Employing Reasoning within the Phenoscape Knowledgebase. - James P. Balhoff; Wasila M. Dahdul; Hilmar Lapp; Peter E. Midford; Todd J. Vision; Monte Westerfield; Paula M. Mabee (ICBO, 2011)

Integrating Anatomy and Phenotype Ontologies with Taxonomic Hierarchies. - James P. Balhoff; Peter E. Midford; Hilmar Lapp (ICBO, 2011)

Phenoscape: Use Cases and Anatomy Ontology Requirements for Linking Evolutionary and Model Organism Phenotypes. - Wasila M. Dahdul; James P. Balhoff; Hilmar Lapp; Peter E. Midford; Todd J. Vision; Monte Westerfield; Paula M. Mabee (ICBO, 2011)

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)

Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: results from a manual alignment. - Matthew A. Bertone; István Mikó; Matthew J. Yoder; Katja C. Seltmann; James P. Balhoff; Andrew R. Deans (Database J. Biol. Databases Curation, 2013)

The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes. - Peter E. Midford; Thomas Dececchi; James P. Balhoff; Wasila M. Dahdul; Nizar Ibrahim; Hilmar Lapp; John G. Lundberg; Paula M. Mabee; Paul C. Sereno; Monte Westerfield; Todd J. Vision; David C. Blackburn (J. Biomed. Semant., 2013)

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. - Arlin Stoltzfus; Hilmar Lapp; Naim Matasci; Helena F. Deus; Brian Sidlauskas; Christian M. Zmasek; Gaurav Vaidya; Enrico Pontelli; Karen Cranston; Rutger A. Vos; Campbell O. Webb; Luke J. Harmon; et al. (BMC Bioinform., 2013)

Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex. - James P. Balhoff; Wasila M. Dahdul; Thomas Dececchi; Hilmar Lapp; Paula M. Mabee; Todd J. Vision (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)

Presence-absence reasoning for evolutionary phenotypes. - James P. Balhoff; T. Alexander Dececchi; Paula M. Mabee; Hilmar Lapp (CoRR, 2014)

CharaParser+EQ: Performance evaluation without gold standard. - Hong Cui; Wasila M. Dahdul; T. Alexander Dececchi; Nizar Ibrahim; Paula M. Mabee; James P. Balhoff; Hariharan Gopalakrishnan (ASIST, 2015)

The Phenoscape Knowledgebase: Tools and APIs for Computing Across Phenotypes from Evolutionary Diversity and Model Organisms. - James P. Balhoff (ICBO/BioCreative, 2016)

Measuring the Importance of Annotation Granularity to the Detection of Semantic Similarity Between Phenotype Profiles. - Prashanti Manda; James P. Balhoff; Todd J. Vision (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)

Scowl: a Scala DSL for programming with the OWL API. - James P. Balhoff (J. Open Source Softw., 2016)

A generic bioinformatics pipeline to integrate large-scale trait data with large phylogenies. - Pasan C. Fernando; Laura M. Jackson; Erliang Zeng; Paula M. Mabee; James P. Balhoff (BIBM, 2017)

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)

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

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)

Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems. - Wasila M. Dahdul; Prashanti Manda; Hong Cui; James P. Balhoff; T. Alexander Dececchi; Nizar Ibrahim; Hilmar Lapp; Todd J. Vision; Paula M. Mabee (Database J. Biol. Databases Curation, 2018)

'Computable' Phenotypes Enable Comparative and Predictive Phenomics Among Plant Species and Across Domains of Life. - Ian Braun; James P. Balhoff; Tanya Z. Berardini; Laurel Cooper; Georgios V. Gkoutos; Lisa C. Harper; Eva Huala; Pankaj Jaiswal; Toni Kazic; Hilmar Lapp; James A. Macklin; Chelsea D. Specht; et al. (Application of Semantic Technology in Biodiversity Science, 2018)

Phenoscape: Semantic analysis of organismal traits and genes yields insights in evolutionary biology. - Paula M. Mabee; Wasila M. Dahdul; James P. Balhoff; Hilmar Lapp; Prashanti Manda; Josef C. Uyeda; Todd J. Vision; Monte Westerfield (Application of Semantic Technology in Biodiversity Science, 2018)

Taxonomy and the Production of Semantic Phenotypes. - Matthew J. Yoder; Michael B. Twidale; Andrea K. Thomer; Lars Vogt; Nico M. Franz; Jinlong Guo; Andrew R. Deans; James P. Balhoff (Application of Semantic Technology in Biodiversity Science, 2018)

ROBOKOP: an abstraction layer and user interface for knowledge graphs to support question answering. - Kenneth Morton; Patrick Wang 003; Chris Bizon; Steven Cox 001; James P. Balhoff; Yaphet Kebede; Karamarie Fecho; Alexander Tropsha (Bioinform., 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)

ROBOKOP KG and KGB: Integrated Knowledge Graphs from Federated Sources. - Chris Bizon; Steven Cox 001; James P. Balhoff; Yaphet Kebede; Patrick Wang 003; Kenneth Morton; Karamarie Fecho; Alexander Tropsha (J. Chem. Inf. Model., 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)

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)

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)

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 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)

Maximizing Interoperability, Enriching EHR Data: Transforming HL7 FHIR Data to RDF Using the FHIR RDF Playground. - James Champion; Eric Prud'hommeaux; David Booth; Gaurav Vaidya; James P. Balhoff; Deepak K. Sharma; Guoqian Jiang; Emily R. Pfaff (AMIA, 2022)

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)

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)

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)

Discovering Novel Biological Traits From Images Using Phylogeny-Guided Neural Networks. - Mohannad Elhamod; Mridul Khurana; Harish Babu Manogaran; Josef C. Uyeda; Meghan A. Balk; Wasila M. Dahdul; Yasin Bakis; Henry L. Bart Jr.; Paula M. Mabee; Hilmar Lapp; James P. Balhoff; Caleb Charpentier; et al. (KDD, 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)

Hierarchical Conditioning of Diffusion Models Using Tree-of-Life for Studying Species Evolution. - Mridul Khurana; Arka Daw; M. Maruf; Josef C. Uyeda; Wasila M. Dahdul; Caleb Charpentier; Yasin Bakis; Henry L. Bart Jr.; Paula M. Mabee; Hilmar Lapp; James P. Balhoff; Wei-Lun Chao; et al. (ECCV (89), 2024)

VLM4Bio: A Benchmark Dataset to Evaluate Pretrained Vision-Language Models for Trait Discovery from Biological Images. - M. Maruf; Arka Daw; Kazi Sajeed Mehrab; Harish Babu Manogaran; Abhilash Neog; Medha Sawhney; Mridul Khurana; James P. Balhoff; Yasin Bakis; Bahadir Altintas; Matthew J. Thompson; Elizabeth G. Campolongo; et al. (NeurIPS, 2024)

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

Horned-OWL: Flying Further and Faster with Ontologies. - Phillip Lord; Björn Gehrke; Martin Larralde; Janna Hastings; Filippo De Bortoli; James A. Overton; James P. Balhoff; Jennifer D. Warrender (TGDK, 2024)

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

Horned-OWL. - Phillip Lord; Björn Gehrke; Martin Larralde; Janna Hastings; Filippo De Bortoli; James A. Overton; James P. Balhoff; Jennifer D. Warrender (DROPS Artifacts, 2024)

BioCLIP 2: Emergent Properties from Scaling Hierarchical Contrastive Learning. - Jianyang Gu; Samuel Stevens 001; Elizabeth G. Campolongo; Matthew J. Thompson; Net Zhang; Jiaman Wu; Andrei Kopanev; Zheda Mai; Alexander E. White; James P. Balhoff; Wasila M. Dahdul; Daniel I. Rubenstein; et al. (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)