bmc_article.tex

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%%  LaTeX template for BioMed Central  %%
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%\documentclass[twocolumn]{bmcart}% uncomment this for twocolumn layout and comment line below
\documentclass{bmcart}

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%\usepackage{amsthm,amsmath}
%\RequirePackage{natbib}
%\RequirePackage[authoryear]{natbib}% uncomment this for author-year bibliography
%\RequirePackage{hyperref}
\usepackage[utf8]{inputenc} % unicode support
\usepackage{url}
\usepackage{graphicx} % used to add figures
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\usepackage{makecell}

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%\def\includegraphic{}
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%%% Put your definitions there:
\startlocaldefs
\endlocaldefs


%%% Begin ...
\begin{document}

%%% Start of article front matter
\begin{frontmatter}

\begin{fmbox}
\dochead{Research}

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\title{Integration of Structured Biological Data Sources using Biological Expression Language}

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\author[
   addressref={scai,bit},
   corref={scai},
   email={charles.hoyt@scai.fraunhofer.de}
]{\inits{CT}\fnm{Charles Tapley} \snm{Hoyt}}
\author[
   addressref={scai,bit},
]{\inits{D}\fnm{Daniel} \snm{Domingo-Fern\'andez}}
\author[
   addressref={scai,bit},
]{\inits{S}\fnm{Sarah} \snm{Mubeen}}
\author[
   addressref={scai},
]{\inits{J}\fnm{Josep} \snm{Mar\'{\i}n-Ll\'ao}}
\author[
   addressref={scai},
]{\inits{A}\fnm{Andrej} \snm{Konotopez}}
\author[
   addressref={scai},
]{\inits{C}\fnm{Christian} \snm{Ebeling}}
\author[
   addressref={scai,bit},
]{\inits{C}\fnm{Colin} \snm{Birkenbihl}}
\author[
   addressref={scai,bit},
]{\inits{\"O}\fnm{\"Ozlem} \snm{Muslu}}
\author[
   addressref={scai,bit},
]{\inits{B}\fnm{Bradley} \snm{English}}
\author[
   addressref={scai,bit},
]{\inits{S}\fnm{Simon} \snm{M\"uller}}
\author[
   addressref={bit},
]{\inits{M}\fnm{Mauricio} \snm{Pio de Lacerda}}
\author[
   addressref={iais,bonn-cs},
]{\inits{M}\fnm{Mehdi} \snm{Ali}}
\author[
   addressref={stanford},
]{\inits{S}\fnm{Scott} \snm{Colby}}
\author[
   addressref={embl,rwth,heidelberg},
]{\inits{D}\fnm{Den\'es} \snm{T\"urei}}
\author[
   addressref={rwth,heidelberg},
]{\inits{N}\fnm{Nicol\`as} \snm{Palacio-Escat}}
\author[
   addressref={scai,bit},
]{\inits{M}\fnm{Martin} \snm{Hofmann-Apitius}}

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\address[id=scai]{
  \orgname{Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI)},
  \street{Konrad Adenauer Strasse},
  \postcode{53754}
  \city{Sankt Augustin},
  \cny{Germany}
}
\address[id=bit]{%
  \orgname{Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universit\"at Bonn},
  %\street{D\"{u}sternbrooker Weg 20},
  \postcode{53115}
  \city{Bonn},
  \cny{Germany}
}
\address[id=iais]{
  \orgname{Department of Enterprise Information Systems, Fraunhofer Institute for Intelligent Analysis and Information Systems (IAIS)},
  \street{Konrad Adenauer Strasse},
  \postcode{53754}
  \city{Sankt Augustin},
  \cny{Germany}
}
\address[id=bonn-cs]{%
  \orgname{Department of Computer Science, Rheinische Friedrich-Wilhelms-Universit\"at Bonn},
  %\street{D\"{u}sternbrooker Weg 20},
  \postcode{53115}
  \city{Bonn},
  \cny{Germany}
}
\address[id=stanford]{%
  \orgname{Department of Chemistry, Stanford University},
  %\street{D\"{u}sternbrooker Weg 20},
  \postcode{94305}
  \city{Stanford},
  \cny{United States of America}
}
\address[id=embl]{%
  \orgname{European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit},
  \street{Meyerhofstrasse 1},
  \postcode{69117}
  \city{Heidelberg},
  \cny{Germany}
}
\address[id=rwth]{%
  \orgname{Faculty of Medicine, Joint Research Centre for Computational Biomedicine, RWTH Aachen University},
  \street{MTZ Pauwelsstrasse 19},
  \postcode{52074}
  \city{Aachen},
  \cny{Germany}
}
\address[id=heidelberg]{%
  \orgname{Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Heidelberg University},
  \street{Bioquant Im Neuenheimer Feld 267},
  \postcode{69120}
  \city{Heidelberg},
  \cny{Germany}
}

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%\note{Sample of title note}     % note to the article
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\begin{abstractbox}

\begin{abstract}
\parttitle{Background}
The integration of heterogeneous, multi-scale, and multi-modal knowledge and data has become a common prerequisite for joint analysis to unravel the mechanisms and aetiologies of complex diseases.
Because of its unique ability to capture this variety, Biological Expression Language (BEL) is well suited to be further used as a platform for semantic integration and harmonization in networks and systems biology.
\parttitle{Results}
We have developed numerous independent packages capable of downloading, structuring, and serializing various biological data sources to BEL. Each Bio2BEL package is implemented in the Python programming language and distributed through GitHub (\url{https://github.com/bio2bel}) and PyPI\@.
\parttitle{Conclusions}
The philosophy of Bio2BEL encourages reproducibility, accessibility, and democratization of biological databases.
We present several applications of Bio2BEL packages including their ability to support the curation of pathway mappings, integration of pathway databases, and machine learning applications.
\end{abstract}

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\begin{keyword}
\kwd{Data Integration}
\kwd{Semantic Web}
\kwd{Biological Expression Language}
\kwd{Knowledge graphs}
\end{keyword}

% MSC classifications codes, if any
%\begin{keyword}[class=AMS]
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\end{abstractbox}
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%\end{fmbox}% uncomment this for twcolumn layout

\end{frontmatter}

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%% http://www.biomedcentral.com/info/authors%%
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%% accordingly for your article type.       %%
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% <put your article body there>

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%% Background %%
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\section*{Background}
\input{background}

\section*{Implementation}
\input{implementation}

\section*{Results}
\input{results}

\section*{Conclusions}
\input{conclusions}

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\begin{backmatter}

\section*{Ethics approval and consent to participate}
Not applicable

\section*{Consent for publication}
Not applicable

\section*{Availability of data and materials}
Each Bio2BEL package is listed on \url{https://github.com/bio2bel} and automatically acquires relevant data from their respective original biological data sources.

\section*{Competing interests}
The authors declare that they have no competing interests.

\section*{Funding}
This work was partially supported by the EU/EFPIA Innovative Medicines Initiative Joint Undertaking under AETIONOMY [grant number 115568], resources of which are composed of financial contribution from the European Union's Seventh Framework Programme (FP7/2007-2013) and EFPIA companies in kind contribution.

This work was also partially supported by the Fraunhofer Society's MAVO program.

The funding bodies did not play a role in the design of the study and collection, analysis, and interpretation of data, nor in writing the manuscript.

\section*{Author's contributions}
CTH conceived and designed the study.
CTH, DDF, and SM drafted the manuscript.
MHA acquired funding and reviewed the manuscript.
All authors performed data curation and developed computational pipelines for extraction, transformation, and loading of various biological data sources.
All authors have read and approved the final manuscript.

\section*{Acknowledgements}
We would like to thank the curators and maintainers of the several databases we have used, without whom none of this work would be possible.

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\end{backmatter}
\end{document}