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diff --git a/public/presentations/opentox-basel16/index.rst b/public/presentations/opentox-basel16/index.rst new file mode 100644 index 0000000..ec1853b --- /dev/null +++ b/public/presentations/opentox-basel16/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 additions: Substance (characterisation of nanoparticles), Ontologies + +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Local service deployment (e.g. for in house services) + +Documentation problems +====================== + +- Scattered/outdated documentation +- Difficult to maintain for developers (no suitable cross-platform solution for code-based documentation) +- Limitations of documentation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) and ontologies +- 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 + |