1 files changed, 146 insertions, 0 deletions
diff --git a/public/presentations/opentox-dublin/index.rst b/public/presentations/opentox-dublin/index.rst
new file mode 100644
index 0000000..9a5846f
--- /dev/null
+++ b/public/presentations/opentox-dublin/index.rst
@@ -0,0 +1,146 @@
+.. |date| date::
+
+=============================================================================
+Extending OpenTox to Nano Safety with eNanoMapper
+=============================================================================
+
+.. class:: center
+
+  Christoph Helma
+
+  in silico toxicology gmbh
+
+  .. image:: logo.png
+ 
+Basic idea
+==========
+
+Webservices as building blocks for computational toxicology
+
+  - avoid reinventing the wheel
+  - reuse existing components
+  - rapid prototyping
+  - interoperability
+  - uses semantic web technologies
+
+Application programming interface (API)
+=======================================
+
+Request messages:
+  - Representational state transfer (*REST*, based on HTTP messages)
+
+Data exchange:
+  - Structure: object dependent
+  - Format: Resource Description Framework (*RDF*), JavaScript Object Notation (*JSON*)
+
+OpenTox
+=======
+
+*Focus on predictive toxicology*
+
+Main objects: Compound, Feature, Dataset, Algorithm, Model, Validation
+
+Helper objects: Task, Authentication and Authorisation, Report, Ontology 
+
+Data format: RDF 
+
+http://opentox.org/dev/apis/api-1.2
+
+ToxBank
+=======
+
+*Extensions for capturing bioassay data* 
+
+Main addition: Investigation (description of biological experiments)
+
+Helper objects: Organisation, Project, Protocol, Search, Session, Template, User, Alert, Data, Index
+
+Data format: RDF, ISA-Tab
+
+http://api.toxbank.net
+
+eNanoMapper
+===========
+
+*Extensions for capturing nanomaterial data*
+
+Main addition: Substance (characterisation of nanoparticles)
+
+Helper objects: Bundle (datasets of substances), Property, Query, Substanceowner, Myaccount, Pmml, Bibtex
+
+Data format: JSON
+
+eNanoMapper APIs
+================
+
+IDEA: http://enanomapper.github.io/API
+
+NTUA: http://app.jaqpot.org:8080/jaqpot/swagger
+
+IST: https://enm.in-silico.ch/api/dist
+
+Technical problems
+==================
+
+- (De)Serialisation of large datasets/investigations
+- Reliability/availability/compatibility of external services
+- Local service deployment (e.g. for in house services)
+
+Documentation problems
+======================
+
+- Scattered/outdated documentation
+- Difficult to maintain for developers (no suitable cross-platform solution for code-based documentation)
+- Limitations of documentation platforms (e.g. SWAGGER) to document important details
+
+API problems
+============
+
+- Lack of orthogonality (large number of partially redundant helper objects)
+- Ad hoc extensions of individual developers
+- Undocumented/silent API/data format changes 
+
+Coordination problems
+=====================
+
+- Individual API changes may be necessary and justified
+- Conflict resolution works one to one, but leaves out other developers (and consistency)
+- No common strategy for conflict resolution and API updates
+- Very limited developer base for testing and feedback
+
+API features
+============
+
+- Covers arbitrary biological and chemical experiments (via ToxBank investigations)
+
+  - storage/search/retrieval of data *and* metadata (experimental layouts)
+  - generic structure for *all* types of experiments (including -omics)
+  - includes preprocessing, data analysis and modelling steps
+  - protocols for experimental and data analysis steps
+
+API features
+============
+
+- Nanomaterial characterisations (via eNM substances)
+- Datasets (bundles) for data analysis 
+- Algorithms for data analysis, modelling, descriptor calculation, ...
+- Models for model predictions
+- Validation for model validation
+
+- User authentication and authorisation
+- Tasks for long running processes
+- ...
+
+OpenTox/ToxBank/eNanoMapper APIs
+================================
+
+http://opentox.org/dev/apis/api-1.2
+
+http://api.toxbank.net
+
+http://enanomapper.github.io/API
+
+http://app.jaqpot.org:8080/jaqpot/swagger
+
+https://enm.in-silico.ch/api/dist
+