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

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Curatorial Procedures at Mouse Genome
Informaticswith an Emphasis on Expression Data
Constance M. SmithThe Jackson LaboratoryBar
Harbor, ME
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Mouse Genome Informatics
Mouse Genome Database Gene Expression
Database Mouse Genome Sequencing Project Mouse
Tumor Biology Database Gene Ontology Consortium
www.informatics.jax.org
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Gene detail page summarizes information in MGI
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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

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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

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Literature Curation at MGI
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As of 10/23/03 32,257 records 8,904
references 5,590 genes Up to date Complete
from early 1990s to the present
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As of 10/23/03 118,576 results 10,329 assays
2,913 genes
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Data entered using customized interface
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The Anatomical Dictionaryessential to integration
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Image storage allows users to analyze primary data
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Allele detail provides description of phenotype
using controlled vocabulary
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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
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Anatomical Dictionary for the adult mouse
multiple hierarchies physiological
systems space / histology sampling
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• Directed Acyclic Graph
• 2405 nodes
• 2922 edges

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Complete image analysis output
Background substraction
Normalization
Additional Data Transformations