastian Köhler,James P. Balhoff,Charles D. Borromeo,Matthew H. Brush,Seth Carbon,Tom Conlin,Nathan A. Dunn,Mark Engelstad,Erin Foster,Jean-Philippe F. Gourdine,Julius O. B. Jacobsen,Dan Keith,Bryan Laraway,Suzanna E. Lewis,Jeremy NguyenXuan,Kent A. Shefchek,Nicole A. Vasilevsky,Zhou Yuan,Nicole L. Washington,Harry Hochheiser,Tudor Groza,Damian Smedley,Peter N. Robinson,Melissa A. Haendel:
  The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species.Nucleic Acids Res.45(Database-Issue):D712-D722 (2017)
• 
  [j43]
  Marina Lizio,Jayson Harshbarger,Imad Abugessaisa,Shuei Noguchi,Atsushi Kondo,Jessica Severin,Chris Mungall,David J. Arenillas,Anthony Mathelier,Yulia A. Medvedeva,Andreas Lennartsson,Finn Drabløs,Jordan A. Ramilowski,Owen J. L. Rackham,Julian Gough,Robin Andersson,Albin Sandelin,Hans Ienasescu,Hiromasa Ono,Hidemasa Bono,Yoshihide Hayashizaki,Piero Carninci,Alistair R. R. Forrest,Takeya Kasukawa,Hideya Kawaji:
  Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals.Nucleic Acids Res.45(Database-Issue):D737-D743 (2017)
• 
  [j42]
  Sebastian Köhler,Nicole A. Vasilevsky,Mark Engelstad,Erin Foster,Julie A. McMurry,Ségolène Aymé,Gareth Baynam,Susan M. Bello,Cornelius F. Boerkoel,Kym M. Boycott,Michael Brudno,Orion J. Buske,Patrick F. Chinnery,Valentina Cipriani,Laureen E. Connell,Hugh J. S. Dawkins,Laura E. DeMare,Andrew Devereau,Bert B. A. de Vries,Helen V. Firth,Kathleen Freson,Daniel Greene,Ada Hamosh,Ingo Helbig,Courtney Hum,Johanna Jähn,Roger James,Roland Krause,Stanley J. F. Laulederkind,Hanns Lochmüller,Gholson J. Lyon,Soichi Ogishima,Annie Olry,Willem H. Ouwehand,Nikolas Pontikos,Ana Rath,Franz Schaefer,Richard H. Scott,Michael Segal,Panagiotis I. Sergouniotis,Richard Sever,Cynthia L. Smith,Volker Straub,Rachel Thompson,Catherine Turner,Ernest Turro,Marijcke W. M. Veltman,Tom Vulliamy,Jing Yu,Julie von Ziegenweidt,Andreas Zankl,Stephan Züchner,Tomasz Zemojtel,Julius O. B. Jacobsen,Tudor Groza,Damian Smedley,Christopher J. Mungall,Melissa A. Haendel,Peter N. Robinson:
  The Human Phenotype Ontology in 2017.Nucleic Acids Res.45(Database-Issue):D865-D876 (2017)
• 
  [c27]
  James P. Balhoff,Matthew H. Brush,Laura Christopherson,Sherri de Coronado,Gilberto Fragoso,Melissa A. Haendel,Christopher J. Mungall,Kimberly Robasky,Nicole A. Vasilevsky,Lawrence W. Wright:
  Tailoring the NCI Thesaurus for Use in The OBO Library.ICBO2017
• 
  [c26]
  Nicole A. Vasilevsky,James P. Balhoff,Christopher J. Mungall,David Osumi-Sutherland,Sebastian Köhler,Susan M. Bello,Cynthia L. Smith,Peter N. Robinson,Melissa A. Haendel:
  Aligning the Human Phenotype and Mammalian Phenotype Ontology using Dead Simple Ontology Design Patterns.ICBO2017
• 
  [i2]
  Christopher J. Mungall,Ian H. Holmes:
  WTFgenes: What's The Function of these genes? Static sites for model-based gene set analysis.F1000Research6:423- (2017)
• 2016
• 
  [j41]
  David P. Hill,Peter D'Eustachio,Tanya Z. Berardini,Christopher J. Mungall,Nikolai Renedo,Judith A. Blake:
  Modeling biochemical pathways in the gene ontology.Database J. Biol. Databases Curation2016 (2016)
• 
  [j40]
  Jerven T. Bolleman,Christopher J. Mungall,Francesco Strozzi,Joachim Baran,Michel Dumontier,Raoul Jean Pierre Bonnal,Robert M. Buels,Robert Hoehndorf,Takatomo Fujisawa,Toshiaki Katayama,Peter J. A. Cock:
  FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation.J. Biomed. Semant.7:39 (2016)
• 
  [j39]
  Alexander D. Diehl,Terrence F. Meehan,Yvonne M. Bradford,Matthew H. Brush,Wasila M. Dahdul,David S. Dougall,Yongqun He,David Osumi-Sutherland,Alan Ruttenberg,Sirarat Sarntivijai,Ceri E. Van Slyke,Nicole A. Vasilevsky,Melissa A. Haendel,Judith A. Blake,Christopher J. Mungall:
  The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.J. Biomed. Semant.7:44 (2016)
• 
  [j38]
  Pier Luigi Buttigieg,Evangelos Pafilis,Suzanna E. Lewis,Mark P. Schildhauer,Ramona L. Walls,Christopher J. Mungall:
  The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation.J. Biomed. Semant.7:57 (2016)
• 
  [c25]
  Pier Luigi Buttigieg,Mark Jensen,Ramona L. Walls,Christopher J. Mungall:
  Environmental Semantics for Sustainable Development in an Interconnected Biosphere.ICBO/BioCreative2016
• 
  [c24]
  Laurel Cooper,Austin Meier,Justin Elser,Justin Preece,Xu Xu,Ryan Kitchen,Botong Qu,Eugene Zhang,Sinisa Todorovic,Pankaj Jaiswal,Marie-Angélique Laporte,Elizabeth Arnaud,Seth Carbon,Chris Mungall,Barry Smith,Georgios V. Gkoutos,John H. Doonan:
  The Planteome Project.ICBO/BioCreative2016
• 
  [c23]
  Mélanie Courtot,James Malone,Chris Mungall:
  Ten Simple Rules for Biomedical Ontology Development.ICBO/BioCreative2016
• 
  [c22]
  Marie-Angélique Laporte,Léo Valette,Laurel Cooper,Chris Mungall,Austin Meier,Pankaj Jaiswal,Elizabeth Arnaud:
  Comparison of Ontology Mapping Techniques to Map Plant Trait Ontologies.ICBO/BioCreative2016
• 
  [c21]
  Botong Qu,Jaden Diefenbaugh,Eugene Zhang,Justin Elser,Pankaj Jaiswal,Seth Carbon,Christopher J. Mungall:
  Planteome Gene Annotation Enrichment Analysis.ICBO/BioCreative2016
• 
  [c20]
  Nicole A. Vasilevsky,Mark Engelstad,Erin Foster,Chris Mungall,Peter N. Robinson,Sebastian Köhler,Melissa A. Haendel:
  Enhancing the Human Phenotype Ontology for Use by the Layperson.ICBO/BioCreative2016
• 
  [c19]
  Prashanti Manda,Christopher J. Mungall,James P. Balhoff,Hilmar Lapp,Todd J. Vision:
  Investigating the Importance of Anatomical Homology for Cross-Species Phenotype Comparisons Using Semantic Similarity.PSB2016:132-143
• 2015
• 
  [j37]
  Warren A. Kibbe,Cesar Arze,Victor Felix,Elvira Mitraka,Evan Bolton,Gang Fu,Christopher J. Mungall,Janos X. Binder,James Malone,Drashtti Vasant,Helen E. Parkinson,Lynn M. Schriml:
  Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data.Nucleic Acids Res.43(Database-Issue):1071-1078 (2015)
• 
  [c18]
  James A. Overton,Heiko Dietze,Shahim Essaid,David Osumi-Sutherland,Christopher J. Mungall:
  ROBOT: A command-line tool for ontology development.ICBO2015
• 2014
• 
  [j36]
  Marcus C. Chibucos,Christopher J. Mungall,Rama Balakrishnan,Karen R. Christie,Rachael P. Huntley,Owen White,Judith A. Blake,Suzanna E. Lewis,Michelle G. Giglio:
  Standardized description of scientific evidence using the Evidence Ontology (ECO).Database J. Biol. Databases Curation2014 (2014)
• 
  [j35]
  Melissa A. Haendel,James P. Balhoff,Frederic B. Bastian,David C. Blackburn,Judith A. Blake,Yvonne M. Bradford,Aurélie Comte,Wasila M. Dahdul,Thomas Dececchi,Robert E. Druzinsky,Terry F. Hayamizu,Nizar Ibrahim,Suzanna E. Lewis,Paula M. Mabee,Anne Niknejad,Marc Robinson-Rechavi,Paul C. Sereno,Christopher J. Mungall:
  Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.J. Biomed. Semant.5:21 (2014)
• 
  [j34]
  Wasila M. Dahdul,Hong Cui,Paula M. Mabee,Christopher J. Mungall,David Osumi-Sutherland,Ramona L. Walls,Melissa A. Haendel:
  Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.J. Biomed. Semant.5:34 (2014)
• 
  [j33]
  Sirarat Sarntivijai,Yu Lin,Zuoshuang Xiang,Terrence F. Meehan,Alexander D. Diehl,Uma D. Vempati,Stephan C. Schürer,Chao Pang,James Malone,Helen E. Parkinson,Yue Liu,Terue Takatsuki,Kaoru Saijo,Hiroshi Masuya,Yukio Nakamura,Matthew H. Brush,Melissa A. Haendel,Jie Zheng,Christian J. Stoeckert Jr.,Bjoern Peters,Christopher J. Mungall,Thomas E. Carey,David J. States,Brian D. Athey,Yongqun He:
  CLO: The cell line ontology.J. Biomed. Semant.5:37 (2014)
• 
  [j32]
  Robert W. Thacker,Maria Díaz,Adeline Kerner,Régine Vignes-Lebbe,Erik Segerdell,Melissa A. Haendel,Christopher J. Mungall:
  The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology.J. Biomed. Semant.5:39 (2014)
• 
  [j31]
  Heiko Dietze,Tanya Z. Berardini,Rebecca E. Foulger,David P. Hill,Jane Lomax,David Osumi-Sutherland,Paola Roncaglia,Christopher J. Mungall:
  TermGenie - A web application for pattern-based ontology class generation.J. Biomed. Semant.5:48 (2014)
• 
  [j30]
  Anika Oellrich,Sebastian Köhler,Nicole L. Washington,Chris Mungall,Suzanna Lewis,Melissa A. Haendel,Peter N. Robinson,Damian Smedley:
  The influence of disease categories on gene candidate predictions from model organism phenotypes.J. Biomed. Semant.5(S-1):S4 (2014)
• 
  [j29]
  Rachael P. Huntley,Midori A. Harris,Yasmin Alam-Faruque,Judith A. Blake,Seth Carbon,Heiko Dietze,Emily C. Dimmer,Rebecca E. Foulger,David P. Hill,Varsha K. Khodiyar,Antonia Lock,Jane Lomax,Ruth C. Lovering,Prudence Mutowo-Meullenet,Tony Sawford,Kimberly Van Auken,Valerie Wood,Christopher J. Mungall:
  A method for increasing expressivity of Gene Ontology annotations using a compositional approach.BMC Bioinform.15:155 (2014)
• 
  [j28]
  Jorrit H. Poelen,James D. Simons,Chris Mungall:
  Global biotic interactions: An open infrastructure to share and analyze species-interaction datasets.Ecol. Informatics24:148-159 (2014)
• 
  [j27]
  Sebastian Köhler,Sandra C. Doelken,Christopher J. Mungall,Sebastian Bauer,Helen V. Firth,Isabelle Bailleul-Forestier,Graeme C. M. Black,Danielle L. Brown,Michael Brudno,Jennifer Campbell,David R. FitzPatrick,Janan T. Eppig,Andrew P. Jackson,Kathleen Freson,Marta Gîrdea,Ingo Helbig,Jane A. Hurst,Johanna Jähn,Laird G. Jackson,Anne M. Kelly,David H. Ledbetter,Sahar Mansour,Christa L. Martin,Celia Moss,Andrew D. Mumford,Willem H. Ouwehand,Soo-Mi Park,Erin Rooney Riggs,Richard H. Scott,Sanjay Sisodiya,Steven Van Vooren,Ronald J. Wapner,Andrew O. M. Wilkie,Caroline F. Wright,Anneke T. Vulto-van Silfhout,Nicole de Leeuw,Bert B. A. de Vries,Nicole L. Washington,Cynthia L. Smith,Monte Westerfield,Paul N. Schofield,Barbara J. Ruef,Georgios V. Gkoutos,Melissa A. Haendel,Damian Smedley,Suzanna E. Lewis,Peter N. Robinson:
  The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.Nucleic Acids Res.42(Database-Issue):966-974 (2014)
• 
  [j26]
  The Fantom Consortium,RIKEN PMII,RIKEN CLST (DGT),Alistair R. R. Forrest,Hideya Kawaji,Michael Rehli,J. Kenneth Baillie,Michiel J. L. de Hoon,Vanja Haberle,Timo Lassmann,Ivan V. Kulakovskiy,Marina Lizio,Masayoshi Itoh,Robin Andersson,Christopher J. Mungall,Terrence F. Meehan,Sebastian Schmeier,Nicolas Bertin,Mette Jørgensen,Emmanuel Dimont,Erik Arner,Christian Schmidl,Ulf Schaefer,Yulia A. Medvedeva,Charles Plessy,Morana Vitezic,Jessica Severin,Colin A. M. Semple,Yuri Ishizu,Robert S. Young,Margherita Francescatto,Intikhab Alam,Davide Albanese,Gabriel M. Altschuler,Takahiro Arakawa,John A. C. Archer,Peter Arner,Magda Babina,Sarah Rennie,Piotr J. Balwierz,Anthony G. Beckhouse,Swati Pradhan-Bhatt,Judith A. Blake,Antje Blumenthal,Beatrice Bodega,Alessandro Bonetti,James Briggs,Frank Brombacher,A. Maxwell Burroughs,Andrea Califano,Carlo V. Cannistraci,Daniel Carbajo,Yun Chen,Marco Chierici,Yari Ciani,Hans Clevers,Emiliano Dalla,Carrie A. Davis,Michael Detmar,Alexander D. Diehl,Taeko Dohi,Finn Drabløs,Albert S. B. Edge,Matthias Edinger,Karl Ekwall,Mitsuhiro Endoh,Hideki Enomoto,Michela Fagiolini,Lynsey Fairbairn,Hai Fang,Mary C. Farach-Carson,Geoffrey J. Faulkner,Alexander V. Favorov,Malcolm E. Fisher,Martin C. Frith,Rie Fujita,Shiro Fukuda,Cesare Furlanello,Masaaki Furuno,Jun-ichi Furusawa,Teunis B. Geijtenbeek,Andrew P. Gibson,Thomas R. Gingeras,Daniel Goldowitz,Julian Gough,Sven Guhl,Reto Guler,Stefano Gustincich,Thomas J. Ha,Masahide Hamaguchi,Mitsuko Hara,Matthias Harbers,Jayson Harshbarger,Akira Hasegawa,Yuki Hasegawa,Takehiro Hashimoto,Meenhard Herlyn,Kelly J. Hitchens,Shannan J. Ho Sui,Oliver M. Hofmann,Ilka Hoof,Fumi Hori,Lukasz Huminiecki,Kei Iida,Tomokatsu Ikawa,Boris R. Jankovic,Hui Jia,Anagha Joshi,Giuseppe Jurman,Bogumil Kaczkowski,Chieko Kai,Kaoru Kaida,Ai Kaiho,Kazuhiro Kajiyama,Mutsumi Kanamori-Katayama,Artem S. Kasianov,Takeya Kasukawa,Shintaro Katayama,Sachi Kato,Shuji Kawaguchi,Hiroshi Kawamoto,Yuki I. Kawamura,Tsugumi Kawashima,Judith S. Kempfle,Tony J. Kenna,Juha Kere,Levon M. Khachigian,Toshio Kitamura,S. Peter Klinken,Alan J. Knox,Miki Kojima,Soichi Kojima,Naoto Kondo,Haruhiko Koseki,Shigeo Koyasu,Sarah Krampitz,Atsutaka Kubosaki,Andrew T. Kwon,Jeroen F. J. Laros,Weonju Lee,Andreas Lennartsson,Kang Li,Berit Lilje,Leonard Lipovich,Alan Mackay-Sim,Ri-ichiroh Manabe,Jessica Cara Mar,Benoit Marchand,Anthony Mathelier,Niklas Mejhert,Alison M. Meynert,Yosuke Mizuno,David A. de Lima Morais,Hiromasa Morikawa,Mitsuru Morimoto,Kazuyo Moro,Efthymios Motakis,Hozumi Motohashi,Christine Mummery,Mitsuyoshi Murata,Sayaka Nagao-Sato,Yutaka Nakachi,Fumio Nakahara,Toshiyuki Nakamura,Yukio Nakamura,Kenichi Nakazato,Erik van Nimwegen,Noriko Ninomiya,Hiromi Nishiyori,Shohei Noma,Tadasuke Nozaki,Soichi Ogishima,Naganari Ohkura,Hiroko Ohmiya,Hiroshi Ohno,Mitsuhiro Ohshima,Mariko Okada-Hatakeyama,Yasushi Okazaki,Valerio Orlando,Dmitry A. Ovchinnikov,Arnab Pain,Robert Passier,Margaret Patrikakis,Helena Persson,Silvano Piazza,James G. D. Prendergast,Owen J. L. Rackham,Jordan A. Ramilowski,Mamoon Rashid,Timothy Ravasi,Patrizia Rizzu,Marco Roncador,Sugata Roy,Morten B. Rye,Eri Saijyo,Antti Sajantila,Akiko Saka,Shimon Sakaguchi,Mizuho Sakai,Hiroki Sato,Hironori Sato,Suzana Savvi,Alka Saxena,Claudio Schneider,Erik A. Schultes,Gundula G. Schulze-Tanzil,Anita Schwegmann,Thierry Sengstag,Guojun Sheng,Hisashi Shimoji,Yishai Shimoni,Jay W. Shin,Christophe Simon,Daisuke Sugiyama,Takaaki Sugiyama,Masanori Suzuki,Naoko Suzuki,Rolf K. Swoboda,Peter A. C. 't Hoen,Michihira Tagami,Naoko Takahashi,Jun Takai,Hiroshi Tanaka,Hideki Tatsukawa,Zuotian Tatum,Mark Thompson,Hiroo Toyoda,Tetsuro Toyoda,Eivind Valen,Marc van de Wetering,Linda M. van den Berg,Roberto Verardo,Dipti Vijayan,Ilya E. Vorontsov,Wyeth W. Wasserman,Shoko Watanabe,Christine A. Wells,Louise N. Winteringham,Ernst Wolvetang,Emily J. Wood,Yoko Yamaguchi,Masayuki Yamamoto,Misako Yoneda,Yohei Yonekura,Shigehiro Yoshida,Susan E. Zabierowski,Peter G. Zhang,Xiaobei Zhao,Silvia Zucchelli,Kim M. Summers,Harukazu Suzuki,Carsten O. Daub,Jun Kawai,Peter Heutink,Winston Hide,Tom C. Freeman,Boris Lenhard,Vladimir B. Bajic,Martin S. Taylor,Vsevolod J. Makeev,Albin Sandelin,David A. Hume,Piero Carninci,Yoshihide Hayashizaki:
  A promoter-level mammalian expression atlas.Nat.507(7493):462-470 (2014)
• 
  [c17]
  Chris Mungall,Heiko Dietze,David Osumi-Sutherland:
  Use of OWL within the Gene Ontology.OWLED2014:25-36
• 2013
• 
  [j25]
  Damian Smedley,Anika Oellrich,Sebastian Köhler,Barbara J. Ruef,Monte Westerfield,Peter N. Robinson,Suzanna Lewis,Christopher J. Mungall:
  PhenoDigm: analyzing curated annotations to associate animal models with human diseases.Database J. Biol. Databases Curation2013 (2013)
• 
  [j24]
  Mikel Egaña Aranguren,Jesualdo Tomás Fernández-Breis,Erick Antezana,Chris Mungall,Alejandro Rodríguez González,Mark D. Wilkinson:
  OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows.J. Biomed. Semant.4:2 (2013)
• 
  [j23]
  Paola Roncaglia,Maryann E. Martone,David P. Hill,Tanya Z. Berardini,Rebecca E. Foulger,Fahim T. Imam,Harold J. Drabkin,Christopher J. Mungall,Jane Lomax:
  The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments.J. Biomed. Semant.4:20 (2013)
• 
  [j22]
  Pier Luigi Buttigieg,Norman Morrison,Barry Smith,Christopher J. Mungall,Suzanna E. Lewis:
  The environment ontology: contextualising biological and biomedical entities.J. Biomed. Semant.4:43 (2013)
• 
  [j21]
  Terrence F. Meehan,Nicole A. Vasilevsky,Christopher J. Mungall,David S. Dougall,Melissa A. Haendel,Judith A. Blake,Alexander D. Diehl:
  Ontology based molecular signatures for immune cell types via gene expression analysis.BMC Bioinform.14:263 (2013)
• 
  [j20]
  Sarah Maynard,Christopher J. Mungall,Suzanna E. Lewis,Fahim T. Imam,Maryann E. Martone:
  A knowledge based approach to matching human neurodegenerative disease and animal models.Frontiers Neuroinformatics7:7 (2013)
• 
  [c16]
  Matthew H. Brush,Chris Mungall,Nicole L. Washington,Melissa A. Haendel:
  What's in a Genotype?: An Ontological Characterization for Integration of Genetic Variation Data.ICBO2013:105-108
• 2012
• 
  [j19]
  David Osumi-Sutherland,Simon Reeve,Christopher J. Mungall,Fabian Neuhaus,Alan Ruttenberg,Gregory S. X. E. Jefferis,J. Douglas Armstrong:
  A strategy for building neuroanatomy ontologies.Bioinform.28(9):1262-1269 (2012)
• 
  [j18]
  David Osumi-Sutherland,Simon Reeve,Christopher J. Mungall,Fabian Neuhaus,Alan Ruttenberg,Gregory S. X. E. Jefferis,J. Douglas Armstrong:
  A strategy for building neuroanatomy ontologies.Bioinform.28(15):2091 (2012)
• 
  [j17]
  Paul D. Thomas,Valerie Wood,Christopher J. Mungall,Suzanna E. Lewis,Judith A. Blake:
  On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report.PLoS Comput. Biol.8(2) (2012)
• 
  [c15]
  Ramona L. Walls,Hong Cui,James A. Macklin,Chris Mungall,Laurel Cooper,Dennis W. Stevenson,Pankaj Jaiswal:
  Mapping of glossary terms from the Flora of North America to the Plant Ontology enhances both resources.ICBO2012
• 2011
• 
  [j16]
  Robert Hoehndorf,Colin R. Batchelor,Thomas Bittner,Michel Dumontier,Karen Eilbeck,Rob Knight,Chris Mungall,Jane S. Richardson,Jesse Stombaugh,Eric Westhof,Craig L. Zirbel,Neocles Leontis:
  The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data.Appl. Ontology6(1):53-89 (2011)
• 
  [j15]
  Syed Hamid Tirmizi,Stuart Aitken,Dilvan A. Moreira,Chris Mungall,Juan F. Sequeda,Nigam H. Shah,Daniel P. Miranker:
  Mapping between the OBO and OWL ontology languages.J. Biomed. Semant.2(S-1):S3 (2011)
• 
  [j14]
  Terrence F. Meehan,Anna Maria Masci,Amina Abdulla,Lindsay G. Cowell,Judith A. Blake,Christopher J. Mungall,Alexander D. Diehl:
  Logical Development of the Cell Ontology.BMC Bioinform.12:6 (2011)
• 
  [j13]
  Sebastian Köhler,Sebastian Bauer,Chris Mungall,Gabriele Carletti,Cynthia L. Smith,Paul N. Schofield,Georgios V. Gkoutos,Peter N. Robinson:
  Improving ontologies by automatic reasoning and evaluation of logical definitions.BMC Bioinform.12:418 (2011)
• 
  [j12]
  Alexander D. Diehl,Alison Deckhut Augustine,Judith A. Blake,Lindsay G. Cowell,Elizabeth S. Gold,Timothy A. Gondré-Lewis,Anna Maria Masci,Terrence F. Meehan,Penelope A. Morel,Anastasia Nijnik,Bjoern Peters,Bali Pulendran,Richard H. Scheuermann,Q. Alison Yao,Martin S. Zand,Christopher J. Mungall:
  Hematopoietic cell types: Prototype for a revised cell ontology.J. Biomed. Informatics44(1):75-79 (2011)
• 
  [j11]
  Christopher J. Mungall,Michael Bada,Tanya Z. Berardini,Jennifer I. Deegan,Amelia Ireland,Midori A. Harris,David P. Hill,Jane Lomax:
  Cross-product extensions of the Gene Ontology.J. Biomed. Informatics44(1):80-86 (2011)
• 
  [j10]
  Christopher J. Mungall,Colin R. Batchelor,Karen Eilbeck:
  Evolution of the Sequence Ontology terms and relationships.J. Biomed. Informatics44(1):87-93 (2011)
• 
  [c14]
  Mélanie Courtot,Chris Mungall,Ryan Remy Brinkman,Alan Ruttenberg:
  Building the OBO Foundry - One Policy at a Time.ICBO2011
• 
  [c13]
  Terrence F. Meehan,Christopher J. Mungall,Judith A. Blake,Alexander D. Diehl:
  Gene Ontology Signatures for Immune Cell-Types Inferred by Gene Expression Analysis.ICBO2011
• 
  [c12]
  Terrence F. Meehan,Christopher J. Mungall,Alexander D. Diehl:
  Revising the Cell Ontology.ICBO2011
• 
  [c11]
  Chris Mungall,David Anderson,Anita E. Bandrowski,Brian A. Canada,Andrew Chatr-aryamontri,Keith C. Cheng,P. Michael Conn,Kara Dolinski,Mark H. Ellisman,Janan T. Eppig,Jeffrey S. Grethe,Joseph W. Kemnitz,Shawn Iadonato,Stephen D. Larson,Charles Magness,Maryann E. Martone,Mike Tyers,Carlo Torniai,Olga G. Troyanskaya,Judith Turner,Monte Westerfield,Melissa A. Haendel:
  An Ontology-Based Approach to Linking Model Organisms and Resources to Human Diseases.ICBO2011
• 
  [c10]
  Christopher J. Mungall,Melissa A. Haendel,Amelia Ireland,Shahid Manzoor,Terry Meehan,David Osumi-Sutherland,Carlo Torniai,Alexander D. Diehl:
  Modularization for the Cell Ontology.ICBO2011
• 
  [c9]
  Zuoshuang Xiang,Chris Mungall,Alan Ruttenberg,Yongqun He:
  Ontobee: A Linked Data Server and Browser for Ontology Terms.ICBO2011
• 
  [c8]
  Chris Mungall:
  Posh - The Prolog OWL Shell.OWLED2011
• 2010
• 
  [j9]
  Jennifer I. Deegan,Emily C. Dimmer,Christopher J. Mungall:
  Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development.BMC Bioinform.11:530 (2010)
• 
  [j8]
  Erick Antezana,Aravind Venkatesan,Chris Mungall,Vladimir Mironov,Martin Kuiper:
  ONTO-ToolKit: enabling bio-ontology engineering via Galaxy.BMC Bioinform.11(S-12):S8 (2010)