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

By Cynthia L. Smith, C. Goldsmith, Janan T. Eppig. Genome Biology, 2004

464 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ab25233b593249a8016353de4b318858a8a2b815

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Citations in the corpus

Integrating phenotype ontologies across multiple species (2010, unknown): “Examples of these species-centric phenotype ontologies include: the Mammalian Phenotype ontology (MP) [15]; the Worm Phenotype ontology (WP); the Plant Trait ontology (TO) [16]; the Human Phenotype ontology (HP) [17]; the Ascomycete Phenotype ontology (APO); and the Mouse Pathology ontology (MPATH).”
The Mouse Genome Database (MGD): mouse biology and model systems (2007, unknown): “MGD collaborates with the bioinformatics community on the development of data and semantic standards such as the Gene Ontology (GO) and the Mammalian Phenotype (MP) Ontology.”
A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility. (2018, unknown): “For example, considering the Mammalian Phenotype Ontology (MPO), an annotated catalog of spontaneous, induced, and genetically engineered mouse mutations (Smith et al., 2005), we found that the genes with DA promoters or linked distal sites in a given cluster were often enriched for cell-type-specif”
WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013 (2013, methodology): “Therefore, we have added phenotype-associated gene sets defined by Mammalian Phenotype Ontology (15) and Human Phenotype Ontology (16) to WebGestalt.”
Massive mining of publicly available RNA-seq data from human and mouse (2017, background): “Gene set libraries from which annotated gene sets are currently derived from are: ChEA (34), ENCODE (35), (36), Gene Ontology (GO) (37), KEGG pathways (38), and MGI mammalian phenotype (39).”
Improved human disease candidate gene prioritization using mouse phenotype (2007, methodology): “The MP Ontology (MPO) supports different levels and richness of phenotypic knowledge and flexible annotations to individual genotypes [17].”
The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease. (2008, methodology): “Analysis of the phenotypic correlates of gene mutations has long been an essential method for discovering biological functions of genes, and more recently, computational analysis of mouse phenotypes related to gene mutations has become possible with tools such as the Mammalian Phenotype Ontology.”
Uberon, an integrative multi-species anatomy ontology (2012, methodology): “In constructing Uberon, we have revealed inconsistencies in related ontologies such as GO, MPO, CL and others.”
The Human Phenotype Ontology (2010, methodology): “The differential diagnosis in clinical genetics can often be challenging (20, 28, 29), for which reason a number of commercial and freely available computational tools have been developed including the LDDB (15), POSSUM (16), OMIM (14), and Orphanet (17).”
Human symptoms–disease network (2014, background): “Resources like the Human Phenotype Ontology 25 (HPO) and the Mammalian Phenotype Ontology 26 provide a standardized vocabulary of phenotypic information that can also be used to transfer detailed knowledge of model organisms to interpret and predict associated phenomena in human 27,28 .”
Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources (2018, methodology): “To that end, we recently organized a Phenotype Ontology development and reconciliation workshop (Phenotype Ontologies Traversing All The Organisms: POTATO).”
A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®) (2011, methodology): “We will add links from the features in each OMIM clinical synopsis to more structured ontologies, such as the Human Phenotype Ontology [Robinson et al., 2008], the Elements of Morphology Terms [Allanson et al., 2009], ICD10, and the Mammalian Phenotype Ontology [Smith et al., 2005].”
Improved exome prioritization of disease genes through cross-species phenotype comparison (2014, methodology): “The pairwise comparisons were performed using OWL representations of the human and mouse phenotype annotations and a merged OWL file of the Phenotype and Trait Ontology (PATO), Uberon (Mungall et al. 2012), MPO and HPO and their logical definitions, as previously described (Doelken et al. 2013; Smed”