COPO - TGAC Documentation

COPO: Collaborative Open Plant Omics
Rob Davey
Data Infrastructure and Algorithms Group Leader
[email protected]
@froggleston
Toni Etuk
Acknowledgements
Oxford eResearch Centre
Susanna Sansone
Alejandra Gonzalez-Beltran
Philippe Rocca-Serra
Alfie Abdul-Rahman
Felix Shaw
Warwick
Jim Beynon
Katherine Denby
Ruth Bastow
EMBL-EBI
Paul Kersey
TGAC
Vicky Schneider
Tanya Dickie
Emily Angiolini
Matt Drew
COPO
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Recently awarded BBSRC BBR grant
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TGAC, Univ. Oxford, Univ. Warwick, EMBL-EBI
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Supported by GARNet, iPlant, Eagle Genomics
Empower bioscience plant researchers to:
1. Enable standards-compliant data collection, curation and
integration
2. Enhance access to data analysis and visualisation pipelines
3. Facilitate data sharing and publication to promote reuse
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Train plant researchers in best practice for data sharing and
producing citable Research Objects
COPO
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(Good) Science is founded on reproducibility
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Reproducibility depends on:
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reducing reinvention (“friction”)*
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describing methods and data
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maximising benefit to the researcher
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Describing methods well established through “traditional” publishing
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Data description sorely under-represented and used
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Benefits are often opaque
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Fear of being scooped, loss of control, reputation, etc
* http://cameronneylon.net/blog/network-enabled-research/
COPO
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What prevents plant scientists from openly depositing their data
and metadata?
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Lack of interoperability between:
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metadata annotation services
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data repository services
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data analysis services
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data publishing services
Researchers might not:
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be aware that the services exist
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have the expertise to use them
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see the value in properly describing their data
COPO
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Data:
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Code:
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figshare, Scientific Data, Dryad, F1000, PeerJ, Gigascience
Beyond the PDF:
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Galaxy, iPlant, Bioconductor, Taverna, local code/services
Publication:
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GitHub, BitBucket, Zenodo
Analysis:
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Sample, Sequence, Genome, Proteome, Metabolome, Imaging
Utopia, GitHub
Training:
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Materials, examples, workshops, bootcamps
COPO
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It's not because these services don't exist!
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Clearly, barriers exist between the scientist and the service
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Infrastructure can help by:
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wiring existing services together
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improving access to services
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facilitating collaboration
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raising profile of the benefits of open science
How do we collaborate successfully to make this happen?
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Mapping services with Application Programming Interfaces
COPO
COPO
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Grace signs into COPO with her ORCID ID
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This signs her into all other services as required
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She starts a new COPO Profile
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She uploads to the COPO platform:
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Three FASTQs (two Illumina HiSeq2500, one PacBio P6-C4)
representing her velociraptor sequencing reads
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She tells COPO to push her data to a Galaxy server and run a workflow,
producing:
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An assembly of the reads from ALLPATHS-LG v51551
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A draft automated annotation from RAST v33-1
The interface prompts her to add metadata to her data in order to deposit
them in the public repositories
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Metadata fields will be shown based on data, and redundant fields will be merged automatically
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Sample name, sample organism, data type, sequencer used, software name, software version....
She clicks “Upload”, and everything is submitted
COPO
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Single-sign on (SSO), e.g. ORCID
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Deposit multi-omics data in one go
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No context-switching between services
Run and deposit analytical workflows
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Describe software used, versions
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Pull into platforms, e.g. Galaxy, iPlant
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Support virtualisation, e.g. iPlant Atmosphere, Docker, Amazon AWS
Data is well-described, open, and everything has DOIs
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Finding and integrating data is improved greatly
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Make suggestions to users based on their data/workflows
Programmatic access to all layers
REPRODUCIBILITY
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Not just raw/processed data is valuable
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COPO supports submission of supplementary data to Figshare
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PDFs (posters, papers)
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CSV/Excel
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movies/images (size permitting)
Zenodo/Github releases for code DOIs
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Marked up with ENCODE Digital Curation Center’s software
metadata descriptors, for example
COPO
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What have we achieved so far?
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TGAC infrastructure to support brokering of data
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iRODS and web server virtual machines
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High speed transfer Aspera links to EBI
Prototype user interface for multi-omics data submissions
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Developing JSON specification for COPO objects
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Oauth2 support (“sign in with” ORCiD, Google, Twitter)
Easily stored in document-based databases, e.g. MongoDB
Interconversion between ISA formats
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ISATab (CSV based) to JSON, and vice versa
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Linked Data specifications
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Community interactions
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Metabolights group at EBI
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Setting up this workshop!
COPO
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COPO will:
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Facilitate easy relevant data description to:
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Submit data and metadata to multiple public repositories
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The reasons most of you are here…
What are the barriers for you and your data?
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Facilitate access to workflows used to analyse the data, e.g. to
GigaDB, Scientific Data
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This will form part of another COPO workshop