Chris Mungall
Orcid: 0000-0002-6601-2165
According to our database1,
Chris Mungall
authored at least 129 papers
between 1996 and 2024.
Collaborative distances:
Collaborative distances:
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Online presence:
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Bibliography
2024
BMC Medical Informatics Decis. Mak., December, 2024
Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning.
Bioinform., March, 2024
2023
The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): connecting toxicology and exposure to human health and beyond.
J. Biomed. Semant., December, 2023
An expectation-maximization framework for comprehensive prediction of isoform-specific functions.
Bioinform., April, 2023
Nat. Comput. Sci., 2023
Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI).
CoRR, 2023
Automated Annotation of Scientific Texts for ML-based Keyphrase Extraction and Validation.
CoRR, 2023
A simple standard for ontological mappings 2023: updates on data model, collaborations and tooling.
Proceedings of the 18th International Workshop on Ontology Matching co-located with the 22nd International Semantic Web Conference (ISWC 2023), 2023
2022
Nucleic Acids Res., 2022
Ontology Development Kit: a toolkit for building, maintaining, and standardising biomedical ontologies.
CoRR, 2022
Biolink Model: A Universal Schema for Knowledge Graphs in Clinical, Biomedical, and Translational Science.
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
A roadmap for the functional annotation of protein families: a community perspective.
Database J. Biol. Databases Curation, 2022
Proceedings of the 17th International Workshop on Ontology Matching (OM 2022) co-located with the 21th International Semantic Web Conference (ISWC 2022), 2022
2021
KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response.
Patterns, 2021
Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale.
Frontiers Bioinform., 2021
Bioinform., 2021
Bioinform., 2021
Database J. Biol. Databases Curation, 2021
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
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
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
KG-Microbe: A Reference Knowledge-Graph and Platform for Harmonized Microbial Information.
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
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
A Semantic Model Leveraging Pattern-based Ontology Terms to Bridge Environmental Exposures and Health Outcomes.
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 Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems.
Patterns, 2020
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.
Nucleic Acids Res., 2020
Nucleic Acids Res., 2020
Data Sci., 2020
Proceedings of the 11th International Conference on Biomedical Ontologies (ICBO) joint with the 10th Workshop on Ontologies and Data in Life Sciences (ODLS) and part of the Bolzano Summer of Knowledge (BoSK 2020), 2020
The Plant Trait Ontology Links Wheat Traits for Crop Improvement and Genomics (short paper).
Proceedings of the 11th International Conference on Biomedical Ontologies (ICBO) joint with the 10th Workshop on Ontologies and Data in Life Sciences (ODLS) and part of the Bolzano Summer of Knowledge (BoSK 2020), 2020
2019
Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery.
npj Digit. Medicine, 2019
Nucleic Acids Res., 2019
ECO, the Evidence & Conclusion Ontology: community standard for evidence information.
Nucleic Acids Res., 2019
Proceedings of the 10th International Conference on Biomedical Ontology (ICBO 2019), Buffalo, New York, USA, July 30, 2019
2018
The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.
Nucleic Acids Res., 2018
J. Biomed. Semant., 2018
FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability.
Database J. Biol. Databases Curation, 2018
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture.
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
Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration.
Nucleic Acids Res., 2017
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species.
Nucleic Acids Res., 2017
Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals.
Nucleic Acids Res., 2017
WTFgenes: What's The Function of these genes? Static sites for model-based gene set analysis.
F1000Research, 2017
Bioinform., 2017
From SNOMED CT to Uberon: Transferability of evaluation methodology between similarly structured ontologies.
Artif. Intell. Medicine, 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
2016
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.
J. Biomed. Semant., 2016
The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation.
J. Biomed. Semant., 2016
FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation.
J. Biomed. Semant., 2016
Database J. Biol. Databases Curation, 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
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016
2015
Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data.
Nucleic Acids Res., 2015
Proceedings of the International Conference on Biomedical Ontology, 2015
2014
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.
Nucleic Acids Res., 2014
Global biotic interactions: An open infrastructure to share and analyze species-interaction datasets.
Ecol. Informatics, 2014
A method for increasing expressivity of Gene Ontology annotations using a compositional approach.
BMC Bioinform., 2014
J. Biomed. Semant., 2014
The influence of disease categories on gene candidate predictions from model organism phenotypes.
J. Biomed. Semant., 2014
Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.
J. Biomed. Semant., 2014
J. Biomed. Semant., 2014
Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.
J. Biomed. Semant., 2014
Database J. Biol. Databases Curation, 2014
Proceedings of the 11th International Workshop on OWL: Experiences and Directions (OWLED 2014) co-located with 13th International Semantic Web Conference on (ISWC 2014), 2014
2013
A knowledge based approach to matching human neurodegenerative disease and animal models.
Frontiers Neuroinformatics, 2013
Ontology based molecular signatures for immune cell types via gene expression analysis.
BMC Bioinform., 2013
The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments.
J. Biomed. Semant., 2013
J. Biomed. Semant., 2013
OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows.
J. Biomed. Semant., 2013
PhenoDigm: analyzing curated annotations to associate animal models with human diseases.
Database J. Biol. Databases Curation, 2013
What's in a Genotype?: An Ontological Characterization for Integration of Genetic Variation Data.
Proceedings of the 4th International Conference on Biomedical Ontology, 2013
2012
On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report.
PLoS Comput. Biol., 2012
Mapping of glossary terms from the Flora of North America to the Plant Ontology enhances both resources.
Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012), 2012
2011
J. Biomed. Informatics, 2011
J. Biomed. Informatics, 2011
BMC Bioinform., 2011
The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data.
Appl. Ontology, 2011
Proceedings of the 8th International Workshop on OWL: Experiences and Directions (OWLED 2011), 2011
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011
An Ontology-Based Approach to Linking Model Organisms and Resources to Human Diseases.
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
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011
2010
Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development.
BMC Bioinform., 2010
2009
BMC Bioinform., 2009
An improved ontological representation of dendritic cells as a paradigm for all cell types.
BMC Bioinform., 2009
Proceedings of the Workshop on Semantic Web Applications and Tools for Life Sciences, 2009
Proceedings of the 5th International Workshop on OWL: Experiences and Directions (OWLED 2009), 2009
Proceedings of the Logic Programming, 25th International Conference, 2009
2008
Proceedings of the Anatomy Ontologies for Bioinformatics, Principles and Practice, 2008
Genome-Wide Analysis of Human Disease Alleles Reveals That Their Locations Are Correlated in Paralogous Proteins.
PLoS Comput. Biol., 2008
A Call for an Abductive Reasoning Feature in OWL-Reasoning Tools toward Ontology Quality Control.
Proceedings of the Fifth OWLED Workshop on OWL: Experiences and Directions, 2008
Proceedings of the Ontologies and Text Mining for Life Sciences: Current Status and Future Perspectives, 24.03., 2008
2007
Proceedings of the OWLED 2007 Workshop on OWL: Experiences and Directions, 2007
A Chado case study: an ontology-based modular schema for representing genome-associated biological information.
Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007
2006
PLoS Comput. Biol., 2006
2001
1998
Bioinform., 1998
1996
Proceedings of the Seventh International Workshop on Database and Expert Systems Applications, 1996