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The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information
Open accessAbstract
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 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].](/paper-figures/81da4303c3354f98b7cc9ea07fcc234f/the-mammalian-phenotype-ontology-as-a-tool-for-annotating-analyzing-and-figure-2.jpg)
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“mining genes associated with phenotypes from the Mammalian Phenotype Ontology resource (Smith et al, 2005; Chen et al, 2007) revealed that, albeit less significant when compared to Hep‐ID TFs, Hep‐IDCONNECT TF‐encoding genes are linked to abnormal liver phenotypes and metabolic functions (Fig 2G).”
From An extended transcription factor regulatory network controls hepatocyte identity (2023) · cites this paper as Smith et al, 2005
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Metadata
- 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
- Venue
- Genome Biology
- Published
- 2004-12-15
- Volume
- 6
- Issue
- 1
- Pages
- R7-R7
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- 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
- 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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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