An Exemplar for Data Integration in the Biomedical Domain Driven by the ISA Framework

7/28/2019 An Exemplar for Data Integration in the Biomedical Domain Driven by the ISA Framework

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An exemplar for data integration in the biomedicaldomain driven by the ISA framework 

Shannan Ho SuiAMIA Summits on Translational Bioinformatics

March 19, 2013

http://stemcellcommons.org

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This is a story aboutcollaboration...

7/28/2019 An Exemplar for Data Integration in the Biomedical Domain Driven by the ISA Framework

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ISA

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ISA

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• Inconsistent data formats, experimental

descriptions and results

Disparate Stem Cell Resources

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Disparate Stem Cell Resources

• Inconsistent data formats, experimental

descriptions and results

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The Stem Cell Commons

• A shared data andanalytical resource

• Bioinformatics support

for research at the HSCI

• A community

Datarepository

Analysissystem

Support/ 

consults

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The Stem Cell Commons

• A shared data andanalytical resource

• Bioinformatics support

for research at the HSCI

• A community

Datarepository

Analysissystem

Support/ 

consults

7/28/2019 An Exemplar for Data Integration in the Biomedical Domain Driven by the ISA Framework

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Susanna-Assunta Sansoneisacommons.org

user community

7/28/2019 An Exemplar for Data Integration in the Biomedical Domain Driven by the ISA Framework

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General-purpose, configurable format,designed to support the use of severalstandards  checklists, terminologies andconversions to (a growing number of) otherme t ad a t a formats , used by publ ic

repositories, e.g.

MAGE-Tab

SRA-xmlSOFT

Pride-xml

Susanna-Assunta Sansoneisacommons.org

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Rationale for developing ISA

§ Capture all salient features of the experimental workflow

§ Make annotation explicit anddiscoverable

§ Support data provenancetracking

§ Use community standards

Susanna-Assunta Sansoneisacommons.org

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ISA

Manual merging process

53 studies

1098 assays

87 studies

1179 assays

Curator

148 studies

2356 assays

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ISA

Conversion driven by ISA-Tab

53 studies

1098 assays

87 studies

1179 assays

ISA-Tab

148 studies

2356 assays

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7/28/2019 An Exemplar for Data Integration in the Biomedical Domain Driven by the ISA Framework

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Current Data Statistics

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7/28/2019 An Exemplar for Data Integration in the Biomedical Domain Driven by the ISA Framework

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Experiment description

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Experimental protocols and data downloads

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ISA-Tab metadata downloads and export

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Linking data to the Galaxy

workflow engine

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Refinery:An analysis and visualization framework

In development

7/28/2019 An Exemplar for Data Integration in the Biomedical Domain Driven by the ISA Framework

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Viewing and selecting samples in list view

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Viewing and selecting samples in matrix view

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Initiating workflows

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Monitoring progress

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Integration with the IGV genome browser

7/28/2019 An Exemplar for Data Integration in the Biomedical Domain Driven by the ISA Framework

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Challenges

• Changing research culture(s) to recognize the valueof data sharing

• Manually curating the data for consistency and

completeness

• Managing large volumes of data

• Standardizing workflows

• Ensuring interoperability when integrating multiplesystems and tools

• Technical complexity of software development effort

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Refinery

Psalm HaseleyNils Gehlenborg Richard Park Ilya SytchevPeter Park Shannan Ho Sui

7/28/2019 An Exemplar for Data Integration in the Biomedical Domain Driven by the ISA Framework

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ISA Commons

Philippe Rocca-Sera

Eamonn MaguireSusanna Sansone

Oxford e-Research Centre

A growing community that uses the ISA metadata trackingframework to facilitate standards-compliant collection, curation,

managementand reuse of datasets.

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WikiPathways

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Meet the Team

Center for Stem Cell Bioinformatics

Winston HideProgram Leader

Shannan Ho SuiAnalytics

Oliver HofmannCore services

Ilya SytchevBioinformatics Developer

John HutchinsonHSCI Analyst

Sudeshna DasRepository

Stéphane CorlosquetBioinformatics Engineer

Emily MerrillBioinformatics Analyst

• Nils Gehlenborg

• Richard Park

• Psalm Haseley

• Peter Park

Collaborators

• Eamonn Maguire

• Philippe Rocca-Sera

• Susanna Sansone