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

Journal of Biomedical Semantics

Janan T Eppig¹  Cynthia L Smith¹ 

[1] Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor 04609, ME, USA

关键词: Database;    Data integration;    Mouse;    Ontology;    Phenotype;   

Others  :  1145429
DOI  :  10.1186/s13326-015-0009-1

 received in 2014-11-03, accepted in 2015-03-03,  发布年份 2015

【 摘 要 】

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.

【 授权许可】

   
2015 Smith and Eppig; licensee BioMed Central.

【 图 表 】

Figure 1.

Figure 2.

【 参考文献 】

• [1]Smith CL, Eppig JT: The mammalian phenotype ontology as a unifying standard for experimental and high-throughput phenotyping data. Mamm Genome 2012, 23(9–10):653-68.
• [2]Smith CL, Eppig JT: The mammalian phenotype ontology: enabling robust annotation and comparative analysis. Wiley Interdiscip Rev Syst Biol Med 2009, 1(3):390-9. Nov-Dec
• [3]Koscielny G, Yaikhom G, Iyer V, Meehan TF, Morgan H, Atienza-Herrero J, et al.: The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data. Nucleic Acids Res 2014, 42(Database issue):D802-9.
• [4]MGI ftp site [ftp://ftp.informatics.jax.org/pub/reports/index.html#pheno]
• [5]Mouse Genome Informatics [www.informatics.jax.org]
• [6]MouseMine [www.mousemine.org]
• [7]Rat Genome Database, RGD [rgd.mcw.edu]
• [8]Morgan H, Beck T, Blake A, Gates H, Adams N, Debouzy G, et al.: EuroPhenome: a repository for high-throughput mouse phenotyping data. Nucleic Acids Res 2010, 38(Database issue):D577-85.
• [9]Ayadi A, Birling MC, Bottomley J, Bussell J, Fuchs H, Fray M, et al.: Mouse large-scale phenotyping initiatives: overview of the European Mouse Disease Clinic (EUMODIC) and of the Wellcome Trust Sanger Institute Mouse Genetics Project. Mamm Genome 2012, 23(9–10):600-10.
• [10]Beck T, Morgan H, Blake A, Wells S, Hancock JM, Mallon AM: Practical application of ontologies to annotate and analyse large scale raw mouse phenotype data. BMC Bioinform 2009, 10(Suppl 5):S2. BioMed Central Full Text
• [11]IMPreSS pipelines [https://www.mousephenotype.org/impress/pipelines]
• [12]IMPReSS Fructosamine Parameter [https://www.mousephenotype.org/impress/parameterontologies/1963/96]
• [13]Hochheiser H, Aronow BJ, Artinger K, Beaty TH, Brinkley JF, Chai Y, et al.: The FaceBase Consortium: a comprehensive program to facilitate craniofacial research. Dev Biol 2011, 355(2):175-82.
• [14]IMPreSS [http://www.mousephenotype.org/impress]
• [15]Lens Opacity Parameter [https://www.mousephenotype.org/impress/parameterontologies/2319/94]
• [16]IMPC [http://www.mousephenotype.org/]
• [17]Cardiovascular system phentypes at IMPC [https://www.mousephenotype.org/data/phenotypes/MP:0005385]
• [18]IMPC RESTfulAPI [https://www.mousephenotype.org/data/documentation/api-help.html]
• [19]Adams D, Baldock R, Bhattacharya S, Copp AJ, Dickinson M, Greene ND, et al.: Bloomsbury report on mouse embryo phenotyping: recommendations from the IMPC workshop on embryonic lethal screening. Dis Model Mech 2013, 6(3):5719.
• [20]Osumi-Sutherland D, Marygold SJ, Millburn GH, Mcquilton PA, Ponting L, Stefancsik R, et al.: The Drosophila phenotype ontology. J Biomed Semantics 2013, 4(1):30. BioMed Central Full Text
• [21]Murray SA, Morgan JL, Kane C, Sharma Y, Heffner CS, Lake J, et al.: Mouse gestation length is genetically determined. PLoS One 2010, 5(8):e12418.
• [22]Cabelof DC: Haploinsufficiency in mouse models of DNA repair deficiency: modifiers of penetrance. Cell Mol Life Sci 2012, 69(5):727-40.
• [23]Sellers RS: The gene or not the gene–that is the question: understanding the genetically engineered mouse phenotype. Vet Pathol 2012, 49(1):5-15.
• [24]Doetschman T: Influence of genetic background on genetically engineered mouse phenotypes. Methods Mol Biol 2009, 530:423-33.
• [25]Jackson Laboratory Repository JAX Mice [http://jaxmice.jax.org]
• [26]European Mouse Mutant Archive, [https://www.infrafrontier.eu]
• [27]Mutant Mouse Regional Resource Centers [http://www.mmrrc.org]
• [28]KOMP Repository [https://www.komp.org]