Download Overview

GUS Overview
June 18, 2002
GUS-3.0
Genomics Unified Schema
• Supports application and data integration
• Uses an extensible architecture.
• Is object-oriented even though it uses an underlying
relational database management system (Oracle).
• Warehouse instead of federation for local stable copy
• Uses standards for bulk data exchange (e.g., MAGE)
• Annotation
GUS Usage
– of genomes - gene models, sequence features
– of genes - gene function, gene expression, gene
regulation
• Data mining
– Develop algorithms and queryable resource
• Publish
– Map identifiers with other resources/ databases
– URL for entry retrieval/ ad hoc queries in web interface
GUS-3.0 Name Spaces
GUS has 5 name spaces compartmentalizing different
types of information.
Namespace
Domain
Features
Core
Data Provenance
Workflows
Sres
Shared resorurces
Ontologies
DoTS
sequence and
annotation
Central dogma
RAD
Gene expresssion
MIAME
TESS
Gene regulation
Grammars
Application Integration: PlasmoDB
Public
Databases
GenBank,
InterPro,
GO, etc
Existing implementation
TIGR
Sanger
Stanford
Genomic
Sequence
Automated
Analysis &
Integration
Plasmodium
Investigators
GSSs &
ESTs
Annotation
Object Layer
DoTS Oracle/SQL TESS
RAD
WWW
queries,
browsing, &
download
Mapping
Data
Java Servlets
&
Perl CGI
Core
Future implementation
microArray
& SAGE
Experiments
Annotator’s
Interface
SRes
GenePlot
Software
QTL,POP,
SNP, Clinical
GenePlot
CD
GUS Supports Multiple Projects
AllGenes
PlasmoDB
EPConDB
Java Servlets
DoTS RAD TESS SRES Core
Oracle RDBMS
Object Layer for Data Loading
Other sites,
Other projects
Main Aspects of GUS Development
• Choice of development tools
– Schema:
• CREATE TABLE statements
• Documentation plug-in: input is tab- delimited text
• UML - Rational Rose, PowerDesigner
– Code: CVS
• Areas to emphasize
–
–
–
–
–
Plug-ins
Work flow
TESS
Proteomics
Images
• Preferred type of user interface
– JSP
– PHP
Data Integration
Core
Data
Provenance
• Ownership
• Protection
• AlgorithmsDoTS
• Similarity
• Versioning Genomic
• Workflow Sequence
SRes
Ontologies
• GO
• Species
• Tissue
• Dev. Stage
Transcribed
Sequence
Protein
Sequence
• Genes, gene models
• STSs, repeats, etc
• Cross-species analysis
RAD
Transcript
• Characterize transcripts
Expression
• RH mapping
• Library analysis
• Cross-species analysis
• DOTS
• Domains
• Function
• Structure
• Cross-species analysis
•Arrays
•SAGE
•Conditions
TESS
Gene
Regulation
• Binding Sites
• Patterns
• Grammars
Transcription factors up-regulated in acute myeloid leukemia
with sequence similarity to c-fos and common promoter motifs
RAD
GUS
EST clustering
and assembly
Identify shared
TF binding sites
TESS
Genomic alignment
and comparative
Sequence analysis
GUS Approach to Schema
• Think objects
– Parents and children
– Subclassing with views
• Views
– Start with generic Imp table (e.g., NAFeatureImp) that
contains base attributes plus generic attributes of
various datatypes
– Superclass view (e.g., NAFeature) just has base
attributes
– Subclass views (e.g., RNAFeature) have additional
attributes using generic attributes
• Strongly-typed
– Tend to avoid “name-value” pairs
DoTS Central Dogma
Gene
Instance
Gene
Feature
RNA
RNA
Instance
NA
Feature
RNA
Feature
Protein
Protein
Instance
Gene
Protein
Feature
AA
Feature
Genomic
Sequence
RNA
Sequence
Protein
Sequence
NA
Sequence
AA
Sequence
DoTS Schema Has Been Driven By Building Gene Indices
Genomic
Sequence
Gene predictions
GenScan/ HMMer, PHAT
mRNA/EST
Sequence
SIM4 or BLAT
Predicted
Genes
Merge Genes
Clustering and
Assembly
DoTS consensus
Sequences
Gene/RNA cluster
assignment
Annotate DoTS
Manual Annotation
Tasks
RNAs
BLASTX
Other computed annotation
(EPCR,
AssemblyAnatomyPercent,
Index Key Words,
SNP analysis)
BLAST Similarities
Gene
Index
framefinder
translation
BLASTP
Functional predictions
GO Functions
Proteins
PFAM, Smart, ProDom
Protein
Motifs
DoTS Gene Indices Are Based on
Clustering and Assembling ESTs
Identify new sequences
In GenBank and dbEST
•Remove vector, polyA tails, ribosomal
and poor quality sequences
•Mask repeats with RepeatMasker
“Quality” AssemblySequences
•BLAST N vs self
•BLASTN vs DoT S
•Connected components analysis to form clusters
Clusters of sequences
(40 bp length, 92% identity)
•Assemble clusters using CAP4
• update database
Iterate to complete build
-Extract consensus sequences
GUS relational database
-Block with RepeatMasker
-BLAST N vs self
-Cluster (95% identity, 75 bp overlap)
-Assemble with CAP4
Annotation of DoTS consensus sequences
-protein translations withframefinder
-BLAST analyses vsnrdb, prodom and CDD
-assign description and index keywords
-GOFunction assignment
-EPCR to generate radiation hybrid mapping
-derive assembly -> anatomy mapping
-alignment to genomic DNA
-assignment to“Gene” clusters
RAD 3.0 Schema Incorporates MAGE and Experience With Microarrays
EXPERIMENTGROUP
AnalysisOutput
0..*
AnalysisImplementation
LABEL
1
0..*
1
0..1
1
1
0..*
AnalysisParameter
GROUPFACTOR
0..*
Analysis
1
0..*
LABELEDEXTRACT
1
AnalysisInput
BIOSAMPLE
BIOSOURCE
0..*
1
BioMaterialImp
ASSAYGROUPFACTOR
0..*
1
1
1
1
ARRAYANNOTATION
0..*
ARRAY
0..*
1
0..*
0..*
BIOMATERIALIMP
1
0..*
RELATEDASSAY
ASSAY
1
1
0..*
1
ASSAYLABELEDEXTRACT
1
0..*
0..*
RELATEDACQUISITION
ACQUISITION
0..1
BIOSOURCECHARACTERISTIC
0..*
0..*
1
0..*
0..*
PROTOCOL
0..1
0..*
0..*
CONTROL
1
1
1
0..*
1
ACQUISITIONPARAMETER
0..1
ONTOLOGYENTRY
ELEMENTIMP
0..*
TREATMENT
0..*
0..*
ELEMENTANNOTATION
0..*
0..*
CONTROLTYPE
0..*
BIOMATERIALMEASUREMENT
1
0..*
1
1
0..*
BioMaterialImp
COMPOSITEELEMENTIMP
1
0..*
1
1
0..11
0..1
0..*
1
0..*
RELATEDQUANTIFICATION
QUANTIFICATION
0..*
0..1
1
0..*
1
COMPOSITEELEMENTANNOTATION
QUANTIFICATIONPARAMETER
0..*
0..*
0..*
ELEMENTRESULTIMP
COMPOSITEELEMENTRESULTIMP
0..*
PROCESSPARAMETER
0..1
0..*
1
0..*
PROCESSTYPE
PROCESS
ProcessInput
1
1
0..*
0..1
0..*
0..*
0..*
0..*
1
PROCESSIMPPARAMETER
1
PROCESSIMPLEMENTATION
ProcessOutput
1
0..*
LIMS for Data Analysis. Also holds SAGE.
0..*
Status of GUS Namespaces
• Core
– Tables exist, Workflow documented
• Sres
– Tables exist
• DoTS
– Tables exist, some documentation
• RAD
– Version 3.0 to include MAGE, experience
• Pretty much complete
– Tables exist, mostly documented
• TESS
– Tables ready but not created
Schema Development
• Releases on Sourceforge:
– CREATE TABLE statements
– Table dumps from Core::TableInfo,
Core::DatabaseDocumentation
– Gifs of ER diagrams
• Adding tables between releases
– In CVS tree?
– Use message forum for discussion
Documentation
• Schema Browser looks at TableInfo
• Plug-in
– Populates DatabaseDocumentation
– Input:
Table\t\tDescription of table
Table\tAttribute\tDescription of
attribute
GUS Schema Browser
• http://www.cbil.upenn.edu/cgibin/GUS30/schemaBrowser.pl?db=GUS30
• Points at GUS30 on CBIL development database
server (erebus).
– Need to move? Maintain release view?
• DoTS Tables:
–
–
–
–
–
Central dogma
Evidence/ Similarity
ProjectLink
SequenceGroupImp/ SequenceGroupExperimentImp
Plasmomap?
• Other tables of interest?