Release 15.0 of Gramene Database

Thu Oct 14 13:35:54 EDT 2004

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,
The Gramene Database

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Gramene website features:
*********************
-Added Frequently Asked Question (FAQ) web pages
(http://www.gramene.org/documentation/faq/index.html) to answer users’
General, Data Curation, BLAST, CMap, Genome Browser, Literature, Mutant,
Ontology, Protein, and QTL questions.

-Added Gramene Glossary web page
(http://www.gramene.org/documentation/glossary/index.html).  It contains a
list of acronyms and abbreviations used in Gramene that have been defined
for users. In the future, this Glossary will grow to include definitions
of the biological and module-specific terms used in Gramene.

Links to the FAQ and Glossary web pages can be found on the Site Map
(http://www.gramene.org/sitemap.html) under “Documents”, or from the “How
to Use Gramene” page (http://www.gramene.org/workshop_tutorial.html), or
also from the navigation bar links present at the bottom of every page on
the Gramene web site.

Databases:
*********

QTL (updated)
************

The Gramene QTL database includes a total of 7,738 QTL identified for
numerous agronomic traits in rice, maize, barley, oat, pearl millet,
foxtail millet and wild rice. In this release, Pearl Millet QTL and
Foxtail millet QTL were added.

A new "QTL Power Search" interface
(http://www.gramene.org/db/qtl/qtl_display?power_search=1) to help users
perform a comprehensive query of the database was also added.  This allows
selection of multiple traits, species, and linkage groups to include or
exclude in queries.

Genome Browser (updated)
**********************
6 New tracks have been added:
Millet_est, Rice_Rufipogon_BACend, Rice_Nivara_BACend,
Ryegrass Assembly, Ryegrass Sequence, Sorghum_CDNA

9 tracks have been remapped:
Barley_est, Maize_est, Rice_Brachyantha_BACend, Rice_CDS, Rice_est,
Rice_tug, Sorghum_cluster_Pratt, Swissprot_Trembl_Proteins, Wheat_est.

BLAST (updated)
**************
Gramene now uses Ensembl version 24 blastview, which shows hit locations
on the genome graphically and matching genome sequences in context.  It
allows for simultaneous searches with multiple query sequences against
multiple target species.  You can use the interface by navigating between
these four pages: SETUP, CONFIG, RESULTS, and DISPLAY. You can navigate
both forward and backwards between these pages. A “Summary” column on the
right shows the states of the current query.  For help on BLAST please
click the "Online Help" button on the BLAST page. We currently support
WU-BLAST 2.0.

6 Added databases:
Millet_est, Rice_Rufipogon_BACend, Rice_Nivara_BACend,
Ryegrass Assembly, Ryegrass Sequence, Sorghum_CDNA

CMap (updated)
*************

In this release, we present 10 new genetic and QTL maps from pearl and
foxtail millet.

Genetic Maps:
Pearl millet-JIC 81B/ICMP 2004
Pearl millet-JIC LGD1/ICMP 2004
Pearl millet-JIC ICMB/863B 2004
Pearl millet-JIC PT732B/P1449 2004

QTL Maps:
Foxtail millet-UM B100/A10 QTL 2004
Pearl millet-FLES Thi/Wil QTL 2002
Pearl millet-FLES Sou/Mol QTL 2000
Pearl millet-IGER H77/BRLT QTL 2002
Pearl millet-GUA LGD1/ICMP F2 RFLP QTL 2004
Pearl millet-IGER ICMB/863B QTL 2004

Updated Maps:
Maize-Curated AGI FPC June 2004
(replaces Maize-Curated AGI FPC Jan23 2004)
Maize-AGI FPC June 2004
(replaces Maize-AGI FPC JAN23 2004)

Protein (updated)
**************

The Gramene protein database includes new and updated information on
43,763 gene products drawn from SwissProt (420) and SP-TREMBL (43,343). 
These proteins are annotated using Pfam, Prosite, TMHMM (for transmembrane
domains), TargetP and Predotar (plastid, mitochrondrial and secretory
pathway targeting) and Interpro categories. A total of 31,187 gene
products are associated with 1,186 Gene Ontology terms.

Mutant (updated)
**************

The Gramene Mutant genes database contains 1,320 genes from rice
characterized by phenotype.  Among them, 424 genes have been fully
annotated with phenotypic descriptions, associations to trait, plant and
gene ontologies, map positions, alleles, phenotypic studies, germplasms,
sequences and gene products, and related public references. Other genes in
the database are currently under curation.

In this release, the anatomy location terms in the associated feature
section have been replaced by plant structure (anatomy) ontology developed
by the Plant Ontology Consortium (POC). In our previous release these
terms were described by using cereal plant anatomy ontology developed by
Gramene. For more information, please see the following section on
Ontology.

Ontology (updated)
****************

For this build, Gramene is pleased to announce three new features:

#1 The first release of the “plant structure” (anatomy) ontology developed
by the Plant Ontology Consortium (www.plantontology.org). You are invited
to browse and evaluate the new ontology at
http://www.gramene.org/db/ontology/search_term?id=PO:0009011. The plant
Structure Ontology replaces the earlier plant anatomy ontology developed
by the Gramene curators.  The plant structure (anatomy) ontology uses the
Plant Ontology Consortium (POC) data using the prefix PO with the term
accession numbers instead of the previous GRO prefix.

#2 The first public version of the implementation state of Environment
Ontology (EO) is released for browsing and feedback. It is available at
http://www.gramene.org/plant_ontology/index.html#eo. The EO is a
controlled vocabulary to describe different types of supplemental
environments that have been reported in the experimental profiles of gene
expression and phenotype (mutant and QTL) studies on cereal plants. The
option to search the associations to genes and phenotypes will be
available soon.

#3 The ontology search interface now allows the optional selection of each
individual type of ontology. In any single search the selection can be
made for more than one type of ontology.

Gene Ontology:
Updated: Total number of terms = 17,601.  A total of 31,187 rice gene
products are associated with 1,186 Gene Ontology terms.

Plant Ontology:
New:  Plant structure (anatomy) ontology developed by POC
(www.plantontology.org) replaces cereal plant anatomy.

Updated:
Total number of terms = 638.   Includes associations to rice mutants

Gramene Plant Growth Stage Ontology:
Total number of terms = 229
The wheat, barley and oat growth stages have a single parent e.g.
http://www.gramene.org/db/ontology/search_term?id=GRO:0007156

Gramene Environment Ontology:
New: Total number of terms = 478

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Molly Fogleman
Gramene Outreach Coordinator
409 Bradfield Hall
Cornell University
Ithaca, NY 14853
(607) 255-9951