Mammalian Phenotype Ontology
Abbreviation: MP
Homepage http://www.informatics.jax.org/vocab/mp_ontology
Countries that developed this resource United States
Created in 2004
Taxonomic range
Knowledge Domains
Subjects
How to cite this record FAIRsharing.org: MP; Mammalian Phenotype Ontology; DOI: https://doi.org/10.25504/FAIRsharing.kg1x4z; Last edited: Dec. 11, 2019, 4:40 p.m.; Last accessed: Apr 11 2021 1:16 a.m.
Record updated: Dec. 10, 2019, 7:31 p.m. by The FAIRsharing Team.
| contact form | User Support Contact Form |
| support email | Support Email |
| forum | GitHub Issue Tracker |
| help | About Phenotypes and Mutant Alleles |
| online documentation | GitHub Repository |
Additional Information
| Contact | Susan M. Bello ORCID |
External Links
| Bioportal | http://bioportal.bioontology.org/ontologies/MP |
| OBO | http://obofoundry.org/ontology/mp.html |
| Mammalian Phenotype Ontology-Download Latest Version | http://www.informatics.jax.org/downloads/reports/index.html#pheno |
No XSD schemas defined
Conditions of Use
Applies to: Data use- MGI Warranty Disclaimer & Copyright Notice
- Creative Commons Attribution 4.0 International (CC BY 4.0)
Data Access
| Search and browse | http://www.informatics.jax.org/vocab/mp_ontology |
REST Web Services
| Access our MouseMine data via our Application Programming Interface (API). We provide client libraries in the following languages: Perl, Python, Ruby, Java | http://www.mousemine.org/mousemine/api.do |
The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information.
Smith CL,Goldsmith CA,Eppig JT
Genome Biol 2005
The mammalian phenotype ontology: enabling robust annotation and comparative analysis.
Smith CL,Eppig JT
Wiley Interdiscip Rev Syst Biol Med 2010
The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data.
Smith CL,Eppig JT
Mamm Genome 2012
Expanding the mammalian phenotype ontology to support automated exchange of high throughput mouse phenotyping data generated by large-scale mouse knockout screens.
Smith CL,Eppig JT
J Biomed Semantics 2015
View in BioPortal.
View in OBO Foundry.
Reporting Guidelines
Terminology Artifacts
Models and Formats
No syntax standards defined
Identifier Schemas
No identifier schema standards defined
Metrics
No metrics standards defined
Characterizations of hundreds of strains of laboratory mice to facilitate translational discoveries and to assist in selection of strains for experimental studies. Data sets are voluntarily contributed by researchers or retrieved by us from public sources. MPD has three major types of strain-centric data sets: phenotype strain surveys, SNP and variation data, and gene expression strain surveys.
neXtProt
neXtProt is a comprehensive human-centric discovery platform, offering its users a seamless integration of and navigation through protein-related data.
PolyDoms
An integrated database of human coding single nucleotide polymorphisms (SNPs) and their annotations.
Rat Genome Database
The Rat Genome Database stores genetic, genomic, phenotype, and disease data generated from rat research. It provides access to corresponding data for eight other species, allowing cross-species comparison. Data curation is performed both manually and via an automated pipeline, giving RGD users integrated access to a wide variety of data to support their research.
Mouse Genome Database - a Mouse Genome Informatics (MGI) Resource
MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. Data includes gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data.
MouseMine @ MGI
A database of integrated mouse data from MGI, powered by InterMine. MouseMine is member of InterMOD, a consortium of model organism databases dedicated to making cross-species data analysis easier through ongoing coordination and collaborative system development.
MGI Mouse Gene Expression Database
The Gene Expression Database (GXD) is a community resource for gene expression information from the laboratory mouse. GXD stores and integrates different types of expression data and makes these data freely available in formats appropriate for comprehensive analysis. There is particular emphasis on endogenous gene expression during mouse development.
GeneWeaver
The GeneWeaver data and analytics website is a publically available resource for storing, curating and analyzing sets of genes from heterogeneous data sources. The system enables discovery of relationships among genes, variants, traits, drugs, environments, anatomical structures and diseases implicitly found through gene set intersections. By enumerating the common and distinct biological molecules associated with all subsets of curated or user submitted groups of gene sets and gene networks, GeneWeaver empowers users with the ability to construct data driven descriptions of shared and unique biological processes, diseases and traits within and across species.
RegenBase
RegenBase is a knowledge base of SCI biology. RegenBase integrates curated literature-sourced facts and experimental details from publications, raw assay data profiling the effect of compounds on enzyme activity and cell growth, and structured SCI domain knowledge in the form of the first ontology for SCI, using Semantic Web representation languages and frameworks. RegenBase enables researchers to organize and interrogate experimental data generated by spinal cord injury (SCI) research, with the ultimate goal of translating SCI experimental findings in model organisms into human therapies.
Deciphering the Mechanisms of Developmental Disorders
Initiated in 2013, DMDD has the ambitious goal of identifying all embryonic lethal knockout lines made at the Wellcome Trust Sanger institute, through their work as a major centre for creation of individual mouse gene knockouts. DMDD uses a combination of comprehensive 3D imaging, tissue histology, immunocytochemistry and transcriptomics to identify abnormalities in embryo and placental structure for each embryonic lethal line. All data is made freely available via this web site, enabling individual researchers to identify lines relevant to their own research. The DMDD programme is coordinating its work with similar international efforts through the umbrella of the International Mouse Phenotyping Consortium.
Open Targets
Open Targets is a data integration platform for access to and visualisation of potential drug targets associated with disease. Each drug target is linked to a disease using integrated genome-wide data from a broad range of data sources.
Alliance of Genome Resources
The primary mission of the Alliance of Genome Resources (the Alliance) is to develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biology, health and disease.
OBO Foundry
The Open Biological and Biomedical Ontology (OBO) Foundry is a collective of ontology developers that are committed to collaboration and adherence to shared principles. The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate. To achieve this, OBO Foundry participants voluntarily adhere to and contribute to the development of an evolving set of principles including open use, collaborative development, non-overlapping and strictly-scoped content, and common syntax and relations, based on ontology models that work well, such as the Gene Ontology (GO). The OBO Foundry is overseen by an Operations Committee with Editorial, Technical and Outreach working groups.
MUGEN mouse database
The MUGEN mouse database (MMdb) is a database of murine models of immune processes and immunological diseases.
Domain-centric GO
Domain-centric GO provides associations between ontological terms and protein domains at the superfamily and family levels. Some functional units consist of more than one domain acting together or acting at an interface between domains; therefore, ontological terms associated with pairs of domains, triplets and longer supra-domains are also provided.
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Record Maintainer
Funds
National Human Genome Research Institute (NHGRI), Bethesda, MD, USA (Government body)
Maintains
Mouse Genome Informatics (MGI) (Consortium) Lead
Grant Number(s)
HG000330 (National Human Genome Research Institute (NHGRI), Bethesda, MD, USA)
