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biosamples
Blockchain4Science Nov2018.pdf
Introduction to Composer.pdf
Introduction to Hyperledger.pdf
README.md
Tracking BioSamples on Hyperledger Paris Nov2018.pdf
bforos@0.0.6.bna

README.md

Using blockchain in biomedical provenance: Tracking BioSamples.

## Representative: Richard Shute

Community


The Pistoia Alliance (www.pistoiaalliance.org)

Leads


  • Carlos Castro
  • Alexander Garcia Castro
  • Olga Giraldo
  • Richard Shute

Background information


Blockchain is a collection of technologies (cryptographic security, decentralization, digital registry, smart contracts, rules and incentives to collaborate among institutions with different levels of trust) that is currently being tested in different industries and organizations (financial, government, shipping,...). OpenScience requires provenance, transparency, and availability. Blockchain delivers the trust layer in OpenScience. Our hacking proposal reuses blockchain tech, Hyperledger in particular, to support provenance and sample supply chain management. We are currently looking at BioSamples as a system that stores and supplies descriptions and metadata about biological samples for industry and academica. The system can be used to track samples through a workflow and provide additional layers of security to the identifiers. In addition, having a blockchain for BioSamples will also make it possible to establish a reward mechanisms that incentivises the creation & curation of samples, so helping to drive improved trust and reputation.

Expected outcomes


  • Identify the added value of Blockchain technologies on BioSamples and similar sample management tools.
  • Create a prototype on Hyperledger Composer of a Business Network (BNA) that includes the data standards and current functionalities (workflows) of BioSamples.
  • Smart contract to track provenance in the curation process.
  • Suggest possible extension in order to implement different layers of curation and generate different states of the samples.

Our code will also contribute to the https://github.com/Blockchain4openscience project. We also expect to start the discussion about using blockchain technology for keeping the trail of evidence in the annotation process.

Expected audience


Bioinformaticians, chemoinformaticians, data scientists, researchers with some programming skills and wet-lab researchers who can provide the context for the problem and can lead the programmers into a useful solution. Participants should have minimal knowledge of JSON and Javascript (ideally Angular). Researchers working with identifiers and also people involved in BioSamples. During the first day of hacking there will be a tutorial on Blockchain technologies and Hyperledger Composer for participants and open to all others that are interested.

Expected hacking days: 4 days

Tasks

Day 1 (Silverstone room)

Blockchain technologies and Biosamples (data and workflows)

  1. Tutorial on Blockchain technologies (9-11)
  2. Tutorial on Hyperledger Composer (11-12, 13-15).
  3. Sample use cases: Blockchain4openscience and Digital Diplomas.
    • Skills: JS.
    • Output: learn Composer-Playground.
  4. Understanding BioSamples: data management and workflows (15-19).
    • Skills: BioSamples.
    • Output: Identify data structures and workflows.
  5. How would BioSamples benefit from blockchain technologies: define provenance in curation.

Day 2 (Main room)

Supply chain management in BioSamples (9-12)

  1. Designing and implementing a business network application (biosamples.bna) on Hyperledger Composer for the project:
    • Define assets, participants, transactions and events in model file (biosamples.cto).
    • Output: BioSamples.bna
    • Example for sample submission (create asset)
  2. Report.

Day 3 (Main room)

Supply chain management in BioSamples

  1. Code transactions logic in JS for curation. Update and document bna with new curation functions.
  2. Extensions.

Day 4 (Main room)

Presentation and roadmap

  1. Writing-up a presentation for the project.
  2. Report.
  3. Documenting (GitHub repo) and roadmap.

Related works and references


GitHub or any other public repositories of your FOSS products (if any)


https://github.com/Blockchain4openscience/B4OS-frontend

Hackers

  • Federico Lopez (EMBL-EBI)
  • Claus Weiland (Senckenberg)
  • Isabelle Perseil (INSERM)
  • Carlos Castro-Iragorri (Urosario)

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