Skip to content
Branch: master
Find file History
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
..
Failed to load latest commit information.
marref_api
.gitignore
BH_Validation_Presentation.pdf
Pipfile
Pipfile.lock
README.md
biosamples_curation.py
biosamples_populate.py
comments_sample_schema.md
configuration.ini.template
docker-compose.yml
marref_sample_bioschemas.example.json
marref_sample_example.json
report.md
sample_schema.json
start_demo.sh

README.md

Data clearinghouse, validation and curation of BioSamples/ENA/Breeding API endpoints/MAR databases

Representative: Luca Cherubin

Community


ELIXIR Data clearinghouse, ELIXIR Data Validation and Bioschemas

Leads


  • Luca Cherubin
  • Melanie Courtot
  • Philippe Rocca Serra
  • Nils Peder Willassen
  • Cyril Pommier

Presentation

https://docs.google.com/presentation/d/1zfH3h-c0g2t_Wna9ixm5ZqKilpJmLEQ5wSPXETJ0-eI/edit?usp=sharing

Background information


Regular practice in life science is to curate and publish high quality metadata describing experiments performed on biological sample(s). Unfortunately this curated, high quality metadata is often not linked to the original assay and results, reducing data FAIRness.

A possible solution to this issue would be to integrate this diversity of resources by

  1. Having metadata that can be easily extracted with bots/crawlers,
  2. Storing it in a central repository and
  3. Validating it against predefined schema.

These overlap with the goals of different ELIXIR implementation studies, including Bioschemas, Data Validation and the Establishment of an ELIXIR Contextual Data Clearinghouse Implementation study.

Expected outcomes


A small subset of publications and curated data resources will be selected to build a proof of concept of an accession mapping - data clearing house - data validation and curation service to support the positive feedback loop to BioSamples, ENA and BrAPi repositories. We will: Create an accessioning mapping service which leverages literature references to establish correspondence between services; Develop a clearinghouse for curation storage; Define JSON schema(s) and validate the metadata;

Expected audience


Developers interested in Bioschemas applications; Developers with knowledge on any of JavaScript, Java, GO, Python, data indexing tools; Developers with knowledge on MongoDB, JSON and JSON Schema; Data resource developers and owners; Curator and data validators; Ontologists Expected hacking days: 4 days

Tasks

During our hacking session we are going to focus on two different use cases:

  1. BioSamples & MarRef use case
  2. Plant phenotype usecase

BioSamples and MarRef use case

For the BioSamples and MarRef use case we are planning the session this way:

Day 1

  • Integration of Bioschemas into MarRef
    • We are going to build a simple API service for MarRef to serve json-ld (Scala)
  • Possibly start to work on a JSON schema version of the Sample bioschemas profile for validation purposes

Day 2

  • Continue to work on JSON schema to validate the bioschemas exported from MarRef
  • Start to curate BioSamples creating curation objects based on MarRef exported metadata

Day 3

  • Continue to work on the curation of BioSamples
  • Start to work on a prototype for the data clearing house

Day 4

  • Continue as much as we can to develop the data clearing house

Plant phenotype use case

For the plant phenotype use case, we are planning the session this way:

Day 1

  • BrAPI v1.2 JSON-LD context
  • BrAPI v1.2 JSON Schemas
  • BrAPI 2 JSON-LD

Day 2

  • Continue with unfinished tasks from day 1
  • Validate BrAPi2ISA on all uses cases
    • Single experiment
    • Phenotyping network
    • Perenial plants

Day 3

  • Continue with unfinished tasks from day 2
  • Integrate BrAPi 2 ISA as a service

Day 4

  • Continue with unfinished tasks from day 3
  • Validate datasets
    • Ontologies & JSON-LD
    • JSON-Schemas
    • ISA framework

Related works and references


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


Hackers

  • Guillaume Cornut
  • ...

You can’t perform that action at this time.
You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session.