From fbfa1f45d93f6b9de111eb95418f4e57a0bb361a Mon Sep 17 00:00:00 2001 From: gebele Date: Mon, 14 Aug 2017 10:49:50 +0000 Subject: fixed qmrf publications order --- qmrf_report.rb | 36 ++++++++++++++++++++++-------------- 1 file changed, 22 insertions(+), 14 deletions(-) diff --git a/qmrf_report.rb b/qmrf_report.rb index a23607f..b52e618 100644 --- a/qmrf_report.rb +++ b/qmrf_report.rb @@ -7,7 +7,6 @@ def qmrf_report id qmrfpath = File.dirname qmrfpath prediction_model = Model::Validation.find id model = prediction_model.model - #validation_template = "./views/model_details.haml" if File.directory?(lazarpath) lazar_commit = `cd #{lazarpath}; git rev-parse HEAD`.strip @@ -40,12 +39,14 @@ def qmrf_report id report.value "model_date", "#{Time.parse(model.created_at.to_s).strftime('%Y')}" # Reference(s) to main scientific papers and/or software package 2.7 - report.change_catalog :publications_catalog, :publications_catalog_1, {:title => "Maunz A., Guetlein M., Rautenberg M., Vorgrimmler D., Gebele D. and Helma C. (2013), lazar: a modular predictive toxicology framework ", :number => "1", :url => "http://dx.doi.org/10.3389/fphar.2013.00038"} + report.change_catalog :publications_catalog, :publications_catalog_4, {:title => "Maunz A., Guetlein M., Rautenberg M., Vorgrimmler D., Gebele D. and Helma C. (2013), lazar: a modular predictive toxicology framework ", :url => "http://dx.doi.org/10.3389/fphar.2013.00038"} + + report.ref_catalog :references, :publications_catalog, :publications_catalog_4 + + report.change_catalog :publications_catalog, :publications_catalog_1, {:title => "Helma C., Gebele D., Rautenberg M. (2017) lazar, software available at https://lazar.in-silico.ch,source code available at #{lazar_commit}", :url => "https://doi.org/10.5281/zenodo.215483"} + report.ref_catalog :references, :publications_catalog, :publications_catalog_1 - report.change_catalog :publications_catalog, :publications_catalog_2, {:title => "Helma C, Gebele D, Rautenberg M (2017) lazar, software available at https://lazar.in-silico.ch,source code available at #{lazar_commit}", :number => "2", :url => "https://doi.org/10.5281/zenodo.215483"} - report.ref_catalog :references, :publications_catalog, :publications_catalog_2 - # Availability of information about the model 2.8 report.value "info_availability", "Prediction interface and validation results available at https://lazar.in-silico.ch" @@ -60,7 +61,7 @@ def qmrf_report id report.value "endpoint_units", "#{prediction_model.unit}" # Dependent variable 3.5 - report.value "endpoint_variable", "#{prediction_model.endpoint} #{prediction_model.regression? ? "regression" : "classification"}" + report.value "endpoint_variable", "#{prediction_model.endpoint}" # Type of model 4.1 model_type = model.class.to_s.gsub('OpenTox::Model::Lazar','') @@ -72,7 +73,7 @@ def qmrf_report id # Descriptors in the model 4.3 if model.algorithms["descriptors"][:type] - report.change_catalog :descriptors_catalog, :descriptors_catalog_1, {:description => "Molprint 2D (Bender et al. 2004)", :name => "#{model.algorithms["descriptors"][:type]} fingerprints", :publication_ref => "", :units => ""} + report.change_catalog :descriptors_catalog, :descriptors_catalog_1, {:description => "(Bender et al. 2004)", :name => "#{model.algorithms["descriptors"][:type]} fingerprints", :publication_ref => "", :units => ""} report.ref_catalog :algorithms_descriptors, :descriptors_catalog, :descriptors_catalog_1 end @@ -198,7 +199,7 @@ def qmrf_report id

Please note that lazar predictions are based on neighbors. - Descriptors are only used for the calculation of similarities. + Descriptors are only used for the calculation of similarities.

" @@ -218,15 +219,22 @@ def qmrf_report id " # Bibliography 9.2 - report.change_catalog :publications_catalog, :publications_catalog_1, {:title => "Helma (2017), Nano-Lazar: Read across Predictions for Nanoparticle Toxicities with Calculated and Measured Properties", :url => "https://dx.doi.org/10.3389%2Ffphar.2017.00377"} - report.change_catalog :publications_catalog, :publications_catalog_2, {:title => "Lo Piparo (2014), Automated and reproducible read-across like models for predicting carcinogenic potency", :url => "https://doi.org/10.1016/j.yrtph.2014.07.010"} - report.change_catalog :publications_catalog, :publications_catalog_3, {:title => "Helma (2006), Lazy structure-activity relationships (lazar) for the prediction of rodent carcinogenicity and Salmonella mutagenicity.", :url => "http://dx.doi.org/10.1007/s11030-005-9001-5"} - report.change_catalog :publications_catalog, :publications_catalog_4, {:title => "Bender et al. (2004), Molecular similarity searching using atom environments, information-based feature selection, and a nave bayesian classifier.", :url => "https://doi.org/10.1021/ci034207y"} + + report.change_catalog :publications_catalog, :publications_catalog_2, {:title => "Helma C., Rautenberg M. and Gebele D. (2017), Nano-Lazar: Read across Predictions for Nanoparticle Toxicities with Calculated and Measured Properties", :url => "https://dx.doi.org/10.3389%2Ffphar.2017.00377"} + + report.change_catalog :publications_catalog, :publications_catalog_3, {:title => "Lo Piparo et al. (2014), Automated and reproducible read-across like models for predicting carcinogenic potency", :url => "https://doi.org/10.1016/j.yrtph.2014.07.010"} + + report.change_catalog :publications_catalog, :publications_catalog_5, {:title => "Maunz A. and Helma C. (2008), Prediction of chemical toxicity with local support vector regression and activity-specific kernels", :url => "http://dx.doi.org/10.1080/10629360802358430"} + + report.change_catalog :publications_catalog, :publications_catalog_6, {:title => "Helma C. (2006), Lazy structure-activity relationships (lazar) for the prediction of rodent carcinogenicity and Salmonella mutagenicity.", :url => "http://dx.doi.org/10.1007/s11030-005-9001-5"} + + report.change_catalog :publications_catalog, :publications_catalog_7, {:title => "Bender et al. (2004), Molecular similarity searching using atom environments, information-based feature selection, and a nave bayesian classifier.", :url => "https://doi.org/10.1021/ci034207y"} - report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_1 report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_2 report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_3 - report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_4 + report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_5 + report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_6 + report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_7 report -- cgit v1.2.3