文档介绍：SRS - A Backbone for Genome Information and Data Grid Systems
Don Gilbert
Indiana University
******@
11/11/2017
Overview
Search/Retrieval in Genome Information systems
Efficiency plexity: RDBMS, SRS†, others
Genome data federation: local and distributed
Directories of data: automated S/R and the Grid
SRS, LDAP and future biodata grids
† Sequence Retrieval System, Lion Bioscience
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SRS - Genomes and Grids
Bioinformatics @ Indiana U. using SRS
Bio-info archiving and distribution
IUBio Archive, / -- public molecular biology data / software archive
Bio-Mirrors, .net/ -- Sequence and related biology databanks
Genome information systems
FlyBase, / -- genome infosystem of Drosophila fruitfly
euGenes, / -- infosystem for 8 important eukaryotes with 180,000 genes
Bio-Data Grids
/ -- experimental puting
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SRS - Genomes and Grids
Genome Information Systems
FlyBase, euGenes (SRS,Perl/Java)
Wormbase (AceDB > RDBMS, BioPerl)
Mouse GD, . GD (RDBMS)
GeneCards (Glimpse > XMLquery)
Ensembl (RDBMS,BioPerls)
Nascent: many newly anism genome systems
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SRS - Genomes and Grids
euGenes
8 eukaryote genomes mon summary data format
Describes 180,000 known, predicted and orphan genes
Gene Homologies parative summaries
Genome map views and feature annotations
Gene Ontology function, process and cell location integration
Efficient information search and retrieval methods
Extends FlyBase information system technology
Updated (semi) automatically from several sources
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SRS - Genomes and Grids
Genome attributes in euGenes July 2002
Genes as extracted from genome project sources. These differ from true gene numbers by orphan gene records, prediction artifacts, unmerged predicted/expt. records, and unfinished sequencing gaps.
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SRS - Genomes and Grids
Search/Retrieval for Genome DBs
Separate management and public search