ASPB 2017 Booth
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 indicated below will be present to demonstrate tools for cutting-edge genomics and genetics research and to answer questions.
You can find us at Booth #215
- 1 Bioinformatics Mini-symposium
- 2 Plant Genome Resources Outreach Booth
- 2.1 Projects with a representative on site
- 2.2 Projects without a Representative On Site (Brochures available!)
- 2.3 Acknowledgements
Plan on attending the ASPB Bioinformatics Workshop, a mini-symposium on Monday, June 26, 11:30 AM – 1:00 PM.
This workshop is intended for researchers at all levels but especially those relatively new to Plant Biology who would like to learn more about the tools and resources available on the web. This is a show-and-tell workshop where each speaker will give a short 6-min overview of the organization, data content and navigation of their resource.
- 11:30-11:32 am --- Introduction
- 11:32-11:40 am --- Araport - Agnes Chan, J. Craig Venter Institute
- 11:40-11:48 am --- Gramene - Marcela Karey Tello-Ruiz, Cold Spring Harbor Laboratory
- 11:48-11:56 am --- BAR - Asher Pasha, University of Toronto
- 11:56-12:04 pm --- TAIR - Leonore Reiser, Phoenix Bioinformatics
- 12:04-12:12 pm --- AtRTD Splicing - Cristiane Calixto, James Hutton Institute
- 12:12-12:20 pm --- Planteome - Laurel Cooper, Oregon State University
- 12:20-12:28 pm --- SGN - Hartmut Foerster, Boyce Thompson Institute
- 12:28-12:36 pm --- PMN - Pascal Schlapfer, Carnegie Science
- 12:36-12:44 pm --- KBase - Vivek Kumar, Cold Spring Harbor Laboratory
- 12:44-12:52 pm --- LegFed - Sam Hokin, National Center for Genome Resources
- 12:52- 1:00 pm --- NRSP10 - Dorrie Main, Washington State University
Plant Genome Resources Outreach Booth
Projects with a representative on site
See Gramene's web page for more information: http://www.gramene.org
Gramene is a curated resource for comparative functional genomics in crops and model plant species currently hosting 44 complete reference genomes. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. Gene evolutionary histories are provided in phylogenetic gene trees using a method that infers orthologous relationships and complements whole genome alignments. Variation data is available for 11 species, including Arabidopsis, rice, and maize, and enriched with variant effect prediction. Gramene hosts metabolic pathways databases developed in house or by our collaborators in the BioCyc platform, which facilitates uploading, visualization and analysis. Recently, we began annotating metabolic pathways using the Reactome model, and have released a beta version of the Plant Reactome, a platform for the comparative analysis of plant metabolic and regulatory networks, featuring at present over 240 curated rice pathways and orthologous pathway projections to 66 plant species. We also host many genetic and QTL maps contributed by the broad research community. Gramene is supported by an NSF grant (IOS-1127112), and works closely with EBI-EMBL, OICR, and ASPB.
An overview of the Gramene comparative genomics database as well as latest developments and future plans will be presented by Marcela Karey Tello-Ruiz during the Bioinformatics Minisymposium on Monday, June 26th at 11:30am.
Gramene talks & posters:
NNN – Gramene: Unifying Comparative Genomics and Pathway Resources for Plant Communities. Presented by Marcela Karey Tello-Ruiz
NNN – Comparative genomics reveals prevalence of coupled R-gene disease resistance systems in 11 species of the Oryzeae tribe. Presented by Joshua Stein
NNN – Presented by Yinping Jiao
Gramene representatives will be available to meet with users and answer questions at booth #205 throughout the meeting.
For more information please contact: Gramene Feedback
Funding: Our participation at this outreach booth is being made possible thanks to the funding support of NSF award #1127112 to "Gramene - Exploring Function through Comparative Genomics and Network Analysis".
Phoenix / TAIR
See Phoenix's web page for more information: 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 weekly from the latest published research literature and community data submissions. Gene structures are updated every 2 years 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.
For more information please contact: email@example.com
Araport (https://www.araport.org) aims to provide Arabidopsis and plant scientists direct access to a new generation web-based data platform. In a nutshell, users can browse and analyze a wide array of data through Araport, and can also publish their own modules for sharing data with the community. The platform collectively host a wide array of information including the latest gene structures and functional annotation Araport11, gene expression, co-expression, orthologs, interactions, pathways, publications, seed stocks, and phenotypes.
- ThaleMine A data warehouse for browsing gene reports, running gene list enrichment analysis, exporting data tables, and saving or sharing work.
- JBrowse A genome browse hosting about 100 data tracks. Users can also upload and view their own data for side-by-side comparison.
- Science Apps A growing collection of data or analysis modules that will serve as building blocks for creating discovery workflows.
- Araport11 Comprehensive updates to Col-0 genome annotation completed and submitted to NCBI.
Araport is funded by the National Science Foundation (#DBI-1262414) and the Biotechnology and Biological Sciences Research Council (BB/L027151/1).
For questions and comments, please contact firstname.lastname@example.org.
See poster: 300-160
The Bio-Analytic Resource for Plant Biology
See BAR's web page for more information: http://www.bar.utoronto.ca
The Bio-Analytic 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. eFP Browsers are available for Arabidopsis, poplar, Medicago truncatula, rice, barley, soybean, maize, potato and cell.
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 28,566 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.
Funding: The BAR is funded in part by Centre for the Analysis of Genome Evolution and Function, grants from the Canada Foundation for Innovation to NJP, and from Genome Canada to the Arabidopsis Research Group at the Department of Cell and Systems Biology, University of Toronto.
For more information please contact: Nick Provart (email@example.com)
See the Planteome Project home page for more information: http://www.planteome.org
The Planteome Project (www.planteome.org) features a suite of reference ontologies for plants, associated with a growing corpus of genomics data in a centralized online plant informatics portal. The species-neutral references, the Plant Ontology, Plant Trait Ontology, and Plant Environment Ontology, (all developed by the project), along with those developed by collaborating groups, (the Gene Ontology, Phenotype and Trait Ontology, and others), are mapped to species-specific, controlled vocabularies for crop plant traits and phenotypes. Data annotations to ontology terms link phenotypes and germplasm to genomics resources, and provide semantic integration of widely diverse datasets with the goal of plant improvement. Analysis and annotation tools are being developed to facilitate studies of plant traits, phenotypes, diseases, gene function and expression, and genetic diversity data across a wide range of plant species. The project database and the online resources provide researchers tools to search and browse the ontologies, and remote access is possible through APIs, for semantic integration into annotation tools and data repositories, providing resources for plant biology, breeding, genomics and genetics. The project is supported by the National Science Foundation award IOS #1340112.
Come see Poster #300-173: The Planteome Project: Reference Ontologies and Tools for Plant Biology
For more information please contact: Planteome Feedback
See KBase's web page for more information: http://kbase.us
The DOE Systems Biology Knowledgebase (KBase) is a collaborative effort designed to accelerate our understanding of microbes, microbial communities, and plants. It will be a community-driven, extensible and scalable open-source software framework and application system. KBase will offer free and open access to data, models and simulations, enabling scientists and researchers to build new knowledge and share their findings.
Projects without a Representative On Site (Brochures available!)
SoyBase, the USDA-ARS soybean genetics and genomics database, provides a comprehensive collection of data, analysis tools and links to external resources of interest to soybean researchers. SoyBase is an actively curated database, with new data regularly being incorporated.The data in SoyBase are provided through intuitive interfaces, and are linked together wherever possible to allow easy identification and browsing of related subjects. The SoyBase home page (http://soybase.org) contains the SoyBase Toolbox, which provides quick access to a search of SoyBase, access to the data download page, a genome sequence BLAST tool, direct links to the genetic and sequence maps, and quick access to the SoyCyc metabolic pathways database. Searching at SoyBase uses an underlying trait-based approach to return all information that is related to the search term. An extensive navigation menu and site description provides facile access to all sections of SoyBase. Numerous data types are available including genetic maps, the soybean reference genome sequence with annotation tracks covering genetic markers, genome organization, gene annotation and expression, and gene knockout mutants. SoyBase includes an extensive RNA-Seq gene atlas and innovative tools for identifying fast neutron-induced mutants affecting genes or which affect traits of interest. Several “omics” tools, for example a GO Term Enrichment tool, enable sophisticated queries and reports on lists of genes.
SoyBase can be publicly accessed at http://soybase.org
Legume Information System
See the Legume Information System page (http://legumeinfo.org).
The mission of the Legume Information System (LIS) is to facilitate basic research and its application to crop improvement in the legumes, which are critical components of global food and agriculture systems. LIS in 2017 includes:
- Genome browsers for a dozen legume species (currently): common bean, pigeonpea, chickpea, Medicago truncatula, Lotus japonicus, narrow-leafed lupin, mungbean, adzuki bean, red clover, soybean (via SoyBase.org) and wild peanut species Arachis duranensis and Arachis ipaensis (via PeanutBase.org). These are interlinked via precomputed synteny between each browser.
- Diverse search methods: Search by sequence (BLAST or BLAT), or by keyword, and see results against any sequenced genome. Or search in the map and trait database for QTLs, markers, traits, publications, etc.
- Gene families: Genes from Medicago, Lotus, chickpea, common bean, pigeonpea, mungbean, soybean, and wild peanut have been placed into ~18,500 gene families â€“ based on and linked to Phytozome gene families.
- Functional annotations of predicted genes and domains.
- Tools for searching and exploring germplasm, including an interactive viewer of GRIN records across global maps.
- Multi-species synteny views using a genome â€œcontext viewerâ€ showing genes by gene family from corresponding genomic regions.
- Integrated QTLs: QTLs from many studies (so far in common bean and peanut) have been collected and integrated into a common database, and projected onto composite genetic maps (in CMap) when possible. Templates for collecting this data are available. Contact us if you would like your data included!
Funding: LIS is funded by the USDA-ARS, and is developed and maintained jointly by the National Center for Genome Resources (NCGR) and the USDA-ARS at Ames, Iowa.
See the Legume Federation page (http://legumefederation.org).
The "Legume Federation" (http://legumefederation.org) is an NSF project to foster data standards, distributed development, and comparative analysis, via gene families and shared phenotypes, to support research across the legume family â€“ and to support robust agriculture for a world that is significantly legume-fed.
Participating Genomic Data Portals (GDPs) currently include, but are not limited to MedicagoGenome (http://medicagogenome.org), SoyBase (http://soybase.org), PeanutBase (http://peanutbase.org), the Legume Information System (http://legumeinfo.org), Climate Resilient Chickpea Lab (http://chickpealab.ucdavis.edu), Alfalfa Genomics Network (http://www.alfalfa-genome.org), Medicago Hapmap project (http://www.medicagohapmap.org), KnowPulse (http://knowpulse.usask.ca), and the Cool Season Food Legume Database (http://www.coolseasonfoodlegume.org). The project also has integral participation by iPlant.
The goals of the Legume Federation include
1) sharing knowledge, development, and data sets across all legume crops; 2) defining standards for data formats, metadata standards, Web service protocols, and ontology use; 3) establishing an open repository for data exchange; and 4) encouraging the use of common, open-source model organism database tools.
Clear standards and formats, with templates and tools for data collection and submission, will enable broader participation. Although a major focus of the project is on methods for distributed development, we emphasize that the fundamental mission is to enable improved agricultural productivity for this important group of crop plants by integrating genetic, genomic, and phenotypic data across species to enable identification of common molecular bases for important traits.
Funding: The Legume Federation project is funded by NSF, award #1444806, "Federated Plant Database Initiative for the Legumes," and in-kind support from USDA-ARS #5030-21000-062-00D.
The Outreach Booth was possible thanks to volunteer organizer:
- Marcela Karey Tello-Ruiz, Gramene