Untitled

Abstract

The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information <p>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.</p> AbstractThe 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.

Interoperability between phenotype and anatomy ontologies

“…At least two kinds of phenotype ontologies can be distinguished: ontologies in which each term contains one specific phenotypic trait (Robinson et al , 2008; Smith et al , 2004), and ontologies and methods that permit the composition of a term through the combination of an entity and a quality (Gkoutos et al , 2004a, b; Mungall et al , 2010). Each of these approaches describes a phenotype through qualities that are attributes of an entity .…”

Integrating phenotype ontologies with PhenomeNET

“…In our experiments, we use the Human Phenotype Ontology (HPO) [12], Mammalian Phenotype Ontology (MP) [13], Human Disease Ontology (DO) [15], and Orphanet Rare Disease Ontology (ORDO) [17] provided as part of the Ontology Alignment Evaluation Initiative 2016 competition.…”

“…We present our results based on three versions of the PhenomeNET ontology: the first version consists of the plain ontology using only the axioms provided in the Human Phenotype Ontology (HPO) [12] and the Mammalian Phenotype Ontology (MP) [13]; in the second version, we extend our original ontology by adding additional lexical and structural mappings generated with the AgreementMakerLight [14] system and represent them as equivalent class axioms in our ontology; and in the third version, we further generate mappings between classes in the PhenomeNET ontology, the Disease Ontology (DO) [15] and the Orphanet Rare Disease Ontology (ORDO) [16]. …”

Mouse Genome Database: From sequence to phenotypes and disease models

“…Ontologies are structured vocabularies and the placement of terms within that structure relay information about the relationships of terms to one another and the type of relationship involved. Within MGD, the Gene Ontology (GO Consortium, 2000) and the Mammalian Phenotype Ontology (Smith et al ., 2005) are used extensively for function and phenotype annotations, respectively. In addition, the EMAP/EMAPA (Edinburgh Mouse Atlas Project/Edinburgh Mouse Atlas Project Abstract version) ontology of mouse developmental anatomy (Hayamizu et al ., 2013; Finger et al ., 2015) is used to coordinate anatomical term use among the ontologies.…”