directory reorganization, evaluation scripts for R CVs

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+@Article{Kazius2005,
+  author = "Kazius, J. and McGuire, R. and Bursi, R.",
+  year = 2005,
+  title = "Derivation and validation of toxicophores for mutagenicity prediction",
+  journal = "J Med Chem",
+  number = 48,
+  pages = "312-20",
+}
+
+@article{Hansen2009,
+  author = {Hansen, Katja and Mika, Sebastian and Schroeter, Timon and Sutter, Andreas and ter Laak, Antonius and Steger-Hartmann, Thomas and Heinrich, Nikolaus and Müller, Klaus-Robert},
+  title = {Benchmark Data Set for in Silico Prediction of Ames Mutagenicity},
+  journal = {Journal of Chemical Information and Modeling},
+  volume = {49},
+  number = {9},
+  pages = {2077-2081},
+  year = {2009},
+  doi = {10.1021/ci900161g},
+  note ={PMID: 19702240},
+  URL = { https://doi.org/10.1021/ci900161g },
+  eprint = { https://doi.org/10.1021/ci900161g }
+}
+
+@article{Yap2011,
+  author = "Yap, CW.",
+  year = 2011,
+  title = "PaDEL-descriptor: an open source software to calculate molecular descriptors and fingerprints",
+  journal = "Journal of computational chemistry",
+  number = 32,
+  pages = "1466-74"
+}
+
+@Article{Bender2004,
+  author =       "Andreas Bender and  Hamse Y. Mussa and Robert C.
+                 Glen and Stephan Reiling",
+  title =        "Molecular Similarity Searching Using Atom
+                 Environments, Information-Based Feature Selection, and
+                 a Naïve Bayesian Classifier",
+  journal =      "Journal of Chemical Information and Computer
+                 Sciences",
+  volume =       "44",
+  number =       "1",
+  pages =        "170--178",
+  year =         "2004",
+  DOI =          "10.1021/ci034207y",
+  note =         "PMID: 14741025",
+  URL =          "http://dx.doi.org/10.1021/ci034207y",
+  eprint =       "http://dx.doi.org/10.1021/ci034207y",
+}
+
+@article{OBoyle2011a,
+  abstract = {{BACKGROUND: A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats.RESULTS: We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion.CONCLUSIONS: Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org.}},
+  added-at = {2019-03-11T21:00:05.000+0100},
+  author = {O'Boyle, Noel and Banck, Michael and James, Craig and Morley, Chris and Vandermeersch, Tim and Hutchison, Geoffrey},
+  biburl = {https://www.bibsonomy.org/bibtex/27ab2699fef73132efcfa6853c3031bf0/fairybasslet},
+  booktitle = {Journal of Cheminformatics},
+  citeulike-article-id = {9866193},
+  citeulike-linkout-0 = {http://dx.doi.org/doi:10.1186/1758-2946-3-33},
+  citeulike-linkout-1 = {http://www.jcheminf.com/content/3/1/33},
+  citeulike-linkout-2 = {http://dx.doi.org/10.1186/1758-2946-3-33},
+  citeulike-linkout-3 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3198950/},
+  citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/21982300},
+  citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=21982300},
+  citeulike-linkout-6 = {http://link.springer.com/article/10.1186/1758-2946-3-33},
+  day = 07,
+  doi = {doi:10.1186/1758-2946-3-33},
+  interhash = {c20842ab14c8a3bbd2dcf3e8072b82d1},
+  intrahash = {7ab2699fef73132efcfa6853c3031bf0},
+  issn = {1758-2946},
+  journal = {J. Cheminf.},
+  keywords = {chemical-file-formats computer-program cpsst open-babel open-source software-library toolkit},
+  month = oct,
+  number = 1,
+  pages = 33,
+  pdf = {file:///H:/publications/OBoyle2011a.pdf},
+  pmcid = {PMC3198950},
+  pmid = {21982300},
+  posted-at = {2011-11-08 10:20:24},
+  priority = {2},
+  publisher = {Chemistry Central Ltd},
+  timestamp = {2019-03-11T21:06:37.000+0100},
+  title = {{Open Babel: An open chemical toolbox}},
+  url = {http://www.jcheminf.com/content/3/1/33},
+  volume = 3,
+  year = 2011
+}
+
+@article{Rücker2007,
+  author = "Rücker, C and Rücker, G and Meringer, M.",
+  year = 2007,
+  title = "y-Randomization and Its Variants in QSPR/QSAR",
+  journal = "J. Chem. Inf. Model.",
+  number = 47,
+  pages = "2345-57"
+}
+
+@Article{Maunz2013,
+  DOI =          "10.3389/fphar.2013.00038",
+  URL =          "http://dx.doi.org/10.3389/fphar.2013.00038",
+  year =         "2013",
+  publisher =    "Frontiers Media {SA}",
+  volume =       "4",
+  author =       "Andreas Maunz and Martin G{\"{u}}tlein and Micha
+                 Rautenberg and David Vorgrimmler and Denis Gebele and
+                 Christoph Helma",
+  title =        "lazar: a modular predictive toxicology framework",
+  journal =      "Frontiers in Pharmacology",
+}
+
+@Article{doi:10.1021/ci00057a005,
+  author =       "David Weininger",
+  title =        "SMILES, a chemical language and information system. 1.
+                 Introduction to methodology and encoding rules",
+  journal =      "Journal of Chemical Information and Computer
+                 Sciences",
+  volume =       "28",
+  number =       "1",
+  pages =        "31--36",
+  year =         "1988",
+  DOI =          "10.1021/ci00057a005",
+  URL =          "http://dx.doi.org/10.1021/ci00057a005",
+  eprint =       "http://dx.doi.org/10.1021/ci00057a005",
+}
+
+@Article{OBoyle2011,
+  DOI =          "10.1186/1758-2946-3-33",
+  URL =          "http://dx.doi.org/10.1186/1758-2946-3-33",
+  year =         "2011",
+  publisher =    "Springer Science and Business Media",
+  volume =       "3",
+  number =       "1",
+  pages =        "33",
+  author =       "Noel M OBoyle and Michael Banck and Craig A James and
+                 Chris Morley and Tim Vandermeersch and Geoffrey R
+                 Hutchison",
+  title =        "Open Babel: An open chemical toolbox",
+  journal =      "Journal of Cheminformatics",
+}
+
+@Article{mazzatorta08,
+  author =       "Paolo Mazzatorta and Manuel Dominguez Estevez and
+                 Myriam Coulet and Benoit Schilter",
+  title =        "Modeling Oral Rat Chronic Toxicity",
+  journal =      "Journal of Chemical Information and Modeling",
+  volume =       "48",
+  number =       "10",
+  pages =        "1949--1954",
+  year =         "2008",
+  DOI =          "10.1021/ci8001974",
+  note =         "PMID: 18803370",
+  URL =          "http://dx.doi.org/10.1021/ci8001974",
+  eprint =       "http://dx.doi.org/10.1021/ci8001974",
+}
+
+@Manual{pls,
+  title =        "pls: Partial Least Squares and Principal Component
+                 Regression",
+  author =       "Bjørn-Helge Mevik and Ron Wehrens and Kristian Hovde
+                 Liland",
+  year =         "2015",
+  note =         "R package version 2.5-0",
+  URL =          "https://CRAN.R-project.org/package=pls",
+}
+
+@Article{Kuhn08,
+  author =       "Max Kuhn",
+  title =        "Building predictive models in R using the caret
+                 package",
+  journal =      "J. of Stat. Soft",
+  year =         "2008",
+}
+
+@Article{Jeliazkova15,
+  author =       "Nina Jeliazkova and Charalampos Chomenidis and Philip
+                 Doganis and Bengt Fadeel and Roland Grafström and
+                 Barry Hardy and Janna Hastings and Markus Hegi and
+                 Vedrin Jeliazkov and Nikolay Kochev and Pekka Kohonen
+                 and Cristian R. Munteanu and Haralambos Sarimveis and
+                 Bart Smeets and Pantelis Sopasakis and Georgia Tsiliki
+                 and David Vorgrimmler and Egon Willighagen",
+  title =        "The eNanoMapper database for nanomaterial safety
+                 information",
+  journal =      "Beilstein J. Nanotechnol.",
+  pages =        "1609–1634",
+  number =       "6",
+  year =         "2015",
+  DOI =          "doi:10.3762/bjnano.6.165",
+}
+
+@TechReport{Fowler2011,
+  author =       "B. Fowler and S. Savage and B. Mendez",
+  year =         "2011",
+  title =        "White paper: Protecting public health in the 21st
+                 century: the case for computational toxicology",
+  institution =  "ICF International, Inc.icfi.com.",
+}
+
+@Article{Cotterill2008,
+  author =       "Cotterill, J.V. and Chaudry, M.Q. and Mattews, W. and R.
+                 W. Watkins",
+  year =         "2008",
+  title =        "In silico assessment of toxicity of heat-generated
+                 food contaminants",
+  journal =      "Food Chemical Toxicology",
+  number =       "46(6)",
+  pages =        "1905--1918",
+}
+
+@Article{Grob2006,
+  author =       "Grob, K. and Biedermann, M. and Scherbaum, E. and Roth, M.
+                 and K. Rieger",
+  year =         "2006",
+  title =       "Food contamination with organic materials in
+                 perspective: packaging materials as the largest and
+                 least controlled source? A view focusing on the
+                 European situation",
+  journal =      "Crit. Rev. Food. Sci. Nutr.",
+  number =       "46",
+  pages =        "529--35",
+  DOI =          "10.1080/10408390500295490",
+}
+
+@Article{LoPiparo2011,
+  author =       "Lo Piparo, E. and Worth, A. and Manibusan, A. and Yang, C. and
+                 Schilter, B. and Mazzatorta, P. and Jacobs, M.N. and
+                 Steinkelner, H. and L. Mohimont",
+  year =         "2011",
+  title =        "Use of Computational tools in the field of food
+                 safety",
+  journal =      "Regulatory Toxicology and Pharmacology",
+  number =       "60(3)",
+  pages =        "354--362",
+}
+
+@Article{LoPiparo2014,
+  author =       "Lo Piparo, E. and Maunz, A. and Helma, C. and Vorgrimmler, D. and Schilter, B.",
+  year =         "2014",
+  title =        "Automated and reproducible read-across like models for
+                 predicting carcinogenic potency",
+  journal =      "Regulatory Toxicology and Pharmacology",
+  number =       "70",
+  pages =        "370--378",
+}
+
+@Article{Schilter2014,
+  author =       "Schilter, B. and Benigni, R. and Boobis, A. and Chiodini, A. and
+                 Cockburn, A. and Cronin, M.T. and Lo Piparo, E. and Modi, S. and
+                 Thiel A. and A. Worth",
+  title =        "Establishing the level of safety concern for chemicals
+                 in food without the need for toxicity testing",
+  year =         "2014",
+  journal =      "Regulatory Toxicology and Pharmacology",
+  number =       "68",
+  pages =        "275--298",
+}
+
+@Article{Stanton2016,
+  author =       "Stanton, K. and F.H. Krusezewski",
+  year =         "2016",
+  title =        "Quantifying the benefits of using read-across and in
+                 silico techniques to fullfill hazard data requirements
+                 for chemical categories",
+  journal =      "Regulatory Toxicology and Pharmacology",
+  number =       "81",
+  pages =        "250--259",
+  DOI =          "10.1016/j-yrtph.2016.09.004.",
+}
+
+@Article{Zarn2011,
+  author =       "Zarn, J.A. and B.E. Engeli and J.R. Schlatter",
+  year =         "2011",
+  title =        "Study parameters influencing {NOAEL} and {LOAEL} in
+                 toxicity feeding studies for pesticides: exposure
+                 duration versus dose decrement, dose spacing, group
+                 size and chemical class",
+  journal =      "Regul. Toxicol. Pharmacol.",
+  number =       "61",
+  pages =        "243--250",
+}
+
+@Article{Zarn2013,
+  author =       "J.A. Zarn and B.E. Engeli and J.R. Schlatter",
+  year =         "2013",
+  title =        "Characterization of the dose decrement in regulatory
+                 rat pesticide toxicity feeding studies",
+  journal =      "Regul. Toxicol. Pharmacol.",
+  number =       "67",
+  pages =        "215--220",
+}
+
+@Article{EFSA2016,
+  author =       {EFSA},
+  year =         "2016",
+  title =        "Guidance on the establishment of the residue
+                  definition for dietary assessment: {EFSA} panel on Plant
+                  Protect Products and their Residues ({PPR})",
+  journal =      "EFSA Journal",
+  number =       "14",
+  pages =        "1--12",
+}
+
+@TechReport{ECHA2008,
+  author =       "{ECHA}",
+  year =         "2008",
+  title =        "Guidance on information requirements and chemical
+                  safety assessment, Chapter R.6: {QSARs} and grouping of
+                 chemicals",
+  institution =  "ECHA",
+}
+
+@Misc{EFSA2014,
+  author =       "{EFSA}",
+  year =         "2014",
+  title =        "Rapporteur Member State assessment reports submitted
+                 for the {EU} peer review of active substances used in
+                 plant protection products",
+  URL =          "http://dar.efsa.europa.eu/dar-web/provision",
+  note =         "accessed 8.1.2015",
+}
+
+@Misc{HealthCanada2016,
+  author =       "{Health Canada}",
+  year =         "2016",
+  URL =          "https://www.canada.ca/en/health-canada/services/chemical-substances/chemicals-management-plan.html",
+}
+
+@InCollection{OECD2015,
+  author =       "{OECD}",
+  year =         "2015",
+  title =        "Fundamental and guiding principles for {(Q)SAR} analysis
+                 of chemicals carcinogens with mechanistic
+                 considerations Monograph 229 {ENV/JM/MONO(2015)46}",
+  chapter =      "229",
+  booktitle =    "Series on Testing and Assessment No 229",
+}
+
+@InCollection{Schilter2013,
+  author =       "Schilter, B. and Constable, A. and Perrin, I.",
+  title =        "Naturally occurring toxicants of plant origin: risk
+                 assessment and management considerations",
+  year =         "2013",
+  booktitle =    "Food Safety Management: a practical guide for
+                 industry",
+  chapter =      "3",
+  editor =       "Y. Motarjemi",
+  publisher =    "Elsevier",
+  pages =        "45--57",
+}
+
+@Misc{EPA2011,
+  title =        "Fact Sheets on New Active Ingredients",
+  author =       "{US EPA}",
+  year =         "2011",
+  note =         "this database was not further maintained by US EPA.
+                 Only data used until 27.11.2014, accessed 27.4.11
+                 A.D.",
+}
+
+@TechReport{WHO2011,
+  author =       "WHO",
+  year =         "2011",
+  title =        "Joint {FAO/WHO} Meeting on Pesticide Residues ({JMPR})
+                 publications",
+  URL =          "http://www.who.int/foodsafety/publications/jmpr-monographs/en/",
+  note =         "accessed 20.3.15 A.D.",
+}