Please use this identifier to cite or link to this item: https://hdl.handle.net/20.500.11851/6849
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dc.contributor.authorGundersen, Sveinung-
dc.contributor.authorKalas, Matus-
dc.contributor.authorAbul, Osman-
dc.contributor.authorFrigessi, Arnoldo-
dc.contributor.authorHovig, Eivind-
dc.contributor.authorSandve, Geir Kjetil-
dc.date.accessioned2021-09-11T15:43:53Z-
dc.date.available2021-09-11T15:43:53Z-
dc.date.issued2011en_US
dc.identifier.issn1471-2105-
dc.identifier.urihttps://doi.org/10.1186/1471-2105-12-494-
dc.identifier.urihttps://hdl.handle.net/20.500.11851/6849-
dc.description.abstractBackground: With the recent advances and availability of various high-throughput sequencing technologies, data on many molecular aspects, such as gene regulation, chromatin dynamics, and the three-dimensional organization of DNA, are rapidly being generated in an increasing number of laboratories. The variation in biological context, and the increasingly dispersed mode of data generation, imply a need for precise, interoperable and flexible representations of genomic features through formats that are easy to parse. A host of alternative formats are currently available and in use, complicating analysis and tool development. The issue of whether and how the multitude of formats reflects varying underlying characteristics of data has to our knowledge not previously been systematically treated. Results: We here identify intrinsic distinctions between genomic features, and argue that the distinctions imply that a certain variation in the representation of features as genomic tracks is warranted. Four core informational properties of tracks are discussed: gaps, lengths, values and interconnections. From this we delineate fifteen generic track types. Based on the track type distinctions, we characterize major existing representational formats and find that the track types are not adequately supported by any single format. We also find, in contrast to the XML formats, that none of the existing tabular formats are conveniently extendable to support all track types. We thus propose two unified formats for track data, an improved XML format, BioXSD 1.1, and a new tabular format, GTrack 1.0. Conclusions: The defined track types are shown to capture relevant distinctions between genomic annotation tracks, resulting in varying representational needs and analysis possibilities. The proposed formats, GTrack 1.0 and BioXSD 1.1, cater to the identified track distinctions and emphasize preciseness, flexibility and parsing convenience.en_US
dc.description.sponsorshipEMBIO; FUGE; UiO; Helse Sor-Ost; eSysbio; Research Council of NorwayResearch Council of Norwayen_US
dc.description.sponsorshipFunding was kindly provided by EMBIO, FUGE, UiO, Helse Sor-Ost, and eSysbio (funded by the Research Council of Norway). This work was performed in association with 'Statistics for Innovation', a Centre for Research-Based Innovation funded by the Research Council of Norway. We thank Kai Trengereid for crucial work in developing the GTrack-related tools, and Inge Jonassen for valuable input on the BioXSD format. We would also like to acknowledge the excellent review work provided by the peer reviewers. These reviews have contributed significantly to the content of this paper.en_US
dc.language.isoenen_US
dc.publisherBmcen_US
dc.relation.ispartofBmc Bioinformaticsen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subject[No Keywords]en_US
dc.titleIdentifying Elemental Genomic Track Types and Representing Them Uniformlyen_US
dc.typeArticleen_US
dc.departmentFaculties, Faculty of Engineering, Department of Computer Engineeringen_US
dc.departmentFakülteler, Mühendislik Fakültesi, Bilgisayar Mühendisliği Bölümütr_TR
dc.identifier.volume12en_US
dc.authorid0000-0002-9103-1077-
dc.authorid0000-0002-1509-4981-
dc.authorid0000-0002-4959-1409-
dc.authorid0000-0001-7103-7589-
dc.authorid0000-0001-9888-7954-
dc.identifier.wosWOS:000302435800001en_US
dc.identifier.scopus2-s2.0-84855180941en_US
dc.institutionauthorAbul, Osman-
dc.identifier.pmid22208806en_US
dc.identifier.doi10.1186/1471-2105-12-494-
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.identifier.scopusqualityQ1-
item.openairetypeArticle-
item.languageiso639-1en-
item.grantfulltextnone-
item.fulltextNo Fulltext-
item.openairecristypehttp://purl.org/coar/resource_type/c_18cf-
item.cerifentitytypePublications-
crisitem.author.dept02.3. Department of Computer Engineering-
Appears in Collections:Bilgisayar Mühendisliği Bölümü / Department of Computer Engineering
PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection
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