Example FAIRtracks JSON document - augmented
DOI10.5281/zenodo.3984947Zenodo3984947MaRDI QIDQ6716777FDOQ6716777
Dataset published at Zenodo repository.
Kieron Taylor, José M. Fernández, Sveinung Gundersen, Radmila Kompova, Salvador Capella-Gutierrez, Finn Drabløs, Dmytro Titov, Eivind Hovig, Daniel Zerbino
Publication date: 15 August 2020
Copyright license: Creative Commons Attribution 4.0 International
Background Many types of data from genomic analyses can be represented as genomic tracks, i.e. features linked to the genomic coordinates of a reference genome. Examples of such data are epigenetic DNA methylation data, ChIP-seq peaks, germline or somatic DNA variants, or RNA-seq expression levels. Researchers often face difficulties in locating, accessing and combining relevant tracks from external sources, as well as locating the raw data, reducing the value of the generated information. FAIRtracks software ecosystem We have, as an output of the ELIXIR Implementation Study FAIRification of Genomic Tracks, developed a basic set of recommendations for genomic track metadata together with an implementationcalled FAIRtracks in the form ofa JSON Schema. We proposeFAIRtracks as a draft standard for genomic track metadata in order toadvance the application of FAIR data principles (Findable, Accessible, Interoperable, and Reusable). We have demonstrated practical usage of this approach by designing a software ecosystem around the FAIRtracks draft standard, integratingglobally identifiable metadata from various track hubs in the Track Hub Registry and other relevant repositories into a novel track search service, called TrackFind. The software ecosystem alsoincludes the FAIRtracks augmentation service, whichassistsmetadata producers by automatically augmenting minimal machine-readable metadata with their human-readable counterparts, as well as the FAIRtracks validation service, which extends basic JSON Schema validation to includeFAIR-related features (global identifiers, ontology terms, and object references).Finally, we have implemented track metadata search and import functionality into relevant analytical tools: EPICO and the GSuite HyperBrowser. For an overview of the FAIRtracks software ecosystem, please visit:http://fairtracks.github.io/ Example FAIRtracks JSON document - augmented The Example FAIRtracks JSON document - augmented is generated as part of the build process of the FAIRtracks draft standard JSON Schema (source code: https://github.com/fairtracks/fairtracks_standard/). The example FAIRtracks document contains a small selection of tracks and objects from the ENCODE project metadata (https://www.encodeproject.org/), adapted to align withthe FAIRtracks draft standard. In addition to being available in the above-mentioned GitHub repository, the Example FAIRtracks JSON document - augmented is also published here on Zenodo in order for the document to be globally uniquely identifiable by aDigital Object Identifier (DOI).
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