QSAR-Report

QMRF and QPRF reporting extension to ruby, OpenTox ruby modules and lazar.

The QSAR-report gem was developed to extend the lazar and nano-lazar toxicity prediction application with QMRF and QPRF reporting features. The library gem is independent from lazar or nano-lazar and can also be used in any other ruby code. The library code is in general public license version 3 (GPLv3). The open source code is freely available and versioned at the Github code hosting platform.

The library has two main classes for the report types OpenTox::QMRFReport and OpenTox::QPRFReport. Instances of these classes can be easily filled with contents. There is a full documentation of the library with examples at RubyDoc.info Code documentation .

Classes for QMRF and QPRF reporting.

  • OpenTox::QMRFReport: Provides a ruby OpenTox class to prepare an initial version of a QMRF report. The XML output is in QMRF version 1.3 and can be finalized with the QMRF editor 2.0 (https://sourceforge.net/projects/qmrf/)
  • OpenTox::QPRFReport: Provides a ruby OpenTox class to prepare an initial version of a QPRF (version 1.1) report in JSON or HTML.

Usage

QMRF

create a new QMRF report, add some content and show output:

    require "qsar-report"

    # create a new report
    report = OpenTox::QMRFReport.new
    
    # add a title
    report.value "QSAR_title", "My QSAR Title"
    
    # change 6.2 'Available information for the training set' set inchi and smiles to Yes
    report.change_attributes "training_set_data", {:inchi => "Yes", :smiles => "Yes"}
    
    # add a publication to the publication catalog
    report.change_catalog :publications_catalog, :publications_catalog_1, {:title => "MyName M (2016) My Publication Title, QSAR News, 10, 14-22", :url => "http://myqsarnewsmag.dom"}
    
    # link/reference the publication to the report bibliography
    report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_1
    
    # output
    puts report.to_xml
    
    # validate a report (as created above) against qmrf.xsd
    report.validate

QPRF

create a new QPRF report, add some content and show output:

    require "qsar-report"
    report = OpenTox::QPRFReport.new
    report.Title = "My QPRF Report"
    report.Version = "1"
    report.Date = Time.now.strftime("%Y/%m/%d")
    report.value "1.1", "7732-18-5" # set CAS number for H²O
    puts report.to_html

Installation

gem install qsar-report

More Documentation



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Published

05 October 2016

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