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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>OpenTox API Working Group</h1> + +</div> +</div> +<div class="presentation"> +<div class="slide" id="slide0"> +<h1 class="title">OpenTox API Working Group</h1> + +<!-- :Date: 30 September 2015 --> +<!-- University College Dublin, Dublin, Ireland --> +<!-- https://docs.google.com/document/d/153ip9ll_pzqMphoJ4d608ujd5GuYysZcTDAODsrXsrc/edit --> + +</div> +<div class="slide" id="workshop-objectives"> +<h1>Workshop Objectives</h1> +<dl class="docutils"> +<dt>Capture</dt> +<dd><ul class="first last simple"> +<li>service provider (developer) experiences</li> +<li>service consumer (client) experiences</li> +</ul> +</dd> +</dl> +<p>Identify open issues</p> +<p>Resolve open issues</p> +<p>Unify and update API documentation</p> +</div> +<div class="slide" id="opentox"> +<h1>OpenTox</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>Focus on predictive toxicology</p> +<p>REST interfaces for: Compound, Feature, Dataset, Algorithm, Model, Validation, Report, Ontology, Task, Authentication and Authorisation</p> +<p>RDF representation</p> +</div> +<div class="slide" id="toxbank"> +<h1>ToxBank</h1> +<p><a class="reference external" href="http://api.toxbank.net">http://api.toxbank.net</a></p> +<p>Extensions for capturing bioassay data</p> +<p>Additional objects: Alert, Data, Index, Investigation, Organisation, Project, Protocol, Search, Session, Template, User.</p> +<p>RDF representation, ISA-Tab (<a class="reference external" href="http://isatab.sourceforge.net/format.html">http://isatab.sourceforge.net/format.html</a>)</p> +</div> +<div class="slide" id="enanomapper"> +<h1>eNanoMapper</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> +<p>Extensions for capturing nanomaterial data</p> +<p>Additional objects: Bundle, Myaccount, Property, Query, Substance, Substanceowner, Pmml, Bibtex</p> +<p>JSON representation</p> +</div> +<div class="slide" id="developer-experiences"> +<h1>Developer experiences</h1> +</div> +<div class="slide" id="de-serialisation-of-large-datasets-investigations"> +<h1>(De)Serialisation of large datasets/investigations</h1> +<blockquote> +<ul class="simple"> +<li>system/infrastructure limitations (time, memory, database/webserver size limits, ...)</li> +<li>impossible for RDF (performance of RDF parsers/serializers, markup size)</li> +<li>even JSON markup can cause problems</li> +<li>we propose CSV/TSV as data exchange format for datasets</li> +</ul> +</blockquote> +</div> +<div class="slide" id="complexity-of-the-one-webservice-class-model"> +<h1>Complexity of the one webservice/class model</h1> +<blockquote> +<ul class="simple"> +<li>code separation, maintenance</li> +<li>performance penalties caused by suboptimal data structures</li> +<li>performance penalties of webservices (data (de)serialisation)</li> +<li>complicated server infrastructure</li> +</ul> +</blockquote> +</div> +<div class="slide" id="communication-with-external-services"> +<h1>Communication with external services</h1> +<blockquote> +<ul class="simple"> +<li>ad hoc requests for features that deviate from official API</li> +<li>reliablity/availability of external services</li> +<li>undocumented API details</li> +<li>undocumented/silent API/data format changes</li> +<li>no common strategy for conflict resolution, API or data representation updates</li> +</ul> +</blockquote> +</div> +<div class="slide" id="local-service-deployment-e-g-for-in-house-services"> +<h1>Local service deployment (e.g. for in house services)</h1> +<blockquote> +<ul class="simple"> +<li>installation far from straightforward</li> +<li>management of additional server instances</li> +<li>duplication of functionality, bloat</li> +<li>update strategy</li> +</ul> +</blockquote> +</div> +<div class="slide" id="documentation"> +<h1>Documentation</h1> +<blockquote> +<ul class="simple"> +<li>scattered/outdated documentation</li> +<li>maintenance +- too many places to consider (error prone) +- ideally autogenerated from code</li> +<li>ideally combined with tests (availability, API coverage, API compliance)</li> +</ul> +</blockquote> +</div> +<div class="slide" id="client-experiences"> +<h1>Client experiences</h1> +</div> +<div class="slide" id="open-issues"> +<h1>Open issues</h1> +<dl class="docutils"> +<dt>Workflow for</dt> +<dd><ul class="first last simple"> +<li>API unification and updates</li> +<li>issue and conflict reporting/resolution</li> +</ul> +</dd> +<dt>Documentation</dt> +<dd><ul class="first last simple"> +<li>location</li> +<li>format (Swagger, Wiki, ...)</li> +<li>maintenance</li> +<li>link to inventories, tests</li> +</ul> +</dd> +</dl> +<p>...</p> +</div> +<div class="slide" id="opentox-apis"> +<h1>OpenTox 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 class="slide" id="next-steps"> +<h1>Next steps</h1> +</div> +</div> +</body> +</html> |