Curatorial Procedures at Mouse Genome Informatics with an Emphasis on Expression Data Constance M. Smith The Jackson Laboratory Bar Harbor, ME

Mouse Genome Informatics Mouse Genome Database Gene Expression Database Mouse Genome Sequencing Project Mouse Tumor Biology Database Gene Ontology Consortium Genotype Objective: Facilitate the use of the mouse as a model for human biology by furthering our understanding of the relationship between genotype and phenotype. PhenotypeExpression

Gene detail page summarizes information in MGI

Gene Expression Database (GXD) Most data obtained via manual curation Emphasis on embryonic expression data Assay types stored are: –In situ: RNA in situ, immunohistochemistry, reporter gene (knock in) –Gels/blots: RT-PCR, Northerns, Westerns, RNase protection, Nuclease S1 –cDNA source data

Principles guiding curation of expression data 1.Different types of expression data are integrated 2.Expression patterns are described using controlled vocabularies 3.Context is provided by integration with other databases

Literature Curation at MGI

As of 10/23/03: 32,257 records 8,904 references 5,590 genes Up to date Complete from early 1990s to the present

As of 10/23/03: 118,576 results 10,329 assays 2,913 genes

Data entered using customized interface

The Anatomical Dictionary—essential to integration

Allele detail Link to images

Image storage allows users to analyze primary data

Allele detail provides description of phenotype using controlled vocabulary

Gene Function Where and When Assay type Chromosomal Location

Mouse Genome Informatics Staff Principal Investigators Janan Eppig Dale Begley Patricia Grant Richard Baldarelli Judith Blake Dirck Bradt Terry Hayamizu Li Ni Carol Bult Donna Burkart David Hill Dong Qi James Kadin Nancy Butler Debra Krupke Deborah Reed Joel Richardson Rebecca Corey Moyha Lennon-Pierce Robert Sinclair Martin Ringwald Howard Dene Ira Lu Constance Smith John Sundberg Harold Drabkin Cathleen Lutz Cynthia Smith Jacqueline Finger Lois Maltais Benjamin Taylor Kenneth Frazer Ingeborg McCright Pierre VandenBorre Carroll Goldsmith TBK Reddy Linda Washburn Igor Mikaelian Yunxia (Sophia) Zhu John Boddy Diane Dahmen Daniel Modrusan Matthew Baya Mary Dolan Leslie Trombley Jonathan Beal Benjamin King Matthew Vincent Jeffrey Campbell Jill Lewis Michael Walker Lori Corbani Michael McCrossin Joshua Winslow Sharon Cousins David Miers Iry Witham David Garippa David Shaw Paul Szauter Daniel Lawrence Lucette Glass Janice Ormsby Masaaki Furuno Alex Diehl Kirk Barsanti Prita Mani David Walton Peter Frost

Anatomical Dictionary for the adult mouse multiple hierarchies physiological systems space / histology sampling

Anatomical Dictionary for the adult mouse multiple hierarchies physiological systems space / histology sampling Describe and view anatomy from different anatomical, physiological, and disease perspectives Directed Acyclic Graph 2405 nodes 2922 edges

Complete image analysis output Background substraction Normalization Additional Data Transformations