James P. Balhoff
Orcid: 0000-0002-8688-6599
According to our database1,
James P. Balhoff
authored at least 51 papers
between 2011 and 2024.
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Book In proceedings Article PhD thesis Dataset OtherLinks
Online presence:
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on orcid.org
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on github.com
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Bibliography
2024
VLM4Bio: A Benchmark Dataset to Evaluate Pretrained Vision-Language Models for Trait Discovery from Biological Images.
Proceedings of the Advances in Neural Information Processing Systems 38: Annual Conference on Neural Information Processing Systems 2024, 2024
Hierarchical Conditioning of Diffusion Models Using Tree-of-Life for Studying Species Evolution.
Proceedings of the Computer Vision - ECCV 2024, 2024
2023
Discovering Novel Biological Traits From Images Using Phylogeny-Guided Neural Networks.
Proceedings of the 29th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 2023
2022
Ontology Development Kit: a toolkit for building, maintaining, and standardising biomedical ontologies.
CoRR, 2022
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies.
Database J. Biol. Databases Curation, 2022
Database J. Biol. Databases Curation, 2022
Proceedings of the International Conference on Biomedical Ontology 2022 (ICBO), Ann Arbor, Michigan, USA, September 25, 2022
Maximizing Interoperability, Enriching EHR Data: Transforming HL7 FHIR Data to RDF Using the FHIR RDF Playground.
Proceedings of the AMIA 2022, 2022
2021
KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response.
Patterns, 2021
Bioinform., 2021
Database J. Biol. Databases Curation, 2021
The Linked Data Modeling Language (LinkML): A General-Purpose Data Modeling Framework Grounded in Machine-Readable Semantics.
Proceedings of the International Conference on Biomedical Ontologies 2021 co-located with the Workshop on Ontologies for the Behavioural and Social Sciences (OntoBess 2021) as part of the Bolzano Summer of Knowledge (BOSK 2021), 2021
2020
PLoS Comput. Biol., 2020
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.
Nucleic Acids Res., 2020
2019
Nucleic Acids Res., 2019
J. Chem. Inf. Model., 2019
ROBOKOP: an abstraction layer and user interface for knowledge graphs to support question answering.
Bioinform., 2019
2018
Proceedings of the Application of Semantic Technology in Biodiversity Science, 2018
Phenoscape: Semantic analysis of organismal traits and genes yields insights in evolutionary biology.
Proceedings of the Application of Semantic Technology in Biodiversity Science, 2018
'Computable' Phenotypes Enable Comparative and Predictive Phenomics Among Plant Species and Across Domains of Life.
Proceedings of the Application of Semantic Technology in Biodiversity Science, 2018
Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems.
Database J. Biol. Databases Curation, 2018
Arachne: an OWL RL Reasoner Applied to Gene Ontology Causal Activity Models (and Beyond).
Proceedings of the ISWC 2018 Posters & Demonstrations, Industry and Blue Sky Ideas Tracks co-located with 17th International Semantic Web Conference (ISWC 2018), Monterey, USA, October 8th - to, 2018
Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), 2018
Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), 2018
2017
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species.
Nucleic Acids Res., 2017
Aligning the Human Phenotype and Mammalian Phenotype Ontology using Dead Simple Ontology Design Patterns.
Proceedings of the 8th International Conference on Biomedical Ontology (ICBO 2017), Newcastle-upon-Tyne, United Kingdom, September 13th, 2017
Proceedings of the 8th International Conference on Biomedical Ontology (ICBO 2017), Newcastle-upon-Tyne, United Kingdom, September 13th, 2017
A generic bioinformatics pipeline to integrate large-scale trait data with large phylogenies.
Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017
2016
Investigating the Importance of Anatomical Homology for Cross-Species Phenotype Comparisons Using Semantic Similarity.
Proceedings of the Biocomputing 2016: Proceedings of the Pacific Symposium, 2016
Measuring the Importance of Annotation Granularity to the Detection of Semantic Similarity Between Phenotype Profiles.
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016
The Phenoscape Knowledgebase: Tools and APIs for Computing Across Phenotypes from Evolutionary Diversity and Model Organisms.
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016
2015
Proceedings of the Information Science with Impact: Research in and for the Community, 2015
2014
Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.
J. Biomed. Semant., 2014
Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex.
J. Biomed. Semant., 2014
2013
BMC Bioinform., 2013
The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes.
J. Biomed. Semant., 2013
Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: results from a manual alignment.
Database J. Biol. Databases Curation, 2013
An overview of the BioCreative 2012 Workshop Track III: interactive text mining task.
Database J. Biol. Databases Curation, 2013
2011
Phenoscape: Use Cases and Anatomy Ontology Requirements for Linking Evolutionary and Model Organism Phenotypes.
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011