All Stories

  1. String of PURLs – frugal migration and maintenance of persistent identifiers

    Article • Data Science, June 2020, IOS Press

    Dr Chris Mungall, Chris Mungall

  2. A logical model of homology for comparative biology

    Article • March 2019, Cold Spring Harbor Laboratory Press

    Chris Mungall

  3. WTFgenes: What's The Function of these genes? Static sites for model-based gene set analysis

    Article • F1000Research, April 2017, Faculty of 1000, Ltd.

    Chris Mungall

  4. WTFgenes: What's The Function of these genes? Static sites for model-based gene set analysis

    Article • March 2017, Cold Spring Harbor Laboratory Press

    Chris Mungall

  5. “Opposite-of”-information improves similarity calculations in phenotype ontologies

    Article • February 2017, Cold Spring Harbor Laboratory Press

    Chris Mungall

  6. The Monarch Initiative: An integrative data and analytic platform connecting phenotypes to genotypes across species

    Article • November 2016, Cold Spring Harbor Laboratory Press

    Chris Mungall

  7. k-BOOM: A Bayesian approach to ontology structure inference, with applications in disease ontology construction

    Article • April 2016, Cold Spring Harbor Laboratory Press

    Chris Mungall

  8. Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity

    Article • October 2015, Cold Spring Harbor Laboratory Press

    Chris Mungall

  9. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

    Article • Nucleic Acids Research, November 2013, Oxford University Press (OUP)

    Chris Mungall

  10. Improved exome prioritization of disease genes through cross-species phenotype comparison

    Article • Genome Research, October 2013, Cold Spring Harbor Laboratory Press

    Chris Mungall

  11. What is an anatomy ontology?

    Article • The Anatomical Record, October 2013, Wiley

    Chris Mungall

  12. Ontology based molecular signatures for immune cell types via gene expression analysis

    Article • BMC Bioinformatics, August 2013, Springer Science + Business Media

    Chris Mungall

  13. PhenoDigm: analyzing curated annotations to associate animal models with human diseases

    Article • Database, May 2013, Oxford University Press (OUP)

    Chris Mungall

  14. Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research

    Article • F1000Research, February 2013, Faculty of 1000, Ltd.

    Suzanna E Lewis, Dr Chris Mungall, Paul Schofield, Chris Mungall

  15. Integrating the Gene Ontology with ChEBI

    Article • BMC Genomics, January 2013, Springer Science + Business Media

    Dr Colin R Batchelor, Chris Mungall

  16. Phenotypic overlap in the contribution of individual genes to CNV pathogenicity revealed by cross-species computational analysis of single-gene mutations in humans, mice and zebrafish

    Article • Disease Models & Mechanisms, January 2013, The Company of Biologists

    Chris Mungall

  17. A knowledge based approach to matching human neurodegenerative disease and animal models

    Article • Frontiers in Neuroinformatics, January 2013, Frontiers

    Chris Mungall

  18. The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments

    Article • Journal of Biomedical Semantics, January 2013, Springer Science + Business Media

    Chris Mungall

  19. The environment ontology: contextualising biological and biomedical entities

    Article • Journal of Biomedical Semantics, January 2013, Springer Science + Business Media

    Chris Mungall

  20. A Unified Anatomy Ontology of the Vertebrate Skeletal System

    Article • PLoS ONE, December 2012, PLOS

    Chris Mungall

  21. The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses

    Article • Plant and Cell Physiology, December 2012, Oxford University Press (OUP)

    Chris Mungall

  22. Ontologies as integrative tools for plant science

    Article • American Journal of Botany, August 2012, Wiley

    Chris Mungall

  23. MouseFinder: Candidate disease genes from mouse phenotype data

    Article • Human Mutation, March 2012, Hindawi Publishing Corporation

    Chris Mungall

  24. A strategy for building neuroanatomy ontologies

    Article • Bioinformatics, March 2012, Oxford University Press (OUP)

    Chris Mungall

  25. On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report

    Article • PLoS Computational Biology, February 2012, PLOS

    Chris Mungall

  26. Uberon, an integrative multi-species anatomy ontology

    Article • Genome Biology, January 2012, Springer Science + Business Media

    Chris Mungall

  27. Taking shortcuts with OWL using safe macros

    Article • Nature Precedings, December 2011, Springer Science + Business Media

    Chris Mungall

  28. Modularization for the Cell Ontology

    Article • Nature Precedings, December 2011, Springer Science + Business Media

    Chris Mungall

  29. The Gene Ontology: enhancements for 2011

    Article • Nucleic Acids Research, November 2011, Oxford University Press (OUP)

    Dr Marcus C Chibucos, Professor Jurg Bahler, Chris Mungall

  30. Improving ontologies by automatic reasoning and evaluation of logical definitions

    Article • BMC Bioinformatics, October 2011, Springer Science + Business Media

    Chris Mungall

  31. Evolution of the Sequence Ontology terms and relationships

    Article • Journal of Biomedical Informatics, February 2011, Elsevier

    Dr Colin R Batchelor, Chris Mungall

  32. Cross-product extensions of the Gene Ontology

    Article • Journal of Biomedical Informatics, February 2011, Elsevier

    Chris Mungall

  33. Hematopoietic cell types: Prototype for a revised cell ontology

    Article • Journal of Biomedical Informatics, February 2011, Elsevier

    Chris Mungall

  34. Logical Development of the Cell Ontology

    Article • BMC Bioinformatics, January 2011, Springer Science + Business Media

    Chris Mungall

  35. The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data

    Article • Applied Ontology, January 2011, IOS Press

    Chris Mungall

  36. ONTO-ToolKit: enabling bio-ontology engineering via Galaxy

    Article • BMC Bioinformatics, December 2010, Springer Science + Business Media

    Chris Mungall

  37. Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development

    Article • BMC Bioinformatics, October 2010, Springer Science + Business Media

    Chris Mungall

  38. Ontology engineering

    Article • Nature Biotechnology, February 2010, Springer Science + Business Media

    Chris Mungall

  39. Integrating phenotype ontologies across multiple species

    Article • Genome Biology, January 2010, Springer Science + Business Media

    Chris Mungall

  40. Linking Human Diseases to Animal Models Using Ontology-Based Phenotype Annotation

    Article • PLoS Biology, November 2009, PLOS

    Chris Mungall

  41. Novel sequence feature variant type analysis of the HLA genetic association in systemic sclerosis

    Article • Human Molecular Genetics, November 2009, Oxford University Press (OUP)

    Chris Mungall

  42. The Gene Ontology in 2010: extensions and refinements

    Article • Nucleic Acids Research, November 2009, Oxford University Press (OUP)

    Dr Marcus C Chibucos, Chris Mungall

  43. Entity/quality-based logical definitions for the human skeletal phenome using PATO

    Article • September 2009, Institute of Electrical & Electronics Engineers (IEEE)

    Dr John M Hancock, Chris Mungall

  44. Mouse, man, and meaning: bridging the semantics of mouse phenotype and human disease

    Article • Mammalian Genome, August 2009, Springer Science + Business Media

    Dr John M Hancock, Chris Mungall

  45. The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species

    Article • PLoS Computational Biology, July 2009, PLOS

    Chris Mungall

  46. JBrowse: A next-generation genome browser

    Article • Genome Research, July 2009, Cold Spring Harbor Laboratory Press

    Chris Mungall

  47. Survey-based naming conventions for use in OBO Foundry ontology development

    Article • BMC Bioinformatics, April 2009, Springer Science + Business Media

    Chris Mungall

  48. An improved ontological representation of dendritic cells as a paradigm for all cell types

    Article • BMC Bioinformatics, February 2009, Springer Science + Business Media

    Chris Mungall

  49. Experiences Using Logic Programming in Bioinformatics

    Article • January 2009, Springer Science + Business Media

    Chris Mungall

  50. AmiGO: online access to ontology and annotation data

    Article • Bioinformatics, November 2008, Oxford University Press (OUP)

    Chris Mungall

  51. Genome-Wide Analysis of Human Disease Alleles Reveals That Their Locations Are Correlated in Paralogous Proteins

    Article • PLoS Computational Biology, November 2008, PLOS

    Chris Mungall

  52. Tools for neuroanatomy and neurogenetics in Drosophila

    Article • Proceedings of the National Academy of Sciences, July 2008, Proceedings of the National Academy of Sciences

    Chris Mungall

  53. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration

    Article • Nature Biotechnology, November 2007, Springer Science + Business Media

    Chris Mungall

  54. A Chado case study: an ontology-based modular schema for representing genome-associated biological information

    Article • Bioinformatics, July 2007, Oxford University Press (OUP)

    Chris Mungall

  55. Phenotype ontologies: the bridge between genomics and evolution

    Article • Trends in Ecology & Evolution, July 2007, Elsevier

    Chris Mungall

  56. The Release 5.1 Annotation of Drosophila melanogaster Heterochromatin

    Article • Science, June 2007, American Association for the Advancement of Science

    Chris Mungall

  57. OBO-Edit an ontology editor for biologists

    Article • Bioinformatics, June 2007, Oxford University Press (OUP)

    Chris Mungall

  58. National Center for Biomedical Ontology: Advancing Biomedicine through Structured Organization of Scientific Knowledge

    Article • OMICS A Journal of Integrative Biology, June 2006, Mary Ann Liebert Inc

    Chris Mungall

  59. Large-Scale Trends in the Evolution of Gene Structures within 11 Animal Genomes

    Article • PLoS Computational Biology, March 2006, PLOS

    Chris Mungall

  60. The Sequence Ontology: a tool for the unification of genome annotations

    Article • April 2005, Springer Science + Business Media

    Chris Mungall

  61. Obol: Integrating Language and Meaning in Bio-Ontologies

    Article • Comparative and Functional Genomics, January 2004, Hindawi Publishing Corporation

    Chris Mungall

  62. The FlyBase database of the Drosophila genome projects and community literature

    Article • Nucleic Acids Research, January 2003, Oxford University Press (OUP)

    Chris Mungall

  63. Genome sequence of the human malaria parasite Plasmodium falciparum

    Article • Nature, October 2002, Springer Science + Business Media

    Professor Alan H Fairlamb, Prof. Jonathan A. Eisen, Chris Mungall

  64. The Bioperl Toolkit: Perl Modules for the Life Sciences

    Article • Genome Research, October 2002, Cold Spring Harbor Laboratory Press

    Chris Mungall

  65. The Generic Genome Browser: A Building Block for a Model Organism System Database

    Article • Genome Research, October 2002, Cold Spring Harbor Laboratory Press

    Chris Mungall

  66. Article • Genome Biology, January 2002, Springer Science + Business Media

    Chris Mungall

  67. Creating the Gene Ontology Resource: Design and Implementation

    Article • Genome Research, August 2001, Cold Spring Harbor Laboratory Press

    Chris Mungall

  68. Comparative Genomics of the Eukaryotes

    Article • Science, March 2000, American Association for the Advancement of Science

    Chris Mungall