From jreecy@iastate.edu  Mon Dec 11 15:05:53 2006
Date: Mon, 11 Dec 2006 15:12:49 -0600
From: James M Reecy <jreecy@iastate.edu>
Subject: NRSP-8 Bioinformatics update #4
Postmaster: Processed by the Listmaster
To: Multiple Recipients of <angenmap@animalgenome.org>

           NRSP-8 Bioinformatics / Database Update 

                    ---===  No. 4  ===--- 

                      December 11, 2006 
---------------------------------------------------------------------- 
 COMMUNITY UPDATES
  1. Improvement to the QTL database has continued
  2. Development of an Animal Trait Ontology
  3. The NAGRP blast server is continuously being updated
  4. Congratulations to two USDA grands winers
  5. New bioinformatics project suggestions

 BIOINFORMATICS RELATED WORKSHOPS PLANNED FOR UPCOMING PAG MEETING
  6. Bovine Genome Annotation workshop
  7. QTL database workshop

  8. Upcoming meetings
---------------------------------------------------------------------- 

COMMUNITY UPDATES

o 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. 

o 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&oldidB85 
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. 

o 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. 

o 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. 

o 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.  Jreecy@iastate.edu 

BIOINFORMATICS RELATED WORKSHOPS PLANNED FOR UPCOMING PAG MEETING:

o 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.

o 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.

UPCOMING BIOINFORMATICS MEETINGS / WORKSHOPS / SHORT COURSES:

 January 7 - 12, 2007 - International Long Oligonucleotide Microarray
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
Location: Ventura Beach Marriott, Ventura,CA Contacts: Patrick C. Phillips,
Email: pphil@uoregon.edu

 March 12 - 16, 2007 Survival Analysis applied to Animal Breeding 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 - 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 Ag. Research
Location: Purdue University, West Lafayette, Indiana Contacts: William M
Muir, Email: bmuir@purdue.edu

 October 23 - 25, 2007 - International Symposium on Animal Genomics
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  
                  Jreecy@iastate.edu  
                  http://www.animalgenome.org