feat(openchallenges): add EDAM concept table to the chalenge service

[tschaffter]

Closes #2520

Description

Add a minimal version of EDAM ontology as a new SQL table in the challenge service DB.

This contribution is a refactored version of #2265 that aims to integrate EDAM into OC one step at a time.

In the near future, I can see us using the following workflow, which the present PR brings us close to.

1. We fork the repo https://github.com/edamontology/edamontology to prevent data from being deleted
2. We have an ETL workflow that
   • E: download the CSV file from the EDAM fork
   • T: a python script that converts the CSV file into a format that OC can work with; optionally validate the input and output data.
   • L: load the processed data into OC DB

Why? The entire EDAM ontology is more than 2MB and too large to be tracked in Sage Monorepo. Using an ETL workflow would allow us to store the raw data externally (e.g. S3 bucket, Synapse).

I actually have implemented this workflow for iAtlas a few weeks ago (see apps/iatlas/data). This workflow could be reused almost as is with OC. Note that the project iatlas-data uses Schematic to validate the iAtlas data, which is a feature that @vpchung suggested recently for OC.

Changelog

• add minimal EDAM ontology to OC Challenge Service
• document in the ticket how the processed EDAM CSV file is generated with minimal manual operations
• add the Google sheet OC_EDAM_1.25 to OC shared folder in Google Drive

Testing

• The new SQL table is created and populated when starting the challenge service
  • using Docker
  • using the development server

Future Work

Add the property Challenge.operation

Preview

[sonarqubecloud]

Quality Gate passed for 'openchallenges-challenge-service'

Issues
0 New issues

Measures
0 Security Hotspots
No data about Coverage
No data about Duplication

See analysis details on SonarCloud

[vpchung]

Minor request, unless it's no longer relevant.

[vpchung]

Works on my end - thanks!