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

  title={The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information},
  author={Cynthia L. Smith and Carroll W Goldsmith and Janan T. Eppig},
  journal={Genome Biology},
  pages={R7 - R7}
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… 

The mammalian phenotype ontology: enabling robust annotation and comparative analysis

A tool, the Mammalian Phenotype (MP) ontology, is described for classifying and organizing phenotypic information related to the mouse and other mammalian species and aids in the discovery of candidate disease genes and molecular signaling pathways.

The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data

The Mammalian Phenotype Ontology is a structured vocabulary for describing mammalian phenotypes and serves as a critical tool for efficient annotation and comprehensive retrieval of phenotype data, providing a standard underpinning to mouse phenotype descriptions for existing and future experimental and large-scale phenotyping projects.

Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research

A cross-species phenotype ontology for human, mouse and zebrafish that contains classes from the Human Phenotype Ontology, Mammalian PhenotypeOntology, and generated classes for zebra fish phenotypes is generated.

Phenotype ontologies for mouse and man: bridging the semantic gap

The current state of the art for phenotype and disease description in mice and humans is reviewed, and ways in which the semantic gap between coding systems might be bridged to facilitate the discovery and exploitation of new mouse models of human diseases are discussed.

Aligning the Human Phenotype and Mammalian Phenotype Ontology using Dead Simple Ontology Design Patterns

This paper describes the development and implementation of the DOSDP in the HP and MP, which are design patterns that can be specified in a YAML text file and can be used to generate new terms, documentation, retrofit old terms, and allows for reuse of patterns.

The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development

The Xenopus phenotype ontology (XPO) is presented to annotate phenotypic data from experiments in Xenopus, one of the major vertebrate model organisms used to study gene function in development and disease.

Integrating phenotype ontologies across multiple species

This work demonstrates how these ontologies can be improved through assignment of logical definitions using a core ontology of phenotypic qualities and multiple additional ontologies from the Open Biological Ontologies library.

Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research.

A cross-species phenotype ontology for human, mouse and zebra fish that contains zebrafish phenotypes is generated and up-to-date annotation data connecting human genes to phenotype classes from the generated ontology is provided.

Using bio-ontologies as data annotation, integration & analytical tools at the Mouse Genome Informatics resource

The mouse genome informatics (MGI) resource, an in-depth resource for the genetics, genomics and biology of the laboratory mouse, provides free access to integrated data on diverse biological



Gene Ontology: tool for the unification of biology

The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.

Using ontologies to describe mouse phenotypes

A novel, compositional approach to the describing phenotypes of mutant mice in a standard, structured manner which combines core ontologies from a variety of sources is described, producing a framework with greater flexibility, power and economy than previous approaches.

Functional Annotation of Mouse Genome Sequences

The International Mouse Mutagenesis Consortium proposes goals and outlines plans for the next 10 years for annotating the mouse genome and compiling data on mouse mutations.

Creating the gene ontology resource: design and implementation.

The Gene Ontology project seeks to provide a set of structured vocabularies for specific biological domains that can be used to describe gene products in any organism, which includes building three extensive ontologies to describe molecular function, biological process, and cellular component.

The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data

An ontology to provide standardized nomenclature for anatomical terms in the postnatal mouse will be used to annotate and integrate different types of data pertinent to anatomy, such as gene expression patterns and phenotype information, which will contribute to an integrated description of biological phenomena in the mouse.

The Mouse Genome Database (MGD): integrating biology with the genome

Recent developments in MGD discussed here include an extensive integration of the mouse sequence data and substantial revisions in the presentation, query and visualization of sequence data.

The Gene Ontology ( GO ) database and informatics resource Gene Ontology Consortium

The Gene Ontology project provides structured, controlled vocabularies and classifications that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of genes, gene products and sequences.

The European dimension for the mouse genome mutagenesis program

The European Mouse Mutagenesis Consortium is the European initiative contributing to the international effort on functional annotation of the mouse genome. Its objectives are to establish and

Pathbase: a database of mutant mouse pathology

High-resolution downloadable images of normal and diseased tissues that are searchable through orthogonal ontologies for pathology, developmental stage, anatomy and gene attributes (GO terms), together with controlled vocabularies for type of genetic manipulation or mutation, genotype and free text annotation for mouse strain and additional attributes.

Algorithms for mutant sorting: the need for phenotype vocabularies

  • J. Eppig
  • Computer Science
    Mammalian Genome
  • 2000
The rationale for developing vocabularies and examples of several vocABularies being developed are described, and the critical nature of community participation in both building and applying phenotypic classification systems is discussed.