Nina Jeliazkova Nina Jeliazkova AMBIT web site updated Nina Jeliazkova https://www.ideaconsult.net/web/ngn/blogs/-/blogs/ambit-web-site-updated 2011-08-20T19:35:23Z 2011-08-20T19:24:46Z <p> AMBIT <a href="http://ambit.sourceforge.net">web site&nbsp;</a>&nbsp;has a new design and a streamlined content. &nbsp;</p> <p> Links to all AMBIT and OpenTox related downloads by <a href="http://www.ideaconsult.net">IdeaConsult</a>&nbsp;can be found &nbsp;in a <a href="http://ambit.sourceforge.net/downloads.html">single page</a>.&nbsp;</p> <p> Guideleness how to install your own instance of <a href="http://ambit.sourceforge.net/download_ambitrest.html">AMBIT REST web services</a>, OpenTox API <a href="http://ambit.sourceforge.net/api.html">examples</a>, and&nbsp;<a href="http://ambit.sourceforge.net/download.html#Libraries">OpenTox Java client libraries</a>&nbsp;releases.</p> <p>  </p> Nina Jeliazkova 2011-08-20T19:24:46Z New Toxtree 2.5.0 release Nina Jeliazkova https://www.ideaconsult.net/web/ngn/blogs/-/blogs/new-toxtree-2-5-0-release 2011-08-08T10:51:20Z 2011-08-08T05:46:43Z <p>  </p> <p> &nbsp;We are&nbsp;pleased to anounce a <a href="http:// http://toxtree.sourceforge.net/download.html#Toxtree_2.5.0">new release</a> of <a href="http://toxtree.sourceforge.net/">Toxtree </a>software. Toxtree was commisioned by the&nbsp;<a href="http://ihcp.jrc.ec.europa.eu/our_labs/computational_toxicology/qsar_tools/toxtree">JRC Computational Toxicology group</a> back in 2005 and the number of Toxtree plugins, predicting different aspects of chemical hazards has been growing ever since.&nbsp;Toxtree's first version&nbsp;included only the&nbsp;Cramer rules scheme. The latest version&nbsp;features 14 plugins, developed by various teams worldwide:</p> <ul> <li> <a href="http://toxtree.sourceforge.net/cramer.html" style="color: rgb(51,102,170); text-decoration: none">Cramer rules</a>&nbsp;&amp;&nbsp;<a href="http://toxtree.sourceforge.net/cramer2.html" style="color: rgb(51,102,170); text-decoration: none">Cramer rules with extensions</a></li> <li> <a href="http://toxtree.sourceforge.net/verhaar.html" style="color: rgb(51,102,170); text-decoration: none">Verhaar scheme</a>&nbsp;&amp;&nbsp;<a href="http://toxtree.sourceforge.net/verhaar2.html" style="color: rgb(51,102,170); text-decoration: none">Modified Verhaar scheme</a></li> <li> <a href="http://toxtree.sourceforge.net/skin.html" style="color: rgb(51,102,170); text-decoration: none">Skin irritation prediction</a></li> <li> <a href="http://toxtree.sourceforge.net/eye.html" style="color: rgb(51,102,170); text-decoration: none">Eye irritation prediction</a></li> <li> <a href="http://toxtree.sourceforge.net/carc.html" style="color: rgb(51,102,170); text-decoration: none">Benigni / Bossa rulebase for mutagenicity and carcinogenicity</a></li> <li> <a href="http://toxtree.sourceforge.net/start.html" style="color: rgb(51,102,170); text-decoration: none">START biodegradation and persistence</a></li> <li> <a href="http://toxtree.sourceforge.net/michaelacceptors.html" style="color: rgb(51,102,170); text-decoration: none">Structure Alerts for identification of Michael Acceptors</a></li> <li> <a href="http://toxtree.sourceforge.net/skinsensitisation.html" style="color: rgb(51,102,170); text-decoration: none">Structure Alerts for skin sensitisation</a></li> <li> <a href="http://toxtree.sourceforge.net/kroes.html" style="color: rgb(51,102,170); text-decoration: none">Kroes TTC Decision tree</a></li> <li> <a href="http://toxtree.sourceforge.net/smartcyp.html" style="color: rgb(51,102,170); text-decoration: none">SMARTCyp - Cytochrome P450-Mediated Drug Metabolism and metabolites prediction</a></li> <li> <a href="http://toxtree.sourceforge.net/mic.html" style="color: rgb(51,102,170); text-decoration: none">Structure Alerts for the in vivo micronucleus assay in rodents (ISSMIC)</a></li> <li> <a href="http://toxtree.sourceforge.net/issfunc.html" style="color: rgb(51,102,170); text-decoration: none">Structural Alerts for Functional Group Identification (ISSFUNC)</a></li> </ul> <p> I would like to&nbsp;specifically draw your attention&nbsp;to the new functionality added to the <a href="http://toxtree.sourceforge.net/smartcyp.html">SMARTCyp plug-in</a>. It supports now metabolite generation, based on sites of metabolism, as predicted by <a href="http://www.farma.ku.dk/index.php/SMARTCyp/7990/0/">SMARTCyp</a>.</p> <p style="text-align: center"> <img alt="Metabolites generated by SMARTCyp" src="http://toxtree.sourceforge.net/images/smartcyp/thumb.jpg" style="width: 275px; height: 161px" /></p> <p>  </p> <p> <a href="http://www.farma.ku.dk/index.php/SMARTCyp/7990/0/">SMARTCyp </a>is developed by <a href="http://www.farma.ku.dk/index.php/SMARTCyp/7990/0/">PatrikRydberg</a> and&nbsp;has been&nbsp;included in Toxtree since<a href="http://toxtree.sourceforge.net/smartcyp.html"> release 2.1.0</a>. &nbsp; It was recently extended to provide information about the reactions (<a href="http://www.daylight.com/dayhtml_tutorials/languages/smirks/index.html">SMIRKS</a>), associated with every predicted site of metabolism. Toxtree 2.5.0 makes use of the reaction SMIRKS and <a href="http://ambit.sf.net">Ambit</a>'s <a href="https://ambit.svn.sourceforge.net/svnroot/ambit/trunk/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/SMIRKSManager.java">SMIRKS engine</a>, in order to generate the structures of the reaction products.&nbsp;</p> <p> Together&nbsp;with Patrik Rydberg we will be holding&nbsp;a <a class="externalLink" href="http://opentox.org/meet/opentox2011/opentox2011metabolites" style="background-image: url(http://toxtree.sourceforge.net/images/window-new.png); padding-right: 18px; background-position: 100% 50%; color: rgb(38,95,194); text-decoration: none; background-origin: initial; background-clip: initial">Hands on exercise</a>&nbsp;for metabolite predictions at&nbsp;the <a class="externalLink" href="http://opentox.org/meet/opentox2011" style="background-image: url(http://toxtree.sourceforge.net/images/window-new.png); padding-right: 18px; background-position: 100% 50%; color: rgb(38,95,194); text-decoration: none; background-origin: initial; background-clip: initial">OpenTox Interaction meeting</a>, using SMARTCyp and Toxtree 2.5.0.</p> <div> Another new functionality in Toxtree is the support for more identifiers in the input text box at the top of the application window. It is no more restricted only to SMILES and accepts InChI, parsed&nbsp;by the&nbsp;<a href="http://jni-inchi.sourceforge.net/">JNI-InChI</a> package, chemical names lookup in&nbsp;<a href="http://opsin.ch.cam.ac.uk/information.html">Open Parser for Systematic IUPAC Names (OPSIN)</a>, as well as&nbsp;CAS and EINECS&nbsp;resolving by calls to a remote&nbsp;<a href="http://www.opentox.org">OpenTox</a> service. Please note that the remote lookup is disabled by default --&nbsp;check the &nbsp;"Method/Decision tree option/Remote Query" menu to enable it<font class="Apple-style-span" color="#555555" face="'Trebuchet MS', Geneva, Arial, Helvetica, SunSans-Regular, sans-serif" size="2"><span class="Apple-style-span" style="line-height: 18px">.</span></font></div> <div>  </div> <div> You could have a look at the <a href="http://toxtree.sourceforge.net/download.html#Toxtree_2.5.0">Toxtree web site</a> for more information on Toxtree 2.5.0's new features and downloads.</div> Nina Jeliazkova 2011-08-08T05:46:43Z Browsing protected OpenTox datasets Nina Jeliazkova https://www.ideaconsult.net/web/ngn/blogs/-/blogs/browsing-protected-opentox-datasets 2011-03-12T23:25:03Z 2011-03-12T22:27:13Z <p> The protected resources at our test server <a href="https://ambit.uni-plovdiv.bg:8443/ambit2">https://ambit.uni-plovdiv.bg:8443/ambit2</a> can be again accessed via web browser, despite the fact the web browsers have no support for <a href="http://opentox.org/dev/apis/api-1.1/AA">OpenSSO authentication scheme, used by OpenTox</a>.</p> <p> For example, accessing a protected <a href="https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/272?page=0&amp;pagesize=10">dataset </a>will return an error, telling the access is forbidden.</p> <p> However, clicking the Login link at the top right , or <a href="https://ambit.uni-plovdiv.bg:8443/ambit2/opentoxuser">https://ambit.uni-plovdiv.bg:8443/ambit2/opentoxuser</a> REST service, will lead to a simple login form, allowing to provide your OpenTox credentials. The OpenTox user and password expected are the same, as used to log in into <a href="http://opentox.org/login_form">www.opentox.org</a> site.&nbsp; If you don't have an OpenTox account, <a href="http://opentox.org/join_form"><span style="text-decoration: underline;">don't hesitate to </span>join </a>!</p> <p> The service will then connect to OpenTox OpenSSO service and retrieve an access token, if the user and password are valid. The token will be saved as a cookie in your browser and used during subsequent accesses to protected resources at&nbsp; <a href="https://ambit.uni-plovdiv.bg:8443/ambit2">https://ambit.uni-plovdiv.bg:8443/ambit2</a>.&nbsp;</p> <p> Now you should be able to view the <a href="https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/272?page=0&amp;pagesize=10">datasets </a>via web browser.</p> <p> Clicking "Logout" will invalidate the OpenSSO token and remove the cookie from your browser.</p> <p> More technically :</p> <p> Log in (HTTP POST) . The OpenSSO token is returned in the Set-Cookie: header.</p> <blockquote> <p> <strong>curl -X POST -H "Accept:text/uri-list"&nbsp; -d "user=&lt;username&gt;" -d "password=&lt;password&gt;" -kL https://ambit.uni-plovdiv.bg:8443/ambit2/opentoxuser -i</strong></p> <p> <em>HTTP/1.1 200 OK<br /> Set-Cookie: subjectid=&lt;THE_TOKEN&gt;; Path=/; Secure<br /> Content-Type: text/uri-list;charset=UTF-8<br /> Content-Length: 59<br /> <br /> <strong>https://ambit.uni-plovdiv.bg:8443/ambit2/opentoxuser/&lt;username&gt;</strong></em></p> </blockquote> <p> Retrieve some data (use the token in the subjectid: HTTP header)</p> <blockquote> <p> <strong>$ curl -H "subjectid:&lt;THE_TOKEN&gt;" -H "Accept:application/rdf+xml" https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/272?max=10 -i</strong><br /> HTTP/1.1 200 OK<br /> Set-Cookie: subjectid=&lt;THE_TOKEN&gt;; Path=/<br /> Content-Type: application/rdf+xml;charset=UTF-8<br /> <br /> <strong>&lt;content skipped&gt;</strong><br />  </p> </blockquote> <p> Alternatively, retrieve some data by sending the token as cookie:</p> <blockquote> <p> <strong>$ curl -H "Cookie:</strong><strong>subjectid=&lt;THE_TOKEN&gt;" -H "Accept:application/rdf+xml" https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/272?max=10 -i</strong><br /> HTTP/1.1 200 OK<br /> Set-Cookie: subjectid=AQIC5wM2LY4Sfcy/kwp5gRN7MG6c7Urnd5bBjNnWqtoFk2U=@AAJTSQACMDE=#; Path=/<br /> Content-Type: application/rdf+xml;charset=UTF-8</p> <p> <strong>&lt;content skipped&gt;</strong></p> </blockquote> <p> Logout (HTTP DELETE)</p> <blockquote> <p> <strong>$ curl -X DELETE -H "Cookie:subjectid=&lt;THE_TOKEN&gt;" -H "Accept:text/uri-list" https://ambit.uni-plovdiv.bg:8443/ambit2/opentoxuser -i</strong></p> <p> <em>HTTP/1.1 200 OK<br /> Content-Type: text/uri-list;charset=UTF-8<br /> Content-Length: 58</em><br />  </p> <blockquote> <p>  </p> </blockquote> </blockquote> Nina Jeliazkova 2011-03-12T22:27:13Z OpenTox Model superbuilder Nina Jeliazkova https://www.ideaconsult.net/web/ngn/blogs/-/blogs/opentox-model-superbuilder 2011-03-07T17:11:20Z 2011-03-07T16:43:18Z <p> A Super Algorithm is a specific instance of an OpenTox algorithm service, that uses other OpenTox services to create a model or a dataset.</p> <p> The <a href="http://apps.ideaconsult.net:8080/ambit2/algorithm/superbuilder">model superbuilder</a>&nbsp; is an initial (and simplified) implementation of a superservice for creating predictive models, as described in <a href="http://opentox.org/dev/apis/api-1.2/Algorithm">OpenTox API 1.2</a> . Such a super algorithm uses descriptor calculation service, feature selection service and a modelling algorithm service to create prediction models. In general,&nbsp; OpenTox <a href="http://opentox.org/dev/apis/api-1.2/Model">Model services</a> execute only learning algorithms (e.g. regression or classification) and assume the input dataset contains all necessary descriptors.</p> <p> The superbuilder accepts URI of descriptor calculation algorithms via <strong>"feature_calculation"</strong> parameters, runs all the calculation, prepares a dataset with all descriptors and the endpoint (URI specified by<strong> "prediction_feature" </strong>parameter), and submits the final dataset to the learning algorithm (URI specified by <strong>"model_learning" </strong>parameter).</p> <blockquote> <p> <em>curl -X POST http://apps.ideaconsult.net:8080/ambit2/algorithm/superbuilder \</em></p> <p> <em>-d "dataset_uri=http://apps.ideaconsult.net:8080/ambit2/dataset/12" \</em></p> <p> <em>-d "prediction_feature=http://apps.ideaconsult.net:8080/ambit2/feature/21686" \</em></p> <p> <em>-d "model_learning=http://apps.ideaconsult.net:8080/ambit2/algorithm/J48" \</em></p> <p> <em>-d "feature_calculation=http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor" \</em></p> <p> <em>-d "feature_calculation=http://apps.ideaconsult.net:8080/ambit2/algorithm/ambit2.descriptors.MolecularWeight" \</em></p> <p> <em>-d "feature_calculation=http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor" -iv</em></p> </blockquote> <p> The model details can be inspected via</p> <blockquote> <p> <em>curl -H "Accept:text/n3" <a href="http://curl -H &quot;Accept:text/n3&quot; http://apps.ideaconsult.net:8080/ambit2/model/157717">http://apps.ideaconsult.net:8080/ambit2/model/157717</a></em></p> </blockquote> <p> The model can be&nbsp; applied directly to a dataset, provided it has all descriptors calculated</p> <blockquote> <p> <em>curl -X POST -d "dataset_uri=http://apps.ideaconsult.net:8080/ambit2/dataset/R710838"<span style="text-decoration: underline;"> </span><a href="http://curl -H &quot;Accept:text/n3&quot; http://apps.ideaconsult.net:8080/ambit2/model/157717">http://apps.ideaconsult.net:8080/ambit2/model/157717</a></em></p> </blockquote> <p> Or via the superservice for applying models :</p> <blockquote> <p> <em>curl -X POST -d "dataset_uri=http://apps.ideaconsult.net:8080/ambit2/dataset/&lt;any&gt;" \</em></p> <p> <em>-d "model_uri=http://apps.ideaconsult.net:8080/ambit2/model/157717<span style="text-decoration: underline;">" \</span></em></p> <p> <a href="http://apps.ideaconsult.net:8080/ambit2/algorithm/superservice"><em>http://apps.ideaconsult.net:8080/ambit2/algorithm/superservice</em></a></p> </blockquote> <p> This will return (intermediate) task URI and finally a dataset URI , containing the predictions, as specified in <a href="http://opentox.org/dev/apis/api-1.2/">OpenTox API.</a></p> <p> The model superbuilder does not support currently all <a href="http://opentox.org/dev/apis/api-1.2/Algorithm">defined parameters</a> but only parameters, shown in the example above.</p> <p>  </p> <p>  </p> <blockquote> <p>  </p> </blockquote> <p>  </p> <blockquote> <p>  </p> </blockquote> Nina Jeliazkova 2011-03-07T16:43:18Z How to find data in OpenTox datasets Nina Jeliazkova https://www.ideaconsult.net/web/ngn/blogs/-/blogs/how-to-find-data-in-opentox-datasets 2011-01-28T16:23:20Z 2011-01-28T11:52:10Z <p> <a href="http://opentox.org"><span style="color: rgb(0, 0, 0);">OpenTox</span></a><span style="color: rgb(0, 0, 0);"> dataset services, currently running at </span><a href="http://apps.ideaconsult.net:8080/ambit2"><span style="color: rgb(0, 0, 0);">IdeaConsult server</span></a><span style="color: rgb(0, 0, 0);">, host a number of datasets, containing chemical structures, toxicity data and calculated properties. Some statistics as of today :</span></p> <blockquote> <p> <tt><span style="color: rgb(0, 0, 205);">$ curl <a href="http://apps.ideaconsult.net:8080/ambit2/stats/dataset">http://apps.ideaconsult.net:8080/ambit2/stats/dataset</a><br /> 4120<br /> <br /> $curl <a href="http://apps.ideaconsult.net:8080/ambit2/stats/structures">http://apps.ideaconsult.net:8080/ambit2/stats/structures</a><br /> 521838<br /> <br /> $ curl <a href="http://apps.ideaconsult.net:8080/ambit2/stats/properties">http://apps.ideaconsult.net:8080/ambit2/stats/properties</a><br /> 31387</span></tt></p> </blockquote> <p> <span style="color: rgb(0, 0, 0);">While all the information is accessible via </span><a href="http://opentox.org/dev/apis/api-1.1"><span style="color: rgb(0, 0, 205);">OpenTox API </span></a><span style="color: rgb(0, 0, 0);">and </span><a href="http://apps.ideaconsult.net:8080/ambit2/dataset"><span style="color: rgb(0, 0, 205);">web browser</span></a><span style="color: rgb(0, 0, 0);">, with the increase of the information available, querying for specific portions of data becomes essential. The examples make use of <a href="http://curl.haxx.se/">cURL</a> </span><span style="color: rgb(0, 0, 0);">, but most links could be followed and viewed in web browser as well.</span></p> <p> <span style="color: rgb(0, 0, 0);">Let's start with two simpe tasks - <a href="#DatasetByName">exploring available datasets </a>and <a href="#FindColumn">finding which datasets contains a column with given name</a>.</span></p> <p> <span style="color: rgb(0, 0, 0);">The most straightforward query is to look for datasets by name<a name="DatasetByName"></a>. The following </span><a href="http://apps.ideaconsult.net:8080/ambit2/dataset?search=ToxCast"><span style="color: rgb(0, 0, 0);">query </span></a><span style="color: rgb(0, 0, 0);">will list all datasets, with name starting with <a href="http://www.epa.gov/ncct/toxcast/data_sets.html">ToxCast</a>.</span></p> <blockquote> <p> <tt><span style="color: rgb(0, 0, 205);">$ curl -H "Accept:text/uri-list" <a href="http://apps.ideaconsult.net:8080/ambit2/dataset?search=ToxCast">http://apps.ideaconsult.net:8080/ambit2/dataset?search=ToxCast</a><br /> http://apps.ideaconsult.net:8080/ambit2/dataset/103<br /> http://apps.ideaconsult.net:8080/ambit2/dataset/104<br /> http://apps.ideaconsult.net:8080/ambit2/dataset/105<br /> http://apps.ideaconsult.net:8080/ambit2/dataset/106<br /> http://apps.ideaconsult.net:8080/ambit2/dataset/107<br /> http://apps.ideaconsult.net:8080/ambit2/dataset/108<br /> http://apps.ideaconsult.net:8080/ambit2/dataset/109<a href="http://apps.ideaconsult.net:8080/ambit2/dataset/110"><br /> http://apps.ideaconsult.net:8080/ambit2/dataset/110</a><br /> http://apps.ideaconsult.net:8080/ambit2/dataset/111<br /> http://apps.ideaconsult.net:8080/ambit2/dataset/112</span></tt></p> <p> <strong>List ToxCast datasets URI</strong></p> </blockquote> <p>  </p> <p> <span style="color: rgb(0, 0, 0);">The RDF/XML representation tells us the URI of the ToxCast dataset, containing Novascreen assays, is </span><a href="http://apps.ideaconsult.net:8080/ambit2/dataset/110">http://apps.ideaconsult.net:8080/ambit2/dataset/110&nbsp;</a><span style="color: rgb(64, 224, 208);"><a href="http://apps.ideaconsult.net:8080/ambit2/dataset/110"><samp> </samp></a>(prefix xml:base="http://apps.ideaconsult.net:8080/ambit2/ and dataset resource and identifier rdf:about="dataset/110")&nbsp;&nbsp; </span><br /> <span style="color: rgb(0, 0, 0);"><span _fck_bookmark="1" style="display: none;">)</span></span></p> <p> The datasets contain rows (chemical compounds) and columns (properties). Finding out which properties a dataset consists of is easy - just append <span style="color: rgb(0, 0, 205);">"/<a href="http://apps.ideaconsult.net:8080/ambit2/dataset/110/feature?max=10 http://apps.ideaconsult.net:8080/ambit2/feature/22687 http://apps.ideaconsult.net:8080/ambit2/feature/22688 http://apps.ideaconsult.net:8080/ambit2/feature/22689 http://apps.ideaconsult.net:8080/ambit2/feature/22690 http://apps.ideaconsult.net:8080/ambit2/feature/22691 http://apps.ideaconsult.net:8080/ambit2/feature/22692 http://apps.ideaconsult.net:8080/ambit2/feature/22693 http://apps.ideaconsult.net:8080/ambit2/feature/22694 http://apps.ideaconsult.net:8080/ambit2/feature/22695 http://apps.ideaconsult.net:8080/ambit2/dataset/110/feature">feature</a>"</span> to the dataset URI:&nbsp;</p> <blockquote> <p> <span style="color: rgb(0, 0, 205);"><tt>$ curl -H "Accept:text/uri-list" <a href="http://apps.ideaconsult.net:8080/ambit2/dataset/110/feature?max=3">http://apps.ideaconsult.net:8080/ambit2/dataset/110/feature?max=10</a><a href="http://apps.ideaconsult.net:8080/ambit2/feature/22687"><br /> http://apps.ideaconsult.net:8080/ambit2/feature/22687</a><a href="http://apps.ideaconsult.net:8080/ambit2/feature/22688"><br /> http://apps.ideaconsult.net:8080/ambit2/feature/22688</a><a href="http://apps.ideaconsult.net:8080/ambit2/feature/22689"><br /> http://apps.ideaconsult.net:8080/ambit2/feature/22689</a><a href="http://apps.ideaconsult.net:8080/ambit2/feature/22690"><br /> http://apps.ideaconsult.net:8080/ambit2/feature/22690</a><a href="http://apps.ideaconsult.net:8080/ambit2/feature/22691"><br /> http://apps.ideaconsult.net:8080/ambit2/feature/22691</a><a href="http://apps.ideaconsult.net:8080/ambit2/feature/22692"><br /> http://apps.ideaconsult.net:8080/ambit2/feature/22692</a><a href="http://apps.ideaconsult.net:8080/ambit2/feature/22693"><br /> http://apps.ideaconsult.net:8080/ambit2/feature/22693</a><a href="http://apps.ideaconsult.net:8080/ambit2/feature/22694"><br /> http://apps.ideaconsult.net:8080/ambit2/feature/22694</a><a href="http://apps.ideaconsult.net:8080/ambit2/feature/22695"><br /> http://apps.ideaconsult.net:8080/ambit2/feature/22695</a><a href="http://apps.ideaconsult.net:8080/ambit2/feature/22696"><br /> http://apps.ideaconsult.net:8080/ambit2/feature/22696</a></tt></span></p> <p> <strong><span style="color: rgb(0, 0, 0);">List URI of first 10 columns form ToxCast NovaScreen dataset </span></strong></p> </blockquote> <p> The same query could be instructed to return information in other formats, for example N3 :</p> <blockquote> <p> <big><small><span style="color: rgb(0, 0, 205);"><tt>$ curl -H "Accept:text/n3" <a href="http://apps.ideaconsult.net:8080/ambit2/dataset/110/feature?max=3">http://apps.ideaconsult.net:8080/ambit2/dataset/110/feature?max=3</a><br /> @prefix ot:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &lt;http://www.opentox.org/api/1.1#&gt; .<br /> @prefix dc:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &lt;http://purl.org/dc/elements/1.1/&gt; .<br /> @prefix :&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &lt;http://apps.ideaconsult.net:8080/ambit2/&gt; .<br /> @prefix otee:&nbsp;&nbsp;&nbsp; &lt;http://www.opentox.org/echaEndpoints.owl#&gt; .<br /> @prefix rdfs:&nbsp;&nbsp;&nbsp; &lt;http://www.w3.org/2000/01/rdf-schema#&gt; .<br /> @prefix owl:&nbsp;&nbsp;&nbsp;&nbsp; &lt;http://www.w3.org/2002/07/owl#&gt; .<br /> @prefix xsd:&nbsp;&nbsp;&nbsp;&nbsp; &lt;http://www.w3.org/2001/XMLSchema#&gt; .<br /> @prefix ac:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &lt;http://apps.ideaconsult.net:8080/ambit2/compound/&gt; .<br /> @prefix ad:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &lt;http://apps.ideaconsult.net:8080/ambit2/dataset/&gt; .<br /> @prefix rdf:&nbsp;&nbsp;&nbsp;&nbsp; &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#&gt; .<br /> @prefix af:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &lt;http://apps.ideaconsult.net:8080/ambit2/feature/&gt; .<br /> <br /> ot:hasSource<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; a&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; owl:ObjectProperty .<br /> ot:units<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; a&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; owl:DatatypeProperty .<br /> ot:Feature<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; a&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; owl:Class .<br /> <br /> ot:NumericFeature<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; a&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; owl:Class ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; rdfs:subClassOf ot:Feature .<br /> <br /> &lt;<a href="http://apps.ideaconsult.net:8080/ambit2/feature/22688">http://apps.ideaconsult.net:8080/ambit2/feature/22688</a>&gt;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; a&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ot:Feature , ot:NumericFeature ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; dc:creator "someone" ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; dc:title "NVS_GPCR_hAdrb1" ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ot:hasSource &lt;http://apps.ideaconsult.net:8080/ambit2/dataset/ToxCast_Novascreen_20091214.txt&gt; ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ot:units "" ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; otee:Receptor_binding_and_gene_expression .<br /> <br /> &lt;<a href="http://apps.ideaconsult.net:8080/ambit2/feature/22687">http://apps.ideaconsult.net:8080/ambit2/feature/22687</a>&gt;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; a&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ot:Feature , ot:NumericFeature ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; dc:creator "someone" ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; dc:title "NVS_IC_rCaChN" ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ot:hasSource &lt;http://apps.ideaconsult.net:8080/ambit2/dataset/ToxCast_Novascreen_20091214.txt&gt; ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ot:units "" ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; otee:Receptor_binding_and_gene_expression .<br /> <br /> &lt;<a href="http://apps.ideaconsult.net:8080/ambit2/feature/22689">http://apps.ideaconsult.net:8080/ambit2/feature/22689</a>&gt;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; a&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ot:Feature , ot:NumericFeature ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; dc:creator "someone" ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; dc:title "NVS_ENZ_hPTPBAS" ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ot:hasSource &lt;<a href="http://apps.ideaconsult.net:8080/ambit2/dataset/ToxCast_Novascreen_20091214.txt">http://apps.ideaconsult.net:8080/ambit2/dataset/ToxCast_Novascreen_20091214.txt</a>&gt; ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ot:units "" ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; otee:Receptor_binding_and_gene_expression .</tt></span></small></big></p> <p> <strong>The first 3 columns from ToxCast NovaScreen dataset in RDF N3 format</strong></p> </blockquote> <p> <span style="color: rgb(0, 0, 0);">The N3 tells us the title of each column (dc:title) </span>, the origin of the column (ot:hasSource) , and asserts the column represent the same entity, as the one, defined in <a href="http://opentox.org/data/documents/development/RDF%20files/Endpoints/view">ECHA Endpoints ontology</a> (otee: Receptor_binding_and_gene_expression).&nbsp;<br />  </p> <p> The full ToxCast NovaScreen dataset can be retrieved&nbsp; in several formats either by name</p> <p> (RDF N3)</p> <blockquote> <p> <span style="color: rgb(0, 0, 205);"><big><small><tt>$curl -H "Accept:text/n3" </tt></small></big></span><big><small><tt><a href="http:// http://apps.ideaconsult.net:8080/ambit2/dataset/ToxCast_Novascreen_20091214.txt"><span style="color: rgb(0, 0, 205);">http://apps.ideaconsult.net:8080/ambit2/dataset/ToxCast_Novascreen_20091214.txt</span></a></tt></small></big><span style="color: rgb(0, 0, 205);"><big><small><tt> </tt></small></big></span></p> </blockquote> <p> or by id</p> <p> (SD File)</p> <blockquote> <p> <span style="color: rgb(0, 0, 205);">$curl -H "Accept:media=chemical/x-mdl-sdfile" <a href="http://apps.ideaconsult.net:8080/ambit2/dataset/110?media=chemical%2Fx-mdl-sdfile&amp;max=320">http://apps.ideaconsult.net:8080/ambit2/dataset/110</a></span></p> </blockquote> <p> (RDF/XML File)</p> <blockquote> <p> <span style="color: rgb(0, 0, 205);">$curl -H "Accept:media=application/rdf+xml" <a href="http://apps.ideaconsult.net:8080/ambit2/dataset/110?media=application%2Frdf%2Bxml&amp;max=320">http://apps.ideaconsult.net:8080/ambit2/dataset/110</a></span></p> </blockquote> <p> To retrieve only specific columns from the entire dataset, one needs to specify the URI of the column as parameters:</p> <blockquote> <p> <a href="http://apps.ideaconsult.net:8080/ambit2/dataset/110?feature_uris[]=http://apps.ideaconsult.net:8080/ambit2/feature/22689">http://apps.ideaconsult.net:8080/ambit2/dataset/110?feature_uris[]=http://apps.ideaconsult.net:8080/ambit2/feature/22689</a></p> </blockquote> <p>  </p> <p> <a name="FindColumn"></a>Finally, let's assume one doesn't know if ToxCast datasets are available via <a href="http://apps.ideaconsult.net:8080/ambit2/dataset">dataset services</a>,&nbsp; but would like to know if there are columns with prefix <span style="color: rgb(0, 0, 205);">"NVS"</span>, which in ToxCast datasets represent NovaScreen assays.</p> <p> Searching for columns (OpenTox features) by name is similar to searching datasets by name:</p> <blockquote> <p> <tt><span style="color: rgb(0, 0, 205);">$ curl -H "Accept:text/n3" "</span><a href="http://apps.ideaconsult.net:8080/ambit2/feature?max=3&amp;search=NVS"><span style="color: rgb(0, 0, 205);">http://apps.ideaconsult.net:8080/ambit2/feature?max=3&amp;search=NVS</span></a><span style="color: rgb(0, 0, 205);">"<br /> @prefix ot:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &lt;http://www.opentox.org/api/1.1#&gt; .<br /> @prefix dc:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &lt;http://purl.org/dc/elements/1.1/&gt; .<br /> @prefix :&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &lt;http://apps.ideaconsult.net:8080/ambit2/&gt; .<br /> @prefix otee:&nbsp;&nbsp;&nbsp; &lt;http://www.opentox.org/echaEndpoints.owl#&gt; .<br /> @prefix rdfs:&nbsp;&nbsp;&nbsp; &lt;http://www.w3.org/2000/01/rdf-schema#&gt; .<br /> @prefix owl:&nbsp;&nbsp;&nbsp;&nbsp; &lt;http://www.w3.org/2002/07/owl#&gt; .<br /> @prefix xsd:&nbsp;&nbsp;&nbsp;&nbsp; &lt;http://www.w3.org/2001/XMLSchema#&gt; .<br /> @prefix ad:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &lt;http://apps.ideaconsult.net:8080/ambit2/dataset/&gt; .<br /> @prefix rdf:&nbsp;&nbsp;&nbsp;&nbsp; &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#&gt; .<br /> @prefix af:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &lt;http://apps.ideaconsult.net:8080/ambit2/feature/&gt; .<br /> <br /> ot:hasSource<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; a&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; owl:ObjectProperty .<br /> <br /> ot:units<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; a&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; owl:DatatypeProperty .<br /> <br /> ot:Feature<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; a&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; owl:Class .<br /> <br /> &lt;http://apps.ideaconsult.net:8080/ambit2/feature/22688&gt;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; a&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ot:Feature ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; dc:creator "194.141.0.136" ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; dc:title "NVS_GPCR_hAdrb1" ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ot:hasSource &lt;http://apps.ideaconsult.net:8080/ambit2/dataset/ToxCast_Novascreen_20091214.txt&gt; ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ot:units "" ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; otee:Receptor_binding_and_gene_expression .<br /> <br /> &lt;http://apps.ideaconsult.net:8080/ambit2/feature/22687&gt;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; a&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ot:Feature ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; dc:creator "194.141.0.136" ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; dc:title "NVS_IC_rCaChN" ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ot:hasSource &lt;http://apps.ideaconsult.net:8080/ambit2/dataset/ToxCast_Novascreen_20091214.txt&gt; ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ot:units "" ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; otee:Receptor_binding_and_gene_expression .<br /> <br /> &lt;http://apps.ideaconsult.net:8080/ambit2/feature/22689&gt;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; a&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ot:Feature ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; dc:creator "194.141.0.136" ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; dc:title "NVS_ENZ_hPTPBAS" ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ot:hasSource &lt;<a href="http://apps.ideaconsult.net:8080/ambit2/dataset/ToxCast_Novascreen_20091214.txt">http://apps.ideaconsult.net:8080/ambit2/dataset/ToxCast_Novascreen_20091214.txt</a>&gt; ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ot:units "" ;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; otee:Receptor_binding_and_gene_expression .</span></tt><br /> <strong>The first 3 columns with names, starting with NVS in RDF N3 format</strong></p> </blockquote> <p> The output contains links (ot:hasSource) to the dataset the NVS* columns belongs to (<tt><span style="color: rgb(0, 0, 205);"><a href="http://apps.ideaconsult.net:8080/ambit2/dataset/ToxCast_Novascreen_20091214.txt">http://apps.ideaconsult.net:8080/ambit2/dataset/ToxCast_Novascreen_20091214.txt</a>)</span></tt>, and the content of the dataset&nbsp; could be easily retrieved in several formats, as explained above.</p> <p>  </p> <p> How to perform more complex queries via <a href="http://apps.ideaconsult.net:8080/ontology">OpenTox ontology service</a> and <a href="http://www.w3.org/TR/rdf-sparql-query/">SPARQL</a>, how to annotate dataset columns with resources, defined in existing ontologies , and how to use all the information and API to calculate properties and build predictive models - in these blogs we will try to provide practical guide and examples, in addition to official documents at <a href="http://opentox.org">OpenTox</a> site.</p> <p>  </p> Nina Jeliazkova 2011-01-28T11:52:10Z