Difference between revisions of "ASPB 2017 Booth"

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[http://plantbiology.aspb.org/ Plant Biology 2017]
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[http://plantbiology.aspb.org/ '''Plant Biology 2017''']
  
'''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.'''
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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 [http://my.aspb.org/?page=Meeting_Exhibitors Booth #215]
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You can find us at [http://conferencemanagersforms.com/fx/aspb17/ '''Booth #215''']
  
  
 
= Bioinformatics Mini-symposium =  
 
= Bioinformatics Mini-symposium =  
 
   
 
   
Plan to attend the '''Bioinformatics''' mini-symposium on Monday, June 26, 11:30 AM – 1:00 PM
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Plan on attending the '''ASPB Bioinformatics Workshop''', a mini-symposium on Monday, June 26, 11:30 AM – 1:00 PM.
  
Plant biology researchers increasingly rely on databases and other informatics resources to organize, integrate and provide access to the flood of plant biology data now available. We will present the latest developments, data and tools for several important plant informatics resources.
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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.
Presentations:
 
  
* Araport - Agnes Chan (J. Craig Venter Institute)
 
* Gramene - Marcela Karey Tello-Ruiz (Cold Spring Harbor Laboratory)
 
* Planteome - Pankaj Jaiswal (Oregon State University)
 
* KBase - Bob Cottingham (Oak Ridge National Laboratory)
 
* TAIR - Eva Huala (Phoenix Bioinformatics)
 
* SGN - Lukas Muller (Boyce Thompson Institute)
 
* Splicing Stuff - John Brown (James Hutton Institute)
 
* BAR - Asher Pasha (University of Toronto)
 
  
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Presentations:
  
=Plant Genome Resources Outreach Booth=
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* 11:30-11:32 am --- Introduction
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 +
* 11:32-11:40 am --- Araport - Agnes Chan, J. Craig Venter Institute
 +
 
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* 11:40-11:48 am --- Gramene - Marcela Karey Tello-Ruiz, Cold Spring Harbor Laboratory
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* 11:48-11:56 am --- BAR - Asher Pasha, University of Toronto
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* 11:56-12:04 pm --- TAIR - Leonore Reiser, Phoenix Bioinformatics
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* 12:04-12:12 pm --- AtRTD Splicing - Cristiane Calixto, James Hutton Institute
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* 12:12-12:20 pm --- Planteome - Laurel Cooper, Oregon State University
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* 12:20-12:28 pm --- SGN - Hartmut Foerster, Boyce Thompson Institute
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* 12:28-12:36 pm --- PMN - Pascal Schlapfer, Carnegie Science
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* 12:36-12:44 pm --- KBase - Vivek Kumar, Cold Spring Harbor Laboratory
  
== Projects with a Representative On Site ==
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* 12:44-12:52 pm --- LegFed - Sam Hokin, National Center for Genome Resources
  
[[File:2013 ASPB plant outreach booth schedule.xls|Schedule]] with a representative present at the booth
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* 12:52- 1:00 pm --- NRSP10 - Dorrie Main, Washington State University
  
----
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=Plant Genome Resources Outreach Booth=
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 +
== Projects with a representative on site ==
  
 
===Gramene===
 
===Gramene===
  
[[File:gramene_logo180new.jpg]]
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[[File:Gramene-2013-logo.png]]
  
  
 
'''See Gramene's web page for more information:  http://www.gramene.org'''
 
'''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 25 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 10 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 121 curated rice pathways. 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.
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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 Joshua Stein during the Genomic Tools Minisymposium on '''Sunday, July 21st at 4:30pm'''.
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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 posters:
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Gramene talks & posters:
  
  
'''P25019''' – ''Gramene: A Resource for Comparative Plant Genomics''.
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'''NNN''' – ''Gramene: Unifying Comparative Genomics and Pathway Resources for Plant Communities''. Presented by Marcela Karey Tello-Ruiz
Presented by Marcela Karey Monaco
 
  
'''P15030''' –  ''Gramene: An Integrated Phylogenomics Resource for the Oryza genus''.
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'''NNN''' –  ''Comparative genomics reveals prevalence of coupled R-gene disease resistance systems in 11 species of the Oryzeae tribe''. Presented by Joshua Stein
Presented by Joshua Stein
 
  
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'''NNN''' – Presented by Yinping Jiao
  
Gramene representatives will be available to meet with users and answer questions at '''booth #200''' throughout the meeting.
 
  
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Gramene representatives will be available to meet with users and answer questions at '''booth #205''' throughout the meeting.
  
For more information please contact:  [http://www.gramene.org/db/feedback/send_feedback?refer_from=/index.html Gramene Feedback]
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For more information please contact:  [http://tools.gramene.org/feedback Gramene Feedback]
  
  
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===TAIR===
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===Phoenix / TAIR===
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[[File:TAIR logo2.gif]]  
 
[[File:TAIR logo2.gif]]  
  
  
'''See TAIR's web page for more information: [http://www.arabidopsis.org http://www.arabidopsis.org]'''
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'''See Phoenix's web page for more information: [http://www.arabidopsis.org http://www.arabidopsis.org]'''
  
 
The Arabidopsis Information Resource (TAIR) maintains a database of
 
The Arabidopsis Information Resource (TAIR) maintains a database of
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For more information please contact: curator@arabidopsis.org
 
For more information please contact: curator@arabidopsis.org
 
 
----
 
 
===Plant Metabolic Network===
 
 
[[File:PMN_logo_highres.gif]]
 
 
 
'''See PMN's web page for more information:  [http://www.plantcyc.org/about/general_information.faces Plant Metabolic Network]'''
 
 
The [http://www.plantcyc.org/about/general_information.faces Plant Metabolic Network] (PMN) provides a broad network of plant metabolic pathway databases that contain curated information from the literature and computational analyses about the genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism in plants.
 
 
The PMN has 17 species-specific databases and PlantCyc, a multi-species database with information from over 350 plant species.
 
 
Researchers can use these resources to analyze results and form new hypotheses for: Arabidopsis, barley, Brachypodium, cassava, Chinese, cabbage, chlamydomonas, corn / maize, grape, moss (''Physcomitrella patens''), papaya, poplar, rice, Selaginella, Setaria, sorghum, soybean, switchgrass, and many other species in PlantCyc.
 
 
Please come meet with a representative at Poster # P07029, the booth, or at Minisymposium #10 at 5:10 PM on Sunday.
 
 
 
'''Funding:''' The PMN is funded by the [http://www.nsf.gov National Science Foundation] (Grants #: [http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1026003 1026003] and [http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0640769 0640769]) and the [http://science.energy.gov/ber Department of Energy] (BER Grant #: [http://www.osti.gov/oberabstracts/detail.jsp?searchpage=search.adv.jsp&projectSerial0=9100 ER65472]).
 
 
  
 
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===Solanaceae Genomics Network===
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===AraPort===
 
 
[[File:sgn_logo_icon.png]] 
 
 
 
 
 
'''See the SGN's web page for more information:  http://solgenomics.net'''
 
 
 
 
 
The [http://solgenomics.net/ 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 [http://solgenomics.net/about/about_solanaceae.pl 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 [http://solgenomics.net/genomes/Solanum_lycopersicum/genome_data.pl 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 [http://solgenomics.net/phenome/ 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.
 
 
 
For more information please contact: [http://solgenomics.net/contact/form SGN Contact]
 
 
 
 
 
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===J. Craig Venter Institute===
 
 
 
[[File:jcvi.png]]
 
 
 
 
 
Plant genomics has been an integral part of the JCVI legacy for many years. Starting with our work on the first sequencing project of a plant, Arabidopsis, we have expanded our activities to genome and EST projects for a wide range of plant species. These include rice, continued work on Arabidopsis, potato, maize, Medicago, soybean, tomato, barley, pine, onion, banana, various pulse crops (legumes) and several microbial pathogens that afflict important crops.
 
Current work is focused primarily on improving the sequence and annotation of Medicago truncatula (barrel medic). We are also involved in consortia sequencing the genomes of Brassica oleracea, Medicago sativa (alfalfa) and Salix purpurea  (willow, a potential bioenergy crop). In addition, we provide informatics support for and host the maize cell genomics database.
 
 
 
'''Medicago truncatula Genome Release v4.0.'''
 
 
 
We have continued to curate and improve the M. truncatula genome sequence and annotation. We have combined NexGen sequences with the previous BAC-based assemblies to produce the current Mt 4.0 release. Pseudomolecules were constructed from ALLPATHS scaffolds on the basis of alignments to both the optical and genetic (genotyping-by-sequencing - GBS) maps. Where possible, high quality contiguous BAC sequences were patched into the new v4 pseudomolecules to close sequencing gaps in the ALLPATHS assembly,. Whereas the Mt 3.5 release consisted of ~ 250 Mb in pseudomolecules and ~ 100 Mb of unanchored sequence, the Mt 4 pseudomolecules now encompass approximately 360 Mb of sequences spanning 390 Mb of which ~ 330 Mb aligns accurately with the optical map. Most of the sequences and genes that were previously on unanchored portion of Mt3.5 have now been incorporated into Mt4.0 pseudomolecules, with the exception of only ~20Mb of unplaced sequences. The new pseudomolecules were annotated by an in-house pipeline that combined Mt3.5 gene models, predictions from Augustus and FGENESH with expression data and protein matches primarily using Evidence Modeler (EVM).  Medtr identifers have been preserved between Mt 3.5 and Mt 4.0. Many new identifiers have been instantiated to replace the gene identifiers previously found on the unanchored contigs. Look-up tables are provided to allow easy navigation between the two data sets.
 
  
An overview of the Medicago truncatula Genome Release v4 and the tools available on the JCVI Website will be given during the Genomic Tools Minisymposium on Sunday, July 21st at 4:10PM.
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[[File:araport-logo.png]]
  
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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.
  
JCVI Poster:
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* '''[https://apps.araport.org/thalemine ThaleMine]''' A data warehouse for browsing gene reports, running gene list enrichment analysis, exporting data tables, and saving or sharing work.
  
'''P15029'''- Medicago truncatula Genome Resources at the J. Craig Venter Institute
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* '''[https://apps.araport.org/jbrowse/?data=arabidopsis JBrowse]''' A genome browse hosting about 100 data tracks. Users can also upload and view their own data for side-by-side comparison.
  
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* '''[https://www.araport.org/apps/catalog Science Apps]''' A growing collection of data or analysis modules that will serve as building blocks for creating discovery workflows.
  
''Medicago truncatula resources at JCVI include:''
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* '''[https://www.araport.org/data/araport11 Araport11]''' Comprehensive updates to Col-0 genome annotation completed and submitted to NCBI.
  
'''BLAST Search''':  Search against Mtv3.5 and Mtv4.0 genome assemblies and annotations.
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Araport is funded by the National Science Foundation (#DBI-1262414) and the Biotechnology and Biological Sciences Research Council (BB/L027151/1).
Gene Information Pages:  Search for your favorite gene by Idnetifier or Keyword.  View all searches completed, functional assignments and gene structure.
 
  
'''JBrowse''':  View any region of the genome in a Google Maps style interface. 
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For questions and comments, please contact araport@jcvi.org.
Community Annotation:  Do you have a favorite gene or gene family?  You can manually curate the Medicago truncatula structure and functions. Our EuCAP interface has been improved to include the ability to associate mutant information.
 
  
'''Coming soon''':  MedicMine (Intermine) and WebApollo for gene structure curation by community annotators.
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See poster: 300-160
 
 
 
 
 
 
'''See the JCVI's web page for more information: http://www.jcvi.org/'''
 
  
 
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===The Bio-Analytic Resource for Plant Functional Genomics===
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===The Bio-Analytic Resource for Plant Biology===
  
 
[[File:Bar_logo_small.gif‎ ]]
 
[[File:Bar_logo_small.gif‎ ]]
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===Planteome===
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[[File:Planteome logo2-1.jpg]]
  
===iPlant===
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'''See the Planteome Project home page for more information:  http://www.planteome.org'''
 
 
[[File:IPL_logo_2C_large.jpg]]
 
 
 
 
 
The ''iPlant Collaborative'' provides a comprehensive cyberinfrastructure (CI) platform for the storage, sharing, and analyses of large datasets – from genomes to image data, and beyond.
 
 
 
''iPlant''’s vision to enable life science researchers and educators to use cyberinfrastructure to solve problems in biology, and ultimately predict the complexity of biological systems.
 
  
 +
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.
 
   
 
   
  
Easy-to-use ''iPlant'' tools cater to every level of user, from bench-biologists to bioinformaticians. Key components of the include:
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Come see Poster #300-173: The Planteome Project: Reference Ontologies and Tools for Plant Biology
  
 
  
·        '''iPlant Discovery Environment'''- web-based solution for managing data, and running analyses; a scalable and extensible platform featuring hundreds of commonly used bioinformatics tools;
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For more information please contact:  [http://planteome.org/contact Planteome Feedback]
  
·        '''Atmosphere'''- customizable on-demand cloud computing;
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----
 
 
·        '''DNA Subway''' – educational platform for genome annotation, DNA barcoding, and RNA-Seq
 
 
 
·        '''Data Store'''- flexibility and control over your data, fast uploads/downloads, and terabytes of storage.
 
 
 
 
 
 
Please visit our website for more information: [http://www.iplantcollaborative.org www.iplantcollaborative.org]
 
 
 
 
 
 
'''Special Events for Plant Biology 2013'''
 
 
 
 
 
 
Please visit our Plant Biology 2013 page to take a survey (Win an iPad mini/ASPB conference pass or membership): [http://www.iplantcollaborative.org/aspb2013 www.iplantcollaborative.org/aspb2013]
 
  
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===GrainGenes===
  
Selected Presentations and Posters:
 
  
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===Tripal===
 
 
·        '''Plant Biology 2013 Education Booth 312/313''': Integrating a Semester-Long Plant Genomics Investigative Research Experience into Introductory and Advanced Courses; Brent Buckner, Truman State University, MO
 
 
 
·        '''Poster P12013''': DNA Subway: Genomics, DNA Barcoding, and RNA-Seq - Bringing Cutting-Edge Biology into the Classroom; Jason Williams, Cold Spring Harbor Laboratory, NY
 
 
 
·        '''Poster P15025''': DNA Barcode Initiative for the Species of Eastern Nigeria; George Ude, Bowie State University, MD
 
 
 
 
 
 
''iPlant'' is funded by the National Science Foundation: DBI-0735191
 
 
 
 
 
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===KBase===
 
===KBase===
  
[[File:Kbase_logo.png]]
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[[File:Kbase_Logo_Final.jpg]]
  
  
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== Projects without a Representative On Site (Brochures available!) ==
 
== Projects without a Representative On Site (Brochures available!) ==
  
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===SoyBase===
  
===SoyKB===
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[[File:Slide1.jpg]]
  
[[File:soykb_logo.png|200px]]
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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.
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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 [http://www.soybase.org/sitemap.php 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.
  
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'''SoyBase can be publicly accessed at http://soybase.org'''
  
Soybean Knowledge Base (SoyKB) is a comprehensive all-inclusive web resource for soybean translational genomics and breeding. SoyKB handles the management and integration of soybean genomics and multi-omics data (including genomics, transcriptomics, proteomics and metabolomics) along with gene function annotations, biological pathway and trait information. It has many useful tools including Affymetrix probeID search, gene family search, multiple gene/metabolite analysis, motif analysis tool, protein 3D structure viewer and download/upload capacity for experimental data and annotations. It has a user-friendly web interface together with genome browser and pathway viewer, which display data in an intuitive manner to the soybean researchers, breeders and consumers. 
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----
 
 
SoyKB has new innovative tools for soybean breeding including a graphical chromosome visualizer targeted towards ease of navigation for breeders. It integrates QTLs, traits, germplasm information along with genomic variation data such as single nucleotide polymorphisms (SNPs) and genome-wide association studies (GWAS) data from multiple genotypes, cultivars and G.soja. QTLs for multiple traits can be queried and visualized in the chromosome visualizer simultaneously and overlaid on top of the genes and other molecular markers as well as multi-omics experimental data for meaningful inferences.
 
 
 
 
 
'''SoyKB can be publicly accessed at http://soykb.org'''
 
  
 
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===Legume Information System===
  
===Plant Ontology and Plant Trait Ontology===
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[[File:legumeinfo_logo.png‎]]
 
 
[[File:PO logo wiki.png‎]]  
 
 
 
 
 
'''See PO's 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 and plant traits. The overall goal is to provide a semantic framework for meaningful cross-species queries across databases. The Plant Ontology (PO) and the Plant Trait Ontology (TO) have been developed with the primary goal to facilitate and accommodate functional annotation efforts in plant databases and by the plant research community at large.  
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See the Legume Information System page (http://legumeinfo.org).
  
As a part of the PO 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.  
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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:
  
Come see [http://precis.preciscentral.com/utils/ip/ShowSummary.asp?AbstractId=521&Presenter= Poster # P28002]: The Plant Ontology: A Tool for Linking Plant Anatomy and Development to Genomics Across Plant Taxa.
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* 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.
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* Gene families: Genes from Medicago, Lotus, chickpea, common bean, pigeonpea, mungbean, soybean, and wild peanut have been placed into ~18,500 gene families – 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 “context viewer” showing genes by gene family from corresponding genomic regions.
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* 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.
  
For more information please contact:  [http://www.plantontology.org/db/feedback/send_feedback?refer_to=/index.html PO Feedback]
 
  
 
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===Legume Federation===
  
===MaizeGDB===
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[[File:LegFed _logo.png‎]]
  
[[File:maizegdb_logo.png]] 
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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 – and to support robust agriculture for a world that is significantly legume-fed.
  
'''See MaizeGDB's web page for more information: http://www.maizegdb.org/'''
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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.
  
MaizeGDB is a community-oriented, long-term informatics service to researchers focused on the crop plant and model organism ''Zea mays'' that is funded by the USDA-ARS.
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The goals of the Legume Federation include
  
MaizeGDB is currently undergoing a full website redesign (see [http://alpha.maizegdb.org]) and we would appreciate help and input on making the new site able to meet your research needs!
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    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.
  
Of interest to most researchers are the integration of genetics and genomics at MaizeGDB. From the [http://gbrowse.maizegdb.org/gb2/gbrowse/maize_v2/ MaizeGDB Genome Browser], cM estimates of genome size are available.  Mechanisms to locate loci of interest on the genome are available via the [http://www.maizegdb.org/cgi-bin/locus_lookup.cgi?id=IBM2&locus= Locus Lookup] and [http://www.maizegdb.org/cgi-bin/locus_pair_lookup.cgi Locus Pair Lookup].
+
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.
  
[http://www.maizegdb.org/expression/expr_tools/expr_tools.php Functional genomics tools] are also coming along at MaizeGDB with access to the eFP Browser images from the Sekhon et al. Maize Gene Expression Atlas via gene model pages (e.g., [http://www.maizegdb.org/cgi-bin/displaygenemodelrecord.cgi?id=GRMZM2G165390]) as well as comparisons and views of the same [http://www.maizegdb.org/expression/expr_tools/two_tissue_comp.php dataset via MapMan] where the data can be visualized online directly.
+
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.
  
 
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== Acknowledgements ==
 
== Acknowledgements ==
  
The Outreach Booth was made possible thanks to volunteer organizers:
+
The Outreach Booth was possible thanks to volunteer organizer:
  
* Kate Dreher, PMN
+
* Marcela Karey Tello-Ruiz, Gramene
* Marcela Karey Monaco, Gramene
 

Latest revision as of 14:55, 21 June 2017

Plant Biology 2017

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


Bioinformatics Mini-symposium

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.


Presentations:

  • 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

Gramene

Gramene-2013-logo.png


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:


NNNGramene: Unifying Comparative Genomics and Pathway Resources for Plant Communities. Presented by Marcela Karey Tello-Ruiz

NNNComparative 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

TAIR logo2.gif


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: curator@arabidopsis.org


AraPort

Araport-logo.png

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 araport@jcvi.org.

See poster: 300-160


The Bio-Analytic Resource for Plant Biology

Bar logo small.gif


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 (nicholas.provart@utoronto.ca)


Planteome

Planteome logo2-1.jpg

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


GrainGenes

Tripal

KBase

File:Kbase Logo Final.jpg


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.


Systems Biology Knowledgebase (KBase)




Projects without a Representative On Site (Brochures available!)

SoyBase

Slide1.jpg

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

Legumeinfo logo.png


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 – 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 “context viewer” 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.



Legume Federation

LegFed logo.png

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 – 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.



Acknowledgements

The Outreach Booth was possible thanks to volunteer organizer:

  • Marcela Karey Tello-Ruiz, Gramene