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Pig Genome Newsletter #075
P I G G E N O M E U P D A T E
__________________________________________________________________
A Bimonthly Newsletter of the U.S. Pig Genome Coordination Program
************** No. 75 **************
* *
* <angenmap@animalgenome.org> *
* November 1, 2005 *
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1. PAG XIV & NRSP8/NC1004 Meeting will be held January 14-18
2. The Online Mendelian Inheritance in Animals are revamped and upgraded
3. Mouse Genome Informatics announced the new database release
4. Send your success stories to CSREES
5. What is new with USDA grants in Washington, DC
6. First European Conference on Pig Genomics will be held in Lodi, Italy
7. AFFY Pig chips available for limited experimentation
8. NRSP-8 Coordinators talk and plan for the future
9. Upcoming meetings (8 items)
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PAG XIV & NRSP8/NC1004 Meeting will be held January 14-18, 2006 at the Town
and Country Hotel, San Diego, CA. A draft program is already available at
www.intl-pag.org/ and looks to be another good year. Abstracts are due
October 7, 2005. The NRSP8 swine committee meets jointly with NC1004 and
will be jointly chaired by Joe Cassidy and Zhihua Jiang. It will be held on
Saturday January 14, 2006 beginning at 8:00 am in Royal Palm Salon 1 & 2.
The International Swine Genome Sequencing meeting will be held Sunday, 15
at noon-2 pm In Royal Palm Salon 5. General information regarding PAG may
be found at http://www.intl-pag.org/. For those wishing to attend the
weekend session only, you may sign-up for the $250 advance registration,
postmarked or submitted by November 1, 2005. Full registration is $475
submitted via the Scherago International secure web site postmarked or
submitted before that date. Some limited travel support may be available
for NRSP-8 members. If interested please contact Max Rothschild at
mfrothsc@iastate.edu.
o o o o o o o o o o o
The Online Mendelian Inheritance in Animals (OMIA) has been revamped and
upgraded. The main change has been to move the master database to a MySQL
platform at the Australian National Genomic Information Service (ANGIS).
The results are: 1) a new web page (http://omia.angis.org.au) that
dynamically queries the master database; 2) access to abstracts (and
sometimes full papers) for papers with a pubmed ID; 3) far greater
possibilities for reciprocal linking with other web sites and 4) on-line
curation, which will enable input from colleagues with specialist
knowledge; and which, in time, will give OMIA a life beyond that of its
creator, Frank Nicholas. Another important development is that at the
request of NCBI, OMIA has been integrated into NCBI?s Entrez search
interface at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIA. This
has given several new dimensions to OMIA, providing enhancements that are
not available from the ANGIS site. The content of the NCBI version will be
updated with regular dumps from the master database. These developments
have been achieved through the sterling efforts of many people (see
http://omia.angis.org.au/acknowledgements.html.) The new master database is
still in its infancy. Input from interested colleagues to make OMIA
continually better is encouraged. The efforts of Frank Nicholas are greatly
appreciated.
o o o o o o o o o o o
Mouse Genome Informatics (MGI, http://www.informatics.jax.org/) is pleased
to announce the release of Version 3.3 of the database. Version 3.3
integrates the data on mouse models of human disease and human disease
etiology from OMIM with existing data for mouse genes and strains in MGI.
This enhances the exploration of phenotypes, sequence, expression,
orthology, and other related data. You can now use three of the MGI query
forms (Phenotypes and Alleles, Genes and Markers, Mouse Sequence) to search
for existing or potential mouse models of a particular human disease and
all human diseases that a particular mouse (genotype plus strain
background) can be used to model. Version 3.3 also incorporates data on
mouse models sought without success, such as models free from particular
confounding diseases or phenotypic traits. The database now links to Online
Mendelian Inheritance in Man (OMIM) descriptions of human diseases,
syndromes, and conditions. The updated query forms are for Phenotypes and
Alleles is: http://www.informatics.jax.org/searches/allele_form.shtml, for
Genes and Markers:
http://www.informatics.jax.org/searches/marker_form.shtml; for Mouse
Sequence: http://www.informatics.jax.org/searches/sequence_form.shtml and
Human Disease Vocabulary Browser:
http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=omimVocab&subset=A
(kindly provided by David Shaw)
o o o o o o o o o o o
Send your success stories to CSREES. Muquarrab Qureshi, NAGRP Leader, is
revising the CSREES Animal Breeding, Genetics and Genomics webpage,
http://www.csrees.usda.gov/ProgView.cfm?prnum=3D4467 . He requests short
features that highlight the impact of your research on animal agriculture
and wellbeing. Pictures and/or web links, links to key publications or
other stories are welcome. Please indicate if the work was supported by
USDA and/or any federal or industry partnership. Send your material to
mqureshi@csrees.usda.gov. Thanks in advance for your help.
o o o o o o o o o o o
What is new with USDA grants in Washington, DC. Agriculture Appropriations
legislation has been passed by both the U.S. House and Senate, but
differences remain to be resolved in Conference Committee and final
outcomes remain in doubt. CSREES has just issued the FY 2006 National
Research Initiative RFA (competitive grant program). You can access it at
http://www.csrees.usda.gov/funding/rfas/nri_rfa.html . The House approved
almost $215 million for the NRI, whereas the Senate approved $190M. Either
would be an increase over this years $179.55M, but with recent emergencies,
the final outcome could be no increase, or even worse. Please stay tuned
and perhaps expect some changes in the FY2006 NRI. The due date for animal
genetics and genomics is June 15 next year. In general, CSREES wishes to
focus research priorities in the program description, hoping to receive a
more targeted set of applications. Concern has been expressed due to the
low overall NRI success rate (14.7%). As reported earlier, the Animal
Genome Reagent & Tool Development Program is expected to continue. At
CSREES request, Coordinators collected and submitted input regarding the
top Tools & Reagents priorities for their respective species (kindly
provided by Jerry Dodgson)
o o o o o o o o o o o
First European Conference on Pig Genomics organized by COST European
Network for Pig Genomics PigNet will be in Lodi, Italy on February 20-21,
2006. The objective of this conference is to provide a broad overview of
cutting-edge genomics in various areas with a strong emphasis on the pig.
This meeting is organized by the PigNet network aimed at connecting search
groups involved in Pig genomics (www.toulouse.inra.fr/pignet). On-line
registration and poster submission is now open at:
http://www.avenuemedia.it/htdocs/linkCONG/Pignet2006/indice_pignet.htm
Early registration and poster submission deadline November 18th.
o o o o o o o o o o o
AFFY Pig chips available for limited experimentation. In a continuing
effort to help researchers try new platforms and ideas the Pig Genome
Coordinator will make available 6 chips to qualified requests. To qualify
you must be a pig NRSP-8 group and have never used this technology. You
must also acknowledge the receipt of these from the Pig Genome Coordination
program in all publications. To request a set of 6 chips please contact Max
Rothschild at mfrothsc@iastate.edu.
o o o o o o o o o o o
NRSP-8 Coordinators talk and plan for the future. As part of efforts to be
more proactive, Dr. Muquarrab A. Qureshi, National Program Leader for
Animal Genetics in USDA-CSREES, has organized phone conferences between the
coordinators. The purpose of these quarterly discussions will be to help
plan for the future of animal genomics. Issues to be covered include
thoughts on FY 2006 and future NRI RFA, evolving NRSP-8 needs (i.e.,
resources, funding, etc.), coordinator issues and updates, DC updates, PAG
meeting/Business meeting, annual reports and other items. Dr. Qureshi's
leadership is appreciated and if you have ideas you feel that need to be
discussed please contact your species coordinator or Dr. Qureshi to relay
those discussion points.
o o o o o o o o o o o
Upcoming meetings (see:
http://www.animalgenome.org/community/meetings.html)
Genetic Analysis: Model Organisms to Human Biology, January 5-7, 2006,
sponsored by the Genetics Society of America, Town and Country Hotel, San
Diego, CA. Please see www.gsa-modelorganisms.org .
Genome Sequence Variation and the Inherited Basis of Common Disease and
Complex Traits, January 8-13, 2006, Keystone Symposia, Big Sky Resort, Big
Sky, Montana. Please see www.keystonesymposia.org .
Genomics of Closely Related Organisms, January 12-14, 2006, Marriott
University Park Hotel, Tucson, Arizona. Please see
www.genomics.arizona.edu/meeting2006.html
Plant and Animal Genome XIV, joint with the NAGRP annual meetings, Jan. 14-
18, 2006, Town & Country Convention Center, San Diego, CA. Please see
www.intl-pag.org/.
7th Annual Advances in Genome Biology and Technology Conf., Feb. 8-11,
2006, Marco Island Resort & Golf Club, Marco Island, FL. Please see
www.agbt.org
First European Conference on Pig Genomics Lodi, Italy, February 20- 21,
2006. For information please contact pignet2006@toulouse.inra.fr
The 8th World Congress on Genetics Applied to Livestock ProductionBelo
Horizonte, MG, Brazil, August 13- 18, 2006. For information please contact
Fernando E. Madalena at iprociencia@terra.com.br
ISAG 2006, 30th International Conference on Animal Genetics, August 20-25,
2006, Porto Seguro - Brazil. See http://www.cbra.org.br/eventos/XXXisag.do
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Items for Pig Genome Update 76 can be sent to me by no later than December 15
please.
Max Rothschild
U.S. Pig Genome Coordinator
2255 Kildee Hall, Department of Animal Science
Iowa State University
Ames, Iowa 50011
Phone: 515-294-6202, Fax: 515-294-2401
mfrothsc@iastate.edu
cc: Muquarrab Qureshi, CSREES and Caird Rexroad II, ARS
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U.S. PIG GENOME COORDINATION PROJECT
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| Paid for by funds from the NRSP-8 | Web: http://www.animalgenome.org/pig
| USDA/CSREES sponsored Pig Genome | Mail: angenmap@animalgenome.org
| Coordination Program |
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