Plant Biology 2011 Outreach Booth

Plant Biology 2011, Minneapolis, Minn

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.

This page is currently under construction- please check back for more information about the groups represented at the booth this year :-)

Projects Represented at the Booth:

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 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 7:30 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

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Plant Metabolic Network

need logo

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 TAIR and the SGN will take place on Sunday, August 7th at 7:30 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'

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Gramene

http://www.gramene.org/plant_ontology/

The Gramene database (www.gramene.org) 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 contact: ???

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Solanaceae Genomics Network

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.

Insert SGN workshop/ Poster links:

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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.

Insert MaizeGDB workshop/ Poster links:

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Other groups....

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