lazar-rest

<p>REST API webservice for lazar and nano-lazar. lazar (lazy structure–activity relationships) is a modular framework for read across predictions of chemical toxicities. Within the European Union’s FP7 eNanoMapper project lazar was extended with capabilities to handle nanomaterial data, interfaces to other eNanoMapper services (databases and ontologies) and a stable and user-friendly graphical interface for nanoparticle read-across predictions. <strong>lazar-rest</strong> provides a new Restful webservice to this developments.</p

nano-lazar

<p>Graphical user interface for nano-lazar read across models. Users can predict nanoparticle toxicities by entering (i) core and coating compounds or (ii) nanoparticle properties or (iii) interactions with human serum proteins.</p> <p>According to our knowledge this is the first program that predicts nanoparticle toxicities from computed properties alone. This makes model (i) especially well suited for cheap and fast nanoparticle toxicity assessments. A detailed description of methods and validation results can be found at https://github.com/enanomapper/nano-lazar-paper/blob/master/nano-lazar.pdf.</p> <p>lazar is a modular framework for read across predictions of chemical toxicities. Within the EU FP7 eNanoMapper project lazar was extended with capabilities to handle nanomaterial data, interfaces to other eNanoMapper services (databases and ontologies) and a stable and user-friendly graphical interface for nanoparticle read-across predictions. nano-lazar is the graphical interface to nanoparticle read-across predictions.</p

qsar-report ruby gem library

<p>QMRF and QPRF reporting extension to OpenTox ruby modules and lazar.<br> The QSAR-report gem was developed to extend the lazar and nano-lazar toxicity prediction application with QMRF and QPRF reporting features.<br> The library gem is independent from lazar or nano-lazar and can also be used in any other ruby code.</p> <p><strong>About:</strong></p> <p>Classes for QMRF and QPRF reporting.</p> <ul> <li><strong>OpenTox::QMRFReport</strong>:<br> Provides a ruby OpenTox class to prepare an initial version of a QMRF report.<br> The XML output is in QMRF version 1.3 and can be finalized with the QMRF editor 2.0 ( https://sourceforge.net/projects/qmrf/ )</li> <li><strong>OpenTox::QPRFReport</strong>:<br> Provides a ruby OpenTox class to prepare an initial version of a QPRF (version 1.1) report in JSON or HTML.</li> </ul> <p><strong>Usage:</strong></p> <p><strong>QMRF </strong></p> <p>create a new QMRF report, add some content and show output:</p> <blockquote>require "qsar-report"<br> <br> # create a new report<br> report = OpenTox::QMRFReport.new<br> <br> # add a title<br> report.value "QSAR_title", "My QSAR Title"<br> <br> # change 6.2 'Available information for the training set' set inchi and smiles to Yes<br> report.change_attributes "training_set_data", {:inchi => "Yes", :smiles => "Yes"}<br> <br> # add a publication to the publication catalog<br> report.change_catalog :publications_catalog, :publications_catalog_1, {:title => "MyName M (2016) My Publication Title, QSAR News, 10, 14-22", :url => "http://myqsarnewsmag.dom"}<br> <br> # link/reference the publication to the report bibliography<br> report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_1<br> <br> # output<br> puts report.to_xml<br> <br> # validate a report (as created above) against qmrf.xsd<br> report.validate</blockquote> <p><strong>QPRF </strong></p> <p>create a new QPRF report, add some content and show output:</p> <blockquote>require "qsar-report"<br> # create a new QPRF report instance<br> report = OpenTox::QPRFReport.new<br> <br> # Set Title of the report<br> report.Title = "My QPRF Report"<br> <br> # Set Version<br> report.Version = "1"<br> <br> # Set Date<br> report.Date = Time.now.strftime("%Y/%m/%d")<br> <br> # Set the CAS number in chapter 1.1<br> report.value "1.1", "7732-18-5" # set CAS number for H²O<br> <br> # print HTML version<br> puts report.to_html<br> <br> # print formated JSON version<br> puts report.pretty_json<br>  </blockquote> <p><strong>Installation </strong></p> <blockquote>gem install qsar-report</blockquote> <p><strong>Documentation:</strong></p> <ul> <li>http://www.rubydoc.info/gems/qsar-report<br> RubyDoc.info Code documentation</li> <li>For full information on QSAR reporting see:<br> https://eurl-ecvam.jrc.ec.europa.eu/databases/jrc-qsar-model-database-and-qsar-model-reporting-formats<br> JRC QSAR Model Database and QSAR Model Reporting Formats</li> </ul

eNanoMapper applications to support the risk assessment of nanomaterials

<p>The infrastructure developed within eNanoMapper project aims to support the data management in the area of nano safety research and to enable an integrated approach for the risk assessment of nanomaterials. To achieve these, eNanoMapper developed an ontology, a data infrastructure and modelling tools with applicability in risk assessment of nanomaterials. By merging the expertise of partners in statistical and data mining tools and in predictive toxicology, biology and nanotechnology research, eNanoMapper developed resources and tools for predicting toxicity of nanomaterials and worked towards improving the standards in risk assessment of nanomaterials. The ontology includes common vocabulary terms used in nanosafety research and aims to provide a clear explanation of nanostructures based on information relating to their characterization, relevant experimental paradigms, biological interactions, safety indications and the integration of data from existing nanotoxicology sources. To support a collaborative safety assessment approach an infrastructure for data management was developed, with a database which includes functionalities for data protection, data sharing, data quality assurance, search and interfaces for different needs and usages, comparability and cross-talk with other databases. Further, a collection of descriptors, computational toxicology models and modelling tools were developed, to enable the use and integration of nanosafety data from various sources. The project provides also a rich source of information and documentation (e.g. tutorials, webinars, publications) to support and guide the users. eNanoMapper is supported by European Commission 7^th Framework Programme for Research and Technological Development Grant (Grant agreement no: 604134).</p