Difference between revisions of "Outreach booth- ASPB Plant Biology 2012"
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| − | [http://austin2012.aspb.org/] | + | [http://austin2012.aspb.org/ Plant Biology 2012] |
'''Visit a collection of Plant Genomics databases and projects with resources for sequenced genomes, ontology development, genetic mapping, functional annotation of genes, mutants and phenotypes, genetic diversity and bioinformatics tools. Representatives from the projects will be present to demonstrate tools for cutting-edge genomics and genetics research and to answer questions.''' | '''Visit a collection of Plant Genomics databases and projects with resources for sequenced genomes, ontology development, genetic mapping, functional annotation of genes, mutants and phenotypes, genetic diversity and bioinformatics tools. Representatives from the projects will be present to demonstrate tools for cutting-edge genomics and genetics research and to answer questions.''' | ||
| − | You can find us at [http://my.aspb.org/?page=Meeting_Exhibitors Booth # | + | You can find us at [http://my.aspb.org/?page=Meeting_Exhibitors Booth #215] |
| + | This page has a tiny URL: http://tinyurl.com/Plant-Genome-Resources | ||
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| + | =Plant Informatics Workshop= | ||
| + | Plan to attend the [http://my.aspb.org/?page=Meetings_PB12Wrkshps Plant Informatics Workshop] Saturday, July 21st, 7:30pm | ||
| − | + | 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. | |
| + | Presentations: | ||
| + | * Eva Huala - TAIR/IAIC transition | ||
| + | * Doreen Ware - Gramene | ||
| + | * Dan Stanzione - iPlant | ||
| + | * Kate Dreher - Plant Metabolic Network | ||
| + | * Laurel Cooper - Plant Ontology and Trait Ontology | ||
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| − | + | =Projects Represented at the Booth:= | |
| − | + | Schedule of Projects reps attendance at the booth: [[Media:ASPB_booth_schedule_2011_v2-2.pdf]] ''needs updated...'' | |
| − | + | ---- | |
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| + | ===Plant Ontology and Plant Trait Ontology=== | ||
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| + | [[File:PO logo wiki.png]] | ||
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| + | '''See our web page for more information: http://www.plantontology.org''' | ||
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| + | 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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| + | 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: [http://precis.preciscentral.com/utils/ip/ShowSummary.asp?AbstractId=521&Presenter= The Plant Ontology: A Tool for Linking Plant Anatomy and Development to Genomics Across Plant Taxa.] | |
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For more information please contact: [http://www.plantontology.org/db/feedback/send_feedback?refer_to=/index.html PO Feedback] | For more information please contact: [http://www.plantontology.org/db/feedback/send_feedback?refer_to=/index.html PO Feedback] | ||
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The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant ''Arabidopsis thaliana''. Data available from TAIR includes the complete genome sequence along with information concerning gene structures, gene product functions, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, useful tools, and members of the Arabidopsis research community. Gene product function data is updated every two weeks from the latest published research literature and community data submissions. Gene structures are updated 1-2 times per year using computational and manual methods as well as community submissions of new and updated genes. TAIR also provides extensive links from our data pages to other Arabidopsis resources. | The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant ''Arabidopsis thaliana''. Data available from TAIR includes the complete genome sequence along with information concerning gene structures, gene product functions, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, useful tools, and members of the Arabidopsis research community. Gene product function data is updated every two weeks from the latest published research literature and community data submissions. Gene structures are updated 1-2 times per year using computational and manual methods as well as community submissions of new and updated genes. TAIR also provides extensive links from our data pages to other Arabidopsis resources. | ||
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* Information on AraCyc, the plant metabolic pathway database connected to TAIR, will be presented in the same workshop | * Information on AraCyc, the plant metabolic pathway database connected to TAIR, will be presented in the same workshop | ||
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| − | Come see the TAIR poster: Abs # | + | Come see the TAIR poster: Abs #XXX |
For more information please contact: [http://www.arabidopsis.org/contact/index.jsp TAIR] | For more information please contact: [http://www.arabidopsis.org/contact/index.jsp TAIR] | ||
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The [http://www.plantcyc.org/about/general_information.faces Plant Metabolic Network] (PMN) is a collaborative project among databases and biochemists with a common goal to build a broad network of plant metabolic pathway databases. A central feature of the PMN is PlantCyc, a comprehensive plant biochemical pathway database, containing curated information from the literature and computational analyses about the genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism. | The [http://www.plantcyc.org/about/general_information.faces Plant Metabolic Network] (PMN) is a collaborative project among databases and biochemists with a common goal to build a broad network of plant metabolic pathway databases. A central feature of the PMN is PlantCyc, a comprehensive plant biochemical pathway database, containing curated information from the literature and computational analyses about the genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism. | ||
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* Researchers are encouraged to bring their published data to the workshop to learn how to directly enter their exciting findings into all three of these public resources | * Researchers are encouraged to bring their published data to the workshop to learn how to directly enter their exciting findings into all three of these public resources | ||
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Gramene Poster links: | Gramene Poster links: | ||
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For more information please see: [http://outreach.gramene.org/gramene-outreach/index.php/ASPB_2011_Workshop Gramene/PO workshop] | For more information please see: [http://outreach.gramene.org/gramene-outreach/index.php/ASPB_2011_Workshop Gramene/PO workshop] | ||
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For more information please contact: [http://www.gramene.org/db/feedback/send_feedback?refer_from=/index.html Gramene Feedback] | For more information please contact: [http://www.gramene.org/db/feedback/send_feedback?refer_from=/index.html Gramene Feedback] | ||
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These tools include: | These tools include: | ||
| − | '''[http://bar.utoronto.ca/efp_arabidopsis/cgi-bin/efpWeb.cgi 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. | + | '''[http://bar.utoronto.ca/efp_arabidopsis/cgi-bin/efpWeb.cgi 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. |
'''[http://www.bar.utoronto.ca/ntools/cgi-bin/ntools_expression_angler.cgi 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. | '''[http://www.bar.utoronto.ca/ntools/cgi-bin/ntools_expression_angler.cgi 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. | ||
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'''[http://www.bar.utoronto.ca/affydb/cgi-bin/affy_db_exprss_browser_in.cgi Expression Browser]''' for performing electronic northerns. | '''[http://www.bar.utoronto.ca/affydb/cgi-bin/affy_db_exprss_browser_in.cgi Expression Browser]''' for performing electronic northerns. | ||
| − | '''''Arabidopsis'' Interactions Viewer''' for querying a database of almost 80,000 predicted and | + | '''''Arabidopsis'' Interactions Viewer''' for querying a database of almost 80,000 predicted and 28,566 documented protein-protein interactions in ''Arabidopsis''. |
'''[http://www.bar.utoronto.ca/ntools/cgi-bin/BAR_Promomer.cgi Promomer]''' for identifying over-represented n-mer words in the promoter of a gene of interest, or in promoters of co-expressed genes. | '''[http://www.bar.utoronto.ca/ntools/cgi-bin/BAR_Promomer.cgi Promomer]''' for identifying over-represented n-mer words in the promoter of a gene of interest, or in promoters of co-expressed genes. | ||
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| − | === | + | ===iPlant=== |
| − | [[File: | + | |
| + | [[File:Iplant logo.png]] | ||
| − | + | '''See our web page for more information http://www.iplantcollaborative.org/''' | |
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| + | ---- | ||
| − | + | ===Solanaceae Genomics Network=== | |
| + | [[File:sgn_logo_icon.png]] '''See our web page for more information:http://solgenomics.net/''' | ||
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| + | 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. |
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| − | [ | + | For more information please contact: [http://solgenomics.net/contact/form SGN Contact] |
| − | + | ---- | |
| − | + | ===Kbase=== | |
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| − | + | [[File:KBase_Final_Logo_4C_white_small.png]] | |
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| − | + | 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 | |
| − | + | [http://kbase.us/ Systems Biology Knowledgebase (KBase)] | |
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Latest revision as of 16:37, 17 July 2012
Visit a collection of Plant Genomics databases and projects with resources for sequenced genomes, ontology development, genetic mapping, functional annotation of genes, mutants and phenotypes, genetic diversity and bioinformatics tools. Representatives from the projects will be present to demonstrate tools for cutting-edge genomics and genetics research and to answer questions.
You can find us at Booth #215
This page has a tiny URL: http://tinyurl.com/Plant-Genome-Resources
Plant Informatics Workshop
Plan to attend the Plant Informatics Workshop Saturday, July 21st, 7:30pm
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. Presentations:
- Eva Huala - TAIR/IAIC transition
- Doreen Ware - Gramene
- Dan Stanzione - iPlant
- Kate Dreher - Plant Metabolic Network
- Laurel Cooper - Plant Ontology and Trait Ontology
Projects Represented at the Booth:
Schedule of Projects reps attendance at the booth: Media:ASPB_booth_schedule_2011_v2-2.pdf needs updated...
Plant Ontology and Plant Trait Ontology
See our web page for more information: http://www.plantontology.org
The main objective of the Plant Ontology Consortium (POC) is to develop, curate and share controlled vocabularies (ontologies) that describe plant structures and growth and developmental stages 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
TAIR:
The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available from TAIR includes the complete genome sequence along with information concerning gene structures, gene product functions, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, useful tools, and members of the Arabidopsis research community. Gene product function data is updated every two weeks from the latest published research literature and community data submissions. Gene structures are updated 1-2 times per year using computational and manual methods as well as community submissions of new and updated genes. TAIR also provides extensive links from our data pages to other Arabidopsis resources.
- Information on AraCyc, the plant metabolic pathway database connected to TAIR, will be presented in the same workshop
- Researchers are encouraged to bring their published data to the workshop to learn how to directly enter their exciting findings into all three of these public resources
Come see the TAIR poster: Abs #XXX
For more information please contact: TAIR
Plant Metabolic Network
See our web page for more information: Plant Metabolic Network
The Plant Metabolic Network (PMN) is a collaborative project among databases and biochemists with a common goal to build a broad network of plant metabolic pathway databases. A central feature of the PMN is PlantCyc, a comprehensive plant biochemical pathway database, containing curated information from the literature and computational analyses about the genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism.
- Researchers are encouraged to bring their published data to the workshop to learn how to directly enter their exciting findings into all three of these public resources
- Please come visit our Poster # P02029 entitled ‘The Plant Metabolic Network: PlantCyc, AraCyc, and more metabolic pathway databases for plant research'
For more information please contact: PMN Feedback
Gramene
See our web page for more information: http://www.gramene.org
The Gramene database is a comparative plant genomics platform. The database allows researchers to carryout online data analysis, hypothetical modeling or confirmation of lab based findings using both forward and reverse genetics approaches to find genes, proteins, phenotypes (mutants and QTLs), function(s), gene-gene interaction(s), metabolic pathways and polymorphisms in a genomic region of interest. It also allows researchers to make comparisons across genetic maps, genomes, genes and gene families and provides a mechanism to find candidate genes associated with phenotype and/or functional characteristics by way of whole genome alignments and synteny views.
Gramene Poster links:
For more information please see: Gramene/PO workshop
For more information please contact: Gramene Feedback
The Bio-Array Resource for Plant Functional Genomics
The Bio-Array Resource at the University of Toronto is a collection of web-based tools for exploring, visualizing and mining large-scale data sets, primarily from Arabidopsis thaliana but also from several other plant species.
These tools include:
eFP Browser (electronic Fluorescent Pictograph Browser) for painting gene expression and other information onto diagrammatic representations of the particular experimental series from which the data were generated. 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.
For more information please contact: Nick Provart (nicholas.provart@utoronto.ca)
iPlant
See our web page for more information http://www.iplantcollaborative.org/
Solanaceae Genomics Network
See our web page for more information:http://solgenomics.net/
The SOL Genomics Network is a Clade Oriented Database (COD) containing genomic, genetic, phenotypic and taxonomic information for species in the Euasterid clade, including the families Solanaceae (e.g. tomato, potato, eggplant, pepper, petunia) and Rubiaceae (coffee). Genomic information is presented in a comparative format and tied to other important plant model species such as Arabidopsis. SGN is also one of the bioinformatics centers involved in tomato genome sequencing.
One of the major efforts at SGN is linking Solanaceae phenotype information with the underlying genes, and subsequently the genome. As part of this goal, SGN puts the control over the information in the hands of community experts. As a result, SGN annotations are more up-to-date, and richer with detailed descriptions and gene-to-phenotype cross links, than would otherwise be possible without a large curatorial staff.
For more information please contact: SGN Contact
Kbase
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)
