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dc.contributor.authorGundersen, Sveinung
dc.contributor.authorBoddu, Sanjay
dc.contributor.authorCapella Gutiérrez, Salvador
dc.contributor.authorDrabløs, Finn
dc.contributor.authorFernández González, Jose María
dc.contributor.authorKompova, Radmila
dc.contributor.authorTaylor, Kieron
dc.contributor.authorTitov, Dmytro
dc.contributor.authorZerbino, Daniel
dc.contributor.authorHovig, Eivind
dc.contributor.otherBarcelona Supercomputing Center
dc.date.accessioned2021-08-31T16:06:57Z
dc.date.available2021-08-31T16:06:57Z
dc.date.issued2021
dc.identifier.citationGundersen, S. [et al.]. FAIRification of genomic track metadata [version 1; peer review: 2 approved]. "F1000 Research", 2021, vol. 10, 268.
dc.identifier.issn2046-1402
dc.identifier.urihttp://hdl.handle.net/2117/350513
dc.description.abstractBackground: 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, as well as 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. Description of work: We propose to advance the application of FAIR data principles (Findable, Accessible, Interoperable, and Reusable) to produce searchable metadata for genomic tracks. Findability and Accessibility of metadata can then be ensured by a track search service that integrates globally identifiable metadata from various track hubs in the Track Hub Registry and other relevant repositories. Interoperability and Reusability need to be ensured by the specification and implementation of a basic set of recommendations for metadata. We have tested this concept by developing such a specification in a JSON Schema, called FAIRtracks, and have integrated it into a novel track search service, called TrackFind. We demonstrate practical usage by importing datasets through TrackFind into existing examples of relevant analytical tools for genomic tracks: EPICO and the GSuite HyperBrowser. Conclusion: We here provide a first iteration of a draft standard for genomic track metadata, as well as the accompanying software ecosystem. It can easily be adapted or extended to future needs of the research community regarding data, methods and tools, balancing the requirements of both data submitters and analytical end-users
dc.description.sponsorshipThe 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. SC-G and JMF received funding through the INB Grant (PT17/0009/0001 - ISCIII-SGEFI / ERDF). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
dc.format.extent22 p.
dc.language.isoeng
dc.publisherF1000 Research
dc.rightsAttribution 3.0 Spain
dc.rightsAttribution 4.0 International (CC BY 4.0)
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/es/
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectÀrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
dc.subject.lcshMetadata
dc.subject.lcshGenomics
dc.subject.otherFAIR
dc.subject.otherFunctional genomics
dc.subject.otherEpigenomics
dc.subject.otherGenomics
dc.subject.otherMetadata
dc.subject.otherInteroperability,
dc.subject.otherGenomic tracks
dc.subject.otherSequence annotations
dc.titleFAIRification of genomic track metadata [version 1; peer review: 2 approved]
dc.typeArticle
dc.subject.lemacMetadades
dc.subject.lemacInteroperabilitat en xarxes d'ordinadors
dc.identifier.doi10.12688/f1000research.28449.1
dc.description.peerreviewedPeer Reviewed
dc.relation.publisherversionhttps://f1000research.com/articles/10-268
dc.rights.accessOpen Access
dc.description.versionPostprint (published version)
local.citation.other268
local.citation.publicationNameF1000 Research
local.citation.volume10


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