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MGI and Phenotyping Projects

MGI and Phenotyping Projects. Mouse Genome Informatics. Data Integration. Centers: mutagenesis, gene trap, etc. Primary literature. Data Loads: GenBank, SNPs, clone collections, SwissProt, RIKEN, etc. Electronic Submissions (individual labs). Processing, QC, and curation.

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MGI and Phenotyping Projects

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  1. MGI and Phenotyping Projects Mouse Genome Informatics

  2. Data Integration Centers: mutagenesis, gene trap, etc Primary literature Data Loads: GenBank, SNPs, clone collections, SwissProt, RIKEN, etc Electronic Submissions (individual labs) Processing, QC, and curation

  3. Lexicon data for Adfp gene trap knockout

  4. Phenotype Expression Mice ES cells

  5. One Goal for MGI in our next grant period is to be able to provide large scale raw phenotyping data to complement and support the analyzed and metadata we already provide from many data resources.

  6. Challenges and Needs for Baseline Strain Phenotypes

  7. Global challenges for baseline phenotype data • making raw/individual animal data available • how much integration of raw data is useful • defining assay SOPs • providing summaries and metadata • center data vs.investigator data • nomenclature

  8. What mouse is being analyzed? • Differentiating background • inbreds: standard, RI, consomic, congenic, etc. • F1 and F2 hybrids and other mixtures • Use of correct and explicit nomenclature • Strain name and substrains • C57BL/6 is not enough: • C57BL/6N, C57BL/6J, C57BL/6JCrl, etc. • Allelic composition • Acvrl1-/- is not enough • Avcrl1tm1Dyl, Avcrl1tm1Enl, Avcrl1tm1Spo • Use of MGI_ids in data and publications

  9. SOPs • Encouraging community use and contributions of SOPs with data • Defining minimal elements • Standard format • Beyond center data: general goal for all publication

  10. Data submission • The ideal • All who submit use same format, the correct nomenclature and include relevant MGI-Ids, GenBank-Ids, etc. • The reality • Even groups who agree on a standard format frequently take liberties • Community database providers need to continue to dedicate effort to disambiguating data, QC for content, and enforce nomenclature.

  11. The End http://www.informatics.jax.org

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