DOI: 10.5281/zenodo.3984946
title: Example FAIRtracks JSON document - augmented

description: <strong>Background</strong> 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. <strong>FAIRtracks software ecosystem</strong> 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 implementation called FAIRtracks in the form of a JSON Schema. We propose FAIRtracks as a draft standard for genomic track metadata in order to advance 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, integrating globally 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 also includes the FAIRtracks augmentation service, which assists metadata 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 include FAIR-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/ <strong>Example FAIRtracks JSON document - augmented</strong> 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 with the 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 a Digital Object Identifier (DOI).
description: The work was funded by ELIXIR through the ELIXIR Implementation Study: "FAIRification of genomic tracks", and through ELIXIR Norway, ELIXIR Spain and EMBL-EBI core funding. Example metadata content was fetched from the ENCODE Project data portal and is subject to the following Data Use Policy: https://www.encodeproject.org/help/citing-encode/. The example ENCODE metadata has been manually transformed to follow the FAIRtracks draft standard for genomic track metadata.
description: {"references": ["ENCODE Project Consortium. \"An integrated encyclopedia of DNA elements in the human genome.\" Nature 489, no. 7414 (2012): 57-74.", "Davis, Carrie A., Benjamin C. Hitz, Cricket A. Sloan, Esther T. Chan, Jean M. Davidson, Idan Gabdank, Jason A. Hilton et al. \"The Encyclopedia of DNA elements (ENCODE): data portal update.\" Nucleic acids research 46, no. D1 (2018): D794-D801."]}