copo kick-off meeting
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ISA tools overview
Alejandra González-Beltrán, PhD Oxford e-Research Centre, University of Oxfordalejandra.gonzalezbeltran@oerc.ox.ac.uk @alegonbel
COPO kick-off meeting September 16, 2014 Norwich, UK
eTRIKS – EUTranslational Information and Knowledge management Services Consortium of academic (Imperial College, CNRS, Un of Luxemburg) and pharmas (Janssen, Merck, AZ, Lilly, Lundbeck, Pfizer, Roche, Sanofi, Bayer, GSK) building a sustainable, open translational research informatics platform
• Nature Publishing Group‘s Scientific Data • BioMedCentral and BGI‘s GigaScience • F1000 Research • Oxford University Press
Ontology and sematic web knowledge representations Ontology for Biomedical Investigation (OBI) for the description of the experimental steps
Statistical ontology (STATO) for the description of statistical results
Applying the linked data and the nanopublication approaches to ISA-Tab
WG in involving PloS, NPG, BMC, BMJ, OUP, etc.
Centre for Extended Data Annotation and Retrieval (pending notification of award) Centre will explore a variety of technique to ease the work of creating and using standards-driven templates for describing and reporting biomedical datasets
A community-driven platform for plant science Coordinated by TGAC and in collaboration with EMBL-European Bioinformatics Institute and Warwick University, COPO will provide platform- and software-as-a-service
Related Funded Project:
http://www.bbsrc.ac.uk/pa/grants/AwardDetails.aspx?FundingReference=BB/L024152/1
Continued Development and Curation of the MetaboLights database
• Large metabolomics lab submission interfaces/integration (API) • Analysis tools (online)• Tools for visualisation of metabolomics data• Enrichment and extension to the reference layer• A curation tool for MetaboLights submissions • Metabolite identification assistant
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Experimental Metadata
Notes in lab notebooks(information for humans)
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Experimental Metadata
Notes in lab notebooks(information for humans) Spreadsheets & tables
ISA-Tab
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Experimental Metadata
Notes in lab notebooks(information for humans) Spreadsheets & tables
ISA-Tab
RDF statements(information for machines)
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Experimental Metadata
It is all about structuring experimental information to make it available to computers and software agents to enable:
! provenance tracking
assessment and evaluation accountability, reliability, trust, evidence
conservation, preservation, storage, archiving and mining
Notes in lab notebooks(information for humans) Spreadsheets & tables
ISA-Tab
RDF statements(information for machines)
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http://www.am
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Rocca-Serra et al, 2010!Bioinformatics!ISA software suite
The format
Why ISA format and Tools?
investigation
assay(s) assay(s)
data data
external files in native or other for-
mats
pointers to data file names/location
investigationhigh level concept to link related studies
studythe central unit, containing information on the subject under study, its characteristics and any treatments applied.a study has associated assays
assaytest performed either on material taken from the sub-ject or on the whole initial subject, which produce quali-tative or quantitative meas-urements (data)
H. Sapiens
33 Years
H. Sapiens
H. Sapiens
H. Sapiens
H1
H1
H2
35
35
33
Years
Years
Years
H1.sample1
H1.sample2
H2.sample1
Labeling
Labeling
H1.sample1.labeled
H2.sample1.labeled
h1-s1.cel
h1-s2.cel
h2-s1.cel
H1
H2
H1.sample1
H1.sample2
H2.sample1
Labeling
Labeling
H1.sample1.labeled
H2.sample1.labeled
h1-s1.cel
h1-s2.cel
h2-s1.cel
H. Sapiens
35 Years
MAGE-Tab Pride-xml SRA-xml
ISA metadata specifications:!• workflow and process orientated• compatible with checklist enforcement• compatible with external vocabulary resources• compatible by design with existing schemas!
The software suite
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Personalized NSAID Therapeutics Consortium [PENTACON]https://pentacon-bii.princeton.edu/
investigation studies assays
measurement technology
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ISA-Tab validation
ISA-Tab to
SRAconversion
Submission to ENA
ISA-Tab creation
(SRA-xml schema)
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The community
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A growing ecosystem of over 30 public and internal resources using the ISA metadata tracking framework (ISA-Tab and/or tools) to facilitate standards-compliant collection, curation, management and reuse of investigations in an increasingly diverse set of life science domains, including: !
• stem cell discovery • system biology • transcriptomics • toxicogenomics • also by communities working to build a library of cellular
signatures
!• environmental health • environmental genomics • metabolomics • metagenomics • nanotechnology • proteomics
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funders
Questions?You can email us...
isatools@googlegroups.com
View our blog http://isatools.wordpress.com
Follow us on Twitter @isatools
View our websites
View our Git repo & contribute http://github.com/ISA-tools
Thanks for your attention!
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