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An exemplar for data integration in the biomedical domain driven by the ISA framework Shannan Ho Sui AMIA Summits on Translational Bioinformatic s March 19, 2013 http://stemcellcommons.org
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
7/28/2019 An Exemplar for Data Integration in the Biomedical Domain Driven by the ISA Framework
http://slidepdf.com/reader/full/an-exemplar-for-data-integration-in-the-biomedical-domain-driven-by-the-isa 2/32
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
7/28/2019 An Exemplar for Data Integration in the Biomedical Domain Driven by the ISA Framework
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ISA
7/28/2019 An Exemplar for Data Integration in the Biomedical Domain Driven by the ISA Framework
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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
7/28/2019 An Exemplar for Data Integration in the Biomedical Domain Driven by the ISA Framework
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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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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
http://slidepdf.com/reader/full/an-exemplar-for-data-integration-in-the-biomedical-domain-driven-by-the-isa 9/32
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
7/28/2019 An Exemplar for Data Integration in the Biomedical Domain Driven by the ISA Framework
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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
7/28/2019 An Exemplar for Data Integration in the Biomedical Domain Driven by the ISA Framework
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ISA
Manual merging process
53 studies
1098 assays
87 studies
1179 assays
Curator
148 studies
2356 assays
7/28/2019 An Exemplar for Data Integration in the Biomedical Domain Driven by the ISA Framework
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ISA
Conversion driven by ISA-Tab
53 studies
1098 assays
87 studies
1179 assays
ISA-Tab
148 studies
2356 assays
7/28/2019 An Exemplar for Data Integration in the Biomedical Domain Driven by the ISA Framework
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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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7/28/2019 An Exemplar for Data Integration in the Biomedical Domain Driven by the ISA Framework
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Current Data Statistics
7/28/2019 An Exemplar for Data Integration in the Biomedical Domain Driven by the ISA Framework
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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
7/28/2019 An Exemplar for Data Integration in the Biomedical Domain Driven by the ISA Framework
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Experimental protocols and data downloads
7/28/2019 An Exemplar for Data Integration in the Biomedical Domain Driven by the ISA Framework
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ISA-Tab metadata downloads and export
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Linking data to the Galaxy
workflow engine
7/28/2019 An Exemplar for Data Integration in the Biomedical Domain Driven by the ISA Framework
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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
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 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
7/28/2019 An Exemplar for Data Integration in the Biomedical Domain Driven by the ISA Framework
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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.
7/28/2019 An Exemplar for Data Integration in the Biomedical Domain Driven by the ISA Framework
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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
