Gramene release September, 2003

[Steven Schmidt]

Dear Cereal Researchers:


The Gramene database (http://www.gramene.org) emails its registered users an
announcement each time a new release is made. The announcement includes
information on new or updated data and software.


Sincerely,
Gramene Database
gramene at gramene.org


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Gramene website features:
*************************
-New look for Gramene web site.
-The new navigation bar on the top of the page allows a quick link to the
respective database searches.
-Site map presents a complete guide to Gramene Database. 
http://www.gramene.org/sitemap.html
-Quick search on top of every web page, with options to limit your search.
-Feedback button relocated to the top of every page.
-Quick links to Documentation, Downloads, Submissions, Mailing List Archive, 
Feedback, Contact Us, Copyright Statement at the bottom of every page.
- View CVS repostory on web at http://gorgonzola.cshl.org/viewcvs. For more 
information on accessing CVS for checkouts, please visit, 
http://brie4.cshl.org/open_cvs.html.



Databases:
**********


1.0-Genome browser (updated)
****************************


The Genome Browser module has been updated with the Ensembl 13 release. The
upgrades include, a mapview that displays statistics on the cereal annotations
for each rice chromosomes and allows the user to enter the genome from the
chromosome view, the addition of a base pair view that provides a nucleotide
level display of the rice genome with alignment to the features found in the
browser, and modification of the detail view section.  The data included in this
release includes a chimera display of the rice genome that includes the
pseudomolecule of 1, 4, and 10 and rice BACs from the remaining chromosomes.  A
total of 35 annotation tracks are available by selecting "Features Advanced" in
the detail view.  The new cereal tracks include, PlantGDB clusters, maize and
sorghum genomic sequences, and the barley clusters from the  Barley1 GeneChip.
For more information on alignments please visit:
http://www.gramene.org/documentation/Alignment_docs


2.0-CMap (updated)
******************


Two new sequence maps for rice:


        -Rice-Gramene BAC 2003Gramene BAC-based Bin Map 2003: contains the three
released pseudomolecules (chromosomes 1, 4 and 10). For the other chromosomes,
we have ordered the BAC/PACs based on data released by the IRGSP.


        -BAC Clone-based Tos17 Insertion Map Rice-Tos17 Insertion Map:is the BAC map
upon which Tos17 insertions have been aligned.  This will serve as the
foundation for the mapping of Tos17 mutant phenotypes.


        Please note that no information is yet available on the orientation of the
BAC/PACs for these unassembled chromosomes.  Hence, nucleotide positions on
these chromosomes should be used as an approximation of the location in the
genome and not a defined point of reference.


New physical maps:
        Maize-AGI FPC 2003
        Maize-Curated FPC 2003
        Sorghum-TAMU FPC 2000


New genetic maps:
        Rice-IGCN sativa/eichingeri RFLP
        Rice-Niigata RFLP 2000
        Maize-IBM2 Neighbors 2003
        Sorghum-Klein 2000


QTL maps:
        57 different QTL reference map_sets used in mapping QTLs presented in the first
release of QTL database. (more information in QTL section)



3.0-Protein(updated)
********************


The Gramene protein database includes 20,785 gene products drawn from SwissProt
(392) and SP-TREMBL (20,393). These proteins are annotated using Pfam, Prosite,
TMHMM (for transmembrane domains), TargetP and Predotar (plastid, mitochrondrial
and secretory pathway targeting) and Interpro category. A total of 14,708 gene
products are associated with 902 Gene Ontology terms.


4.0-QTL(new)
************
We are pleased to announce the first release of the Gramene QTL Database. This
includes entries on 3843 curated QTLs for rice and maize mapped on 57 QTL
reference maps. The current version provides core information for QTL, including
published symbol, trait, linkage group, and map position. Users can search QTLs
via trait name, trait symbol, and trait category by using Gramene QTL Search.
The QTL reference maps are provided via CMap section.
Since this is a first release of the QTL database, we advice our users to browse
through the demonstration pages before starting. The demonstration is available
at http://www.gramene.org/qtl/qtl_demo.


5.0-Mutant(updated)
*******************
Rice mutant genes and alleles database now contains 1320 genes characterized by
phenotype. Among them, 424 genes have been fully annotated with phenotypic
description, associations to trait, plant and gene ontologies, map positions,
allele, phenotypic study, germplasm, sequence and gene product, and related
public references. Other genes in the database are currently under curation.
However, we are providing core information such as gene name and symbol,
phenotypic image(s), map position, and cross-reference to Oryzabase. Users can
search for the gene symbol or gene name by using Gramene Mutant Search.


6.0-Ontology(updated)
*********************
        Trait Ontology: Organization of Trait Ontology was revised to present different
Plant traits in higher level categories such as: biochemical trait, fertility or
sterility trait, yield related trait, plant anatomy and morphology related
trait, plant development related trait, quality related trait, stature or vigor
related trait, stress related trait. Includes associations to rice mutants


        Gene Ontology: Updated with GO database, go_200306 release, by Gene Ontology
Consortium. Includes associations to proteins


        Plant ontology: Organized by anatomy and growth stages. Includes associations
to rice mutants.
           -Cereal Plant Anatomy: The controlled vocabulary of cereal plant morphology,
anatomy representing tissue and cell types.
           -Cereal Plant growth stage ontology: The controlled vocabulary of growth and
developmental stages for rice, maize, sorghum, wheat, oat and barley.



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-- 
Steven Schmidt
www.gramene.org
Cold Spring Harbor Laboratory
516-367-8892