The Mammalian Phenotype Ontology: enabling robust annotation and comparative analysis

By Cynthia L. Smith, Janan T. Eppig. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 2009

341 citations recorded by the source corpus.

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 (MP) ontology, 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 (MGI) Database (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, facilitates comparisons across mammalian species, assists in identifying appropriate experimental disease models, and aids in the discovery of candidate disease genes and molecular signaling pathways. Copyright © 2009 John Wiley & Sons, Inc.

Subfields: Artificial Intelligence, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d7099858306d09b503a60af307e8767a716ee5ed

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Citations in the corpus

Concept annotation in the CRAFT corpus (2012, background): “…mouse genes or gene products in the Mouse Genome Database (MGD) [68] to one or more terms from the GO and/or the Mammalian Phenotype Ontology (MP) [69], and (b) for their unrestric-tive licensing terms, i.e. , available in PubMed Central in the form of Open Access XML. Table 4 shows counts for…”
Finding Our Way through Phenotypes (2015, methodology): “quantitative and qualitative phenotype assay data for the mouse using the Mammalian Phenotype Ontology (MP) [54].”
The International Mouse Phenotyping Consortium: comprehensive knockout phenotyping underpinning the study of human disease (2022, methodology): “These phenotypic similarity computations between mouse knockouts and known human disorders are performed by the PhenoDigm algorithm (34), which relies on the availability of standardised phenotypic annotations (2,3).”
Protein Networks as Logic Functions in Development and Cancer (2011, background): “A systematic functional analysis of the modules (Materials and Methods) indicated that they were highly enriched for genes whose perturbation is linked to prenatal lethality or improper organ development in mammals (Figure 3B), as reported in the Mouse Genome Informatics (MGI) database [39] — an est”
Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models (2012, methodology): “In addition, our method advances the ﬁeld with its unique ability to anno-tate the molecular and phenotypic consequences of AASs using several domain-centric ontologies [de Lima Morais et al., 2011] including the Human Phenotype Ontology [Robinson et al., 2008] and the Mammalian Phenotype Ontology [”