fairtracks/fairtracks_augment repository overview

⁠The FAIRtracks augmentation service

The FAIRtracks draft standard⁠ is a set of JSON Schemas that define a minimal standard for genomic track metadata. The FAIRtracks augmentation service is a simple Flask-based service written in Python that provides a HTTP-based API for augmenting a minimal FAIRtracks JSON document with automatically generated content for all the properties defined in the FAIRtracks JSON schemas with augmented=true.

The FAIRtracks augmentation service fills out the following fields:

• The newest versions of all ontologies required by the FAIRtracks standard are fetched and the versioned URLs are added to the doc_info-> doc_ontology_versions object.
• All term_value properties are generated by the related term_id property by lookup in the relevant ontology.
• track->file_name is generated from the track->file_url property.a
• The two properties sample->sample_type->summary and experiment->target->summary are generated based upon the relevant rule as defined by sample->biospecimen_class->term_id and target->technique->term_id, respectively, as described in the top-level FAIRtracks schema.
• sample->species_name is generated by a lookup in the NCBI Taxonomy Database⁠