REST API TO CREATE OR UPDATE SUBMISSIONS IN BIOMODELS

In this repo, the directories and files are explained as below:

• models4test: includes all model directories and BASH scripts
• files: includes all files to be uploaded
• cmd.sh: bash script to run the create/update pipeline
• submission-metadata.json

Notes: The names of the files and directories are not necessary identical to the ones in this repo but you should make sure that its references in the bash script are correspondingly matched.

cmd.sh script

Please comment or uncomment the variables ACCESS_TOKEN, PREFIX_DOWNUP_SVR, and BM_SVR to your proper values.

Please contact us to support to gain an ACCESS_TOKEN for your work.

Create a new submission

The REST API endpoint is https://$BM_SVR.ebi.ac.uk/biomodels/api/submission/create.

Update an existing submission

The REST API endpoint is https://$BM_SVR.ebi.ac.uk/biomodels/api/submission/update.

uploading files

Update the variable FILES_DIR in the cmd.sh script to the path where your model files are located. Both absolute and relative path perfectly work. Make sure the names of all files match with the names defined in the submission-metadata.json file, otherwise the process will definitely fail.

The REST API endpoint for uploading files: https://$BM_SVR.ebi.ac.uk/biomodels/services/upload.

input file: submission-metadata.json

A copy of the input file like submission-metadata.json is downloaded from BioModels. When viewing an individual model in BioModels in JSON format, we can hit, for example, https://wwwdev.ebi.ac.uk/biomodels/MODEL1703310000?format=json in on the dev instance.

Then, appending some other properties to that JSON file. These properties are explained below.

• "type": "PubMed ID"|"DOI": required in the publication section.
• "accession": "34380040": required in the publication section.
• "isAmend": true|false: required for UPDATE.
• "comment": "A free text describing what you have modified your model.": required for UPDATE.
• "submissionId" : "MODEL2406050001": required for UPDATE.
• "modelling_approach": "ordinary differential equation model": required.
• "readme_submission": "This is the first sumbmission done via API": optional.
• "other_info": "SBML Model Format": optional.
• "isMetadataSubmission": true|false: optional.
• "contributorRole": "Curator", "Modeller", "Submitter", etc. It is an optional attribute. See the full list of the curator roles using the following service: https://www(dev).ebi.ac.uk/biomodels/contributor/role

The other fields are explainable as what their names are.