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

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-...

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Bibliographic Details
Published in:Journal of biomedical semantics 2016-06, Vol.7 (1), p.39-39, Article 39
Main Authors: Bolleman, Jerven T, Mungall, Christopher J, Strozzi, Francesco, Baran, Joachim, Dumontier, Michel, Bonnal, Raoul J P, Buels, Robert, Hoehndorf, Robert, Fujisawa, Takatomo, Katayama, Toshiaki, Cock, Peter J A
Format: Article
Language:English
Subjects:
60 APPLIED LIFE SCIENCES
Annotation
BASIC BIOLOGICAL SCIENCES
Biological Ontologies
Data integration
Databases, Genetic
Databases, Protein
Fuzzy Logic
Genomics
Humans
KNOWLEDGE MANAGEMENT AND PRESERVATION
Molecular Sequence Annotation - standards
Nucleotides - genetics
Nucleotides - metabolism
Protein binding
Proteins - chemistry
Proteins - metabolism
RDF
Reference Books
Semantic Web
Semantics
Sequence feature
Sequence ontology
SPARQL
Standardisation
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Summary: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. 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. 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.
ISSN:2041-1480
2041-1480
DOI:10.1186/s13326-016-0067-z