NRSP-8 Bioinformatics/Database Update # 4
December 10, 2006 |
COMMUNITY UPDATES
Improvement to the QTL database has continued. QTL data for
cattle, swine and chickens are now available in the database. A new
feature recently added to the cattle QTL display tools is that the
underlining markers for a QTL can be linked to either NCBI MapViewer
or Ensembl Bovine Map (pre) tools for map details, where the QTL
location can be tracked to the newly available cattle genome
sequences by location. (http://www.animalgenome.org/QTLdb/ ) This
feature will be available for chicken and pigs as well when data
becomes available.
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To facilitate comparison of QTL data, we are in the process of
developing an Animal Trait Ontology.
http://www.animalgenome.org/bioinfo/projects/ATO/ . The initial goal
of the project is to develop this ontology so that all curated QTL
are linked to at least one ontology term. Recently, we attended the
PATO meeting hosted by the National Center for Biomedical Ontology at
Stanford University
http://www.bioontology.org/wiki/index.php?title=PATO:Main_Page&oldid=4285.
This workshop had a number of presentations on current phenotype
ontology development in different organisms (Fly, zebrafish, rat,
mouse, worm, human). Extensive discussions ensued on what tools were
available for ontology development, what is needed, what can be done
to link organism ontologies together, pre- vs. post-composition of
phenotypes, natural language processing.
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The NAGRP blast server (http://www.animalgenome.org/blast/ ) is
continuously being updated. The most recent addition to the blast
sequence database is the cattle and chicken genome sequences
(annotated by chromosomes). Please let us know if you need some
other datasets to be available for blast.
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Congratulations to Dr. Chris Elsik and her collaborators on
obtaining funding from USDA-NRI for development of the bovine genome
database http://racerx00.tamu.edu/cgi-bin/gbrowse/bovine2 . In
addition, congratulations to Dr. Shane Burgess and his collaborators
on receiving USDA-NRI funding for AgBase
http://www.agbase.msstate.edu/. I would encourage labs to contact
Drs. Elsik and Burgess for additional details to see how your ongoing
efforts may interact with their projects.
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New projects: As always if you have suggestions about what needs
to be developed/improved or how we can help please do not hesitate to
contact us. Jre...@iastate.edu
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Bovine Genome Annotation Workshop planned at PAG in San Diego.
On Monday January 15 at 1PM, in conjunction with Dr. Chris Elsik,
Texas A&M University, we will be hosting a bovine genome annotation
workshop. Presentation will be given outlining the annotation phase
of the bovine genome sequencing project, how to use available tools
to annotate bovine genes, how to fix misassembled portion of the
genome. Additional information will be sent as soon as the meeting
schedule is set. If you know anyone who wishes to participate in
annotation of the bovine genome, please help spread the word.
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QTL database Workshop planned at PAG in San Diego.
On Tuesday January 16th at 1PM, we will be hosting a workshop.
involving databases actively curating QTL data from rat, mouse,
chicken, cattle, and swine. The goals of the workshop are 1) Define
the minimal amount of information needed for QTL publication. Can we
develop MIAME guidelines for QTL publication?; 2) Integration of
phenotype ontologies; and 3) Exchange of curated QTL information. At
3PM, we would like to invite all users of QTL databases to come and
discuss with us what they would like QTL databases to be able to do.
This is your chance to help set priorities for future development of
QTL databases.
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UPCOMING BIOINFORMATICS MEETINGS / WORKSHOPS / SHORT COURSES:
-
January 7 - 12, 2007 - 7th International Long Oligonucleotide
Microarray Workshop
Location: University of Arizona, Tucson, AZ
Lecturer D.A. Henderson, D.W. Galbraith
Contacts: David Galbraith, Email: galbraith@arizona.edu
- January 13 - 17, 2007 - Plant and Animal Genome XV (PAG-XV)
Location: Town and Country Convention Center, San Diego, CA
Contacts: Sherago, Sherago International, Email: pag@scherago.com
- February 18 - 23, 2007 Gordon Conference on Quantitative Genetics and
Genomics
Location: Ventura Beach Marriott, Ventura,CA
Contacts: Patrick C. Phillips, Email: pphil@uoregon.edu
- March 12 - 16, 2007 Survival Analysis applied to Animal Breeding and
Epidemiology
Location: Christian-Albrechts-University in Kiel, Germany
Lecturer Vincent P. Ducrocq
Contacts: Georg Thaller, Email: gthaller@tierzucht.uni-kiel.de
- March 21 - 23, 2007 - Storage and Annotation of Reaction Kinetics
Data
Location: Heidelberg, Germany
Contacts: Ulrike Wittig, Email: Ulrike.Wittig@eml-r.villa-bosch.de
- July 19 - 25, 2007 Intelligent Systems for Molecular Biology (ISMB)
Location: Austria Center, Vienna, Austria
Contacts: Steven Leard, Email: steven@iscb.org
- August 18 - 24, 2007 - 3rd International Conference on Quantitative
Genetics
Location: Zheijiang University, Hangzhou, China
Contacts: Jun Zhu, Email: jzhu@zju.edu.cn
- September 10 - 12, 2007 - Convergence of Genomics and the Land Grant
Mission: Emerging Trends in the Application of Genomics in
Agricultural Research
Location: Purdue University, West Lafayette, Indiana
Contacts: William M Muir, Email: bmuir@purdue.edu
- October 23 - 25, 2007 - International Symposium on Animal Genomics
for Animal Health
Location: OIE Headquarters, Paris, France
Contacts: Cyril Gay, Email: cyril.gay@ars.usda.gov
James Reecy
U.S. Database/Bioinformatics Coordinator
2255 Kildee Hall
Department of Animal Science
Iowa State University
Ames, Iowa 50011-3150
Phone: 515-294-9269
Fax: 515-294-2401
Jre...@iastate.edu
http://www.animalgenome.org
© NAGRP Bioinformatics Coordination Program