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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> |