The Zebrafish Information Network: the zebrafish model organism database. - Judy Sprague; Leyla Bayraktaroglu; Dave Clements; Tom Conlin; David Fashena; Ken Frazer; Melissa A. Haendel; Douglas G. Howe; Prita Mani; Sridhar Ramachandran; Kevin Schaper; Erik Segerdell; et al. (Nucleic Acids Res., 2006)

OBO-Edit - an ontology editor for biologists. - John Day-Richter; Midori A. Harris; Melissa A. Haendel; Suzanna Lewis (Bioinform., 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)

The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. - Judy Sprague; Leyla Bayraktaroglu; Yvonne M. Bradford; Tom Conlin; Nathan A. Dunn; David Fashena; Ken Frazer; Melissa A. Haendel; Douglas G. Howe; Jonathan Knight; Prita Mani; Sierra A. T. Moxon; et al. (Nucleic Acids Res., 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)

Developing a Reagent Application Ontology within the OBO Foundry Framework. - Matthew H. Brush; Nicole A. Vasilevsky; Carlo Torniai; Tenille Johnson; Chris Shaffer; Melissa A. Haendel (ICBO, 2011)

Aligning Research Resource and Researcher Representation: The eagle-i and VIVO Use Case. - Stella Mitchell; Carlo Torniai; Brian Lowe; Jon Corson-Rikert; Melanie Wilson; Mansoor Ahmed; Shanshan Chen; Ying Ding 001; Nicholas Rejack; Melissa A. Haendel (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)

Developing an Application Ontology for Biomedical Resource Annotation and Retrieval: Challenges and Lessons Learned. - Carlo Torniai; Matthew H. Brush; Nicole A. Vasilevsky; Erik Segerdell; Melanie Wilson; Tenille Johnson; Karen Corday; Chris Shaffer; Melissa A. Haendel (ICBO, 2011)

Research resources: curating the new eagle-i discovery system. - Nicole A. Vasilevsky; Tenille Johnson; Karen Corday; Carlo Torniai; Matthew H. Brush; Erik Segerdell; Melanie Wilson; Chris Shaffer; David Robinson; Melissa A. Haendel (Database J. Biol. Databases Curation, 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)

Alignment of Cultured Cell Modeling Across OBO Foundry Ontologies: Key Outcomes, Insights. - Matthew H. Brush; Jie Zheng 001; Yongqun He; Sirarat Sarntivijai; Bjoern Peters; Alexander D. Diehl; Christian J. Stoeckert Jr.; Melissa A. Haendel (ICBO, 2013)

Enabling semantic search in a bio-specimen repository. - Shahim Essaid; Carlo Torniai; Melissa A. Haendel (ICBO, 2013)

eagle-i: ontology-driven federated search and data entry tools for discovering biomedical research resources. - Melissa A. Haendel; Carlo Torniai; Nicole A. Vasilevsky; Scott Hoffmann; Daniela Bourges-Waldegg (ICBO, 2013)

Finding common ground: integrating the eagle-i and VIVO ontologies. - Carlo Torniai; Shahim Essaid; Brian Lowe; Jon Corson-Rikert; Melissa A. Haendel (ICBO, 2013)

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. - Cecilia N. Arighi; Ben Carterette; K. Bretonnel Cohen; Martin Krallinger; W. John Wilbur; Petra Fey; Robert J. Dodson; Laurel Cooper; Ceri E. Van Slyke; Wasila M. Dahdul; Paula M. Mabee; Donghui Li; et al. (Database J. Biol. Databases Curation, 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)

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)

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)

Thematic series on biomedical ontologies in JBMS: challenges and new directions. - Robert Hoehndorf; Dietrich Rebholz-Schuhmann; Melissa A. Haendel; Robert Stevens 001 (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 zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio. - Ceri E. Van Slyke; Yvonne M. Bradford; Monte Westerfield; Melissa A. Haendel (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 sea of standards for omics data: sink or swim? - Jessica D. Tenenbaum; Susanna-Assunta Sansone; Melissa A. Haendel (J. Am. Medical Informatics Assoc., 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)

Summarizing and visualizing structural changes during the evolution of biomedical ontologies using a Diff Abstraction Network. - Christopher Ochs; Yehoshua Perl; James Geller; Melissa A. Haendel; Matthew H. Brush; Sivaram Arabandi; Samson W. Tu (J. Biomed. Informatics, 2015)

Achieving human and machine accessibility of cited data in scholarly publications. - Joan Starr; Eleni Castro; Mercè Crosas; Michel Dumontier; Robert R. Downs; Ruth E. Duerr; Laurel L. Haak; Melissa A. Haendel; Iván Herman; Simon Hodson; Joe Hourclé; John Ernest Kratz; et al. (PeerJ Prepr., 2015)

Gold-Standard Ontology-Based Annotation of Concepts in Biomedical Text in the CRAFT Corpus: Updates and Extensions. - Michael Bada; Nicole A. Vasilevsky; Melissa A. Haendel; Lawrence Hunter (ICBO/BioCreative, 2016)

SEPIO: A Semantic Model for the Integration and Analysis of Scientific Evidence. - Matthew H. Brush; Kent A. Shefchek; Melissa A. Haendel (ICBO/BioCreative, 2016)

Building a Molecular Glyco-phenotype Ontology to Decipher Undiagnosed Diseases. - Jean-Philippe F. Gourdine; Thomas O. Metz; David Koeller; Matthew H. Brush; Melissa A. Haendel (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)

Enhancing SciENcv through Semantic Research Profile Integration with the VIVO-ISF Ontology. - Marijane White; Matthew H. Brush; Shahim Essaid; Robin Champieux; Adrienne Zell; Melissa A. Haendel; Colin Grove; Syeda Momina Tabish; David Eichmann (ICBO/BioCreative, 2016)

Session Introduction. - Melissa A. Haendel; Maricel G. Kann; Nicole L. Washington (PSB, 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)

The Resource Identification Initiative: A Cultural Shift in Publishing. - Anita E. Bandrowski; Matthew H. Brush; Jeffrey S. Grethe; Melissa A. Haendel; David N. Kennedy; Sean L. Hill; Patrick R. Hof; Maryann E. Martone; Maaike Pols; Serena S. Tan; Nicole L. Washington; Elena V. Zudilova-Seinstra; et al. (Neuroinformatics, 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)

Gold-standard ontology-based anatomical annotation in the CRAFT Corpus. - Michael Bada; Nicole A. Vasilevsky; William A. Baumgartner Jr.; Melissa A. Haendel; Lawrence E. Hunter (Database J. Biol. Databases Curation, 2017)

OpenVIVO: Transparency in Scholarship. - Violeta Ilik; Michael Conlon 001; Graham Triggs; Marijane White; Muhammad Javed 002; Matthew H. Brush; Karen Gutzman; Shahim Essaid; Paul Friedman; Simon Porter 001; Martin Szomszor; Melissa Anne Haendel; et al. (Frontiers Res. Metrics Anal., 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)

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)

Expanding the Molecular Glycophenotype Ontology to include model organisms and acquired diseases. - Jean-Philippe F. Gourdine; Nicole A. Vasilevsky; Lilly Winfree; Matthew H. Brush; Melissa A. Haendel (ICBO, 2018)

Making it count: a computational approach to attribution. - Kristi L. Holmes; Karen Gutzman; Patricia Smith; David Eichmann; Melissa A. Haendel (RO, 2018)

Architecting Attribution: expanding the scope of academic credit. - Kristi L. Holmes; Nicole A. Vasilevsky; Marijane White; Matthew H. Brush; Lisa O'Keefe; Karen Gutzman; Melissa A. Haendel (RO, 2019)

Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery. - Jean-Philippe F. Gourdine; Matthew H. Brush; Nicole A. Vasilevsky; Kent A. Shefchek; Sebastian Köhler 001; Nicolas Matentzoglu; Monica C. Munoz-Torres; Julie A. McMurry; Xingmin Aaron Zhang; Peter N. Robinson; Melissa A. Haendel (Database J. Biol. Databases Curation, 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)

Ten quick tips for biocuration. - Y. Amy Tang; Klemens Pichler; Anja Füllgrabe; Jane Lomax; James Malone; Monica C. Munoz-Torres; Drashtti Vasant; Eleanor Williams; Melissa A. Haendel (PLoS Comput. Biol., 2019)

Global research consortia and data harmonization projects drive the clinical interpretation of cancers. - Justin Guinney; Subha Madhavan; Melissa A. Haendel; Alex H. Wagner; Ratna R. Thangudu (AMIA, 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)

Structuring, reuse and analysis of electronic dental data using the Oral Health and Disease Ontology. - William D. Duncan; Thankam Thyvalikakath; Melissa A. Haendel; Carlo Torniai; Pedro Hernández; Mei Song; Amit Acharya; Daniel J. Caplan; Titus Schleyer; Alan Ruttenberg (J. Biomed. Semant., 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)

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)

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)

The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research. - Lauren E. Chan; Nicole A. Vasilevsky; Anne E. Thessen; Julie A. McMurry; Melissa A. Haendel (Database J. Biol. Databases Curation, 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)

An Open Natural Language Processing Development Framework for EHR-based Clinical Research: A case demonstration using the National COVID Cohort Collaborative (N3C). - Sijia Liu 002; Andrew Wen; Liwei Wang 010; Huan He; Sunyang Fu; Robert T. Miller; Andrew E. Williams; Daniel R. Harris; Ramakanth Kavuluru; Mei Liu; Noor Abu-El-Rub; Rui Zhang 028; et al. (CoRR, 2021)

Beyond Low Earth Orbit: Biomonitoring, Artificial Intelligence, and Precision Space Health. - Ryan T. Scott; Erik L. Antonsen; Lauren M. Sanders; Jaden J. A. Hastings; Seung-Min Park; Graham Mackintosh; Robert J. Reynolds; Adrienne L. Hoarfrost; Aenor Sawyer; Casey S. Greene; Benjamin S. Glicksberg; Corey A. Theriot; et al. (CoRR, 2021)

Beyond Low Earth Orbit: Biological Research, Artificial Intelligence, and Self-Driving Labs. - Lauren M. Sanders; Jason H. Yang; Ryan T. Scott; Amina Ann Qutub; Héctor García Martín; Daniel C. Berrios; Jaden J. A. Hastings; Jon Rask; Graham Mackintosh; Adrienne L. Hoarfrost; Stuart J. Chalk; John Kalantari; et al. (CoRR, 2021)

The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment. - Melissa A. Haendel; Christopher G. Chute; Tellen D. Bennett; David A. Eichmann; Justin Guinney; Warren A. Kibbe; Philip R. O. Payne; Emily R. Pfaff; Peter N. Robinson; Joel H. Saltz; Heidi Spratt; Christine Suver; et al. (J. Am. Medical Informatics Assoc., 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)

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)

Analyzing historical diagnosis code data from NIH N3C and RECOVER Programs using deep learning to determine risk factors for Long Covid. - Saurav Sengupta; Johanna Loomba; Suchetha Sharma; Donald E. Brown; Lorna E. Thorpe; Melissa A. Haendel; Christopher G. Chute; Stephanie S. Hong (BIBM, 2022)

From Survey to Ontology, the Challenges and Opportunities in Ontologizing Questions and Answers. - Lauren E. Chan; Jimmy Phuong; Anne E. Thessen; Stephanie S. Hong; Shahim Essaid; Melissa A. Haendel (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 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)

Ontologizing Health Systems Data at Scale: Making Translational Discovery a Reality. - Tiffany J. Callahan; Adrianne L. Stefanski; Jordan M. Wyrwa; Chenjie Zeng; Anna Ostropolets; Juan M. Banda; William A. Baumgartner Jr.; Richard D. Boyce; Elena Casiraghi; Ben D. Coleman; Janine H. Collins; Sara J. Deakyne Davies; et al. (CoRR, 2022)

Harmonizing units and values of quantitative data elements in a very large nationally pooled electronic health record (EHR) dataset. - Katie R. Bradwell; Jacob T. Wooldridge; Benjamin R. C. Amor; Tellen D. Bennett; Adit Anand; Carolyn Bremer; Yun Jae Yoo; Zhenglong Qian; Steven G. Johnson; Emily R. Pfaff; Andrew T. Girvin; Amin Manna; et al. (J. Am. Medical Informatics Assoc., 2022)

Synergies between centralized and federated approaches to data quality: a report from the national COVID cohort collaborative. - Emily R. Pfaff; Andrew T. Girvin; Davera Gabriel; Kristin Kostka; Michele Morris; Matvey B. Palchuk; Harold P. Lehmann; Benjamin R. C. Amor; Mark Bissell; Katie R. Bradwell; Sigfried Gold; Stephanie S. Hong; et al. (J. Am. Medical Informatics Assoc., 2022)

Demonstrating an approach for evaluating synthetic geospatial and temporal epidemiologic data utility: results from analyzing >1.8 million SARS-CoV-2 tests in the United States National COVID Cohort Collaborative (N3C). - Jason A. Thomas; Randi E. Foraker; Noa Zamstein; Jon D. Morrow; Philip R. O. Payne; Adam B. Wilcox; Melissa A. Haendel; Christopher G. Chute; Kenneth R. Gersing; Anita Walden; Tellen D. Bennett; David A. Eichmann; et al. (J. Am. Medical Informatics Assoc., 2022)

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)

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)

Clinical encounter heterogeneity and methods for resolving in networked EHR data: a study from N3C and RECOVER programs. - Peter Leese; Adit Anand; Andrew T. Girvin; Amin Manna; Saaya Patel; Yun Jae Yoo; Rachel Wong; Melissa A. Haendel; Christopher G. Chute; Tellen D. Bennett; Janos G. Hajagos; Emily R. Pfaff; et al. (J. Am. Medical Informatics Assoc., 2023)

Ontologizing health systems data at scale: making translational discovery a reality. - Tiffany J. Callahan; Adrianne L. Stefanski; Jordan M. Wyrwa; Chenjie Zeng; Anna Ostropolets; Juan M. Banda; William A. Baumgartner Jr.; Richard D. Boyce; Elena Casiraghi; Ben D. Coleman; Janine H. Collins; Sara J. Deakyne Davies; et al. (npj Digit. Medicine, 2023)

Biological research and self-driving labs in deep space supported by artificial intelligence. - Lauren M. Sanders; Ryan T. Scott; Jason H. Yang; Amina Ann Qutub; Héctor García Martín; Daniel C. Berrios; Jaden J. A. Hastings; Jon Rask; Graham Mackintosh; Adrienne L. Hoarfrost; Stuart J. Chalk; John Kalantari; et al. (Nat. Mac. Intell., 2023)

Biomonitoring and precision health in deep space supported by artificial intelligence. - Ryan T. Scott; Lauren M. Sanders; Erik L. Antonsen; Jaden J. A. Hastings; Seung-Min Park; Graham Mackintosh; Robert J. Reynolds; Adrienne L. Hoarfrost; Aenor Sawyer; Casey S. Greene; Benjamin S. Glicksberg; Corey A. Theriot; et al. (Nat. Mac. Intell., 2023)

De-black-boxing health AI: demonstrating reproducible machine learning computable phenotypes using the N3C-RECOVER Long COVID model in the All of Us data repository. - Emily R. Pfaff; Andrew T. Girvin; Miles Crosskey; Srushti Gangireddy; Hiral Master; Wei-Qi Wei; Vern Eric Kerchberger; Mark G. Weiner; Paul A. Harris; Melissa A. Basford; Christopher Lunt; Christopher G. Chute; et al. (J. Am. Medical Informatics Assoc., 2023)

An open natural language processing (NLP) framework for EHR-based clinical research: a case demonstration using the National COVID Cohort Collaborative (N3C). - Sijia Liu 002; Andrew Wen; Liwei Wang 010; Huan He; Sunyang Fu; Robert T. Miller; Andrew E. Williams; Daniel R. Harris; Ramakanth Kavuluru; Mei Liu; Noor Abu-El-Rub; Dalton Schutte; et al. (J. Am. Medical Informatics Assoc., 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)

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)

Finding Long-COVID: temporal topic modeling of electronic health records from the N3C and RECOVER programs. - Shawn T. O'Neil; Charisse R. Madlock-Brown; Kenneth Wilkins; Brenda M. McGrath; Hannah E. Davis; Gina S. Assaf; Hannah Wei; Parya Zareie; Evan T. French; Johanna Loomba; Julie A. McMurry; Andrea Zhou; et al. (npj Digit. Medicine, 2024)

Code for Publication: Insights from an N3C RECOVER EHR-based cohort study characterizing SARS-CoV-2 reinfections and Long COVID. - Emily Hadley; Yun Jae Yoo; Saaya Patel; Andrea Zhou; Bryan Laraway; Rachel Wong; Alexander Preiss; Hannah E. Davis; Daniel Brannock; Christopher G. Chute; Emily R. Pfaff; Johanna Loomba; et al. (Zenodo, 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)

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)

National COVID Cohort Collaborative data enhancements: a path for expanding common data models. - Kellie M. Walters; Marshall Clark; Sofia Dard; Stephanie S. Hong; Elizabeth Kelly; Kristin Kostka; Adam M. Lee; Robert T. Miller; Michele Morris; Matvey B. Palchuk; Emily R. Pfaff; Adam B. Wilcox; et al. (J. Am. Medical Informatics Assoc., 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)