Curatorial Procedures at Mouse Genome Informaticswith an Emphasis on Expression Data

Constance M. SmithThe Jackson Laboratory

Bar Harbor, ME

Mouse Genome Informatics

www.informatics.jax.org

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

Gene is in MGI?

Gene is NOT in MGI

Secondary Triage

Marker Association

New Genes

Indexing

Nomenclature

Primary Triage:

Pick Paper Based On:

ExpressionMapping

HomologyNew Genes

Alleles & PhenotypesSequences

Inbred Strain TumorNomenReview

General Interest

Expert Curation for:

ExpressionMapping

HomologyNew GenesAlleles &

PhenotypesSequences

Inbred Strain Tumor

Master Bibliography

Papers are read and

information entered into the database

using controlled

vocabularies

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 toimages

Image storage allows users to analyze primary data

Allele detail provides description of phenotype using controlled vocabulary

Gene

GeneFunction

Where and When

Assay type

ChromosomalLocation

Mouse Genome Informatics StaffPrincipal 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