Generic Feature Database

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Generic Feature Database
A Simple Scheme for Feature Storage
Shawn Hoon Fugu Informatics Group Institute of
Molecular and Cell Biology
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Associated Gene Family
Splicing Enhancer/Repressor Elements
Gene
Transcript
Protein Sequence
Exon
GenomicSequence
Promoter Elements
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(No Transcript)
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A Converter
BioSeq
BioEnsEMBLSeq
Aggregator
GFD
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A Converter
BioSeq
BioEnsEMBLSeq
Aggregator
Drivers
HSP
Exon
Seq
Protein
Gene
GFD
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my _at_ens_seqfeature get_ens_seqfeatures() my
db BioGFDDBAdaptor-gtnew(-dbnamegt
somedb,-hostgtmysql,-usergtroot) my
entity_id db-gtget_AggregatorAdaptor-gtstore(-dr
iverSeqFeature,
-methodgtstore_ens_seq,
-store_objsgt_at_ens_seq) my _at_bio_seq
db-gtget_AggregatorAdaptor-gtfetch(-driverSeq,
-methodgt fetch_Bio_Seq,
-idgt entity_id)
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Efficiency?

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

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In the works
BioperlDB
GMOD Browser
DASI
GFD
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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.
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Availability
GFD Web site
cvs -d pservercvs_at_cvs.fugu-sg.org/home/cvs/rep
ository co GFD fugui_at_fugu-sg.org
http//www.fugu-sg.org
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Acknowledgements
Alumni Tania Oh
FuguI Team Elia Stupka Jer-Ming Chia Kiran Kumar
Ratnapu Shawn Hoon