title: Preserving sequence annotations across reference sequences.
abstract: BACKGROUND
  Matching and comparing sequence annotations of different reference sequences is vital to genomics research, yet many annotation formats do not specify the reference sequence types or versions used. This makes the integration of annotations from different sources difficult and error prone.
  
  
  RESULTS
  As part of our effort to create linked data for interoperable sequence annotations, we present an RDF data model for sequence annotation using the ontological framework established by the OBO Foundry ontologies and the Basic Formal Ontology (BFO). We defined reference sequences as the common domain of integration for sequence annotations, and identified three semantic relationships between sequence annotations. In doing so, we created the Reference Sequence Annotation to compensate for gaps in the SO and in its mapping to BFO, particularly for annotations that refer to versions of consensus reference sequences. Moreover, we present three integration models for sequence annotations using different reference assemblies.
  
  
  CONCLUSIONS
  We demonstrated a working example of a sequence annotation instance, and how this instance can be linked to other annotations on different reference sequences. Sequence annotations in this format are semantically rich and can be integrated easily with different assemblies. We also identify other challenges of modeling reference sequences with the BFO.
authors.affiliation: Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands ; Department of Rheumatology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands.
authors.forename: Zuotian
authors.initials: Z
authors.lastname: Tatum
authors.affiliation: Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands ; Informatics Institute of the Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands.
authors.forename: Marco
authors.initials: M
authors.lastname: Roos
authors.affiliation: Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands.
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Gibson
authors.affiliation: Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands.
authors.forename: Peter Em
authors.initials: PE
authors.lastname: Taschner
authors.affiliation: Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands.
authors.forename: Mark
authors.initials: M
authors.lastname: Thompson
authors.affiliation: Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands.
authors.forename: Erik A
authors.initials: EA
authors.lastname: Schultes
authors.affiliation: Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands ; Leiden Genome Technology Center, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands.
authors.forename: Jeroen Fj
authors.initials: JF
authors.lastname: Laros
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