FALDO: A semantic standard for describing the location of nucleotide and protein feature annotation

Jerven T. Bolleman*, Christopher J. Mungall, Francesco Strozzi, Joachim Baran, Michel Dumontier, Raoul J.P. Bonnal, Robert Buels, Robert Hoehndorf, Takatomo Fujisawa, Toshiaki Katayama, Peter J.A. Cock

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

14 Scopus citations

Abstract

Background: Nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, there was no standard that described this potentially complex location information as subject-predicate-object triples. Description: We have developed an ontology, the Feature Annotation Location Description Ontology (FALDO), to describe the positions of annotated features on linear and circular sequences. FALDO can be used to describe nucleotide features in sequence records, protein annotations, and glycan binding sites, among other features in coordinate systems of the aforementioned "omics" areas. Using the same data format to represent sequence positions that are independent of file formats allows us to integrate sequence data from multiple sources and data types. The genome browser JBrowse is used to demonstrate accessing multiple SPARQL endpoints to display genomic feature annotations, as well as protein annotations from UniProt mapped to genomic locations. Conclusions: Our ontology allows users to uniformly describe - and potentially merge - sequence annotations from multiple sources. Data sources using FALDO can prospectively be retrieved using federalised SPARQL queries against public SPARQL endpoints and/or local private triple stores.

Original languageEnglish (US)
Article number39
JournalJournal of Biomedical Semantics
Volume7
Issue number1
DOIs
StatePublished - Jun 13 2016

Keywords

  • Annotation
  • Data integration
  • RDF
  • SPARQL
  • Semantic Web
  • Sequence feature
  • Sequence ontology
  • Standardisation

ASJC Scopus subject areas

  • Information Systems
  • Computer Science Applications
  • Health Informatics
  • Computer Networks and Communications

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