RGD Demo ISMB Scotland 8/03/04 Rat Genome Database RGD Dean Pasko Norie de la Cruz.

RGD Demo ISMB Scotland 8/03/04

Rat Genome DatabaseRGD

http://rgd.mcw.edu

Dean PaskoNorie de la Cruz


• 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’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


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’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 Home Page


Advanced and QuickSearches


Quick & Advanced Search


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


Quick Search-keyword

Enter Search

keyword keyword

*keyword ends with keyword

keyword* begins with keyword

*keyword* contains keyword

Results ordered: equals, begins, contains


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


Ontology searches

• searches term and descendants– if search for “antioxidant”, returns genes

annotated to glutathione dehydrogenase (ascorbate) activity, peroxidase activity, etc.


Advanced Search

• Boolean Logic– AND, OR, NOT

• Limit to 1 or more objects


Quick Search


Advanced Search


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


Search Results-Genes

Genesspeciessymbolnamegene descriptionchromosomelocation


Search Results Report


Search Results-QTL

QTLspeciessymbolnamechromosometraitsubtraitlocation


Search Results-Strains

Strainsspeciessymbolnamelocation


Search Results

Sort on any column

Show only selected itemsDownload reportGo back to summary pageSelect some or all records


Alternative search

Ontology search

Object search


Object Specific Searches


QTL Query


10:8

QTL Report

8

10


Gene Query


Gene Report


Virtual Comparative MapsVCMap


VCMap


The Gene Annotation Tool

(GATool)


Bioinformatics and biological databases

• bioinformatics is an oxymoron– biology is complex– informatics wants to abstract to general

principles



• 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



• the needs of biological research– focus on particular phenomena

• disease• organism• toxin• biomolecule

– "omics"

• data needs to be pulled from various sources



• 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



• 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



• 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



• inputs– species

• rat• mouse• human

– data format• comma delimited line• file• interval



• 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



• Inputs: species, input data format, data type



• Inputs: data fields



• Inputs: data field and output format



• outputs– HTML– delimited file



• outputs



• Outputs: with chromosomal region as input



• Outputs: with TIGR ids as input



• Outputs: with Affy ids as input



• internals– identifiers– data processing– scripts



– identifiers

GA idRGD id

Ll id

SP id

KEGG id

Unigene id

GB est id

GB mRNA idTIGR id

Affy id



• integration– predefined queries

• ontology browser• genome browser• reports

– linkouts• Other tools• Rgd reports• Data from other web dbs



• integration– predefined queries: ontology browser



• integration– predefined queries: genome browser



• upcoming developments– saved queries– notebook– advanced data mining (?)


GBrowseGenome Browser


Genome Browser


Search forQTL names

Genome Browser

Displays matchingQTLs on eachchromosome


Genome Browser


Genome browser -- ontology tracks

• annotated objects

• best evidence

• high level aggregators


Genome browser -- annotated object tracks


Genome browser -- best evidence tracks


Genome browser -- higher level aggregators


Genome browser -- Integration -- visual inspection


Genome browser -- Integration -- linkouts


Ontologies


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)



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


Information integration – navigating through ontologies and objects


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 Rat Genome Database RGD Dean Pasko Norie de la Cruz.

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