Validating an SDRF

Before submitting to ProteomeXchange, researchers and submitters should validate their SDRF-Proteomics file format. While the PX submission tool allows users to validate their SDRF-Proteomics files, we recommend users to validate locally their files before submission. How can this be done?

sdrf-pipelines validator

The sdrf-pipelines Python tool can be used to locally validate SDRF-Proteomics files.

Installing with pip:

pip install sdrf-pipelines

Installing with conda:

conda install sdrf-pipelines

and update with:

conda update sdrf-pipelines

or use the docker container:

docker pull quay.io/biocontainers/sdrf-pipelines:<tag>

Validating and SDRF-Proteomics file

parse_sdrf validate-sdrf --sdrf_file {here_the_path_to_sdrf_file}

The validation will run two levels of validation: schema validation and semantic validation. The schema validation checks that the structure of the file is valid: the columns, the spaces, etc... The semantic validation checks that the values in the properties can be found in OLS ontology service and they are valid for the corresponding property. For example, the values in characteristics[organism] should be present in the OLS ontology service under the following term in EFO ontology