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Generic Feature Database A Simple Scheme for Feature Storage Shawn Hoon Fugu Informatics Group Institute of Molecular and Cell Biology
Associated Gene Family Splicing Enhancer/Repressor Elements Gene Transcript Protein Sequence Exon GenomicSequence Promoter Elements
Trees Alignments Seqfetcher Analysis Relationship SeqFeature GFD Entity Aggregator DBSeq Splicing Enhancer/ Repressor Elements Promoter Elements Protein Sequence Genomic Sequence Gene Family
A Converter Bio::Seq Bio::EnsEMBL::Seq Aggregator GFD
A Converter Bio::Seq Bio::EnsEMBL::Seq Aggregator Drivers HSP Seq Exon Protein Gene GFD
my @ens_seqfeature = get_ens_seqfeatures(); my $db = Bio::GFD::DBAdaptor->new(-dbname=> “somedb”,-host=>”mysql”,-user=>”root”) my $entity_id = $db->get_AggregatorAdaptor->store(-driver=“SeqFeature”, -method=>”store_ens_seq”, -store_objs=>@ens_seq); my @bio_seq = $db->get_AggregatorAdaptor->fetch(-driver=“Seq”, -method=> “fetch_Bio_Seq”, -id=> “entity_id”);
Efficiency? • Spawn off denormalized slice of the GFD for specific • Features or Analysis for web display • Easy to dump out using the aggregator layer
In the works BioperlDB DASI GMOD Browser GFD
Development We welcome thoughts/critiques on the design and whether there are other things we should in corporate. We welcome development in way of coding aggregators for objects of interest.
Availability GFD Web site: cvs -d :pserver:email@example.com:/home/cvs/repository co GFD firstname.lastname@example.org http://www.fugu-sg.org
Acknowledgements Alumni Tania Oh FuguI Team Elia Stupka Jer-Ming Chia Kiran Kumar Ratnapu Shawn Hoon