MGI and Phenotyping Projects Mouse Genome Informatics

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

Lexicon data for Adfp gene trap knockout

Phenotype Expression Mice ES cells

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.

Challenges and Needs for Baseline Strain Phenotypes

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

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 –Avcrl1 tm1Dyl, Avcrl1 tm1Enl, Avcrl1 tm1Spo –Use of MGI_ids in data and publications

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

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.

The End