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


METHODS
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.
Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel, Servet, Geneva 4, 1211, Switzerland. jerven.bolleman@sib.swiss.
Jerven T
JT
Bolleman
Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, 94720, CA, US.
Christopher J
CJ
Mungall
CeRSA, Parco Tecnologico Padano, Lodi, 26900, Italy.
Francesco
F
Strozzi
CODAMONO, 5-121 Marion Street, Toronto, M6R 1E6, Ontario, Canada.
Joachim
J
Baran
Stanford Center for Biomedical Informatics Research, 1265 Welch Road, Room X223, Stanford, 94305-5479, CA, US.
Michel
M
Dumontier
Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan, Italy.
Raoul J P
RJ
Bonnal
University of California, Berkeley, Berkeley, CA, USA.
Robert
R
Buels
Department of Computer Science, Aberystwyth, SY23 3DB, UK.
Robert
R
Hoehndorf
Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka, 411-08540, Japan.
Takatomo
T
Fujisawa
Database Center for Life Science, Research Organization of Information and Systems, 2-11-16, Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
Toshiaki
T
Katayama
The James Hutton Institute, Dundee, DD2 5DA, UK.
Peter J A
PJ
Cock
D064229:Biological Ontologies; D030541:Databases, Genetic; D030562:Databases, Protein; D017143:Fuzzy Logic; D006801:Humans; D058977:Molecular Sequence Annotation / Q000592:standards*; D009711:Nucleotides / Q000235:genetics* / Q000378:metabolism*; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012013:Reference Books; D012660:Semantics
D009711:Nucleotides; D011506:Proteins
Annotation; Data integration; RDF; SPARQL; Semantic Web; Sequence feature; Sequence ontology; Standardisation