1. QTL Annotation in MGI Susan M Bello, Ira Lu, Cynthia L Smith, Janan T Eppig, and the Mouse Genome Informatics Group

2. Overview of Mouse Genome Informatics (MGI)
Genes & Gene Products
nomenclature
gene characterization
transcripts, proteins, gene products
functional annotation
orthologs & paralogs
Sequences & Maps
sequence representation
C57BL/6J genomic sequence
SNPs and strain variants
adding biological context to computational gene models
Gene Expression
mouse anatomy
time, tissue, level of expression
range of assays & results
emphasis on embryonic stages
Tumor Biology
tumor classifications & descriptions
strain incidence
histopathology images
tumor genetics
Phenotype
mutant allele definitions
QTL
strain characteristics
phenotype vocabularies
disease models (human)
comparative phenotypes

3. QTL Annotation: Present and Future
Current format
Problems with using the Mammalian Phenotype (MP) ontology to annotate QTL
Display of mapping information
Display of variant and parent strain phenotypes
over 3000 QTL markers, over 2200 with annotation

4. Current QTL Display

5. Current QTL display + +

7. Mammalian Trait Ontology
Purpose: annotate QTL and strains
Adapted from the MP Ontology
Absolute traits rather than relative phenotypes
~3700 trait terms compared to ~4800 phenotype terms
example trait - phenotype - disease
auditory threshold or startle reflex (trait) - deaf - Cowchock syndrome (muscle weakness and metal retardation also)

8. Mammalian Trait Ontology
Mammalian Phenotype Ontology
Mammalian Trait Ontology

9. Mammalian Trait Ontology

10. Proposed QTL Display Genome coordinates: 132851306-135646474
(MGI Mouse GBrowse)

11. Current QTL display in MGI

12. MGI Staff PI Janan T. Eppig Judith A. Blake Carol J. Bult
Martin Ringwald
James A. Kadin
Joel E. Richardson GO
Alexander D. Diehl
Harold J. Drabkin
David P.Hill
Dmitry Sitnikov
Software Engineering
Jon S. Beal
Lori E. Corbani
Sharon L. Giannatto
Diane J. Dahmen
Mary Dolan
Richard M. Balderelli
David B. Miers
Matt Vincent
Peter Frost
Michael B. Walker
GXD
Terry E. Hayamizu
Ingeborg J. McCright
Constance M. Smith
Jacqueline H. Finger
Phenotypes
Donna L. Burkart
Anna Anagostopoulos
Ira Lu
Cynthia L. Smith
Susan M. Bello
Megan Updegraff
Howard Dene
Beverly Richards-Smith
Linda L. Washburn
Randal Babiuk
Hiroaki Onda
Monika Tomczuk
Software QA
Mark Airey
Jeffrey W. Campbell
Jill R. Lewis
MTB
Debra M. Krupke
Dale A. Begley
Sequences and Maps
Dirck W. Bradt
Yunxia Zhu
Kenneth Frazer
Deborah J. Reed
Robert Sinclair
T.B.K. Reddy
SysAdmin
Matthew J. Baya
Mike J. McCrossin
Leslie A. Miller
Iry T. Witham
Point out Pis and phenotypes staff
Administrative
Deborah E. Geel
Janice E. Ormsby
User Support
David R. Shaw
Paul Szauter
Susan McClatchy
Genes/Gene Products
Nancy E. Butler
Lois J. Maltais
Monica McAndrews-Hill
Li Ni
Funding
NHGRI (HG000330, HG002273) NIH/NICHD (HD033745)
NCI (CA089713) 2

13. disease
phenotype 1
phenotype 2
trait A
trait B
trait C
trait D

14. Mammalian Trait Ontology vs Mammalian Phenotype Ontology

15. Mammalian Phenotype Ontology