feat(openchallenges): add EDAM terms SQL table and update Challenge.inputDataTypes

[vpchung]

Changelog

• add 2 new tables to challenge-service db
  • edam_ontology_term : a table consisting of EDAM ontology terms currently used to annotate challenges in the OC; includes parent classes
  • challenge_input_data_annotation : a table mapping challenges to their EDAM annotation(s)
• update API spec
• update Angular API client
• update Java files
• automated script that dumps the CSV files has been updated to include the EDAM terms and annotations into the dump

References

• https://github.com/edamontology/edamontology
• https://bioportal.bioontology.org/ontologies/EDAM (used as reference for the EDAM schema)

Preview

API docs

edam_ontology_term table

challenge_input_data_annotation table

[vpchung]

2024 update:

• automated script that dumps the CSV files has been updated to include the EDAM terms and annotations into the dump

[tschaffter]

@vpchung Please update the information included in the first comment of this PR.

[sonarqubecloud]

Quality Gate passed for 'openchallenges-app'

Issues
0 New issues

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

See analysis details on SonarCloud

[sonarqubecloud]

Quality Gate passed for 'openchallenges-challenge-service'

Issues
0 New issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
28.3% Duplication on New Code

See analysis details on SonarCloud

[sonarqubecloud]

Quality Gate passed for 'openchallenges-organization-service'

Issues
0 New issues

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

See analysis details on SonarCloud

[sonarqubecloud]

Quality Gate passed for 'openchallenges-image-service'

Issues
0 New issues

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

See analysis details on SonarCloud

[tschaffter]

Does the change to this file break the existing stack? Does the web app rely on this object?

The name and description of the object don't seem related. Shall the schema be renamed as EdamAnnotation?

Another question is whether we want to replace the existing data input object by an edam annotation object, or do we augment the existing data input data type object with an EDAM annotation?

[vpchung]

Does the change to this file break the existing stack? Does the web app rely on this object?

I tested the app, and no breakage was encountered. But it was a superficial test, so perhaps I didn't hit all of the edge cases.

Shall the schema be renamed as EdamAnnotation?

This makes sense to me.

Another question is whether we want to replace the existing data input object by an edam annotation object, or do we augment the existing data input data type object with an EDAM annotation?

I think this depends. Do we see the OC using other ontologies in the future? If so, I'd be inclined to keep it as SimpleChallengeInputData (or ChallengeInputData)

[tschaffter]

Replaced by #2557