WebinTool: A Generic Web to Database Interface Building Tool. - Jian Hu; David Nicholson; Chris Mungall; Alan L. Hillyard; Alan L. Archibald (DEXA Workshop, 1996)

Design and implementation of a CORBA-based genome mapping system prototype. - Jian Hu; Chris Mungall; David Nicholson; Alan L. Archibald (Bioinform., 1998)

The ARKdb: genome databases for farmed and other animals. - Jian Hu; Chris Mungall; Andy Law; Richard Papworth; J. Paul Nelson; Alison Brown; Irene Simpson; Shirley Leckie; David W. Burt; Alan L. Hillyard; Alan L. Archibald (Nucleic Acids Res., 2001)

Large-Scale Trends in the Evolution of Gene Structures within 11 Animal Genomes. - Mark Yandell; Chris Mungall; Chris Smith; Simon Prochnik; Joshua S. Kaminker; George Hartzell; Suzanna Lewis; Gerald M. Rubin (PLoS Comput. Biol., 2006)

A Chado case study: an ontology-based modular schema for representing genome-associated biological information. - Chris Mungall; David B. Emmert (ISMB/ECCB (Supplement of Bioinformatics), 2007)

Representing Phenotypes in OWL. - Chris Mungall (OWLED, 2007)

NLP and Phenotypes: using Ontologies to link Human Diseases to Animal Models. - Nicole L. Washington; M. Gibson; Chris Mungall; Michael Ashburner; Georgios V. Gkoutos; Monte Westerfield; Melissa A. Haendel; Suzanna E. Lewis (Ontologies and Text Mining for Life Sciences, 2008)

A Call for an Abductive Reasoning Feature in OWL-Reasoning Tools toward Ontology Quality Control. - Michael Bada; Chris Mungall; Lawrence Hunter (OWLED, 2008)

Genome-Wide Analysis of Human Disease Alleles Reveals That Their Locations Are Correlated in Paralogous Proteins. - Mark Yandell; Barry Moore; Fidel Salas; Chris Mungall; Andrew MacBride; Charles White; Martin G. Reese (PLoS Comput. Biol., 2008)

CARO - The Common Anatomy Reference Ontology. - Melissa A. Haendel; Fabian Neuhaus; David Osumi-Sutherland; Paula M. Mabee; José L. V. Mejino Jr.; Chris Mungall; Barry Smith 001 (Anatomy Ontologies for Bioinformatics, 2008)

Experiences Using Logic Programming in Bioinformatics. - Chris Mungall (ICLP, 2009)

Processing OWL2 Ontologies using Thea: An Application of Logic Programming. - Vangelis Vassiliadis; Jan Wielemaker; Chris Mungall (OWLED, 2009)

OBO & OWL: Roundtrip Ontology Transformations. - Syed Hamid Tirmizi; Stuart Aitken; Dilvan A. Moreira; Chris Mungall; Juan F. Sequeda; Nigam H. Shah; Daniel P. Miranker (SWAT4LS, 2009)

AmiGO: online access to ontology and annotation data. - Seth Carbon; Amelia Ireland; Christopher J. Mungall; Shengqiang Shu; Brad Marshall; Suzanna Lewis (Bioinform., 2009)

An improved ontological representation of dendritic cells as a paradigm for all cell types. - Anna Maria Masci; Cecilia N. Arighi; Alexander D. Diehl; Anne E. Lieberman; Chris Mungall; Richard H. Scheuermann; Barry Smith 001; Lindsay G. Cowell (BMC Bioinform., 2009)

Survey-based naming conventions for use in OBO Foundry ontology development. - Daniel Schober; Barry Smith 001; Suzanna E. Lewis; Waclaw Kusnierczyk; Jane Lomax; Chris Mungall; Chris F. Taylor; Philippe Rocca-Serra; Susanna-Assunta Sansone (BMC Bioinform., 2009)

ONTO-ToolKit: enabling bio-ontology engineering via Galaxy. - Erick Antezana; Aravind Venkatesan; Chris Mungall; Vladimir Mironov; Martin Kuiper (BMC Bioinform., 2010)

Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development. - Jennifer I. Deegan; Emily C. Dimmer; Christopher J. Mungall (BMC Bioinform., 2010)

Building the OBO Foundry - One Policy at a Time. - Mélanie Courtot; Chris Mungall; Ryan Remy Brinkman; Alan Ruttenberg (ICBO, 2011)

Gene Ontology Signatures for Immune Cell-Types Inferred by Gene Expression Analysis. - Terrence F. Meehan; Christopher J. Mungall; Judith A. Blake; Alexander D. Diehl (ICBO, 2011)

Revising the Cell Ontology. - Terrence F. Meehan; Christopher J. Mungall; Alexander D. Diehl (ICBO, 2011)

An Ontology-Based Approach to Linking Model Organisms and Resources to Human Diseases. - 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; et al. (ICBO, 2011)

Modularization for the Cell Ontology. - Christopher J. Mungall; Melissa A. Haendel; Amelia Ireland; Shahid Manzoor; Terry Meehan; David Osumi-Sutherland; Carlo Torniai; Alexander D. Diehl (ICBO, 2011)

Ontobee: A Linked Data Server and Browser for Ontology Terms. - Zuoshuang Xiang; Chris Mungall; Alan Ruttenberg; Yongqun He (ICBO, 2011)

Posh - The Prolog OWL Shell. - Chris Mungall (OWLED, 2011)

The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data. - Robert Hoehndorf; Colin R. Batchelor; Thomas Bittner; Michel Dumontier; Karen Eilbeck; Rob Knight 001; Chris Mungall; Jane S. Richardson; Jesse Stombaugh; Eric Westhof; Craig L. Zirbel; Neocles Leontis (Appl. Ontology, 2011)

Mapping between the OBO and OWL ontology languages. - Syed Hamid Tirmizi; Stuart Aitken; Dilvan A. Moreira; Chris Mungall; Juan F. Sequeda; Nigam H. Shah; Daniel P. Miranker (J. Biomed. Semant., 2011)

Improving ontologies by automatic reasoning and evaluation of logical definitions. - Sebastian Köhler 001; Sebastian Bauer 002; Chris Mungall; Gabriele Carletti; Cynthia L. Smith; Paul N. Schofield; Georgios V. Gkoutos; Peter N. Robinson (BMC Bioinform., 2011)

Logical Development of the Cell Ontology. - Terrence F. Meehan; Anna Maria Masci; Amina Abdulla; Lindsay G. Cowell; Judith A. Blake; Christopher J. Mungall; Alexander D. Diehl (BMC Bioinform., 2011)

Hematopoietic cell types: Prototype for a revised cell ontology. - 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; et al. (J. Biomed. Informatics, 2011)

Cross-product extensions of the Gene Ontology. - Christopher J. Mungall; Michael Bada; Tanya Z. Berardini; Jennifer I. Deegan; Amelia Ireland; Midori A. Harris; David P. Hill; Jane Lomax (J. Biomed. Informatics, 2011)

Evolution of the Sequence Ontology terms and relationships. - Christopher J. Mungall; Colin R. Batchelor; Karen Eilbeck (J. Biomed. Informatics, 2011)

Mapping of glossary terms from the Flora of North America to the Plant Ontology enhances both resources. - Ramona L. Walls; Hong Cui; James A. Macklin; Chris Mungall; Laurel Cooper; Dennis W. Stevenson; Pankaj Jaiswal (ICBO, 2012)

A strategy for building neuroanatomy ontologies. - David Osumi-Sutherland; Simon Reeve; Christopher J. Mungall; Fabian Neuhaus; Alan Ruttenberg; Gregory S. X. E. Jefferis; J. Douglas Armstrong (Bioinform., 2012)

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report. - Paul D. Thomas; Valerie Wood; Christopher J. Mungall; Suzanna E. Lewis; Judith A. Blake (PLoS Comput. Biol., 2012)

What's in a Genotype?: An Ontological Characterization for Integration of Genetic Variation Data. - Matthew H. Brush; Chris Mungall; Nicole L. Washington; Melissa A. Haendel (ICBO, 2013)

PhenoDigm: analyzing curated annotations to associate animal models with human diseases. - Damian Smedley; Anika Oellrich; Sebastian Köhler 001; Barbara J. Ruef; Monte Westerfield; Peter N. Robinson; Suzanna Lewis; Christopher J. Mungall (Database J. Biol. Databases Curation, 2013)

OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows. - Mikel Egaña Aranguren; Jesualdo Tomás Fernández-Breis; Erick Antezana; Chris Mungall; Alejandro Rodríguez González; Mark D. Wilkinson (J. Biomed. Semant., 2013)

The environment ontology: contextualising biological and biomedical entities. - Pier Luigi Buttigieg; Norman Morrison; Barry Smith 001; Christopher J. Mungall; Suzanna E. Lewis (J. Biomed. Semant., 2013)

The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments. - 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 (J. Biomed. Semant., 2013)

Ontology based molecular signatures for immune cell types via gene expression analysis. - Terrence F. Meehan; Nicole A. Vasilevsky; Christopher J. Mungall; David S. Dougall; Melissa A. Haendel; Judith A. Blake; Alexander D. Diehl (BMC Bioinform., 2013)

A knowledge based approach to matching human neurodegenerative disease and animal models. - Sarah Maynard; Christopher J. Mungall; Suzanna E. Lewis; Fahim T. Imam; Maryann E. Martone (Frontiers Neuroinformatics, 2013)

Use of OWL within the Gene Ontology. - Chris Mungall; Heiko Dietze; David Osumi-Sutherland (OWLED, 2014)

Standardized description of scientific evidence using the Evidence Ontology (ECO). - 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 (Database J. Biol. Databases Curation, 2014)

Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. - Wasila M. Dahdul; Hong Cui; Paula M. Mabee; Christopher J. Mungall; David Osumi-Sutherland; Ramona L. Walls; Melissa A. Haendel (J. Biomed. Semant., 2014)

TermGenie - A web application for pattern-based ontology class generation. - Heiko Dietze; Tanya Z. Berardini; Rebecca E. Foulger; David P. Hill; Jane Lomax; David Osumi-Sutherland; Paola Roncaglia; Christopher J. Mungall (J. Biomed. Semant., 2014)

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. - 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; et al. (J. Biomed. Semant., 2014)

The influence of disease categories on gene candidate predictions from model organism phenotypes. - Anika Oellrich; Sebastian Köhler 001; Nicole L. Washington; Chris Mungall; Suzanna Lewis; Melissa A. Haendel; Peter N. Robinson; Damian Smedley (J. Biomed. Semant., 2014)

CLO: The cell line ontology. - 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; et al. (J. Biomed. Semant., 2014)

The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology. - Robert W. Thacker; Maria Díaz; Adeline Kerner; Régine Vignes-Lebbe; Erik Segerdell; Melissa A. Haendel; Christopher J. Mungall (J. Biomed. Semant., 2014)

A method for increasing expressivity of Gene Ontology annotations using a compositional approach. - 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; et al. (BMC Bioinform., 2014)

Global biotic interactions: An open infrastructure to share and analyze species-interaction datasets. - Jorrit H. Poelen; James D. Simons; Chris Mungall (Ecol. Informatics, 2014)

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. - Sebastian Köhler 001; Sandra C. Doelken; Christopher J. Mungall; Sebastian Bauer 002; Helen V. Firth; Isabelle Bailleul-Forestier; Graeme C. M. Black; Danielle L. Brown; Michael Brudno; Jennifer Campbell; David R. FitzPatrick; Janan T. Eppig; et al. (Nucleic Acids Res., 2014)

A promoter-level mammalian expression atlas. - 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; et al. (Nat., 2014)

ROBOT: A command-line tool for ontology development. - James A. Overton; Heiko Dietze; Shahim Essaid; David Osumi-Sutherland; Christopher J. Mungall (ICBO, 2015)

Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. - 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 (Nucleic Acids Res., 2015)

Environmental Semantics for Sustainable Development in an Interconnected Biosphere. - Pier Luigi Buttigieg; Mark Jensen; Ramona L. Walls; Christopher J. Mungall (ICBO/BioCreative, 2016)

The Planteome Project. - 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; et al. (ICBO/BioCreative, 2016)

Ten Simple Rules for Biomedical Ontology Development. - Mélanie Courtot; James Malone; Chris Mungall (ICBO/BioCreative, 2016)

Comparison of Ontology Mapping Techniques to Map Plant Trait Ontologies. - Marie-Angélique Laporte; Léo Valette; Laurel Cooper; Chris Mungall; Austin Meier; Pankaj Jaiswal; Elizabeth Arnaud (ICBO/BioCreative, 2016)

Planteome Gene Annotation Enrichment Analysis. - Botong Qu; Jaden Diefenbaugh; Eugene Zhang; Justin Elser; Pankaj Jaiswal; Seth Carbon; Christopher J. Mungall (ICBO/BioCreative, 2016)

Enhancing the Human Phenotype Ontology for Use by the Layperson. - Nicole A. Vasilevsky; Mark Engelstad; Erin Foster; Chris Mungall; Peter N. Robinson; Sebastian Köhler 001; Melissa A. Haendel (ICBO/BioCreative, 2016)

Investigating the Importance of Anatomical Homology for Cross-Species Phenotype Comparisons Using Semantic Similarity. - Prashanti Manda; Christopher J. Mungall; James P. Balhoff; Hilmar Lapp; Todd J. Vision (PSB, 2016)

Modeling biochemical pathways in the gene ontology. - David P. Hill; Peter D'Eustachio; Tanya Z. Berardini; Christopher J. Mungall; Nikolai Renedo; Judith A. Blake (Database J. Biol. Databases Curation, 2016)

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation. - 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 (J. Biomed. Semant., 2016)

The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation. - Pier Luigi Buttigieg; Evangelos Pafilis; Suzanna E. Lewis; Mark P. Schildhauer; Ramona L. Walls; Christopher J. Mungall (J. Biomed. Semant., 2016)

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. - 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; et al. (J. Biomed. Semant., 2016)

Tailoring the NCI Thesaurus for Use in The OBO Library. - 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 (ICBO, 2017)

Aligning the Human Phenotype and Mammalian Phenotype Ontology using Dead Simple Ontology Design Patterns. - Nicole A. Vasilevsky; James P. Balhoff; Christopher J. Mungall; David Osumi-Sutherland; Sebastian Köhler 001; Susan M. Bello; Cynthia L. Smith; Peter N. Robinson; Melissa A. Haendel (ICBO, 2017)

From SNOMED CT to Uberon: Transferability of evaluation methodology between similarly structured ontologies. - Gai Elhanan; Christopher Ochs; José L. V. Mejino Jr.; Hao Liu 025; Christopher J. Mungall; Yehoshua Perl (Artif. Intell. Medicine, 2017)

BioMake: a GNU make-compatible utility for declarative workflow management. - Ian H. Holmes; Christopher J. Mungall (Bioinform., 2017)

Dead simple OWL design patterns. - David Osumi-Sutherland; Mélanie Courtot; James P. Balhoff; Christopher J. Mungall (J. Biomed. Semant., 2017)

WTFgenes: What's The Function of these genes? Static sites for model-based gene set analysis. - Christopher J. Mungall; Ian H. Holmes (F1000Research, 2017)

The Human Phenotype Ontology in 2017. - Sebastian Köhler 001; 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; et al. (Nucleic Acids Res., 2017)

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. - 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; et al. (Nucleic Acids Res., 2017)

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. - Christopher J. Mungall; Julie A. McMurry; Sebastian Köhler 001; James P. Balhoff; Charles D. Borromeo; Matthew H. Brush; Seth Carbon; Tom Conlin; Nathan A. Dunn; Mark Engelstad; Erin Foster; Jean-Philippe F. Gourdine; et al. (Nucleic Acids Res., 2017)

Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration. - Edison Ong; Zuoshuang Xiang; Bin Zhao; Yue Liu; Yu Lin; Jie Zheng 001; Chris Mungall; Mélanie Courtot; Alan Ruttenberg; Yongqun He (Nucleic Acids Res., 2017)

Reasoning over Anatomical Homology in the Phenoscape KB. - Paula M. Mabee; James P. Balhoff; Wasila M. Dahdul; Hilmar Lapp; Christopher J. Mungall; Todd J. Vision (ICBO, 2018)

Standardizing Ontology Workflows Using ROBOT. - Rebecca Tauber; James P. Balhoff; Eric Douglass; Chris Mungall; James A. Overton (ICBO, 2018)

Arachne: an OWL RL Reasoner Applied to Gene Ontology Causal Activity Models (and Beyond). - James P. Balhoff; Benjamin M. Good; Seth Carbon; Chris Mungall (ISWC (P&D/Industry/BlueSky), 2018)

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. - 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; et al. (Database J. Biol. Databases Curation, 2018)

FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability. - Randi Vita; James A. Overton; Christopher J. Mungall; Alessandro Sette; Bjoern Peters (Database J. Biol. Databases Curation, 2018)

MIRO: guidelines for minimum information for the reporting of an ontology. - Nicolas Matentzoglu; James Malone; Chris Mungall; Robert Stevens 001 (J. Biomed. Semant., 2018)

The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics. - Laurel Cooper; Austin Meier; Marie-Angélique Laporte; Justin Elser; Chris Mungall; Brandon T. Sinn; Dario Cavaliere; Seth Carbon; Nathan A. Dunn; Barry Smith 001; Botong Qu; Justin Preece; et al. (Nucleic Acids Res., 2018)

Medical Action Ontology (MAxO). - Leigh C. Carmody; Xingmin Aaron Zhang; Nicole A. Vasilevsky; Christopher J. Mungall; Nicolas Matentzoglu; Peter N. Robinson (ICBO, 2019)

ROBOT: A Tool for Automating Ontology Workflows. - Rebecca C. Jackson; James P. Balhoff; Eric Douglass; Nomi L. Harris; Christopher J. Mungall; James A. Overton (BMC Bioinform., 2019)

ECO, the Evidence & Conclusion Ontology: community standard for evidence information. - 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; et al. (Nucleic Acids Res., 2019)

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. - Sebastian Köhler 001; 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; et al. (Nucleic Acids Res., 2019)

Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery. - 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; et al. (npj Digit. Medicine, 2019)

The Plant Trait Ontology Links Wheat Traits for Crop Improvement and Genomics (short paper). - Laurel Cooper; Marie-Angélique Laporte; Justin Elser; Victoria Carollo Blake; Taner Z. Sen; Chris Mungall; Elizabeth Arnaud; Pankaj Jaiswal (ICBO/ODLS, 2020)

Mondo Disease Ontology: Harmonizing Disease Concepts Across the World (short paper). - Nicole A. Vasilevsky; Shahim Essaid; Nicolas Matentzoglu; Nomi L. Harris; Melissa A. Haendel; Peter N. Robinson; Christopher J. Mungall (ICBO/ODLS, 2020)

String of PURLs - frugal migration and maintenance of persistent identifiers. - James A. Overton; Michael Cuffaro; Christopher J. Mungall (Data Sci., 2020)

Alliance of Genome Resources Portal: unified model organism research platform. - 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; et al. (Nucleic Acids Res., 2020)

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. - 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; et al. (Nucleic Acids Res., 2020)

The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems. - 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; et al. (Patterns, 2020)

Transforming the study of organisms: Phenomic data models and knowledge bases. - 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 (PLoS Comput. Biol., 2020)

A Semantic Model Leveraging Pattern-based Ontology Terms to Bridge Environmental Exposures and Health Outcomes. - Lauren E. Chan; Nicole A. Vasilevsky; Anne E. Thessen; Nicolas Matentzoglu; William D. Duncan; Christopher J. Mungall; Melissa A. Haendel (ICBO, 2021)

Leveraging Ontologies within the National Microbiome Data Collaborative. - 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; et al. (ICBO, 2021)

KG-Microbe: A Reference Knowledge-Graph and Platform for Harmonized Microbial Information. - Marcin P. Joachimiak; Harshad Hegde; William D. Duncan; Justin T. Reese; Luca Cappelletti; Anne E. Thessen; Christopher J. Mungall (ICBO, 2021)

Bringing Schemas to the Schemaless. - Mark A. Miller; Rebecca C. Jackson; Christopher J. Mungall (ICBO, 2021)

The Linked Data Modeling Language (LinkML): A General-Purpose Data Modeling Framework Grounded in Machine-Readable Semantics. - 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 A. Miller; Matthew H. Brush; Nomi L. Harris; et al. (ICBO, 2021)

Reclassification of Infectious Disease in the Mondo Disease Ontology. - Nicole A. Vasilevsky; Sabrina Toro; Nicolas Matentzoglu; Dazhi Jiao; Melissa A. Haendel; Peter N. Robinson; Christopher J. Mungall (ICBO, 2021)

OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies. - 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; et al. (Database J. Biol. Databases Curation, 2021)

Reactome and the Gene Ontology: digital convergence of data resources. - 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 (Bioinform., 2021)

The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). - 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; et al. (Bioinform., 2021)

GraPE: fast and scalable Graph Processing and Embedding. - 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 (CoRR, 2021)

Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale. - Bin Hu 025; 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; et al. (Frontiers Bioinform., 2021)

The Human Phenotype Ontology in 2021. - Sebastian Köhler 001; 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; et al. (Nucleic Acids Res., 2021)

The Gene Ontology resource: enriching a GOld mine. - 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; et al. (Nucleic Acids Res., 2021)

KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response. - 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; et al. (Patterns, 2021)

Ubergraph: Integrating OBO Ontologies into a Unified Semantic Graph. - James P. Balhoff; Ugur Bayindir; Anita R. Caron; Nicolas Matentzoglu; David Osumi-Sutherland; Christopher J. Mungall (ICBO, 2022)

COB: A Core Ontology for Biology and Biomedicine. - James A. Overton; Rebecca C. Jackson; Nicolas Matentzoglu; William D. Duncan; Randi Vita; Nomi L. Harris; Christopher J. Mungall; Bjoern Peters (ICBO, 2022)

Classifying Animal Breeds with the Vertebrate Breed Ontology (VBO). - 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 (ICBO, 2022)

A simple standard for ontological mappings 2022: updates of data model and outlook. - Nicolas Matentzoglu; Joe E. Flack; John B. Graybeal; Nomi L. Harris; Harshad B. Hegde; Charles Tapley Hoyt; Hyeongsik Kim 001; Sabrina Toro; Nicole A. Vasilevsky; Christopher J. Mungall (OM@ISWC, 2022)

A roadmap for the functional annotation of protein families: a community perspective. - 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; et al. (Database J. Biol. Databases Curation, 2022)

A Simple Standard for Sharing Ontological Mappings (SSSOM). - 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; et al. (Database J. Biol. Databases Curation, 2022)

Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies. - 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; et al. (Database J. Biol. Databases Curation, 2022)

Biolink Model: A Universal Schema for Knowledge Graphs in Clinical, Biomedical, and Translational Science. - 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; et al. (CoRR, 2022)

Ontology Development Kit: a toolkit for building, maintaining, and standardising biomedical ontologies. - 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; et al. (CoRR, 2022)

ECO: the Evidence and Conclusion Ontology, an update for 2022. - 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; et al. (Nucleic Acids Res., 2022)

A simple standard for ontological mappings 2023: updates on data model, collaborations and tooling. - 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 001; Huanyu Li 001; et al. (OM@ISWC, 2023)

KG-Hub - Building and Exchanging Biological Knowledge Graphs. - 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; et al. (CoRR, 2023)

Gene Set Summarization using Large Language Models. - Marcin P. Joachimiak; J. Harry Caufield; Nomi L. Harris; Hyeongsik Kim 001; Christopher J. Mungall (CoRR, 2023)

An Open-Source Knowledge Graph Ecosystem for the Life Sciences. - 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; et al. (CoRR, 2023)

MapperGPT: Large Language Models for Linking and Mapping Entities. - Nicolas Matentzoglu; J. Harry Caufield; Harshad B. Hegde; Justin T. Reese; Sierra A. T. Moxon; Hyeongsik Kim 001; Nomi L. Harris; Melissa A. Haendel; Christopher J. Mungall (CoRR, 2023)

Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI). - 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; et al. (CoRR, 2023)

GRAPE for fast and scalable graph processing and random-walk-based embedding. - 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 (Nat. Comput. Sci., 2023)

An expectation-maximization framework for comprehensive prediction of isoform-specific functions. - Guy Karlebach; Leigh Carmody; Jagadish Chandrabose Sundaramurthi; Elena Casiraghi; Peter Hansen; Justin T. Reese; Christopher J. Mungall; Giorgio Valentini; Peter N. Robinson (Bioinform., 2023)

The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): connecting toxicology and exposure to human health and beyond. - 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 (J. Biomed. Semant., 2023)

Initial achievements in relation extraction from RNA-focused scientific papers. - 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 (SEBD, 2024)

SPIREX: Improving LLM-based relation extraction from RNA-focused scientific literature using graph machine learning. - 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 (VLDB Workshops, 2024)

The Artificial Intelligence Ontology: LLM-Assisted Construction of AI Concept Hierarchies. - Marcin P. Joachimiak; Mark A. Miller; J. Harry Caufield; Ryan Ly; Nomi L. Harris; Andrew J. Tritt; Christopher J. Mungall; Kristofer E. Bouchard (Appl. Ontology, 2024)

FAIR Header Reference genome: a TRUSTworthy standard. - 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; et al. (Briefings Bioinform., 2024)

Methods for Linking Data to Online Resources and Ontologies with Applications to Neurophysiology. - Matthew Avaylon; Ryan Ly; Andrew J. Tritt; Benjamin K. Dichter; Kristofer E. Bouchard; Christopher J. Mungall; Oliver Rübel (CoRR, 2024)

The Vertebrate Breed Ontology: Towards Effective Breed Data Standardization. - Kathleen R. Mullen; Imke Tammen; Nicolas A. Matentzoglu; Marius Mather; Christopher J. Mungall; Melissa A. Haendel; Frank W. Nicholas; Sabrina Toro; Vertebrate Breed Ontology Consortium (CoRR, 2024)

CurateGPT: A flexible language-model assisted biocuration tool. - 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; et al. (CoRR, 2024)

Predicting nutrition and environmental factors associated with female reproductive disorders using a knowledge graph and random forests. - 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; et al. (Int. J. Medical Informatics, 2024)

Whelk: An OWL EL+RL Reasoner Enabling New Use Cases. - James P. Balhoff; Christopher J. Mungall (TGDK, 2024)

Automated annotation of scientific texts for ML-based keyphrase extraction and validation. - Oluwamayowa O. Amusat; Harshad Hegde; Christopher J. Mungall; Anna Giannakou; Neil P. Byers; Dan Gunter; Kjiersten Fagnan; Lavanya Ramakrishnan (Database J. Biol. Databases Curation, 2024)

Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning. - J. Harry Caufield; Harshad Hegde; Vincent Emonet; Nomi L. Harris; Marcin P. Joachimiak; Nicolas Matentzoglu; Hyeongsik Kim 001; Sierra A. T. Moxon; Justin T. Reese; Melissa A. Haendel; Peter N. Robinson; Christopher J. Mungall (Bioinform., 2024)

Whelk reasoner. - James P. Balhoff; Christopher J. Mungall (DROPS Artifacts, 2024)

Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI). - 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; et al. (J. Biomed. Semant., 2024)

An evaluation of GPT models for phenotype concept recognition. - Tudor Groza; J. Harry Caufield; Dylan Gration; Gareth Baynam; Melissa A. Haendel; Peter N. Robinson; Christopher J. Mungall; Justin T. Reese (BMC Medical Informatics Decis. Mak., 2024)

A change language for ontologies and knowledge graphs. - 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 (Database J. Biol. Databases Curation, 2025)

Chemical classification program synthesis using generative artificial intelligence. - Christopher J. Mungall; Adnan Malik; Daniel R. Korn; Justin T. Reese; Noel M. O'Boyle; Janna Hastings (CoRR, 2025)

A Dynamic Framework for Semantic Grouping of Common Data Elements (CDE) Using Embeddings and Clustering. - Madan Krishnamurthy; Daniel R. Korn; Melissa A. Haendel; Christopher J. Mungall; Anne E. Thessen (CoRR, 2025)

The Cell Ontology in the age of single-cell omics. - Shawn Zheng Kai Tan; Aleix Puig-Barbe; Damien Goutte-Gattat; Caroline Eastwood; Brian D. Aevermann; Alida Avola; James P. Balhoff; Ismail Ugur Bayindir; Jasmine Belfiore; Anita R. Caron; David S. Fischer; Nancy George; et al. (CoRR, 2025)

Towards a standard benchmark for phenotype-driven variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework. - Yasemin Bridges; Vinicius de Souza; Katherina G. Cortes; Melissa A. Haendel; Nomi L. Harris; Daniel R. Korn; Nikolaos M. Marinakis; Nicolas Matentzoglu; James A. McLaughlin; Christopher J. Mungall; Aaron Odell; David Osumi-Sutherland; et al. (BMC Bioinform., 2025)