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

Jerven Bolleman, View ORCID ProfileChristopher J. Mungall, Francesco Strozzi, Joachim Baran, View ORCID ProfileMichel Dumontier, Raoul J. P. Bonnal, Robert Buels, View ORCID ProfileRobert Hoehndorf, Takatomo Fujisawa, Toshi-aki Katayama, View ORCID ProfilePeter J. A. Cock
doi: https://doi.org/10.1101/002121
Jerven Bolleman
1Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
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  • For correspondence: jerven.bolleman@isb-sib.ch
Christopher J. Mungall
2Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, US
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Francesco Strozzi
3CeRSA, Parco Tecnologico Padano, Lodi 26900, Italy
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Joachim Baran
4Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario, M5G 0A3, Canada
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Michel Dumontier
5Stanford Center for Biomedical Informatics Research, 1265 Welch Road, Room X223, Stanford, CA, 94305-5479, US
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Raoul J. P. Bonnal
6Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan, Italy,
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Robert Buels
7University of California, Berkeley, Berkeley, CA, USA
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Robert Hoehndorf
8Department of Computer Science, Aberystwyth, SY23 3DB, UK
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  • ORCID record for Robert Hoehndorf
Takatomo Fujisawa
9Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka 411-08540, Japan
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Toshi-aki Katayama
10Database Center for Life Science, Research Organization of Information and Systems, 2-11-16, Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
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Peter J. A. Cock
11The James Hutton Institute, Dundee, DD2 5DA, UK
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  • ORCID record for Peter J. A. Cock
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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.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND Unported 3.0 license.
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Posted February 02, 2014.
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FALDO: A semantic standard for describing the location of nucleotide and protein feature annotation
Jerven Bolleman, Christopher J. Mungall, Francesco Strozzi, Joachim Baran, Michel Dumontier, Raoul J. P. Bonnal, Robert Buels, Robert Hoehndorf, Takatomo Fujisawa, Toshi-aki Katayama, Peter J. A. Cock
bioRxiv 002121; doi: https://doi.org/10.1101/002121
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FALDO: A semantic standard for describing the location of nucleotide and protein feature annotation
Jerven Bolleman, Christopher J. Mungall, Francesco Strozzi, Joachim Baran, Michel Dumontier, Raoul J. P. Bonnal, Robert Buels, Robert Hoehndorf, Takatomo Fujisawa, Toshi-aki Katayama, Peter J. A. Cock
bioRxiv 002121; doi: https://doi.org/10.1101/002121

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