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

Slides:

Advertisements

Similar presentations

A Comparative mapping resource ONTOLOGY DEVELOPMENT AND INTEGRATION IN GRAMENE Pankaj Jaiswal Cornell University.

Advertisements

Annotation of Gene Function …and how thats useful to you.

MRC Human Genetics Unit 7-Feb-02Richard Baldock 1 The Mouse Gene-Expression Information Resource Richard Baldock MRC Human Genetics.

Implementing Dictionary-Based NER Solutions for Mining Biomedical Literature Karen Dowell, Monica McAndrews-Hill, David Hill, Harold Drabkin, Judith Blake.

Data Integration, Gene Ontology, and the Mouse* Joel Richardson, Ph.D. Mouse Genome Informatics Group The Jackson Laboratory Bar Harbor, Maine *

Mouse Genome Informatics Online Resource Joanne Berghout, PhD Oct 13,

Working in Real Time: Building Ontologies While Annotating the Mouse from Genotype to Phenotype Judith Blake, Ph.D. Mouse Genome Informatics The Jackson.

MouseMine: Mouse Gene Lists (and a whole lot more) Joel Richardson.

Using Ontologies to Annotate Phenotypic Data Janan T. Eppig December Mouse Genome Informatics.

Vlad: A Visual Annotation Display Tool Joel Richardson Mouse Genome Informatics The Jackson Laboratory.

Revising the Cell Ontology Terrence Meehan, Christopher Mungall, Alexander Diehl The Jackson Laboratory Lawrence Berkeley National Laboratory University.

Alignment of Ontologies for Biological Research Judith A. Blake, Ph.D. Bioinformatics and Computational Biology The Jackson Laboratory.

A Study on Variations of HDL Levels in Female vs. Male Mice The Battle of the Sexes: Presented by: Sean Roney Teresa Leslie Courtney Deshayes.

Terry F. Hayamizu Mouse Genome Informatics, The Jackson Laboratory M OUSE A NATOMY O NTOLOGIES AND GXD.

Extending to the GO model OBO open biology ontologies aka - extended go - (ego)

Comprehensive Annotation System for Infectious Disease Data Alexander Diehl University at Buffalo/The Jackson Laboratory IDO Workshop /9/2010.

Mouse Genome Informatics November 2008 Paul Szauter MGI User Support.

Presented by Karen Xu. Introduction Cancer is commonly referred to as the “disease of the genes” Cancer may be favored by genetic predisposition, but.

Ontologies and vocabularies supporting data integration: emphasis on mouse phenotypes and disease model Control C3H/HeJ Homozygous Fasl gld /Fasl gld The.

Integration of PRO and UniProtKB Amherst, NY May 16, 2013 Cathy H. Wu, Ph.D. PRO-PO-GO Meeting.

Computational Biology and Informatics Laboratory Development of an Application Ontology for Beta Cell Genomics Based On the Ontology for Biomedical Investigations.

Managing Big Scientific Data Capturing, Integrating and Presenting Mouse Data at MGI Cynthia Smith Canberra April Mouse Genome.

Gramene Objectives Develop a database and tools to store, visualize and analyze data on genetics, genomics, proteomics, and biochemistry of grass plants.

Gene Expression Databases: Where and When Dave Clements EuReGene and Mouse Atlas projects Medical Research Council Human Genetics.

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

Gene Ontology Overview and Perspective Lung Development Ontology Workshop.

Data Analysis Summary. Elephant in the room General Comments General understanding that informatics is integral in medical sequencing and other –omics.

MMAP: mouse Metabolomics Analysis Platform Preeti Bais 09/09/2014.

Cell Ontology 2.0 Elimination of multiple is_a inheritance through instantiation of relationships to terms in outside ontologies, such as the GO cellular.

Functional Genomics Carol Bult, Ph.D. Course coordinator The Jackson Laboratory Winter/Spring 2012 Keith Hutchison, Ph.D. Course co-coordinator.

Jessica Dantzer Mooney Lab Center for Computational Biology and Bioinformatics Indiana University School of Medicine

1 of 38 Data Mining in Ensembl with BioMart. 2 of 38 Simple Text-based Search Engine.

Ontologies GO Workshop 3-6 August Ontologies  What are ontologies?  Why use ontologies?  Open Biological Ontologies (OBO), National Center for.

DAVID R. SMITH DR. MARY DOLAN DR. JUDITH BLAKE Integrating the Cell Cycle Ontology with the Mouse Genome Database.

Integrating the Cell Cycle Ontology with the Mouse Genome Database David R. Smith Mary Dolan Dr. Judith Blake.

Linking Animal Models and Human Diseases Supported by NIH P41 HG002659, U54 HG004028, & R01 HG Cambridge University & the University of Oregon.

PGA Workshop August 2003 Rat Genome Database an introduction Simon N. Twigger, Ph.D. Bioinformatics Research Center Medical College of Wisconsin, Milwaukee.

Maps & Markers - Noel Yap Proteins - Pankaj Jaiswal Phenotypes Mutants –Junjian Ni QTLs- Literature - all Curation.

DAVID R. SMITH DR. MARY DOLAN DR. JUDITH BLAKE Integrating the Cell Cycle Ontology with the Mouse Genome Database.

Copyright OpenHelix. No use or reproduction without express written consent1.

TRPGR Gramene: A Platform for Comparative Plant Genomics Doreen Ware USDA ARS Cold Spring Harbor Laboratory Pankaj Jaiswal Oregon State University Joshua.

Exploring Rice Phenotypes Using Gramene A Comparative Mapping Resource GRAMENE.

Scope of the Gene Ontology Vocabularies. Compile structured vocabularies describing aspects of molecular biology Describe gene products using vocabulary.

Gene Mapping ROBERT SANTOS ENGLISH 100 ESP NOVEMBER

Cell Ontology Workshop 2010 May 18-19, 2010 Highseas Conference Center The Jackson Laboratory Supported by NHGRI HG Z “an ARRA stimulus grant at.

Copyright OpenHelix. No use or reproduction without express written consent1.

What do we already know ? The rice disease resistance gene Pi-ta Genetically mapped to chromosome 12 Rybka et al. (1997). It has also been sequenced Bryan.

生物資料庫搜尋 ( 第八組 ) 連威森王鼎黃智楹張鈞淵

Linking Animal Models and Human Diseases

Towards a unified MOD resource: An Overview

Pathway Informatics 16th August, 2017

Ontologies, Databases, Knowledgebases: How should they interoperate?

Annotating with GO: an overview

Behavior and Phenotype in GMOD Natural Diversity in GMOD

National Human Genome Research Institute

Revisions to the Disease Ontology in support of

Functional Annotation of the Horse Genome

QTL Database Round Table Discussion:

Browsing the GO at MGI Harold Drabkin, Ph.D. Senior Scientific Curator

TAMU Bovine QTL db and viewer

Mendelian Inheritance

FaceBase Hub Demonstration

Structural Architecture of SNP Effects on Complex Traits

A systems view of genetics in chronic kidney disease

Key CottonGen Features For more information contact:

Important Vocabulary Genetics.

3q29 Microdeletion Syndrome: Clinical and Molecular Characterization of a New Syndrome Lionel Willatt, James Cox, John Barber, Elisabet Dachs Cabanas,

Germplasm Overview Page Trait Descriptor Standard Images

Investigation 2 Part 2 Vocabulary

For more information contact:

Presentation transcript:

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

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

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

Current QTL Display

Current QTL display + +

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)

Mammalian Trait Ontology Mammalian Phenotype Ontology Mammalian Trait Ontology

Mammalian Trait Ontology

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

Current QTL display in MGI

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

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

Mammalian Trait Ontology vs Mammalian Phenotype Ontology

Mammalian Phenotype Ontology