Expanding the mammalian phenotype ontology to support automated exchange of high throughput mouse phenotyping data generated by large-scale mouse knockout screens

Abstract

Background: A vast array of data is about to emerge from the large scale high-throughput mouse knockout phenotyping projects worldwide. It is critical that this information is captured in a standardized manner, made accessible, and is fully integrated with other phenotype data sets for comprehensive querying and analysis across all phenotype data types. The volume of data generated by the high-throughput phenotyping screens is expected to grow exponentially, thus, automated methods and standards to exchange phenotype data are required.

Results: The IMPC (International Mouse Phenotyping Consortium) is using the Mammalian Phenotype (MP) ontology in the automated annotation of phenodeviant data from high throughput phenotyping screens. 287 new term additions with additional hierarchy revisions were made in multiple branches of the MP ontology to accurately describe the results generated by these high throughput screens.

Conclusions: Because these large scale phenotyping data sets will be reported using the MP as the common data standard for annotation and data exchange, automated importation of these data to MGI (Mouse Genome Informatics) and other resources is possible without curatorial effort. Maximum biomedical value of these mutant mice will come from integrating primary high-throughput phenotyping data with secondary, comprehensive phenotypic analyses combined with published phenotype details on these and related mutants at MGI and other resources.

Keywords: Data integration; Database; Mouse; Ontology; Phenotype.

Figure 1

Mouse prenatal lethality stages. Defined mouse prenatal stages incorporated in Mammalian Phenotype lethality terms and new time points required to support IMPC prenatal screening (Not drawn to scale).

Figure 2

Allelic series for mouse Fgfr2 gene shows range of phenotypes. Screenshot of MGI Allele Summary Page listing seven of the twenty-seven known alleles of Fgfr2 that exist in mice. Different mutations in this gene result in a range of phenotypes and disease models in the homozygous and heterozygous states. An additional eighty-eight mutations that exist only in gene trapped or targeted ES cell lines are also known.