locations.tex

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\begin{document}
\begin{bmcformat}
\title{Semantic standard for describing the location of nucleotide and protein feature annotation.}
\author{Jerven Bolleman\correspondingauthor$^1$\email{Jerven Bolleman\correspondingauthor - jerven.bolleman@isb-sib.ch}%
    \and Robert Buels$^2$%
    \and Robert Hoehndorf$^3$%
    \and Peter Cock$^3$%
    \and Toshiaki Katayama$^4$%
    \and Raoul J. P. Bonnal$^5$%
    \and Michel Dumontier$^5$%
    \and Takatomo Fujisawa$^6$%
    \and Francesco Strozzi$^7$%
    \and Joachim Baran$^8$%
}
\address{
 \iid(1) SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel
Servet, 1211 Geneva 4, Switzerland,
 \iid(2) University of California, Berkeley, Berkeley, CA, USA,
 \iid(3) The James Hutton Institute, Dundee, DD2 5DA, UK,
 \iid(4) Database Center for Life Science, Research Organization of Information and Systems, 2-11-16, Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan,
 \iid(5) Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan, Italy,
 \iid(6) Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka 411-08540, Japan,
 \iid(7) CeRSA, Parco Tecnologico Padano, Lodi 26900, Italy, and
 \iid(8) Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario, M5G 0A3, Canada.
}
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\section*{Keywords}
SPARQL, RDF, semantic-web, standardization, sequence ontology

\input{background}
\input{implementation}
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\input{discussion}
\input{conclusions}
\input{avareq}


\section*{List of abbreviations}

\begin{description}
\item[SPARQL] SPARQL Protocol and RDF Query Language
\item[UniProtKB] Universal Protein Knowledgebase 
\item[RDF] Resource Description Framework
\item[DNA] Deoxyribonucleic acid
\item[INSDC] International Nucleotide Sequence Database Collaboration
\item[DDBJ] DNA Data Bank of Japan
\item[ENA] European Nucleotide Archive
\end{description}
\bigskip

\section*{Authors contributions}

Jerven Bolleman wrote the basic ontology file and mapping to UniProt RDF.
Robert Hoehndorf did the GFF3 to OWL conversion.
Peter Cock adapted the Biopython data object model to this format (TODO).
Raoul JP Bonnal adapted BioRuby to match the ontology and wrote the cufflink to locations.rdf converter with Francesco Strozzi.
Totokama Fujisawa implemented the DDBJ RDF in terms of this format.
Robert Beuels adapted JBrowse to query SPARQL endpoints that use this format to generate custom tracks. 

\section*{Acknowledgments}



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