The mammalian phenotype ontology: enabling robust annotation and comparative analysis
Open accessAbstract
The mouse has long been an important model for the study of human genetic disease. Through the application of genetic engineering and mutagenesis techniques, the number of unique mutant mouse models and the amount of phenotypic data describing them are growing exponentially. Describing phenotypes of mutant mice in a computationally useful manner that will facilitate data mining is a major challenge for bioinformatics. Here we describe a tool, the Mammalian Phenotype Ontology (MP), for classifying and organizing phenotypic information related to the mouse and other mammalian species. The MP Ontology has been applied to mouse phenotype descriptions in the Mouse Genome Informatics Database (MGI, http://www.informatics.jax.org/), the Rat Genome Database (RGD, http://rgd.mcw.edu), the Online Mendelian Inheritance in Animals (OMIA, http://omia.angis.org.au/) and elsewhere. Use of this ontology allows comparisons of data from diverse sources, can facilitate comparisons across mammalian species, assists in identifying appropriate experimental disease models, and aids in the discovery of candidate disease genes and molecular signaling pathways.
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The Disease Ontology data were further extended and newer ontologies such as Rat Disease Ontology and Mammalian Phenotype Ontology were added to facilitate comparison of target-disease and target-phenotype associations across multiple species.
“The Disease Ontology (DO) (8) data were further extended and newer ontologies such as Rat Disease Ontology (9) and Mammalian Phenotype Ontology (10) were added to facilitate comparison of target-disease and target-phenotype associations across multiple species.”
From TCRD and pharos 2021: mining the human proteome for disease biology (2021) · cites this paper as [10]
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“…of the gene set in the MSigDB M5 subcollection MPT: Mammalian Phenotype Tumor Ontology, which consists of ontology terms related to tumor phenotypes mined from the Mammalian Phenotype Ontology database [49], and {text_desc} is the ’description’ field of that gene set (as collected in m5.mpt.v2023.”
Method
- Authors
- Smith, C. L., & Eppig, J. T.
- Affiliations
- Jackson Laboratory (US)
- Corresponding author
- Eppig, Janan T.
- Venue
- WIREs Systems Biology and Medicine
- Publisher
- Wiley
- Published
- 2009-11
- Volume
- 1
- Issue
- 3
- Pages
- 390-399
- ISSN
- 1939-005X (ISSN-L)
- 1939-5094
- PMC
- PMC2801442
- OpenAlex
- W2010798628
- Cited by
- 353
- References
- 29
- Citations by year
- 2026: 14 · 2025: 32 · 2024: 35 · 2023: 36 · 2022: 52 · 2021: 25 · 2020: 21 · 2019: 21 · 2018: 12 · 2017: 8 · 2016: 17 · 2015: 14 · 2014: 11 · 2013: 12 · 2012: 24
- FWCI
- 5.78
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- WIREs Systems Biology and Medicine (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- The Mouseion at the JAXlibrary (Jackson Laboratory) (submittedVersion)
- Funders
- National Human Genome Research Institute (HG000330, P41HG000330)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Physical Sciences › Computer Science › Artificial Intelligence › Semantic Web and Ontologies
- Keywords
- Mammalian Phenotype Ontology, phenotype annotation, mutant mouse models, mouse phenotypes, Mouse Genome Informatics, Rat Genome Database, candidate disease genes, molecular pathways, phenotypic data integration
- MeSH terms
- Animals, Classification, Disease Models, Animal, Humans, Mammals, Mutation, Phenotype, Software, User-Computer Interface, Genomics, Mice, Data Mining
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