http://precedings.nature.com/users/9e02a42d81d489a9ed5101306d1a6ec9/ Documents posted by Naama Menda 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.2009.3160.1 Quantitative trait loci (QTL) analysis is used to dissect the genetic basis underlying polygenic traits. Several public databases have been storing and making QTL data available to research communities. To our knowledge, current QTL databases rely on manual curation where curators read literature and extract relevant QTL information to store in databases. Evidently, this approach is expensive in terms of expert manpower and time use and limits the type of data that can be curated. At the Solanaceae Genomics Network (SGN) (http://sgn.cornell.edu), we have developed a database to store raw phenotype and genotype data from QTL studies, perform, on the fly, QTL analysis using R/QTL statistical software (http://www.rqtl.org) and visualize QTLs on a genetic map. Users can identify peak, and flanking markers for QTLs of traits of interest. The QTL database is integrated with other SGN databases (eg. Marker, BACs, and Unigenes), and analysis tools such as the Comparative Map Viewer. Using the comparative map viewer, users can compare chromosome with QTL regions to genetic maps of interest from the same or different Solanaceae species. As the tomato genome sequencing advances, users can also identify corresponding BAC sequences or locations on the tomato physical map, which can be suggestive of candidate genes for a trait of interest.Furthermore at SGN, images, quantitative phenotype and genotype data, publications, genetic maps generated by QTL studies are displayed and available for download. Currently, data from three F2 and two backcross population QTL studies on fruit morphology traits (18 – 46 traits per population) is available at the SGN website for viewing at population, accession, and trait levels. Traits are described using ontology terms. Phenotype data is presented in tabular and graphical formats such as frequency distributions with basic descriptive statistics. Mapping data showing location of parental alleles on individual accession genetic maps is also available.SGN is a public database hosted at Boyce Thomson Institute, Cornell University, and funded by USDA CSREES and NSF. http://dx.doi.org/10.1038/npre.2009.3160.1 Thu, 23 Apr 2009 17:11:49 UTC SGN Database: From QTLs to Genomes doi:10.1038/npre.2009.3160.1 2009-09-18 Isaak Y. Tecle Nature Precedings 2009-04-23T17:11:49Z Poster Genetics & Genomics Bioinformatics Plant Biology http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3192.1 MetaCyc is a metabolic encyclopedia of experimentally validated biochemical pathways curated from scientific literature, that spans all organisms, with an emphasis on plants and microbes. The Pathway tools is a complex curation software suite that enables curation of reactions, construction of pathways and annotation with one or more representative enzymes, that include information such as substrate specificity, kinetic properties, activators, inhibitors, cofactor requirements, genes if cloned and links to external databases. In addition curators are able to provide concise, review-level summaries and extensive literature citations. The present database release includes more than 1200 pathways from more than 1549 organisms, 7312 reactions, 5127 enzymes, 4748 genes, 7234 chemical compounds, curated from 17916 citations. The MetaCyc database is the reference database on which the pathways are predicted from annotated genomes by PathoLogic called Pathway/genome Databases (PGDB’s). The Biocyc Database (biocyc.org) has a collection over 300 PGDB’s. Each BioCyc Database describes the genome and predicted metabolic pathways of a single organism, which are then taken up by interested groups for curation. SolCyc is one such PGDB, developed for the clade oriented Solanceae Genomics Network (SGN) database. It has predicted metabolic pathway databases of significant species belonging to Solanaceae and includes Lycocyc(tomato), Solacyc (eggplant), Nicotianacyc (tobacco),Petuniacyc (Petunia), Capcyc (Capsicum) , Potatocyc (potato). An interactive webinterface has been developed for the seamless flow of information from the SGN phenotype and locus database with SolCyc. This facilitates researchers with the capacity to search for underlying metabolic pathway information of genes and phenotypes that has been curated into the SolCyc database. http://dx.doi.org/10.1038/npre.2009.3192.1 Tue, 28 Apr 2009 18:40:24 UTC Plant Metabolic Pathways in MetaCyc and SolCyc doi:10.1038/npre.2009.3192.1 2009-04-28 Anuradha Pujar Nature Precedings 2009-04-28T18:40:24Z Poster Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3134.1 The concept of community annotation is a growing discipline for achieving participation of the research community in depositing up‐to‐date knowledge in biological databases.The Solanaceae Genomics Network (SGN) is a clade‐oriented database (COD) focusing on plants of the nightshade family, including tomato, potato, pepper, eggplant, and tobacco, and is one of the bioinformatics nodes of the international tomato genome sequencing project. One of our major efforts is linking Solanaceae phenotype information with the underlying genes, and subsequently the genome. As part of this goal, SGN has introduced a database for locus names and descriptors, and a database for phenotypes of natural and induced variation. These two databases have web interfaces that allow cross references, associations with tomato gene models, and in‐house curated information of sequences, literature, ontologies, gene networks, and the Solanaceae biochemical pathways database (SolCyc). All of our curator tools are open for online community annotation, through specially assigned “submitter” accounts. Currently the community database consists of 5,548 phenotyped accessions, and 5,739 curated loci, out of which more than 300 loci where contributed or annotated by 66 active submitters, creating a database that is truly community driven.This framework is easily adaptable for other projects working on other taxa (for example see http://chlamybase.org), greatly expanding the application of this user‐friendly online annotation system. Community participation is fostered by an active outreach program that includes contacting potential submitters via emails, at meetings and conferences, and by promoting featured user submitted annotations on the SGN homepage. The source code and database schema for all SGN functionalities are freely available. Please contact SGN at sgn‐feedback[at]sgn.cornell.edu for more information. http://dx.doi.org/10.1038/npre.2009.3134.1 Wed, 22 Apr 2009 21:15:52 UTC The SOL Genomics Network Model: Making Community Annotation Work doi:10.1038/npre.2009.3134.1 2009-04-22 Naama Menda Nature Precedings 2009-04-22T21:15:52Z Poster Bioinformatics Plant Biology http://creativecommons.org/licenses/by/3.0/