PAG 2016 Booth

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Plant and Animal Genome 2016

Visit a collection of Plant and Animal 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 #504





Gramene

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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 39 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 200 curated rice pathways and orthologous pathway projections to 58 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.


Gramene workshop: Tuesday, January 12 of 2015 1:30 - 3:40 pm PST in the California Room.


Gramene posters on the following sessions:

  • Bioinformatics
  • Genome Mapping, Tagging & Characterization (Rice)


Gramene representatives will also be available to meet with users and answer questions at booth #504 throughout the meeting.


For more information please contact: Gramene Feedback or e-mail feedback@gramene.org


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" and USDA-ARS #1907-21000-030-00D.



MaizeGDB

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See MaizeGDB's web page for more information: http://www.maizegdb.org/

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.

Of interest to most researchers are the integration of genetics and genomics at MaizeGDB. From the MaizeGDB Genome Browser, cM estimates of genome size are available. Mechanisms to locate loci of interest on the genome are available via the Locus Lookup and Locus Pair Lookup.

Functional genomics tools at MaizeGDB with access to the eFP Browser images from the Sekhon et al. Maize Gene Expression Atlas via gene model pages (e.g., [1]) as well as comparisons and views of the same dataset via MapMan where the data can be visualized online directly.


Crop Ontology

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The Crop Ontology is a service of the Integrated Breeding Platform (IBP) developed in collaboration with the CGIAR centers and partners, under the leadership of Bioversity international. The Crop Ontology (www.cropontology.org) provides harmonized and validated breeders’ trait names, measurement methods, scales and standard variables for currently 19 CGIAR crops: banana, barley cassava, cowpea, chickpea, common bean, groundnut, lentil, maize, pearl millet, pigeonpea, potato, sorghum, soybean, sweet potato, rice, wheat, yam. Partners provided their ontologies for oat (Oat Global), solanaceae (SGN) and vitis (INRA).


Crop Ontology is used by the Breeding Management System (BMS) of the IBP and the Next Generation Breeding Databases developed by Boyce Thompson Institute. The Crop Ontology contributes to the content enrichment of the reference ontologies of the Planteome project (http://www.planteome.org/).


To fully understand the implications of varying factors within any cropping system, it is important to combine results of field management practices with crop traits. Therefore, an Agronomy Ontology is being developed to index key agronomic variables that will power an Agronomy Management System and Fieldbook, modeled on a CGIAR Breeding Management System and Fieldbook. The ontology development started with the compilation of existing lists of variables, factors, and methods commonly used by agronomists to described the trial management.



Integrated Breeding Platform (IBP)

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Plant breeders are at the forefront of the next food revolution, most particularly in developing countries. The Integrated Breeding Platform (IBP) provides the tools and knowledge they need to rise to a new level of breeding innovation. It offers a suite of integrated software solutions (the IBP Breeding Management System); several breeding services such as genotyping; and breeding materials and related information for a broad range of crops, including germplasm, trait dictionaries and predictive markers. Furthermore, the IBP empowers plant breeders through training, funding opportunities, dedicated support and community spaces, making it the most comprehensive source for best practices in plant breeding. At the core of this offer, the IBP Breeding Management System (BMS) is a comprehensive and easy-to-use software suite designed to help breeders conduct their routine activities with more efficiency, so that they may develop improved cultivars faster and at lower cost. It combines information management, data analysis and decision-support tools that accommodate common breeding schemes, from conventional breeding through increasing levels of marker use, providing all the tools they need in just one place.To Register and Download: [2].


RAP-DB

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The Rice Annotation Project (RAP) was conceptualized in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project with the aim of providing the scientific community with an accurate and timely annotation of the rice genome sequence. One of the major objectives of this project is to facilitate a comprehensive analysis of the genome structure and function of rice on the basis of the annotation.

For more information please see RAP-DB's web page: http://rapdb.dna.affrc.go.jp/



Solanaceae Genomics Network

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See the SGN's 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.

For more information please contact: SGN Contact



Araport

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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 or building analysis workflows. Araport has also assumed the responsibility for updating and revising genome annotation (Araport11) and the reference genome sequence.

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.


PAG Workshop: Monday, January 11, 2016, 12:50 PM - 03:00 PM, Pacific Salon 6-7 (2nd Floor) PAG Poster: Bioinformatics, Databases PAG Booth: 504



Medicago Database

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The Medicago truncatula database at JCVI (www.medicagogenome.org) has been migrated to a customized Tripal interface and database. The database includes the latest M. truncatula genome assembly and annotation (Mt 4.0) as well as access to earlier versions of these data. You can search for your favorite gene by Identifier or Keyword, as well as by sequence BLASTing.

  • JBrowse provides genome browsing capability that includes annotation, RNA-seq and synteny and ortholog data.
  • MedicMine is based upon the increasingly popular InterMine data mining tool and will soon be enriched with additional features.
  • Textpresso gives quick access to Medicago literature indexed in PubMed.
  • EuCAP, the community annotation interface has been improved to include the ability to associate mutant information with annotated genes.

This project is also part of the Legume Federation (www.legumefederation.org)


See the JCVI's web page for more information: http://www.jcvi.org/


BAR: The Bio-Analytic Resource for Plant Functional Genomics

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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, moss 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)


Legume Information System

See the Legume Information System page: [3]

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 2015 includes:

  • Genome browsers for ten legume species (currently): common bean, pigeonpea, chickpea, Medicago truncatula, Lotus japonicus, mungbean, 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

See the Legume Federation page: [4], and additional information about the Legume Federation project at PAG: [5]

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.



SoyBase

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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. 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.


SoyKB

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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.

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



Plant Ontology and Plant Trait Ontology

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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.

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.

Come see Poster # P28002: The Plant Ontology: A Tool for Linking Plant Anatomy and Development to Genomics Across Plant Taxa.


For more information please contact: PO Feedback


Nottingham Arabidopsis Stock Centre (NASC)

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The Nottingham Arabidopsis Stock Centre (NASC), based at the University of Nottingham, collects, preserves, reproduces and distributes diverse seed and other stocks of the model plant Arabidopsis thaliana and related species for research and education. Established in April 1991 with British public funding, NASC’s seed collection approaches one million stocks. NASC’s activities are coordinated with those of the Arabidopsis Biological Resource Center (ABRC, [6]) based at Ohio State University, USA. Both stock centres offer several advantages: they provide security and stability as seed stocks are preserved under the best possible conditions and they maintain and curate large numbers of stocks according to common standards. NASC has traditionally been funded by the Biotechnology and Biological Sciences Research Council (BBSRC, [7]) with a small proportion of operational costs also covered through user fees. This combination of government funding and cost recovery represents a reasonable balance between community services provided and financial support required. The usage of NASC resources has increased year on year continuously since introducing user fees and has shown a recent acceleration in distribution. The number of seed and DNA stocks sent annually is now over 100,000, a rate that substantially exceed anything imagined in the beginning. As part of the AIP community [8], our data are freely available through web services and we are currently expanding our integration with other community resources.



National BioResource Project (NBRP)

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The National BioResource Project (NBRP) is a Japanese project to establish a system for collecting, preserving and providing biological resources to be utilized as experimental materials in life science researches. It is promoted by one information center and by 29 core resource facilities, each focusing on a particular group of organisms. Information of all resources is accessible through the NBRP home page ([9]) and all materials (6.5 million items) are available for distribution. NBRP provides an integrated database, BRW (BioResource World), where users can search for resources across species such as animals, plant, and microbes. NBRP-Plant is a plant subset of NBRP members consisting of Arabidopsis, Rice, Wheat, Barley, Algae, Lotus/Glycine, Morning Glory, Chrysanthemum and Tomato. SABRE2 is a database of plant DNA clones available from the core facilities of NBRP-Plant members. NBRP resources are directly accessible from PubMed LinkOut.


  • Poster #P19667
  • Poster #P0311

Animal QTLdb

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The Animal Quantitative Trait Loci (QTL) Database (Animal QTLdb) strives to collect all publicly available trait mapping data, i.e. QTL (phenotype/expression, eQTL), candidate gene and association data (GWAS), and copy number variations (CNV) mapped to livestock animal genomes, in order to facilitate locating and comparing discoveries within and between species. New data and database tools are continually developed to align various trait mapping data to map-based genome features such as annotated genes. Many scientific journals require or recommend that any original QTL/association data be deposited into a public database before a paper may be accepted for publication. We provide user/curator accounts for direct data submission and supply users with a data summary link to facilitate the manuscript review process. The QTL/association data are freely accessible via online browser, download, and built-in visualization tools. In addition, the data is also ported for map viewing in GBrowse and JBrowse on AnimalGenome.org, and at NCBI, Ensembl, and UCSC using their respective web tools.

Currently, QTL/association data from the following species have been curated into the database:

  • Cattle
  • Chicken
  • Horse
  • Pig
  • Rainbow trout
  • Sheep

Work is underway to add catfish QTL/association data.

Related projects include but are not limited to:

  • Vertebrate Trait Ontology (VT)
  • Livestock Product Trait Ontology (LPT)
  • Clinical Measurement Ontology (CMO)
  • Livestock Breed Ontology (LBO)
  • Virtual Comparative Map (VCmap)

Each of these projects is closely associated with, and co-developed with, the Animal QTLdb. While they provide enhanced functionality for QTLdb, each has a wider range of applications as well.

See [10] for more information or find us at the PAG Booth #504 (Jim Reecy and Zhiliang Hu from our team are on this PAG meeting). Please feel free to talk to one of us on things you are interested).


Bovine Genome Database (BGD)

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The Bovine Genome Database (BGD, http://BovineGenome.org) provides data mining, genome navigation and annotation tools for the bovine genome. BGD catalogues genome features, including protein-coding and non-coding RNA genes from RefSeq, Ensembl and the bovine Official Gene Set version 2 (OGSv2), pseudogenes, repetitive elements, single nucleotide polymorphisms (SNP), and quantitative trait loci (QTL). Genome viewing and annotation tools are based on JBrowse and Apollo. BGD also includes BovineMine, which is based on the InterMine data warehousing system. It integrates BGD data with external sources of orthology, gene ontology, gene interaction and pathway information. BovineMine provides powerful query building tools, as well as customized query templates, and allows users to analyze and download genome-wide datasets. BovineMine allows researchers to use orthology to leverage the curated gene pathways of model organisms, such as human, mouse and rat.



Acknowledgements

The Outreach Booth was made possible thanks to volunteer organizers:

  • Mary Schaeffer, MaizeGDB (University of Missouri)
  • Marcela Karey Tello-Ruiz, Gramene (Cold Spring Harbor Laboratory)
  • Lisa Harper, MaizeGDB
  • Carson Anderson, MaizeGDB (Iowa University)