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links --> -<script src="ui/small-white/slides.js" type="text/javascript"></script> -<link rel="stylesheet" href="ui/small-white/slides.css" - type="text/css" media="projection" id="slideProj" /> -<link rel="stylesheet" href="ui/small-white/outline.css" - type="text/css" media="screen" id="outlineStyle" /> -<link rel="stylesheet" href="ui/small-white/print.css" - type="text/css" media="print" id="slidePrint" /> -<link rel="stylesheet" href="ui/small-white/opera.css" - type="text/css" media="projection" id="operaFix" /> - -<style type="text/css"> -#currentSlide {display: none;} -</style> -</head> -<body> -<div class="layout"> -<div id="controls"></div> -<div id="currentSlide"></div> -<div id="header"> - -</div> -<div id="footer"> -<h1>Extending OpenTox to Nano Safety with eNanoMapper</h1> - -</div> -</div> -<div class="presentation"> -<div class="slide" id="slide0"> -<h1 class="title">Extending OpenTox to Nano Safety with eNanoMapper</h1> - -<p class="center">Christoph Helma</p> -<p class="center">in silico toxicology gmbh</p> -<img alt="logo.png" class="center" src="logo.png" /> - -</div> -<div class="slide" id="basic-idea"> -<h1>Basic idea</h1> -<p>Webservices as building blocks for computational toxicology</p> -<blockquote> -<ul class="simple"> -<li>avoid reinventing the wheel</li> -<li>reuse existing components</li> -<li>rapid prototyping</li> -<li>interoperability</li> -<li>uses semantic web technologies</li> -</ul> -</blockquote> -</div> -<div class="slide" id="application-programming-interface-api"> -<h1>Application programming interface (API)</h1> -<dl class="docutils"> -<dt>Request messages:</dt> -<dd><ul class="first last simple"> -<li>Representational state transfer (<em>REST</em>, based on HTTP messages)</li> -</ul> -</dd> -<dt>Data exchange:</dt> -<dd><ul class="first last simple"> -<li>Structure: object dependent</li> -<li>Format: Resource Description Framework (<em>RDF</em>), JavaScript Object Notation (<em>JSON</em>)</li> -</ul> -</dd> -</dl> -</div> -<div class="slide" id="opentox"> -<h1>OpenTox</h1> -<p><em>Focus on predictive toxicology</em></p> -<p>Main objects: Compound, Feature, Dataset, Algorithm, Model, Validation</p> -<p>Helper objects: Task, Authentication and Authorisation, Report, Ontology</p> -<p>Data format: RDF</p> -<p><a class="reference external" href="http://opentox.org/dev/apis/api-1.2">http://opentox.org/dev/apis/api-1.2</a></p> -</div> -<div class="slide" id="toxbank"> -<h1>ToxBank</h1> -<p><em>Extensions for capturing bioassay data</em></p> -<p>Main addition: Investigation (description of biological experiments)</p> -<p>Helper objects: Organisation, Project, Protocol, Search, Session, Template, User, Alert, Data, Index</p> -<p>Data format: RDF, ISA-Tab</p> -<p><a class="reference external" href="http://api.toxbank.net">http://api.toxbank.net</a></p> -</div> -<div class="slide" id="enanomapper"> -<h1>eNanoMapper</h1> -<p><em>Extensions for capturing nanomaterial data</em></p> -<p>Main addition: Substance (characterisation of nanoparticles)</p> -<p>Helper objects: Bundle (datasets of substances), Property, Query, Substanceowner, Myaccount, Pmml, Bibtex</p> -<p>Data format: JSON</p> -</div> -<div class="slide" id="enanomapper-apis"> -<h1>eNanoMapper APIs</h1> -<p>IDEA: <a class="reference external" href="http://enanomapper.github.io/API">http://enanomapper.github.io/API</a></p> -<p>NTUA: <a class="reference external" href="http://app.jaqpot.org:8080/jaqpot/swagger">http://app.jaqpot.org:8080/jaqpot/swagger</a></p> -<p>IST: <a class="reference external" href="https://enm.in-silico.ch/api/dist">https://enm.in-silico.ch/api/dist</a></p> -</div> -<div class="slide" id="technical-problems"> -<h1>Technical problems</h1> -<ul class="simple"> -<li>(De)Serialisation of large datasets/investigations</li> -<li>Reliability/availability/compatibility of external services</li> -<li>Local service deployment (e.g. for in house services)</li> -</ul> -</div> -<div class="slide" id="documentation-problems"> -<h1>Documentation problems</h1> -<ul class="simple"> -<li>Scattered/outdated documentation</li> -<li>Difficult to maintain for developers (no suitable cross-platform solution for code-based documentation)</li> -<li>Limitations of documentation platforms (e.g. SWAGGER) to document important details</li> -</ul> -</div> -<div class="slide" id="api-problems"> -<h1>API problems</h1> -<ul class="simple"> -<li>Lack of orthogonality (large number of partially redundant helper objects)</li> -<li>Ad hoc extensions of individual developers</li> -<li>Undocumented/silent API/data format changes</li> -</ul> -</div> -<div class="slide" id="coordination-problems"> -<h1>Coordination problems</h1> -<ul class="simple"> -<li>Individual API changes may be necessary and justified</li> -<li>Conflict resolution works one to one, but leaves out other developers (and consistency)</li> -<li>No common strategy for conflict resolution and API updates</li> -<li>Very limited developer base for testing and feedback</li> -</ul> -</div> -<div class="slide" id="api-features"> -<h1>API features</h1> -<ul class="simple"> -<li>Covers arbitrary biological and chemical experiments (via ToxBank investigations)<ul> -<li>storage/search/retrieval of data <em>and</em> metadata (experimental layouts)</li> -<li>generic structure for <em>all</em> types of experiments (including -omics)</li> -<li>includes preprocessing, data analysis and modelling steps</li> -<li>protocols for experimental and data analysis steps</li> -</ul> -</li> -</ul> -</div> -<div class="slide" id="id1"> -<h1>API features</h1> -<ul class="simple"> -<li>Nanomaterial characterisations (via eNM substances)</li> -<li>Datasets (bundles) for data analysis</li> -<li>Algorithms for data analysis, modelling, descriptor calculation, ...</li> -<li>Models for model predictions</li> -<li>Validation for model validation</li> -<li>User authentication and authorisation</li> -<li>Tasks for long running processes</li> -<li>...</li> -</ul> -</div> -<div class="slide" id="opentox-toxbank-enanomapper-apis"> -<h1>OpenTox/ToxBank/eNanoMapper APIs</h1> -<p><a class="reference external" href="http://opentox.org/dev/apis/api-1.2">http://opentox.org/dev/apis/api-1.2</a></p> -<p><a class="reference external" href="http://api.toxbank.net">http://api.toxbank.net</a></p> -<p><a class="reference external" href="http://enanomapper.github.io/API">http://enanomapper.github.io/API</a></p> -<p><a class="reference external" href="http://app.jaqpot.org:8080/jaqpot/swagger">http://app.jaqpot.org:8080/jaqpot/swagger</a></p> -<p><a class="reference external" href="https://enm.in-silico.ch/api/dist">https://enm.in-silico.ch/api/dist</a></p> -</div> -</div> -</body> -</html> |