Limits...
Gramene: a growing plant comparative genomics resource.

Liang C, Jaiswal P, Hebbard C, Avraham S, Buckler ES, Casstevens T, Hurwitz B, McCouch S, Ni J, Pujar A, Ravenscroft D, Ren L, Spooner W, Tecle I, Thomason J, Tung CW, Wei X, Yap I, Youens-Clark K, Ware D, Stein L - Nucleic Acids Res. (2007)

Bottom Line: Since our last NAR publication 2 years ago, we have updated these data types to include new datasets and new connections among them.Completely new features include rice pathways for functional annotation of rice genes; genetic diversity data from rice, maize and wheat to show genetic variations among different germplasms; large-scale genome comparisons among Oryza sativa and its wild relatives for evolutionary studies; and the creation of orthologous gene sets and phylogenetic trees among rice, Arabidopsis thaliana, maize, poplar and several animal species (for reference purpose).We have significantly improved the web interface in order to provide a more user-friendly browsing experience, including a dropdown navigation menu system, unified web page for markers, genes, QTLs and proteins, and enhanced quick search functions.

View Article: PubMed Central - PubMed

Affiliation: Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA.

ABSTRACT
Gramene (www.gramene.org) is a curated resource for genetic, genomic and comparative genomics data for the major crop species, including rice, maize, wheat and many other plant (mainly grass) species. Gramene is an open-source project. All data and software are freely downloadable through the ftp site (ftp.gramene.org/pub/gramene) and available for use without restriction. Gramene's core data types include genome assembly and annotations, other DNA/mRNA sequences, genetic and physical maps/markers, genes, quantitative trait loci (QTLs), proteins, ontologies, literature and comparative mappings. Since our last NAR publication 2 years ago, we have updated these data types to include new datasets and new connections among them. Completely new features include rice pathways for functional annotation of rice genes; genetic diversity data from rice, maize and wheat to show genetic variations among different germplasms; large-scale genome comparisons among Oryza sativa and its wild relatives for evolutionary studies; and the creation of orthologous gene sets and phylogenetic trees among rice, Arabidopsis thaliana, maize, poplar and several animal species (for reference purpose). We have significantly improved the web interface in order to provide a more user-friendly browsing experience, including a dropdown navigation menu system, unified web page for markers, genes, QTLs and proteins, and enhanced quick search functions.

Show MeSH
Conceptual data organization and relationship in Gramene. Gramene contains primary data, such as genome sequences, maps, genes, QTLs, proteins and markers, as well as complex data, such as comparative mappings, gene families, genetic diversities and pathways. Ontology terms are used to provide annotations and associations for other data. Gramene also provides literature for the data source. Please note the size of each line segment is not in proportional to the real size of any biological objects it represents.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2238951&req=5

Figure 1: Conceptual data organization and relationship in Gramene. Gramene contains primary data, such as genome sequences, maps, genes, QTLs, proteins and markers, as well as complex data, such as comparative mappings, gene families, genetic diversities and pathways. Ontology terms are used to provide annotations and associations for other data. Gramene also provides literature for the data source. Please note the size of each line segment is not in proportional to the real size of any biological objects it represents.

Mentions: Figure 1 shows how Gramene is organized from the end-user's point of view. Gramene annotates data using vertical information association (e.g. through controlled vocabularies) as well as horizontal comparative studies among species, and provides users with easy access to the integrated data through a user-friendly web interface. Gramene provides several ways to access data. Data searches can be conducted through either the general search, which is found on every page, or through data type specific search functions, which are located on the module home pages. Other search tools include Gramene Blast, for sequence similarity, and GrameneMart, a data-mining tool for searching data from several datasets [such as gene annotations and rice single-nucleotide polymorphisms (SNPs)] with a comprehensive set of predefined user-selectable filters. Gramene data and tools are freely available for local installation and customization.Figure 1.


Gramene: a growing plant comparative genomics resource.

Liang C, Jaiswal P, Hebbard C, Avraham S, Buckler ES, Casstevens T, Hurwitz B, McCouch S, Ni J, Pujar A, Ravenscroft D, Ren L, Spooner W, Tecle I, Thomason J, Tung CW, Wei X, Yap I, Youens-Clark K, Ware D, Stein L - Nucleic Acids Res. (2007)

Conceptual data organization and relationship in Gramene. Gramene contains primary data, such as genome sequences, maps, genes, QTLs, proteins and markers, as well as complex data, such as comparative mappings, gene families, genetic diversities and pathways. Ontology terms are used to provide annotations and associations for other data. Gramene also provides literature for the data source. Please note the size of each line segment is not in proportional to the real size of any biological objects it represents.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238951&req=5

Figure 1: Conceptual data organization and relationship in Gramene. Gramene contains primary data, such as genome sequences, maps, genes, QTLs, proteins and markers, as well as complex data, such as comparative mappings, gene families, genetic diversities and pathways. Ontology terms are used to provide annotations and associations for other data. Gramene also provides literature for the data source. Please note the size of each line segment is not in proportional to the real size of any biological objects it represents.
Mentions: Figure 1 shows how Gramene is organized from the end-user's point of view. Gramene annotates data using vertical information association (e.g. through controlled vocabularies) as well as horizontal comparative studies among species, and provides users with easy access to the integrated data through a user-friendly web interface. Gramene provides several ways to access data. Data searches can be conducted through either the general search, which is found on every page, or through data type specific search functions, which are located on the module home pages. Other search tools include Gramene Blast, for sequence similarity, and GrameneMart, a data-mining tool for searching data from several datasets [such as gene annotations and rice single-nucleotide polymorphisms (SNPs)] with a comprehensive set of predefined user-selectable filters. Gramene data and tools are freely available for local installation and customization.Figure 1.

Bottom Line: Since our last NAR publication 2 years ago, we have updated these data types to include new datasets and new connections among them.Completely new features include rice pathways for functional annotation of rice genes; genetic diversity data from rice, maize and wheat to show genetic variations among different germplasms; large-scale genome comparisons among Oryza sativa and its wild relatives for evolutionary studies; and the creation of orthologous gene sets and phylogenetic trees among rice, Arabidopsis thaliana, maize, poplar and several animal species (for reference purpose).We have significantly improved the web interface in order to provide a more user-friendly browsing experience, including a dropdown navigation menu system, unified web page for markers, genes, QTLs and proteins, and enhanced quick search functions.

View Article: PubMed Central - PubMed

Affiliation: Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA.

ABSTRACT
Gramene (www.gramene.org) is a curated resource for genetic, genomic and comparative genomics data for the major crop species, including rice, maize, wheat and many other plant (mainly grass) species. Gramene is an open-source project. All data and software are freely downloadable through the ftp site (ftp.gramene.org/pub/gramene) and available for use without restriction. Gramene's core data types include genome assembly and annotations, other DNA/mRNA sequences, genetic and physical maps/markers, genes, quantitative trait loci (QTLs), proteins, ontologies, literature and comparative mappings. Since our last NAR publication 2 years ago, we have updated these data types to include new datasets and new connections among them. Completely new features include rice pathways for functional annotation of rice genes; genetic diversity data from rice, maize and wheat to show genetic variations among different germplasms; large-scale genome comparisons among Oryza sativa and its wild relatives for evolutionary studies; and the creation of orthologous gene sets and phylogenetic trees among rice, Arabidopsis thaliana, maize, poplar and several animal species (for reference purpose). We have significantly improved the web interface in order to provide a more user-friendly browsing experience, including a dropdown navigation menu system, unified web page for markers, genes, QTLs and proteins, and enhanced quick search functions.

Show MeSH