QSAR-Report

QMRF and QPRF reporting extension to 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.

About

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"

# create a new QPRF report instance
report = OpenTox::QPRFReport.new

# Set Title of the report
report.Title = "My QPRF Report"

# Set Version
report.Version = "1"

# Set Date
report.Date = Time.now.strftime("%Y/%m/%d")

# Set the CAS number in chapter 1.1
report.value "1.1", "7732-18-5" # set CAS number for H²O

# print HTML version
puts report.to_html

# print formated JSON version
puts report.pretty_json

Installation

gem install qsar-report

Documentation

Copyright

Copyright (c) 2016 Christoph Helma, Micha Rautenberg, Denis Gebele. See LICENSE for details.

Lazar QMRF Example

Here is an advanced example of the usage of the gem in lazar code: