Contributor documentation

Contributor documentation

Contributors are welcome to provide new spectra to MassBank. New spectra should meet the format described in the MassBank record format specification. All MassBank spectra are stored in the MassBank-data repository. To submit new spectra create a pull request to MassBank-data or open an issue to get in contact.

Generation of new records for upload to MassBank-data

The preferred software to generate MassBank records is RMassBank. RMassBank is in continuous development. Hence, use the latest version available, please. If you are using your own pipeline please consider to provide it to other users(please open an issue).

Validate new record files locally

Before new record files are accepted to MassBank-data, they need to pass the validation. This will be done automatically if a pull request is created. Its also possible to validate record files locally in advance. To validate new record files locally please clone the [MassBank-web] repo and compile it.

git clone --depth 1 -q https://github.com/MassBank/MassBank-web.git
mvn -f MassBank-web/MassBank-Project/MassBank-lib/pom.xml package

The Validator executable can be found at MassBank-web/MassBank-Project/MassBank-lib/target/MassBank-lib/MassBank-lib/bin/Validator. If you want to copy the executable to a different place, make sure that the environment variable LIB_DIR inside the executable points to the abolute path of MassBank-web/MassBank-Project/MassBank-lib/target/MassBank-lib/MassBank-lib/lib. Now its possible to validate record files locally. Validator supports validation of a single record file, several files as well as one or several directories containing record files, eg.

MassBank-web/MassBank-Project/MassBank-lib/target/MassBank-lib/MassBank-lib/bin/Validator <my record directory>

Submit new records to MassBank-data or modify existing records

To submit data or to change existing records:

  1. Please fork the MassBank-data repo, clone it to your place and make your changes or add new content in the dev branch.
  2. Commit and push your changes to the dev branch of your repo.
  3. Create a pull request against the dev branch.

Your pull request will be validated and you will receive a report whether your records meet the MassBank specs. If everything is ok, your content will be integrated into MassBank.

If you are not able to provide your contribution via a pull request, please fill a issue at the issue board or get in contact via email.