Haider Embrace Bosc2008

EMBRACE – BioMart Developments & Future

Syed HaiderRice Group - EBIJuly 2008

EMBRACEwww.embracegrid.info

European Model for Bioinformatics Research and Community Education

Objective:

to integrate the major databases and software

tools in bioinformatics

A Collaboration:

- European Bioinformatics Institute (EBI)

- Ontario Institute for Cancer Research (OICR)

BioMartwww.biomart.org

BioMart

A generic data management system with a particular focus on supporting biological research featuring:

- Built-in query optimisation for fast data retrieval- Data Federation- Easy to use interfaces and APIs- Web Services and DAS

In a nutshell

ATGCTGTTGTGCATGCTGGACTGGATGGCCCGATGGATGCTGTTGTGCATGCTGGACTGGATGGCCCGATGG

Source data(MySQL, Oracle, Postgres)

DB

Mart

Deploying BioMart

– STEP 1 - Transformation– STEP 2 - Configuration

1. Transformation

ATGCTGTTGTGCATGCTGGACTGGATGGCCCGATGGATGCTGTTGTGCATGCTGGACTGGATGGCCCGATGG

DB

Mart

Source data(MySQL, Oracle, Postgres)

1. TransformationMartBuilder

2. Configuration

Mart

Mart

Mart

2. ConfigurationMartEditor

User Interfaces

Concepts for End Users

1.Dataset

2.Filter

3.Attribute

Examples of all rat genes

located on chromosome 1, expressed in lungs

name, chromosome, description

of all mouse genes

ENSMUSG00000042351

exon sequences in FASTA format

of all rat genes

up-regulated in brain and associated with a QTL for

a neurological disorder

Upstream sequences

Web Service Access

<Query>

<Dataset name="hsapiens_gene_ensembl" >

<Filter name="chromosome_name" value="1"/><Attribute name="ensembl_gene_id"/><Attribute name="ensembl_transcript_id"/><Attribute name="biotype"/>

</Dataset> </Query>

wget --post-data 'query=

‘http://www.biomart.org/biomart/martservice

Web Service Access

<Query>

<Dataset name="hsapiens_gene_ensembl" >

<Filter name="chromosome_name" value="1"/><Attribute name="ensembl_gene_id"/><Attribute name="ensembl_transcript_id"/><Attribute name="biotype"/>

</Dataset> </Query>

wget --post-data 'query=

‘http://www.biomart.org/biomart/martservicemartview

VIRTUALSCHEMANAME=default

&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.

ensembl_gene_id

&FILTERS=hsapiens_gene_ensembl.default.filters.

chromosome_name."1"

Web Service AccessXML Free URL

http://biomart.org/biomart/martview?

BioMart DAS Access

http://www.YourBioMart.org/biomart/das/DATASET/features? segment=FILTERS

http://www.biomart.org/biomart/das/default__hsapiens_gene_ensembl__ensembl_das_chr/features? segment=1:1,100000

http://www.biomart.org/biomart/das/default__hsapiens_gene_ensembl__ensembl_das_gene/features? segment=ENSG00000197194

Web based AccessHow far it has gone ?

Taverna

BiomaRt - BioConductor package

Cytoscape

Galaxy

Template Queries

Learn as you go....

Show URL Request

Show XML Query

Show Perl Script

- Scalability - Maintaining large databases and configurations

- Security- UserName/Password based access for clinical and

experimental data etc

- Multiple and Custom GUIs

Future

- Beyond rows and columns- Framework for Visualisations and Analysis Tools

Future

Visualisation: Gene List Analysis & Clinical Significance

Gene List

Query

Visualisation

Gene list analysis

Clinical SignificanceResponse to

therapy

Map genes onto genome

Map genes onto GO

Map genes onto Pathways

Map Genes onto Genome

Visualisation: Gene List Analysis & Clinical Significance

Gene List

Query

Visualisation

Gene list analysis

Clinical SignificanceResponse to

therapy

Map genes onto genome

Map genes onto GO

Map genes onto Pathways

Map Genes onto GO

GO

Biological process (32)

Cellular component (18)

Molecular Function (24)

Stem cell maintenance (7)

Positive regulation of developmental process (8)

Leukocyte mediated cytotoxicity (5)

regulation of cell killing (12)

Developmental process (15)

Cell killing (17)

Visualisation: Gene List Analysis & Clinical Significance

Gene List

Query

Visualisation

Gene list analysis

Clinical SignificanceResponse to

therapy

Map genes onto genome

Map genes onto GO

Map genes onto Pathways

Map Genes onto Pathways

Reactome

Apoptosis (43)

Intrinsic pathway for apoptosis (26)

Signaling by Wnt (10)

Signaling by TGFβ (23)

Activation of BH3-only proteins (5)

Permeabilization of mitochondria (3)

Release of apoptotic factors from mitochondria (18)

Future- Summary Pages

Annotation for each gene

1. Entrez/Ensembl gene info

2. Gene ontology/pathways

3. Biblography

4. Transcript & protein info, etc.

Genomic variations for each gene

1. for each cancer studied

Information for each patient

1. Demographics

2. History of cancer

3. Progress & outcome

4. Types of samples available

5. Histopathology of tumor

Submission support

Galaxy

BioMart TeamArek Kasprzyk (OICR-Toronto)

Syed Haider (Rice Group-EBI)

AcknowledgementsBenoit Ballester (Ensembl) Richard Holland (Ensembl)

Andreas Kahari (Ensembl) Craig Melsopp (Ensembl)

Damian Smedley (Ensembl) Arne Stabenau (Ensembl)

Asif Kibria (EBI) Gulam Patel (EBI)

Stephen Robinson (EBI) Katerina Tzouvara (EBI)

Will Spooner (CSHL) Gudmundur Thorisson (CSHL)

Darin London (Duke University) Don Gilbert (Indiana University)

Steffen Durinck (NCI NIH) Eric Just (Northwestern University)

Paul Donlon (Unilever) Christina Yung (OICR)

Igor Antoshechkin (Caltech)

Credits

References

Thanks.

BioMart Central Portal – queries served

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