article.bib

@Manual{devtools,
    title = {devtools: Tools to Make Developing R Packages Easier},
    author = {Hadley Wickham and Winston Chang},
    year = {2015},
    note = {R package version 1.7.0},
    url = {http://CRAN.R-project.org/package=devtools},
}

@article{Mons2011,
    abstract = {Data citation and the derivation of semantic constructs directly from datasets have now both found their place in scientific communication. The social challenge facing us is to maintain the value of traditional narrative publications and their relationship to the datasets they report upon while at the same time developing appropriate metrics for citation of data and data constructs.},
    author = {Mons, Barend and van Haagen, Herman and Chichester, Christine and Hoen, Peter-Bram and den Dunnen, Johan T. and van Ommen, Gertjan and van Mulligen, Erik and Singh, Bharat and Hooft, Rob and Roos, Marco and Hammond, Joel and Kiesel, Bruce and Giardine, Belinda and Velterop, Jan and Groth, Paul and Schultes, Erik},
    citeulike-article-id = {9075469},
    citeulike-linkout-0 = {http://dx.doi.org/10.1038/ng0411-281},
    citeulike-linkout-1 = {http://dx.doi.org/10.1038/ng0411-281},
    citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/21445068},
    citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=21445068},
    day = {29},
    doi = {10.1038/ng0411-281},
    issn = {1061-4036},
    journal = {Nature Genetics},
    month = mar,
    number = {4},
    pages = {281--283},
    pmid = {21445068},
    posted-at = {2014-03-15 12:23:58},
    priority = {2},
    publisher = {Nature Publishing Group},
    title = {The value of data},
    url = {http://dx.doi.org/10.1038/ng0411-281},
    volume = {43},
    year = {2011}
}

@article{Gentleman2004,
    abstract = {The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples.},
    address = {Department of Biostatistical Science, Dana-Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA. rgentlem@jimmy.harvard.edu},
    author = {Gentleman, Robert and Carey, Vincent and Bates, Douglas and Bolstad, Ben and Dettling, Marcel and Dudoit, Sandrine and Ellis, Byron and Gautier, Laurent and Ge, Yongchao and Gentry, Jeff and Hornik, Kurt and Hothorn, Torsten and Huber, Wolfgang and Iacus, Stefano and Irizarry, Rafael and Leisch, Friedrich and Li, Cheng and Maechler, Martin and Rossini, Anthony and Sawitzki, Gunther and Smith, Colin and Smyth, Gordon and Tierney, Luke and Yang, Jean and Zhang, Jianhua},
    booktitle = {Genome Biology},
    citeulike-article-id = {166220},
    citeulike-linkout-0 = {http://dx.doi.org/10.1186/gb-2004-5-10-r80},
    citeulike-linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC545600/},
    citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/15461798},
    citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=15461798},
    citeulike-linkout-4 = {http://link.springer.com/article/10.1186/gb-2004-5-10-r80},
    doi = {10.1186/gb-2004-5-10-r80},
    issn = {1465-6906},
    journal = {Genome Biology},
    number = {10},
    pages = {R80--16},
    pmcid = {PMC545600},
    pmid = {15461798},
    posted-at = {2014-03-15 11:36:27},
    priority = {2},
    publisher = {BioMed Central},
    title = {Bioconductor: open software development for computational biology and bioinformatics},
    url = {http://dx.doi.org/10.1186/gb-2004-5-10-r80},
    volume = {5},
    year = {2004}
}

@article{Durinck2005,
    abstract = {Summary: {biomaRt} is a new Bioconductor package that integrates {BioMart} data resources with data analysis software in Bioconductor. It can annotate a wide range of gene or gene product identifiers (e.g. {Entrez-Gene} and Affymetrix probe identifiers) with information such as gene symbol, chromosomal coordinates, Gene Ontology and {OMIM} annotation. Furthermore {biomaRt} enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis. Fast and up-to-date data retrieval is possible as the package executes direct {SQL} queries to the {BioMart} databases (e.g. Ensembl). The {biomaRt} package provides a tight integration of large, public or locally installed {BioMart} databases with data analysis in Bioconductor creating a powerful environment for biological data {mining.Availability}: http://www.bioconductor.org. {LGPLContact}: steffen.durinck@esat.kuleuven.ac.be},
    author = {Durinck, Steffen and Moreau, Yves and Kasprzyk, Arek and Davis, Sean and De Moor, Bart and Brazma, Alvis and Huber, Wolfgang},
    citeulike-article-id = {299529},
    citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/bti525},
    citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/16/3439},
    citeulike-linkout-2 = {http://www.ingentaconnect.com/content/oup/cabios/2005/00000021/00000016/art03439},
    citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/16082012},
    citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=16082012},
    day = {15},
    doi = {10.1093/bioinformatics/bti525},
    issn = {1367-4803},
    journal = {Bioinformatics},
    month = aug,
    number = {16},
    pages = {3439--3440},
    pmid = {16082012},
    posted-at = {2013-12-26 09:07:53},
    priority = {2},
    publisher = {Oxford University Press},
    title = {{BioMart} and Bioconductor: a powerful link between biological databases and microarray data analysis},
    url = {http://dx.doi.org/10.1093/bioinformatics/bti525},
    volume = {21},
    year = {2005}
}

@article{Dix2007,
    author = {Dix, David J. and Houck, Keith A. and Martin, Matthew T. and Richard, Ann M. and Setzer, R. Woodrow and Kavlock, Robert J.},
    citeulike-article-id = {1002785},
    citeulike-linkout-0 = {http://dx.doi.org/10.1093/toxsci/kfl103},
    citeulike-linkout-1 = {http://toxsci.oxfordjournals.org/cgi/content/abstract/95/1/5},
    citeulike-linkout-2 = {http://www.ingentaconnect.com/content/oup/toxsci/2007/00000095/00000001/art00005},
    citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/16963515},
    citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=16963515},
    day = {1},
    doi = {10.1093/toxsci/kfl103},
    issn = {1096-6080},
    journal = {Toxicological Sciences},
    keywords = {toxcast},
    month = jan,
    number = {1},
    pages = {5--12},
    pmid = {16963515},
    posted-at = {2011-05-20 12:59:43},
    priority = {2},
    publisher = {Oxford University Press},
    title = {The {ToxCast} Program for Prioritizing Toxicity Testing of Environmental Chemicals},
    url = {http://dx.doi.org/10.1093/toxsci/kfl103},
    volume = {95},
    year = {2007}
}

@article{Hardy2010,
    author = {Hardy, Barry and Douglas, Nicki and Helma, Christoph and Rautenberg, Micha and Jeliazkova, Nina and Jeliazkov, Vedrin and Nikolova, Ivelina and Benigni, Romualdo and Tcheremenskaia, Olga and Kramer, Stefan and Girschick, Tobias and Buchwald, Fabian and Wicker, Joerg and Karwath, Andreas and Gutlein, Martin and Maunz, Andreas and Sarimveis, Haralambos and Melagraki, Georgia and Afantitis, Antreas and Sopasakis, Pantelis and Gallagher, David and Poroikov, Vladimir and Filimonov, Dmitry and Zakharov, Alexey and Lagunin, Alexey and Gloriozova, Tatyana and Novikov, Sergey and Skvortsova, Natalia and Druzhilovsky, Dmitry and Chawla, Sunil and Ghosh, Indira and Ray, Surajit and Patel, Hitesh and Escher, Sylvia},
    citeulike-article-id = {7750823},
    citeulike-linkout-0 = {http://dx.doi.org/10.1186/1758-2946-2-7},
    citeulike-linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2941473/},
    citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/20807436},
    citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=20807436},
    day = {31},
    doi = {10.1186/1758-2946-2-7},
    issn = {1758-2946},
    journal = {Journal of Cheminformatics},
    keywords = {cheminformatics, chemistry, opentox, toxicity},
    month = aug,
    number = {1},
    pages = {7+},
    pmcid = {PMC2941473},
    pmid = {20807436},
    posted-at = {2010-09-01 05:24:27},
    priority = {2},
    title = {Collaborative development of predictive toxicology applications},
    url = {http://dx.doi.org/10.1186/1758-2946-2-7},
    volume = {2},
    year = {2010}
}

@Manual{Lang2013,
  title = {RCurl: General network (HTTP/FTP/...) client interface for R},
  author = {Duncan Temple Lang},
  year = {2013},
  note = {R package version 1.95-4.1},
  url = {http://CRAN.R-project.org/package=RCurl},
}


@misc{dumontier2013semanticscience,
  title={The Semanticscience Integrated Ontology (SIO) for Biomedical Research and Knowledge Discovery},
  author={Dumontier, Michel and Baker, Christopher JO and Baran, Joachim and Callahan, Alison and Hoehndorf, Robert},
  howpublished={\url{http://code.google.com/p/semanticscience/wiki/SIO}},
  year={2013}
}

@article{d2009bibliographic,
  title={Bibliographic Ontology Specification. Specification Document, 4 November 2009},
  author={D'Arcus, B and Giasson, F},
  volume={10},
  pages={2011},
  howpublished = {\url{http://bibliontology.com/specification}},
  year={2009}
}

@article{Shotton2010,
    author = {Shotton, David},
    citeulike-article-id = {7351537},
    citeulike-linkout-0 = {http://dx.doi.org/10.1186/2041-1480-1-s1-s6},
    citeulike-linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2903725/},
    citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/20626926},
    citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=20626926},
    doi = {10.1186/2041-1480-1-s1-s6},
    issn = {2041-1480},
    journal = {Journal of Biomedical Semantics},
    keywords = {ontology, publishing, rdf},
    number = {Suppl 1},
    pages = {S6+},
    pmcid = {PMC2903725},
    pmid = {20626926},
    posted-at = {2010-10-21 14:26:04},
    priority = {2},
    title = {{CiTO}, the Citation Typing Ontology},
    url = {http://dx.doi.org/10.1186/2041-1480-1-s1-s6},
    volume = {1},
    year = {2010}
}

@article{Luciano2011,
    author = {Luciano, Joanne and Andersson, Bosse and Batchelor, Colin and Bodenreider, Olivier and Clark, Tim and Denney, Christine and Domarew, Christopher and Gambet, Thomas and Harland, Lee and Jentzsch, Anja and Kashyap, Vipul and Kos, Peter and Kozlovsky, Julia and Lebo, Timothy and Marshall, Scott and McCusker, James and McGuinness, Deborah and Ogbuji, Chimezie and Pichler, Elgar and Powers, Robert and Prud'hommeaux, Eric and Samwald, Matthias and Schriml, Lynn and Tonellato, Peter and Whetzel, Patricia and Zhao, Jun and Stephens, Susie and Dumontier, Michel},
    citeulike-article-id = {9336575},
    citeulike-linkout-0 = {http://dx.doi.org/10.1186/2041-1480-2-s2-s1},
    citeulike-linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3102889/},
    citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/21624155},
    citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=21624155},
    doi = {10.1186/2041-1480-2-s2-s1},
    issn = {2041-1480},
    journal = {Journal of Biomedical Semantics},
    number = {Suppl 2},
    pages = {S1+},
    pmcid = {PMC3102889},
    pmid = {21624155},
    posted-at = {2013-11-06 15:36:10},
    priority = {2},
    title = {The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside},
    url = {http://dx.doi.org/10.1186/2041-1480-2-s2-s1},
    volume = {2},
    year = {2011}
}

@techreport{Haupt2013,
    author = {Haupt, Carina and Waagmeester, Andra and Zimmermann, Marc and Willighagen, Egon},
    citeulike-article-id = {12870877},
    citeulike-linkout-0 = {http://www.openphacts.org/specs/2013/WD-rdfguide-20131007/},
    day = {7},
    howpublished = {\url{http://www.openphacts.org/specs/2013/WD-rdfguide-20131007/}},
    month = oct,
    organization = {Open PHACTS},
    posted-at = {2013-12-26 09:48:38},
    priority = {2},
    title = {Guidelines for exposing data as {RDF} in Open {PHACTS}},
    url = {http://www.openphacts.org/specs/2013/WD-rdfguide-20131007/},
    year = {2013}
}

@misc{VanHage2013,
    author = {Van Hage, Willem R.},
    citeulike-article-id = {12870876},
    day = {25},
    howpublished = {\url{http://cran.r-project.org/web/packages/SPARQL/}},
    month = oct,
    posted-at = {2013-12-26 09:46:08},
    priority = {2},
    publisher = {The Comprehensive R Archive Network},
    title = {{SPARQL}: {SPARQL} client},
    year = {2013}
}

@article{Noy2009,
    abstract = {Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, data annotation, natural-language processing and decision support. {BioPortal} (http://bioportal.bioontology.org) is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in {OWL}, {RDF}, {OBO} format and Prot\'{e}g\'{e} frames. {BioPortal} functionality includes the ability to browse, search and visualize ontologies. The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content by providing features to add notes to ontology terms, mappings between terms and ontology reviews based on criteria such as usability, domain coverage, quality of content, and documentation and support. {BioPortal} also enables integrated search of biomedical data resources such as the Gene Expression Omnibus ({GEO}), {ClinicalTrials}.gov, and {ArrayExpress}, through the annotation and 
indexing of these resources with ontologies in {BioPortal}. Thus, {BioPortal} not only provides investigators, clinicians, and developers 'one-stop shopping' to programmatically access biomedical ontologies, but also provides support to integrate data from a variety of biomedical resources.},
    author = {Noy, Natalya F. and Shah, Nigam H. and Whetzel, Patricia L. and Dai, Benjamin and Dorf, Michael and Griffith, Nicholas and Jonquet, Clement and Rubin, Daniel L. and Storey, Margaret-Anne and Chute, Christopher G. and Musen, Mark A.},
    citeulike-article-id = {4716987},
    citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gkp440},
    citeulike-linkout-1 = {http://nar.oxfordjournals.org/content/37/suppl\_2/W170.abstract},
    citeulike-linkout-2 = {http://nar.oxfordjournals.org/content/37/suppl\_2/W170.full.pdf},
    citeulike-linkout-3 = {http://nar.oxfordjournals.org/cgi/content/abstract/37/suppl\_2/W170},
    citeulike-linkout-4 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703982/},
    citeulike-linkout-5 = {http://view.ncbi.nlm.nih.gov/pubmed/19483092},
    citeulike-linkout-6 = {http://www.hubmed.org/display.cgi?uids=19483092},
    day = {1},
    doi = {10.1093/nar/gkp440},
    issn = {1362-4962},
    journal = {Nucleic Acids Research},
    month = jul,
    number = {suppl 2},
    pages = {W170--W173},
    pmcid = {PMC2703982},
    pmid = {19483092},
    posted-at = {2013-12-26 09:40:31},
    priority = {2},
    title = {{BioPortal}: ontologies and integrated data resources at the click of a mouse},
    url = {http://dx.doi.org/10.1093/nar/gkp440},
    volume = {37},
    year = {2009}
}

@article{Williams2012,
    abstract = {Open {PHACTS} is a public–private partnership between academia, publishers, small and medium sized enterprises and pharmaceutical companies. The goal of the project is to deliver and sustain an 'open pharmacological space' using and enhancing state-of-the-art semantic web standards and technologies. It is focused on practical and robust applications to solve specific questions in drug discovery research. {OPS} is intended to facilitate improvements in drug discovery in academia and industry and to support open innovation and in-house non-public drug discovery research. This paper lays out the challenges and how the Open {PHACTS} project is hoping to address these challenges technically and socially. \^{a}–º We discuss Open {PHACTS}, a project using semantic web standards and technologies. \^{a}–º We discuss integration and mapping of disparate chemical and biological data types. \^{a}–º The influence of data quality, crowdsourcing and curation is discussed. \^{a}–º Open {PHACTS} will 
facilitate improvements in drug discovery in academia and industry.},
    author = {Williams, Antony J. and Harland, Lee and Groth, Paul and Pettifer, Stephen and Chichester, Christine and Willighagen, Egon L. and Evelo, Chris T. and Blomberg, Niklas and Ecker, Gerhard and Goble, Carole and Mons, Barend},
    citeulike-article-id = {10770367},
    citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.drudis.2012.05.016},
    citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/22683805},
    citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=22683805},
    day = {7},
    doi = {10.1016/j.drudis.2012.05.016},
    issn = {13596446},
    journal = {Drug Discovery Today},
    keywords = {openphacts},
    month = nov,
    number = {21-22},
    pages = {1188--1198},
    pmid = {22683805},
    posted-at = {2012-06-10 06:48:25},
    priority = {2},
    title = {Open {PHACTS}: semantic interoperability for drug discovery},
    url = {http://dx.doi.org/10.1016/j.drudis.2012.05.016},
    volume = {17},
    year = {2012}
}

@article{Durinck2005,
    abstract = {Summary: {biomaRt} is a new Bioconductor package that integrates {BioMart} data resources with data analysis software in Bioconductor. It can annotate a wide range of gene or gene product identifiers (e.g. {Entrez-Gene} and Affymetrix probe identifiers) with information such as gene symbol, chromosomal coordinates, Gene Ontology and {OMIM} annotation. Furthermore {biomaRt} enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis. Fast and up-to-date data retrieval is possible as the package executes direct {SQL} queries to the {BioMart} databases (e.g. Ensembl). The {biomaRt} package provides a tight integration of large, public or locally installed {BioMart} databases with data analysis in Bioconductor creating a powerful environment for biological data {mining.Availability}: http://www.bioconductor.org. {LGPLContact}: steffen.durinck@esat.kuleuven.ac.be},
    author = {Durinck, Steffen and Moreau, Yves and Kasprzyk, Arek and Davis, Sean and De Moor, Bart and Brazma, Alvis and Huber, Wolfgang},
    citeulike-article-id = {299529},
    citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/bti525},
    citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/16/3439},
    citeulike-linkout-2 = {http://www.ingentaconnect.com/content/oup/cabios/2005/00000021/00000016/art03439},
    citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/16082012},
    citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=16082012},
    day = {15},
    doi = {10.1093/bioinformatics/bti525},
    issn = {1367-4803},
    journal = {Bioinformatics},
    month = aug,
    number = {16},
    pages = {3439--3440},
    pmid = {16082012},
    posted-at = {2013-12-26 09:07:53},
    priority = {2},
    publisher = {Oxford University Press},
    title = {{BioMart} and Bioconductor: a powerful link between biological databases and microarray data analysis},
    url = {http://dx.doi.org/10.1093/bioinformatics/bti525},
    volume = {21},
    year = {2005}
}

@article{Gaulton2012,
    abstract = {{ChEMBL} is an Open Data database containing binding, functional and {ADMET} information for a large number of drug-like bioactive compounds. These data are manually abstracted from the primary published literature on a regular basis, then further curated and standardized to maximize their quality and utility across a wide range of chemical biology and drug-discovery research problems. Currently, the database contains 5.4 million bioactivity measurements for more than 1 million compounds and 5200 protein targets. Access is available through a web-based interface, data downloads and web services at: https://www.ebi.ac.uk/chembldb.},
    author = {Gaulton, Anna and Bellis, Louisa J. and Bento, A. Patricia and Chambers, Jon and Davies, Mark and Hersey, Anne and Light, Yvonne and McGlinchey, Shaun and Michalovich, David and Al-Lazikani, Bissan and Overington, John P.},
    citeulike-article-id = {9801263},
    citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gkr777},
    citeulike-linkout-1 = {http://nar.oxfordjournals.org/content/early/2011/09/22/nar.gkr777.abstract},
    citeulike-linkout-2 = {http://nar.oxfordjournals.org/content/early/2011/09/22/nar.gkr777.full.pdf},
    citeulike-linkout-3 = {http://nar.oxfordjournals.org/cgi/content/abstract/40/D1/D1100},
    citeulike-linkout-4 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245175/},
    citeulike-linkout-5 = {http://view.ncbi.nlm.nih.gov/pubmed/21948594},
    citeulike-linkout-6 = {http://www.hubmed.org/display.cgi?uids=21948594},
    day = {01},
    doi = {10.1093/nar/gkr777},
    issn = {1362-4962},
    journal = {Nucleic Acids Research},
    keywords = {assay, chembl, cheminformatics, qsar, toxicology},
    month = jan,
    number = {D1},
    pages = {D1100--D1107},
    pmcid = {PMC3245175},
    pmid = {21948594},
    posted-at = {2012-03-07 10:56:43},
    priority = {2},
    publisher = {Oxford University Press},
    title = {{ChEMBL}: a large-scale bioactivity database for drug discovery},
    url = {http://dx.doi.org/10.1093/nar/gkr777},
    volume = {40},
    year = {2012}
}

@TechReport{Seaborne2009,
  author      = "Andy Seaborne and Steve Harris",
  title       = "{SPARQL} 1.1 Query",
  month       = oct,
  url         = "http://www.w3.org/TR/2009/WD-sparql11-query-20091022/",
  year        = "2009",
  bibsource   = "http://w2.syronex.com/jmr/w3c-biblio",
  type        = "{W3C} Working Draft",
  institution = "W3C",
}

@misc{EBIRDFPlatform,
  title = "{EBI RDF Platform}",
  year = "2013",
  url = "http://www.ebi.ac.uk/rdf/"
}

@Manual{RMan,
  title = {R: A Language and Environment for Statistical Computing},
  author = {{R Core Team}},
  organization = {R Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2013},
  url = {http://www.R-project.org/},
}

@misc{Jena,
  title = "{Apache Jena 2.12.1}",
  year = "2014",
  url = "http://jena.apache.org/"
}

@misc{RJava,
  author = "Urbanek, S.",
  title = "{rJava - Low-level R to Java interface}",
  year = "2013",
  month = 12,
  day = 3,
  url = "http://cran.r-project.org/web/packages/rJava/"
}

@article{Williams2012,
    abstract = {Open {PHACTS} is a public–private partnership between academia, publishers, small and medium sized enterprises and pharmaceutical companies. The goal of the project is to deliver and sustain an 'open pharmacological space' using and enhancing state-of-the-art semantic web standards and technologies. It is focused on practical and robust applications to solve specific questions in drug discovery research. {OPS} is intended to facilitate improvements in drug discovery in academia and industry and to support open innovation and in-house non-public drug discovery research. This paper lays out the challenges and how the Open {PHACTS} project is hoping to address these challenges technically and socially. \^{a}–º We discuss Open {PHACTS}, a project using semantic web standards and technologies. \^{a}–º We discuss integration and mapping of disparate chemical and biological data types. \^{a}–º The influence of data quality, crowdsourcing and curation is discussed. \^{a}–º Open {PHACTS} will 
facilitate improvements in drug discovery in academia and industry.},
    author = {Williams, Antony J. and Harland, Lee and Groth, Paul and Pettifer, Stephen and Chichester, Christine and Willighagen, Egon L. and Evelo, Chris T. and Blomberg, Niklas and Ecker, Gerhard and Goble, Carole and Mons, Barend},
    citeulike-article-id = {10770367},
    citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.drudis.2012.05.016},
    citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/22683805},
    citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=22683805},
    day = {7},
    doi = {10.1016/j.drudis.2012.05.016},
    issn = {13596446},
    journal = {Drug Discovery Today},
    keywords = {openphacts},
    month = nov,
    number = {21-22},
    pages = {1188--1198},
    pmid = {22683805},
    posted-at = {2012-06-10 06:48:25},
    priority = {2},
    title = {Open {PHACTS}: semantic interoperability for drug discovery},
    url = {http://dx.doi.org/10.1016/j.drudis.2012.05.016},
    volume = {17},
    year = {2012}
}

@article{Samwald2011,
    abstract = {There is an abundance of information about drugs available on the Web. Data sources range from medicinal chemistry results, over the impact of drugs on gene expression, to the outcomes of drugs in clinical trials. These data are typically not connected together, which reduces the ease with which insights can be gained. Linking Open Drug Data ({LODD}) is a task force within the World Wide Web Consortium's ({W3C}) Health Care and Life Sciences Interest Group ({HCLS} {IG}). {LODD} has surveyed publicly available data about drugs, created Linked Data representations of the data sets, and identified interesting scientific and business questions that can be answered once the data sets are connected. The task force provides recommendations for the best practices of exposing data in a Linked Data representation. In this paper, we present past and ongoing work of {LODD} and discuss the growing importance of Linked Data as a foundation for pharmaceutical {R\&D} data sharing.},
    author = {Samwald, Matthias and Jentzsch, Anja and Bouton, Christopher and Kallesoe, Claus and Willighagen, Egon and Hajagos, Janos and Marshall, M. and Prud'hommeaux, Eric and Hassanzadeh, Oktie and Pichler, Elgar and Stephens, Susie},
    citeulike-article-id = {9301838},
    citeulike-linkout-0 = {http://dx.doi.org/10.1186/1758-2946-3-19},
    citeulike-linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3121711/},
    citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/21575203},
    citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=21575203},
    doi = {10.1186/1758-2946-3-19},
    issn = {1758-2946},
    journal = {Journal of Cheminformatics},
    keywords = {acsrdf2010, chemistry, lifesciences, rdf},
    number = {1},
    pages = {19+},
    pmcid = {PMC3121711},
    pmid = {21575203},
    posted-at = {2011-05-16 11:56:36},
    priority = {2},
    title = {Linked open drug data for pharmaceutical research and development},
    url = {http://dx.doi.org/10.1186/1758-2946-3-19},
    volume = {3},
    year = {2011}
}

@article{Willighagen2013,
    abstract = {{BACKGROUND}:Making data available as Linked Data using Resource Description Framework ({RDF}) promotes integration with other web resources. {RDF} documents can natively link to related data, and others can link back using Uniform Resource Identifiers ({URIs}). {RDF} makes the data machine-readable and uses extensible vocabularies for additional information, making it easier to scale up inference and data {analysis.RESULTS}:This paper describes recent developments in an ongoing project converting data from the {ChEMBL} database into {RDF} triples. Relative to earlier versions, this updated version of {ChEMBL}-{RDF} uses recently introduced ontologies, including {CHEMINF} and {CiTO}; exposes more information from the database; and is now available as dereferencable, linked data. To demonstrate these new features, we present novel use cases showing further integration with other web resources, including {Bio2RDF}, {Chem2Bio2RDF}, and {ChemSpider}, and showing the use of standard ontologies for 
{querying.CONCLUSIONS}:We have illustrated the advantages of using open standards and ontologies to link the {ChEMBL} database to other databases. Using those links and the knowledge encoded in standards and ontologies, the {ChEMBL}-{RDF} resource creates a foundation for integrated semantic web cheminformatics applications, such as the presented decision support.},
    author = {Willighagen, Egon and Waagmeester, Andra and Spjuth, Ola and Ansell, Peter and Williams, Antony and Tkachenko, Valery and Hastings, Janna and Chen, Bin and Wild, David},
    citeulike-article-id = {12333337},
    citeulike-linkout-0 = {http://dx.doi.org/10.1186/1758-2946-5-23},
    citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/23657106},
    citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=23657106},
    doi = {10.1186/1758-2946-5-23},
    issn = {1758-2946},
    journal = {Journal of Cheminformatics},
    keywords = {chembl, pharmacology, rdf, semantic\_web},
    number = {1},
    pages = {23+},
    pmid = {23657106},
    posted-at = {2013-05-09 11:05:56},
    priority = {5},
    title = {The {ChEMBL} database as linked open data},
    url = {http://dx.doi.org/10.1186/1758-2946-5-23},
    volume = {5},
    year = {2013}
}

@article{Belleau2008,
    abstract = {Presently, there are numerous bioinformatics databases available on different websites. Although {RDF} was proposed as a standard format for the web, these databases are still available in various formats. With the increasing popularity of the semantic web technologies and the ever growing number of databases in bioinformatics, there is a pressing need to develop mashup systems to help the process of bioinformatics knowledge integration. {Bio2RDF} is such a system, built from rdfizer programs written in {JSP}, the Sesame open source triplestore technology and an {OWL} ontology. With {Bio2RDF}, documents from public bioinformatics databases such as Kegg, {PDB}, {MGI}, {HGNC} and several of {NCBI}'s databases can now be made available in {RDF} format through a unique {URL} in the form of http://bio2rdf.org/namespace:id. The {Bio2RDF} project has successfully applied the semantic web technology to publicly available databases by creating a knowledge space of {RDF} documents linked together with 
normalized {URIs} and sharing a common ontology. {Bio2RDF} is based on a three-step approach to build mashups of bioinformatics data. The present article details this new approach and illustrates the building of a mashup used to explore the implication of four transcription factor genes in Parkinson's disease. The {Bio2RDF} repository can be queried at http://bio2rdf.org.},
    address = {Centre de Recherche du CHUL, Universit\'{e} Laval, 2705 Boulevard Laurier, Que., Canada G1V 4G2.},
    author = {Belleau, Fran\c{c}ois and Nolin, Marc-Alexandre and Tourigny, Nicole and Rigault, Philippe and Morissette, Jean},
    citeulike-article-id = {2794985},
    citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.jbi.2008.03.004},
    citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/18472304},
    citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=18472304},
    citeulike-linkout-3 = {http://www.sciencedirect.com/science/article/B6WHD-4S3S2HJ-2/2/e60cdd078bdf86af287bc5926bcd1254},
    day = {21},
    doi = {10.1016/j.jbi.2008.03.004},
    issn = {15320464},
    journal = {Journal of Biomedical Informatics},
    month = oct,
    number = {5},
    pages = {706--716},
    pmid = {18472304},
    posted-at = {2009-09-02 10:53:30},
    priority = {2},
    title = {{Bio2RDF}: Towards a mashup to build bioinformatics knowledge systems},
    url = {http://dx.doi.org/10.1016/j.jbi.2008.03.004},
    volume = {41},
    year = {2008}
}

@article{Chen2010,
    abstract = {{BACKGROUND}:Recently there has been an explosion of new data sources about genes, proteins, genetic variations, chemical compounds, diseases and drugs. Integration of these data sources and the identification of patterns that go across them is of critical interest. Initiatives such as {Bio2RDF} and {LODD} have tackled the problem of linking biological data and drug data respectively using {RDF}. Thus far, the inclusion of chemogenomic and systems chemical biology information that crosses the domains of chemistry and biology has been very {limitedRESULTS}:We have created a single repository called {Chem2Bio2RDF} by aggregating data from multiple chemogenomics repositories that is cross-linked into {Bio2RDF} and {LODD}. We have also created a linked-path generation tool to facilitate {SPARQL} query generation, and have created extended {SPARQL} functions to address specific chemical/biological search needs. We demonstrate the utility of {Chem2Bio2RDF} in investigating polypharmacology, 
identification of potential multiple pathway inhibitors, and the association of pathways with adverse drug {reactions.CONCLUSIONS}:We have created a new semantic systems chemical biology resource, and have demonstrated its potential usefulness in specific examples of polypharmacology, multiple pathway inhibition and adverse drug reaction - pathway mapping. We have also demonstrated the usefulness of extending {SPARQL} with cheminformatics and bioinformatics functionality.},
    author = {Chen, Bin and Dong, Xiao and Jiao, Dazhi and Wang, Huijun and Zhu, Qian and Ding, Ying and Wild, David},
    citeulike-article-id = {7179733},
    citeulike-linkout-0 = {http://dx.doi.org/10.1186/1471-2105-11-255},
    citeulike-linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881087/},
    citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/20478034},
    citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=20478034},
    day = {17},
    doi = {10.1186/1471-2105-11-255},
    issn = {1471-2105},
    journal = {BMC Bioinformatics},
    month = may,
    number = {1},
    pages = {255+},
    pmcid = {PMC2881087},
    pmid = {20478034},
    posted-at = {2010-09-29 15:08:14},
    priority = {2},
    title = {{Chem2Bio2RDF}: a semantic framework for linking and data mining chemogenomic and systems chemical biology data},
    url = {http://dx.doi.org/10.1186/1471-2105-11-255},
    volume = {11},
    year = {2010}
}