Skip to main content

Accessing data from the International Mouse Phenotyping Consortium: state of the art and future plans

Abstract

The International Mouse Phenotyping Consortium (IMPC) (http://www.mousephenotype.org) will reveal the pleiotropic functions of every gene in the mouse genome and uncover the wider role of genetic loci within diverse biological systems. Comprehensive informatics solutions are vital to ensuring that this vast array of data is captured in a standardised manner and made accessible to the scientific community for interrogation and analysis. Here we review the existing EuroPhenome and WTSI phenotype informatics systems and the IKMC portal, and present plans for extending these systems and lessons learned to the development of a robust IMPC informatics infrastructure.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

References

  • Bogue MA, Grubb SC (2004) The Mouse Phenome Project. Genetica 122:71–74

    PubMed  Article  CAS  Google Scholar 

  • Brown SD, Moore MW (2012) Towards an encyclopaedia of mammalian gene function: the International Mouse Phenotyping Consortium. Dis Model Mech 5:289–292

    PubMed  Article  CAS  Google Scholar 

  • Brown SD, Chambon P, de Angelis MH (2005) EMPReSS: standardized phenotype screens for functional annotation of the mouse genome. Nat Genet 37:1155

    PubMed  Article  CAS  Google Scholar 

  • Brown SD, Hancock JM, Gates H (2006) Understanding mammalian genetic systems: the challenge of phenotyping in the mouse. PLoS Genet 2:e118

    PubMed  Article  Google Scholar 

  • Collins FS, Rossant J, Wurst W (2007) A mouse for all reasons. Cell 128:9–13

    PubMed  Article  CAS  Google Scholar 

  • Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, Gordon L, Hendrix M, Hourlier T, Johnson N, Kahari AK, Keefe D, Keenan S, Kinsella R, Komorowska M, Koscielny G, Kulesha E, Larsson P, Longden I, McLaren W, Muffato M, Overduin B, Pignatelli M, Pritchard B, Riat HS, Ritchie GR, Ruffier M, Schuster M, Sobral D, Tang YA, Taylor K, Trevanion S, Vandrovcova J, White S, Wilson M, Wilder SP, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernandez-Suarez XM, Harrow J, Herrero J, Hubbard TJ, Parker A, Proctor G, Spudich G, Vogel J, Yates A, Zadissa A, Searle SM (2012) Ensembl 2012. Nucleic Acids Res 40:D84–D90

    PubMed  Article  CAS  Google Scholar 

  • Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D (2005) Using ontologies to describe mouse phenotypes. Genome Biol 6:R8

    PubMed  Article  Google Scholar 

  • Kapushesky M, Adamusiak T, Burdett T, Culhane A, Farne A, Filippov A, Holloway E, Klebanov A, Kryvych N, Kurbatova N, Kurnosov P, Malone J, Melnichuk O, Petryszak R, Pultsin N, Rustici G, Tikhonov A, Travillian RS, Williams E, Zorin A, Parkinson H, Brazma A (2012) Gene Expression Atlas update—a value-added database of microarray and sequencing-based functional genomics experiments. Nucleic Acids Res 40:D1077–D1081

    PubMed  Article  CAS  Google Scholar 

  • Kasprzyk A (2011) BioMart: driving a paradigm change in biological data management. Database (Oxford) 2011:bar049

  • Mallon AM, Blake A, Hancock JM (2008) EuroPhenome and EMPReSS: online mouse phenotyping resource. Nucleic Acids Res 36:D715–D718

    PubMed  Article  CAS  Google Scholar 

  • Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N, Zhukova A, Brazma A, Parkinson H (2010) Modeling sample variables with an Experimental Factor Ontology. Bioinformatics 26:1112–1118

    PubMed  Article  CAS  Google Scholar 

  • Morgan H, Beck T, Blake A, Gates H, Adams N, Debouzy G, Leblanc S, Lengger C, Maier H, Melvin D, Meziane H, Richardson D, Wells S, White J, Wood J, de Angelis MH, Brown SD, Hancock JM, Mallon AM (2010) EuroPhenome: a repository for high-throughput mouse phenotyping data. Nucleic Acids Res 38:D577–D585

    PubMed  Article  CAS  Google Scholar 

  • Prlic A, Down TA, Kulesha E, Finn RD, Kahari A, Hubbard TJ (2007) Integrating sequence and structural biology with DAS. BMC Bioinformatics 8:333

    PubMed  Article  Google Scholar 

  • Ringwald M, Iyer V, Mason JC, Stone KR, Tadepally HD, Kadin JA, Bult CJ, Eppig JT, Oakley DJ, Briois S, Stupka E, Maselli V, Smedley D, Liu S, Hansen J, Baldock R, Hicks GG, Skarnes WC (2011) The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium. Nucleic Acids Res 39:D849–D855

    PubMed  Article  Google Scholar 

  • Skarnes WC, Rosen B, West AP, Koutsourakis M, Bushell W, Iyer V, Mujica AO, Thomas M, Harrow J, Cox T, Jackson D, Severin J, Biggs P, Fu J, Nefedov M, de Jong PJ, Stewart AF, Bradley A (2011) A conditional knockout resource for the genome-wide study of mouse gene function. Nature 474:337–342

    PubMed  Article  CAS  Google Scholar 

  • Tanaka N, Waki K, Kaneda H, Suzuki T, Yamada I, Furuse T, Kobayashi K, Motegi H, Toki H, Inoue M, Minowa O, Noda T, Takao K, Miyakawa T, Takahashi A, Koide T, Wakana S, Masuya H (2010) SDOP-DB: a comparative standardized-protocol database for mouse phenotypic analyses. Bioinformatics 26:1133–1134

    PubMed  Article  CAS  Google Scholar 

  • Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, Fostel J, Ghazal P, Gibson F, Gray T, Grimes G, Hancock JM, Hardy NW, Hermjakob H, Julian RK Jr, Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Le Novere N, Leebens-Mack J, Lewis SE, Lord P, Mallon AM, Marthandan N, Masuya H, McNally R, Mehrle A, Morrison N, Orchard S, Quackenbush J, Reecy JM, Robertson DG, Rocca-Serra P, Rodriguez H, Rosenfelder H, Santoyo-Lopez J, Scheuermann RH, Schober D, Smith B, Snape J, Stoeckert CJ Jr, Tipton K, Sterk P, Untergasser A, Vandesompele J, Wiemann S (2008) Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol 26:889–896

    PubMed  Article  CAS  Google Scholar 

  • Valentin F, Squizzato S, Goujon M, McWilliam H, Paern J, Lopez R (2010) Fast and efficient searching of biological data resources—using EB-eye. Brief Bioinform 11:375–384

    PubMed  Article  CAS  Google Scholar 

  • Wilkinson P, Sengerova J, Matteoni R, Chen CK, Soulat G, Ureta-Vidal A, Fessele S, Hagn M, Massimi M, Pickford K, Butler RH, Marschall S, Mallon AM, Pickard A, Raspa M, Scavizzi F, Fray M, Larrigaldie V, Leyritz J, Birney E, Tocchini-Valentini GP, Brown S, Herault Y, Montoliu L, de Angelis MH, Smedley D (2010) EMMA—mouse mutant resources for the international scientific community. Nucleic Acids Res 38:D570–D576

    PubMed  Article  CAS  Google Scholar 

  • Zheng-Bradley X, Rung J, Parkinson H, Brazma A (2010) Large scale comparison of global gene expression patterns in human and mouse. Genome Biol 11:R124

    PubMed  Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Ann-Marie Mallon.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Mallon, AM., Iyer, V., Melvin, D. et al. Accessing data from the International Mouse Phenotyping Consortium: state of the art and future plans. Mamm Genome 23, 641–652 (2012). https://doi.org/10.1007/s00335-012-9428-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00335-012-9428-9

Keywords

  • Laboratory Information Management System
  • Mammalian Phenotype
  • Wellcome Trust Sanger Institute
  • Data Coordination Centre
  • Phenotyping Centre