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Generic Feature Database

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. Genomic Sequence. Promoter Elements. Trees

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Generic Feature Database

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  1. Generic Feature Database A Simple Scheme for Feature Storage Shawn Hoon Fugu Informatics Group Institute of Molecular and Cell Biology

  2. Associated Gene Family Splicing Enhancer/Repressor Elements Gene Transcript Protein Sequence Exon GenomicSequence Promoter Elements

  3. Trees Alignments Seqfetcher Analysis Relationship SeqFeature GFD Entity Aggregator DBSeq Splicing Enhancer/ Repressor Elements Promoter Elements Protein Sequence Genomic Sequence Gene Family

  4. A Converter Bio::Seq Bio::EnsEMBL::Seq Aggregator GFD

  5. A Converter Bio::Seq Bio::EnsEMBL::Seq Aggregator Drivers HSP Seq Exon Protein Gene GFD

  6. 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”);

  7. Efficiency? • Spawn off denormalized slice of the GFD for specific • Features or Analysis for web display • Easy to dump out using the aggregator layer

  8. In the works BioperlDB DASI GMOD Browser GFD

  9. 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.

  10. Availability GFD Web site: cvs -d :pserver:cvs@cvs.fugu-sg.org:/home/cvs/repository co GFD fugui@fugu-sg.org http://www.fugu-sg.org

  11. Acknowledgements Alumni Tania Oh FuguI Team Elia Stupka Jer-Ming Chia Kiran Kumar Ratnapu Shawn Hoon

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