The DOI matches its Crossref record; 22 of the 22 references it cites were found in a registry or an index.
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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Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206
Self-citationThe Gene Ontology (GO) database and informatics resource
Gene Ontology Consortium (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh036 · Cited by 4,596
Mutation nomenclature extensions and suggestions to describe complex mutations: A discussion
den Dunnen, J. T., & Antonarakis, S. E. (2000) · Human Mutation · doi:10.1002/(sici)1098-1004(200001)15:1 · Cited by 1,757
Creating the Gene Ontology Resource: Design and ImplementationPreprint
The Gene Ontology Consortium (2001) · Genome Research · doi:10.1101/gr.180801 · Cited by 957
Online Mendelian Inheritance in Man 'OMIM'.
Amladi, S. (2007) · PubMed · Cited by 871
Creating the gene ontology resource: design and implementation.
Blake, J. A., Corradi, J., Eppig, J. T., Hill, D. P., Richardson, J. E., & Ringwald, M. (2001) · The Mouseion at the JAXlibrary (Jackson Laboratory) · Cited by 826
Self-citationBiology of the Laboratory Mouse
(1941) · JAMA · doi:10.1001/jama.1941.02820440081034 · Cited by 805
The Comprehensive Knockout Mouse Project Consortium (2004) · Nature Genetics · doi:10.1038/ng0904-921 · Cited by 608
Self-citationGene Ontology Consortium. The Gene Ontology (GO) database and informatics resource
Harris, M. A., Clark, J., Ireland, A., Lomax, J., Ashburner, M., Foulger, R. E., Eilbeck, K. L., Lewis, S., Marshall, B., Mungall, C., et al. (2004) · Cited by 295
Self-citationUsing ontologies to describe mouse phenotypes
Gkoutos, G. V., Green, E. C. J., Mallon, A., Hancock, J. M., & Davidson, D. R. (2004) · Genome biology · doi:10.1186/gb-2004-6-1-r8 · Cited by 241
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WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013
Wang, J., Duncan, D. T., Shi, Z., & Zhang, B. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt439 · Cited by 1,512
Convergence of genes and cellular pathways dysregulated in autism spectrum disorders
Pinto, D., Delaby, E., Merico, D., Barbosa, M., Merikangas, A., Klei, L., Thiruvahindrapuram, B., Xu, X., Ziman, R., Wang, Z., et al. (2014) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.03.018 · Cited by 969
The human phenotype ontology: a tool for annotating and analyzing human hereditary disease
Robinson, P. N., Köhler, S., Bauer, S., Seelow, D., Horn, D., & Mundlos, S. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2008.09.017 · Cited by 1,034
Massive mining of publicly available RNA-seq data from human and mouse
Lachmann, A., Torre, D., Keenan, A. B., Jagodnik, K. M., Lee, H. J., Wang, L., Silverstein, M. C., & Ma’ayan, A. (2018) · Nature Communications · doi:10.1038/s41467-018-03751-6 · Cited by 701
A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility
Cusanovich, D. A., Hill, A. J., Aghamirzaie, D., Daza, R. M., Pliner, H. A., Berletch, J. B., Filippova, G. N., Huang, X., Christiansen, L., DeWitt, W. S., et al. (2018) · Cell · doi:10.1016/j.cell.2018.06.052 · Cited by 759
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
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