Plant Biology 2011 Outreach Booth

Plant Biology 2011

Visit a collection of Plant Genomics databases and projects with resources for sequenced genomes, ontology development, genetic mapping, functional annotation of genes, mutants and phenotypes, genetic diversity and bioinformatics tools. Representatives from the projects will be present to demonstrate tools for cutting-edge genomics and genetics research and to answer questions.

You can find us at Booth #415

Projects Represented at the Booth:

'Schedule of Projects reps attendance at the booth: Media:ASPB_booth_schedule_2011_v2-2.pdf

Plant Ontology Consortium

See our web page for more information: http://www.plantontology.org

The main objective of the Plant Ontology Consortium (POC) is to develop, curate and share controlled vocabularies (ontologies) that describe plant structures and growth and developmental stages, providing a semantic framework for meaningful cross-species queries across databases. The Plant Ontology (PO) has been developed and maintained with the primary goal to facilitate and accommodate functional annotation efforts in plant databases and by the plant research community at large. As a part of the POC project, participating databases such as TAIR, NASC, Gramene and MaizeGDB have been using PO to describe expression patterns of genes and phenotypes of mutants and natural variants.

Come see Poster # P21013: Expanding the Plant Ontology: linking plant anatomy and development to genomics across plant taxa

Plan to attend the Gramene and Plant Ontology Gene Annotation Workshop Monday, Aug 8th, 7:30pm – 10:30pm (pre-registration required)

For more information please see: Gramene/PO workshop

For more information please contact: PO Feedback

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TAIR:

http://www.arabidopsis.org/

The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available from TAIR includes the complete genome sequence along with information concerning gene structures, gene product functions, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, useful tools, and members of the Arabidopsis research community. Gene product function data is updated every two weeks from the latest published research literature and community data submissions. Gene structures are updated 1-2 times per year using computational and manual methods as well as community submissions of new and updated genes. TAIR also provides extensive links from our data pages to other Arabidopsis resources.

• A joint workshop with the PMN and the SGN will take place on Sunday, August 7th at 7:00 PM in Auditorium 1

• Information on AraCyc, the plant metabolic pathway database connected to TAIR, will be presented in the same workshop

• Researchers are encouraged to bring their published data to the workshop to learn how to directly enter their exciting findings into all three of these public resources

Come see the TAIR poster: Abs # P05022: An Equation For A Vibrant Database: Curators + Journals + Community = Success

For more information please contact: TAIR

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Plant Metabolic Network

See our web page for more information: Plant Metabolic Network

The Plant Metabolic Network (PMN) is a collaborative project among databases and biochemists with a common goal to build a broad network of plant metabolic pathway databases. A central feature of the PMN is PlantCyc, a comprehensive plant biochemical pathway database, containing curated information from the literature and computational analyses about the genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism.

• A joint workshop with the TAIR and the SGN will take place on Sunday, August 7th at 7:00 PM in Auditorium 1

• Researchers are encouraged to bring their published data to the workshop to learn how to directly enter their exciting findings into all three of these public resources

• Please come visit our Poster # P02029 entitled ‘The Plant Metabolic Network: PlantCyc, AraCyc, and more metabolic pathway databases for plant research'

For more information please contact: PMN Feedback

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Gramene

See our web page for more information: http://www.gramene.org

The Gramene database is a comparative plant genomics platform. The database allows researchers to carryout online data analysis, hypothetical modeling or confirmation of lab based findings using both forward and reverse genetics approaches to find genes, proteins, phenotypes (mutants and QTLs), function(s), gene-gene interaction(s), metabolic pathways and polymorphisms in a genomic region of interest. It also allows researchers to make comparisons across genetic maps, genomes, genes and gene families and provides a mechanism to find candidate genes associated with phenotype and/or functional characteristics by way of whole genome alignments and synteny views.

Gramene Poster links:

P21021: Metabolic and Regulatory Networks for Cereals

P15050: Gramene: A Resource For Comparative Plant Genomics

Plan to attend the Gramene and Plant Ontology Gene Annotation Workshop Monday, Aug 8th, 7:30pm – 10:30pm (pre-registration required)

For more information please see: Gramene/PO workshop

For more information please contact: Gramene Feedback

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Solanaceae Genomics Network

See our web page for more information:http://solgenomics.net/

The SOL Genomics Network is a Clade Oriented Database (COD) containing genomic, genetic, phenotypic and taxonomic information for species in the Euasterid clade, including the families Solanaceae (e.g. tomato, potato, eggplant, pepper, petunia) and Rubiaceae (coffee). Genomic information is presented in a comparative format and tied to other important plant model species such as Arabidopsis. SGN is also one of the bioinformatics centers involved in tomato genome sequencing.

One of the major efforts at SGN is linking Solanaceae phenotype information with the underlying genes, and subsequently the genome. As part of this goal, SGN puts the control over the information in the hands of community experts. As a result, SGN annotations are more up-to-date, and richer with detailed descriptions and gene-to-phenotype cross links, than would otherwise be possible without a large curatorial staff.

• A joint workshop with the PMN and TAIR will take place on Sunday, August 7th at 7:00 PM in Auditorium 1

For more information please contact: SGN Contact

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Maize Genetics and Genomics Database

http://www.maizegdb.org/

MaizeGDB is a community database designed to disseminate biological information on the important crop plant, Zea mays ssp. mays to a user community that is as diverse as maize itself.

A variety of datatypes are served through MaizeGDB including genetic, genomic, DNA sequence, gene product, functional characterization, and literature resources.

Accordingly, MaizeGDB is serving as the long-term home of the recently completed maize genome sequence through the MaizeGDB Genome Browser.

In addition, MaizeGDB provides community support services including: person/organization contact information, coordination of annual meetings, conducting elections and surveys, and dissemination of the annual Maize Newsletter.

Challenges to be met in the immediate future include: development of tools and capacities to handle large datasets from Next Generation DNA sequencing, expansion of mutant and phenotype datasets, expansion of structural and genetic maps, and providing access to gene models developed by gene structure prediction groups.

For more information please contact: MaizeGDB

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The Bio-Array Resource for Plant Functional Genomics

http://www.bar.utoronto.ca/

The Bio-Array Resource at the University of Toronto is a collection of web-based tools for exploring, visualizing and mining large-scale data sets, primarily from Arabidopsis thaliana but also from several other plant species.

These tools include:

eFP Browser (electronic Fluorescent Pictograph Browser) for painting gene expression and other information onto diagrammatic representations of the particular experimental series from which the data were generated. An Arabidopsis, poplar, Medicago truncatula, rice, barley,soybean, maize and cell eFP Browsers are available.

Expression Angler for identifying co-expressed, anti-correlated, or condition/tissue-specific genes using the "custom bait feature" in 5 of the gene expression data sets from the AtGenExpress Consortium, from our in-house database or from NASCArrays, or several other data sets.

Expression Browser for performing electronic northerns.

Arabidopsis Interactions Viewer for querying a database of almost 80,000 predicted and 22,150 documented protein-protein interactions in Arabidopsis.

Promomer for identifying over-represented n-mer words in the promoter of a gene of interest, or in promoters of co-expressed genes.

ePlant: - A suite of interactive web-based tools that enables users to explore Arabidopsis data from the kilometre to nanometre scale, including natural variation data, organ and cell-type-specific gene expression patterns, subcellular localization, protein-protein interactions, and protein tertiary structures predicted for ~70% of the proteome.

Next-Gen Mapping: - allows for the rapid localization of recessive EMS induced mutations within an F2 mapping population that has been pooled and sequenced en masse using a next-generation sequencing platform.

For more information please contact: Nick Provart (nicholas.provart@utoronto.ca)

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Legume Information System

Visit our web site for more information http://www.comparative-legumes.org/

Steven Cannon

The mission of the Legume Information System (LIS) is to facilitate discoveries and crop improvement in the legumes. LIS stores datasets from numerous legume species, and uses the reference species Glycine max, Lotus japonicus, and Medicago truncatula as a basis for comparisons between diverse legume species.

LIS maintains genome browsers for the model legumes Lotus japonicus , Medicago truncatula and soybean (in cooperation with SoyBase). LIS also features genetic maps.

The LIS multi-sequence, multi-target search tool, Seqqle, serves as a portal to a variety of genomic resources, including genome browsers, the JCVI Medicago truncatula Project, the Medicago truncatula HapMap Project, Kazusa’s Lotus japonicus site, Uniprot and the Medicago truncatula Gene Expression Atlas at the Noble Foundation. Also, coming soon are a multi-genome comparative viewer and search tool, and resources for searching and navigating legume gene families.

Please visit our Poster #P21012, titled: ‘The Legume Information System 2011'

For more information please contact: steven.cannon@ars.usda.gov or lis_feedback@ncgr.org

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SoyBase

See our web page for more information: http://soybase.org/

SoyBase, the USDA-ARS soybean database, is a central location for genetics, genomics and related data. The main SoyBase page provides access to the SoyBase Toolbox where simple searches can be done or a jump can be done directly to a specific genetic or sequence map. A comprehensive navigation toolbar provides access to the all parts of the Soybean Breeder’s Toolbox (SBT), the user interface to the data in SoyBase, and to a number of data mining and analysis tools.

SoyBase is organized around two related data types: the genetic and physical maps and the whole genome sequence. Genetic and physical map displays allow side-by-side presentations of multiple maps for comparing homoeologous regions of the genome. Annotation tracks for the JGI “Williams 82” genomic sequence include sequenced genetic markers, soybean BACs, repetitive sequences, EST-based unigene sets, the JGI automated gene calls and several expression data sets. Features on the genetic, physical and sequence maps (eg. markers, QTL, BACs and FPC contigs) are linked to additional detailed textual data in SoyBase, and also provide connections between the genetic maps and the whole genome sequence. Controlled vocabularies for soybean growth, development and phenotypic traits are presented and have been integrated with the Plant Ontology Consortium and Plant Trait Ontologies. Soybean ontologies are linked as appropriate to genes and QTL in SoyBase, thus allowing searching by trait or developmental stage as well as by gene or QTL name.

There won't be a SoyBase poster at the meeting but here is a link to recent one: SoyBase Poster

For more information please contact: David Grant (not present at the meeting)

David Grant: david.grant@ars.usda.gov

USDA-ARS, G304 Agronomy Hall

Iowa State University

Ames, IA 50011 USA

(515) 294 1205