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The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information

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Smith, Cynthia L, Goldsmith, Carroll-Ann W, Eppig, Janan T·2004·Genome Biology

DOI 10.1186/gb-2004-6-1-r7PMC PMC549068

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Abstract

The Mammalian Phenotype (MP) Ontology enables robust annotation of mammalian phenotypes in the context of mutations, quantitative trait loci and strains that are used as models of human biology and disease. The MP Ontology supports different levels and richness of phenotypic knowledge and flexible annotations to individual genotypes. It continues to develop dynamically via collaborative input from research groups, mutagenesis consortia, and biological domain experts. The MP Ontology is currently used by the Mouse Genome Database and Rat Genome Database to represent phenotypic data.

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Figure 1 Screen shot of the Mammalian Phenotype (MP) Browser in which the term 'lethality-embryonic/perinatal' was selected. At the top (yellow shading) the term, its synonym and MP unique identifier appear. The number of paths to term (in this case, one) indicates how many paths through the DAG structure can be traversed to reach the term. The main body of the browser page shows the selected term highlighted and within the context of the hierarchical path(s) of the MP Ontology. In this example page, three levels of the hierarchy are visible (Phenotype Ontology, its 34 sub-terms, and the two sub-terms that fall beneath 'lethality-embryonic/perinatal'. The plus sign, appearing for many of the terms on this page, indicates that these terms have additional sub-terms that can be viewed by clicking on the term to expand the view of that portion of the ontology. The number of genotypes and annotations following the term 'lethality-embryonic/perinatal' is a hypertext link to those data. This latter feature will be available in early 2005.CC BY · PubMed Central

Figure 2 Example showing a portion of the MGI web display of the phenotype annotations for homozygotes for the Ccm1tm1Dmar genetically engineered allele (the first targeted mutation from the Douglas Marchuk laboratory in the cerebral cavernous malformations 1 gene). Homozygotes are embryonic lethal, showing developmental and cardiac abnormalities. Note the organization of annotations under the high level phenotype categories and the link to OMIM where the mouse and human show similar phenotypic characteristics. See [30] to view the complete record for the Ccm1tm1Dmar phenotypic allele. Searches for phenotypes at MGI can be done via the Alleles and Phenotypes Query Form [31].CC BY · PubMed Central

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Authors: Smith, C. L., Goldsmith, C.-A. W., & Eppig, J. T.
Affiliations: Jackson Laboratory (US)
Massachusetts College of Pharmacy and Health Sciences (US)
Corresponding author: Eppig, Janan T
ORCID: Smith, Cynthia L
Eppig, Janan T
Venue: Genome Biology
Publisher: Springer Science and Business Media LLC
Published: 2004-12-15
Volume: 6
Issue: 1
Pages: R7-R7
ISSN: 1465-6906 (ISSN-L)
1474-760X
DOI: 10.1186/gb-2004-6-1-r7
PMC: PMC549068
OpenAlex: W2126434293
Cited by: 417
References: 22
Citations by year: 2026: 6 · 2025: 8 · 2024: 8 · 2023: 8 · 2022: 9 · 2021: 10 · 2020: 17 · 2019: 14 · 2018: 24 · 2017: 14 · 2016: 17 · 2015: 19 · 2014: 30 · 2013: 31 · 2012: 41
FWCI: 5.81
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/2.0/ (tdm)
creativecommons.org/licenses/by/2.0/ (vor)
Locations: Genome biology (publishedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
The Mouseion at the JAXlibrary (Jackson Laboratory) (submittedVersion)
Topics: Health Sciences › Medicine › Health Informatics › 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, mouse model, rat model, quantitative trait loci, mutant strain, Mouse Genome Database, Rat Genome Database, disease models
MeSH terms: Animals, Genotype, Humans, Mammals, Mutation, Terminology as Topic, Phenotype, Genome, Vocabulary, Controlled, Computational Biology, Databases, Genetic, Quantitative Trait Loci, Mice, Rats

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The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information

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