rgd demo ismb scotland 8/03/04 rat genome database rgd dean pasko norie de la cruz
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RGD Demo ISMB Scotland 8/03/04
Rat Genome DatabaseRGD
http://rgd.mcw.edu
Dean PaskoNorie de la Cruz
RGD Demo ISMB Scotland 8/03/04
• Rat Genome Database is a NIH funded project NHLBI (grant HL64541) Database went public on June 1, 2000
RGD’s mission statement:
“RGD curates and integrates all rat genetic and genomic data and provides access to this data to support research using the rat as a genetic model to study human diseases.”
RGD Background
RGD Demo ISMB Scotland 8/03/04
RGD’s curation and integration involves many processes:
• Manual curation of literature• Informatic curation/validation of both curated and non-curated data loaded into the database• Leveraging of comparative genomic and functional data to annotate rat data
RGD Background
RGD Demo ISMB Scotland 8/03/04
Rat offers many resources for comparative genomics
• Rat is a great model organism for human disease• RGD has tools to relate phenotype and disease
Rat QTL data Mouse QTL data Human QTL data
• New genome sequence (Nature, April of 2004) • Human and Mouse homolog data and reports• Gene ontology data• Phenotype ontology data• Disease ontology data
Comparative Genomics
RGD Demo ISMB Scotland 8/03/04
RGD’s multi-species and comparative tools• Advance/quick search
Comprehensive for rat data (annotations, ontologies, etc.) Homologs - searches symbol and name and ontologies (coming soon!)
• Virtual Comparative Map (VCMap) – EST/Unigene based• Gene Annotation – query tool for multiple databases for Rat, Mouse, and Human
RGD’s genome browser• GBrowse (GMOD open source tool)
RGD object specific query tools• Genes, QTLs, Strains, Ontologies, Homologs, etc.
RGD Tools
RGD Demo ISMB Scotland 8/03/04
RGD Home Page
RGD Demo ISMB Scotland 8/03/04
Advanced and QuickSearches
RGD Demo ISMB Scotland 8/03/04
Quick & Advanced Search
RGD Demo ISMB Scotland 8/03/04
Search for RGD_ID Quick Search & Advanced Search
• enter: one RGD_ID or RGD:RGD_ID• returns: report page for the object with
that RGD_ID• no other numbers (e.g., Entrez Gene or
Ratmap ID) can be searched• only one ID can be searched at a time
RGD Demo ISMB Scotland 8/03/04
Quick Search-keyword
Enter Search
keyword keyword
*keyword ends with keyword
keyword* begins with keyword
*keyword* contains keyword
Results ordered: equals, begins, contains
RGD Demo ISMB Scotland 8/03/04
Special CasesQuick Search & Advanced Search
Enter Search
keyword1 keyword2 “keyword1 keyword2”
a; the; as; etc. will not perform search (returns not found)
am performs search
NM_, A1- NM; A1
RGD Demo ISMB Scotland 8/03/04
Ontology searches
• searches term and descendants– if search for “antioxidant”, returns genes
annotated to glutathione dehydrogenase (ascorbate) activity, peroxidase activity, etc.
RGD Demo ISMB Scotland 8/03/04
Advanced Search
• Boolean Logic– AND, OR, NOT
• Limit to 1 or more objects
RGD Demo ISMB Scotland 8/03/04
Quick Search
RGD Demo ISMB Scotland 8/03/04
Advanced Search
RGD Demo ISMB Scotland 8/03/04
Results Summary Page
Found Returns
more than one object intermediate page: list of objects and # of each found
> 10 of a single object found
intermediate page: # of the object found
< 10 of a single object found
results page
RGD Demo ISMB Scotland 8/03/04
Search Results-Genes
Genesspeciessymbolnamegene descriptionchromosomelocation
RGD Demo ISMB Scotland 8/03/04
Search Results Report
RGD Demo ISMB Scotland 8/03/04
Search Results-QTL
QTLspeciessymbolnamechromosometraitsubtraitlocation
RGD Demo ISMB Scotland 8/03/04
Search Results-Strains
Strainsspeciessymbolnamelocation
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Search Results
Sort on any column
Show only selected itemsDownload reportGo back to summary pageSelect some or all records
RGD Demo ISMB Scotland 8/03/04
Alternative search
Ontology search
Object search
RGD Demo ISMB Scotland 8/03/04
Object Specific Searches
RGD Demo ISMB Scotland 8/03/04
QTL Query
RGD Demo ISMB Scotland 8/03/04
10:8
QTL Report
8
10
RGD Demo ISMB Scotland 8/03/04
Gene Query
RGD Demo ISMB Scotland 8/03/04
Gene Report
RGD Demo ISMB Scotland 8/03/04
Virtual Comparative MapsVCMap
RGD Demo ISMB Scotland 8/03/04
VCMap
RGD Demo ISMB Scotland 8/03/04
VCMap
RGD Demo ISMB Scotland 8/03/04
VCMap
RGD Demo ISMB Scotland 8/03/04
VCMap
RGD Demo ISMB Scotland 8/03/04
VCMap
RGD Demo ISMB Scotland 8/03/04
VCMap
RGD Demo ISMB Scotland 8/03/04
VCMap
RGD Demo ISMB Scotland 8/03/04
VCMap
RGD Demo ISMB Scotland 8/03/04
The Gene Annotation Tool
(GATool)
RGD Demo ISMB Scotland 8/03/04
Bioinformatics and biological databases
• bioinformatics is an oxymoron– biology is complex– informatics wants to abstract to general
principles
RGD Demo ISMB Scotland 8/03/04
Bioinformatics and biological databases
• proliferation reflects complexity of biology
• classes of biological databases defined by NAR DB issue
– major sequence repositories
– gene expression
– comparative genomics
– gene identification and structure
– genetic and physical maps
– genomic databases
– intermolecular interactions
– metabolic pathways and cellular regulation
– mutation database
– pathology
– model organism
• uncontrolled: so much data, so little time
RGD Demo ISMB Scotland 8/03/04
Bioinformatics and biological databases
• the needs of biological research– focus on particular phenomena
• disease• organism• toxin• biomolecule
– "omics"
• data needs to be pulled from various sources
RGD Demo ISMB Scotland 8/03/04
Bioinformatics and biological databases
• challenges
– gather and collate data from various objects
– link object data in one coherent package
– provide some customizability in output
– provide capability for user to do further analyses on output
– allow link backs to original sources for more detailed study
• uses
– hypothesis generation
– knowledge base
– data mining
RGD Demo ISMB Scotland 8/03/04
The Gene Annotation Tool
RGD Demo ISMB Scotland 8/03/04
The Gene Annotation Tool
• overview– history
• llparser• gene annotation tool with
locuslink,swissprot,kegg data• gene annotation tool with RGD data and
HTML option for linkouts• gene annotation tool with host of new
functions and input under development
RGD Demo ISMB Scotland 8/03/04
The Gene Annotation Tool
• overview– The tool
• Receive inputs from user via web form• Packages data and information from several
web dbs and returns the output as HTML or a delimited text file
RGD Demo ISMB Scotland 8/03/04
The Gene Annotation Tool
• inputs– species
• rat• mouse• human
– data format• comma delimited line• file• interval
RGD Demo ISMB Scotland 8/03/04
The Gene Annotation Tool
• inputs– data type
• gene symbol• gene ids• sequence ids• interval
– data field• objects in a given interval• from RGD• from KEGG• from SwissProt• from LocusLink
RGD Demo ISMB Scotland 8/03/04
The Gene Annotation Tool
• Inputs: species, input data format, data type
RGD Demo ISMB Scotland 8/03/04
The Gene Annotation Tool
• Inputs: data fields
RGD Demo ISMB Scotland 8/03/04
The Gene Annotation Tool
• Inputs: data field and output format
RGD Demo ISMB Scotland 8/03/04
The Gene Annotation Tool
• outputs– HTML– delimited file
RGD Demo ISMB Scotland 8/03/04
The Gene Annotation Tool
• outputs
RGD Demo ISMB Scotland 8/03/04
The Gene Annotation Tool
• Outputs: with chromosomal region as input
RGD Demo ISMB Scotland 8/03/04
The Gene Annotation Tool
• Outputs: with TIGR ids as input
RGD Demo ISMB Scotland 8/03/04
The Gene Annotation Tool
• Outputs: with Affy ids as input
RGD Demo ISMB Scotland 8/03/04
The Gene Annotation Tool
• internals– identifiers– data processing– scripts
RGD Demo ISMB Scotland 8/03/04
The Gene Annotation Tool
– identifiers
GA idRGD id
Ll id
SP id
KEGG id
Unigene id
GB est id
GB mRNA idTIGR id
Affy id
RGD Demo ISMB Scotland 8/03/04
The Gene Annotation Tool
• integration– predefined queries
• ontology browser• genome browser• reports
– linkouts• Other tools• Rgd reports• Data from other web dbs
RGD Demo ISMB Scotland 8/03/04
The Gene Annotation Tool
• integration– predefined queries: ontology browser
RGD Demo ISMB Scotland 8/03/04
The Gene Annotation Tool
• integration– predefined queries: genome browser
RGD Demo ISMB Scotland 8/03/04
The Gene Annotation Tool
• upcoming developments– saved queries– notebook– advanced data mining (?)
RGD Demo ISMB Scotland 8/03/04
GBrowseGenome Browser
RGD Demo ISMB Scotland 8/03/04
Genome Browser
RGD Demo ISMB Scotland 8/03/04
Search forQTL names
Genome Browser
Displays matchingQTLs on eachchromosome
RGD Demo ISMB Scotland 8/03/04
Genome Browser
RGD Demo ISMB Scotland 8/03/04
Genome Browser
RGD Demo ISMB Scotland 8/03/04
Genome browser -- ontology tracks
• annotated objects
• best evidence
• high level aggregators
RGD Demo ISMB Scotland 8/03/04
Genome browser -- annotated object tracks
RGD Demo ISMB Scotland 8/03/04
Genome browser -- best evidence tracks
RGD Demo ISMB Scotland 8/03/04
Genome browser -- higher level aggregators
RGD Demo ISMB Scotland 8/03/04
Genome browser -- Integration -- visual inspection
RGD Demo ISMB Scotland 8/03/04
Genome browser -- Integration -- linkouts
RGD Demo ISMB Scotland 8/03/04
Ontologies
RGD Demo ISMB Scotland 8/03/04
Implementation of Multiple Ontologies at the Rat Genome Database
Ontologies are controlled vocabularies that orderconcepts in a hierarchical fashion
Currently three ontologies are being usedto annotate genes, QTLs, strains and homologs
Gene Ontology (GO) Component Function Process
Phenotype Ontology (PO)
Disease Ontology (DO)
RGD Demo ISMB Scotland 8/03/04
Implementation of Multiple Ontologies at the Rat Genome Database
RGD Demo ISMB Scotland 8/03/04
Implementation of Multiple Ontologies at the Rat Genome Database
Multiple object type reports – genes, QTLs and strains –can be retrieved using terms for any of the
ontologies used for annotations
Multiple ontology reports can be accessed from the annotations associated with any particular object type
Program for Genetic ApplicationPhysGen - Physiogenomics of Stressors
in Derived Consomic Rats
RGD Demo ISMB Scotland 8/03/04
Information integration – navigating through ontologies and objects
RGD Demo ISMB Scotland 8/03/04
Information integration – navigating through ontologies and objects
RGD Demo ISMB Scotland 8/03/04
Information integration – navigating through ontologies and objects
RGD Demo ISMB Scotland 8/03/04
Information integration – navigating through ontologies and objects
RGD Demo ISMB Scotland 8/03/04
Information integration – navigating through ontologies and objects
RGD Demo ISMB Scotland 8/03/04
Information integration – navigating through ontologies and objects
RGD Demo ISMB Scotland 8/03/04
Information integration – navigating through ontologies and objects
RGD Demo ISMB Scotland 8/03/04
RGD Demo ISMB Scotland 8/03/04
Rat Genome DatabaseHoward Jacob, Principal Investigator
Simon Twigger, Co-Principal InvestigatorAnne Kwitek, Advisor
Weihong Jin, WebmasterPeter Tonellato, Advisor
Collaborators: MGI, RGSC, NCBI, UniProt, Ensembl, RatMap, BIND
Data Integration and Comparative Analysis
Susan Bromberg, Team LeaderCindy Foote, Offsite Curator
Glenn Harris, CuratorRajni Nigam, Curator
Dorothy Reilly, Offsite CuratorAngela Zuniga-Meyer, Curation Assistant
Data Exploration and Discovery
Mary Shimoyama, Team leaderNataliya Nenasheva, Curation Assistant
Victoria Petri, GO CuratorCharles Wang, Curator
Database and Tool Management
Dean Pasko, Team LeaderJiali Chen, Analyst/Project Programmer Henry Fan, Analyst/Project Programmer Wenhua Wu, Bioinformatics Specialist Lan Zhao, Analyst/Project Programmer
Data Mining and Advanced Tool Development
Norie de la Cruz, Team Leader
Hang Liu , Analyst/Project Programmer Jed Mathis, Data Analyst/Programmer
RGD Demo ISMB Scotland 8/03/04
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