http://precedings.nature.com/users/c96085c42a575a31d291aabc66209074/ Documents posted by Diego Mauricio Riaño-Pachón Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://dx.doi.org/10.1038/npre.2009.3218.1 GabiPD (http://www.gabipd.org/) at the Max Planck Institute of Molecular Plant Physiology constitutes a repository and analysis platform of genomic, transcriptomic, proteomic, and metabolomic plant data provided by the GABI community (Riaño-Pachón et al., 2009). Beside the data, current versions of useful tools are being made accessible via GabiPD, such as MapMan (Usadel et al., 2005) and SATlotyper (Neigenfind et al., 2008). Access to GabiPD is provided via either the web interface or WebServices.In GabiPD, twenty different plant species are currently represented with the model plant A. thaliana on top followed by the crop plants S. tuberosum and H. vulgare. Innovative user interfaces allow interactive access to the different data types, e.g. (i) GreenCards to all text-based information, like sequences and comparative SNP information (e.g., Pajerowska-Mukhtar et al., 2009) (ii) YAMB to comparative genetic maps, (iii) MapManWeb to gene expression or metabolite profiling data mapped onto pathways, or (iv) 2DGelViewer to annotated 2DE gel images. All data types (e.g., clones, protein spots, gene expression data) in GabiPD are pointing to the central Gene GreenCard, where gene information is retrieved from genome annotation projects or UniGene sets (provided by NCBI). With the Gene GreenCards, we provide MapMan and Gene Ontology annotations and ortholog information (currently only between A. thaliana and O. sativa ssp. japonica). Recently, a new graphical representation of transcripts was integrated displaying gene structure (untranslated regions, start and stop codons and exon-exon junctions). Protein domains as well as ESTs, are mapped on the transcript displays. In order to ease the transfer of knowledge from model to crop plants, we have performed similarity-based mappings between closely related species, i.e., O. sativa ssp. japonica and H. vulgare. By the integration of complex data in a framework of existing knowledge, GabiPD provides new insights and allows for new interpretations of plant data.This work is/was supported by the BMBF (GABI grants 0312272, 0313112, 0315046).Neigenfind J et al. (2008) Haplotype inference from unphased SNP data in heterozygous polyploids based on SAT. BMC Genomics 9:356.Pajerowska-Mukhtar K et al. (2009) Single nucleotide polymorphisms in the allene oxide synthase 2 gene are associated with field resistance to late blight in populations of tetraploid potato cultivars. Genetics, doi:10.1534/genetics.108.094268Riano-Pachon DM et al. (2009) GabiPD: The GABI Primary Database – a plant integrative ‘omics’ database. Nucleic Acids Research 37(Database issue):D954-9, DOI 10.1093/nar/gkn611Usadel B et al (2006) PageMan: an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments. BMC Bioinformatics 7:535. http://dx.doi.org/10.1038/npre.2009.3218.1 Wed, 06 May 2009 20:39:02 UTC The GABI Primary Database: GABIPD – Integration of Plant ‘Omics’-Data in Gene Context doi:10.1038/npre.2009.3218.1 2009-05-06 Birgit Kersten Nature Precedings 2009-05-06T20:39:02Z Poster Genetics & Genomics Bioinformatics Plant Biology http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2007.243.1 We present the Plant Transcription Factor Database (PlnTFDB), and the putative complete set of TFs in the algae Chlamydomonas reinhardtii, Ostreococcus tauri and the vascular plants Oryza sativa and Arabidopsis thaliana. http://dx.doi.org/10.1038/npre.2007.243.1 Tue, 26 Jun 2007 10:35:10 UTC Plant Transcription Factors @ uni-potsdam.de doi:10.1038/npre.2007.243.1 2008-12-04 Diego Mauricio Riaño-Pachón Nature Precedings 2007-06-26T10:35:10Z Poster Ecology Bioinformatics Plant Biology http://creativecommons.org/licenses/by/2.5/ http://dx.doi.org/10.1038/npre.2007.1094.1 PlnTFDB is a publicly available computational resource comprising putative complete sets of transcription factors from plants. The original database listed the putative complete sets of TFs from five different green plant (viridiplantae) species. Up to date, summer 2007, PlnTFDB have had more than one hundred thousand hits from more than one thousand different clients, showing the importance that this resource had acquired for the plant community. In this first major update, we extended the coverage of the database to additional completed viridiplantae genomes, i.e., the moss Physcomitrella patens and the rice Oryza sativa spp indica. The scope of PlnTFDB was broadened to encompass other eukaryote photosynthetic organisms, such as the rhodophyte algae Galdieria sulphuraria and Cyanidioschyzon merolae, and the diatom Thalassiosira pseudonana. This will allow acquiring a better knowledge of plant evolution and on differentiation events. Moreover, the inclusion of large EST collections (i.e., Hordeum vulgare) have further extended the range of this resource to species whose genome are not yet sequenced but that have, nevertheless, highthroughput EST sequencing projects ongoing. http://dx.doi.org/10.1038/npre.2007.1094.1 Wed, 26 Sep 2007 08:33:19 UTC PlnTFDB: Plant Transcription Factor Database – Update doi:10.1038/npre.2007.1094.1 2008-12-04 Diego Mauricio Riaño-Pachón Nature Precedings 2007-09-26T08:33:19Z Poster Ecology Bioinformatics Plant Biology http://creativecommons.org/licenses/by/2.5/ http://dx.doi.org/10.1038/npre.2008.1684.1 GabiPD (http://gabi.rzpd.de) was established within GABI-I and further developed in GABI-II and constitutes a repository and analysis platform for a wide array of heterogeneous data arising from high throughput experiments developed by members of the GABI/WPG community. Currently, data from different fronts (genomics, transcriptomics, proteomics, metabolomics) are incorporated in GabiPD, representing 14 different biological species. Last year GabiPD moved to the Max Planck Institute of Molecular Plant Physiology. In the progressing GABI-FUTURE phase, the GabiPD team has been creating a more integrative data view, expanding the tools and information provided by our well-known GreenCards. Links to different species-specific (Arabidopsis thaliana so far) GABI-resources (e.g., Aramemnon, GABI-KAT) as well as external resources (e.g., ProMEX) are being added or updated. All data types (e.g., protein spots, clones) in GabiPD are pointing to the central Gene’s GreenCard, where gene information is retrieved from genome annotation projects or large UniGene sets provided by NCBI. Moreover, the GabiPD team will perform new types of data computations, like analysis of conserved domains in protein sequences. http://dx.doi.org/10.1038/npre.2008.1684.1 Thu, 13 Mar 2008 12:46:38 UTC GabiPD: Gabi Primary Database – a plant integrative ‘omics’ database in GABI-FUTURE doi:10.1038/npre.2008.1684.1 2008-12-04 Diego Mauricio Riaño-Pachón Nature Precedings 2008-03-13T12:46:38Z Poster Bioinformatics Plant Biology http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2008.2221.1 The GABI Primary Database, GabiPD, was established eight years ago in the frame of the German initiative for Genome Analysis of the Plant Biological System (Genomanalyse im biologischen System Pflanze, GABI), funded by the German Federal Ministry of Education, Research and Technology (BMBF) as well as a number of private enterprise companies. The main goal of GabiPD is to collect, integrate, visualize and link primary information from GABI projects. GabiPD, in contrast to other plant databases constitutes a repository and analysis platform for a wide array of heterogeneous data arising from high-throughput experiments in several plant species. Currently, data from different ‘omics’ fronts are incorporated in GabiPD (i.e., genomics, transcriptomics, metabolomics, proteomics), originating from 14 different model or crop species. We have developed the concept of GreenCards for text based retrieval of all data types in GabiPD (e.g., clones, genes, mutant plant lines, markers). All data types are pointing to the central Gene’s GreenCard, where gene information is integrated from genome annotation projects. Within the Gene’s GreenCards links to all GabiPD data related to the corresponding genes as well as cross references to large UniGene sets from NCBI and to useful gene-based external data bases are displayed. A collection of ~400000 ESTs from different species, generated in different GABI projects, is made publicly available though GabiPD. These ESTs have been cross referenced to UniGene sets from NCBI and to sequences from different plant genome projects, in an effort to ease the transfer of functional information. The centralized Gene’s GreenCard also allows visualizing ESTs aligned to annotated transcripts as well as identified protein domains and gene structure. Moreover GabiPD makes available interactive genetic maps from Solanum tuberosum (potato) and Hordeum vulgare (barley). Gene expression data in GabiPD can be visualized through MapManWeb, the web interface of MapMan. Access to the data in GabiPD is provided via either the web interface (http://www.gabipd.org) or webservices that are currently available for Arabidopsis-related information. GabiPD was accessed by more than 30000 unique visitors last year from around the world. http://dx.doi.org/10.1038/npre.2008.2221.1 Fri, 22 Aug 2008 20:56:52 UTC GabiPD: GABI primary database – a plant integrative ‘omics’ database doi:10.1038/npre.2008.2221.1 2008-12-04 Diego Mauricio Riaño-Pachón Nature Precedings 2008-08-22T20:56:52Z Poster Bioinformatics Plant Biology http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2008.2210.1 The GABI Primary Database, GabiPD (http://www.gabipd.org/), was established in the frame of the German initiative for Genome Analysis of the Plant Biological System (GABI). The goal of GabiPD is to collect, integrate, analyse and visualise primary information from GABI projects. GabiPD constitutes a repository and analysis platform for a wide array of heterogeneous data from high-throughput experiments in several plant species. Data from different ‘omics’ fronts are incorporated (i.e., genomics, transcriptomics, proteomics and metabolomics), originating from 14 different model or crop species. We have developed the concept of GreenCards for text based retrieval of all data types in GabiPD (e.g., clones, genes, mutant lines). All data types point to a central Gene GreenCard, where gene information is integrated from genome projects or NCBI UniGene sets. The centralised Gene GreenCard allows visualising ESTs aligned to annotated transcripts as well as displaying identified protein domains and gene structure. Moreover GabiPD makes available interactive genetic maps from potato and barley, and 2DE-gels from Arabidopsis thaliana and Brassica napus. Gene expression and metabolic profiling data can be visualised through MapManWeb. By the integration of complex data in a framework of existing knowledge, GabiPD provides new insights and allows for new interpretations of the data. http://dx.doi.org/10.1038/npre.2008.2210.1 Fri, 22 Aug 2008 09:31:55 UTC GabiPD: The GABI Primary Database – a plant integrative ‘omics’ database doi:10.1038/npre.2008.2210.1 2008-08-22 Diego Mauricio Riaño-Pachón Nature Precedings 2008-08-22T09:31:55Z Manuscript Genetics & Genomics Molecular Cell Biology Bioinformatics http://creativecommons.org/licenses/by/3.0/