Frequently Asked Questions#

Validation#

  • Can the FAIR Data Station interact with other validation libraries such as the ELIXIR Biovalidator?
    The FAIR Data Station can export metadata into a multitude of JSON files (one for each package). These files can be used with external validation libraries (such as the ELIXIR Biovalidator). The JSON package files can be found in the Git repository.

  • Is there a mechanism for users to add a new regular expression?
    Yes, field–value pairs, value specifications, examples and regular expressions are stored in an external metadata file in an open excel format. When running a local or Docker instance the FAIR Data Station, this template file can be modified to:

    • add new or update existing regular expressions

    • add new metadata fields

    • define or modify packages

  • Where do the checklists and regular expressions come from?
    The checklists are directly obtained from ENA checklists, and the ENA supplied regular expressions are reused when the field format is restricted. The regular expression for DOI are obtained from https://registry.identifiers.org/registry/doi.

  • Is there a way to validate ontology terms against the relevant ontologies?
    We are currently exploring the validation of ontology terms. The FAIR Data Station metadata file (metadata.xlsx) regular expression field now also accepts an URL-link to an OWL-file. During start-up of the app, the OWL-file is retrieved and transformed into a RDF database. During the validation process the user-recorded terms are checked against rdfs:label values of the selected ontology. As a working example we have implemented a first version of term validation of the Environment Ontology (http://purl.obolibrary.org/obo/envo.owl).

ISA alignment#

  • The FAIR Data Station uses an amended version of the original three-tier Investigation, Study, Assay (ISA) metadata framework. What changes were implemented and how does it affect metadata database searches?
    The FAIR Data station extends the original ISA model by introducing Observation Unit and Sample as separate entities. This change reflects how experimentalists tend to work, where the entity that is studied (e.g. patient, bioreactor, plant) is conceptually distinct from the samples taken.

  • Observation Unit: the entity being observed, adopted from the MIAPPE v1.1 ISA-Tab format

  • Sample: material derived from observed entity, adopted from the Just Enough Results Model For compatibility with existing RDF models, these levels are mapped to source material and sample material. See example mappings.

Metadata#

  • I messed up my metadata template file and my FAIR Data Station instance no longer functions properly, what should I do?
    Remove the Excel file from the fairds_storage folder and restart the application. A new file with default settings will be automatically generated.

  • I want to use the metadata template developed by my colleague
    Make sure the template complies with the required format and simply replace the Excel file and restart the application. Keep a backup of your original file if needed.