Abstract
AbstractThe 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":http://sgn.cornell.edu/) 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":http://solcyc.sgn.cornell.edu). 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":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":mailto:sgn-feedback@sgn.cornell.edu for more information.
Highlights
Solanaceae share conserved genomes, yet show rich phenotypic diversity. These characteristics allow us to address one of today's greatest challenges in biology: how do we reveal the phenotypes encoded by genome sequences? The clade-oriented approach is utilized for studying related species in one database
Since genes occur in networks, we can learn about putative function and phenotypes based on the relationship of one gene with its orthologs, paralogs, interacting genes, and pathway members
We have developed a 'network-browser' tool for visualising the complexity of gene-to-gene relationships
Summary
SGN is part of the bioinformatics platform for the International Solanaceae Project (SOL), which is currently sequencing the euchromatic portion (about 25%) of the 850 Mb tomato genome. With an SGN submitter account you can contribute your data to SGN on the web!
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