sbd-data-elixir-fairsharing

        

This repository converts FAIRsharing content to SbD4Nano landscape data. The followin instructions use the FAIRSharing API. The ELIXIR Toxicology Community, in collaboration with FAIRsharing, maintains the FAIRSharing Toxicology collection.

Update protocol

Step 1: login

Copy the login.json to login_private.json and add your account info. Then run:

curl --location --request POST 'https://api.fairsharing.org/users/sign_in' \
  --header 'Accept: application/json' \
  --header 'Content-Type: application/json' \
  --data '@login_private.json'

Step 2: Search for toxicology-related records

This returns a JSON file with embeded a string for your jwt. This you use to replace $JWT in the next command:

curl --location --request POST 'https://api.fairsharing.org/search/fairsharing_records?q=toxicology' \
  --header 'Accept: application/json' \
  --header 'Content-Type: application/json' \
  --header 'Authorization: Bearer $JWT' \
  | jq . > toxicology.json

This creates a toxicology.json file under the CC-BY-SA license and can be converted into landscape content.

Step 3: Convert the results to landscape content

groovy convert.groovy > toxicology.ttl

References

• Sansone, SA., McQuilton, P., Rocca-Serra, P. et al. FAIRsharing as a community approach to standards, repositories and policies. Nat Biotechnol 37, 358–367 (2019). https://doi.org/10.1038/s41587-019-0080-8
• Martens, M. et al. ELIXIR and Toxicology: a community in development. F1000Research 10(ELIXIR):1129 (2023). https://doi.org/10.12688/f1000research.74502.2