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diff --git a/public/presentations/opentox-basel16/index.rst b/public/presentations/opentox-basel16/index.rst deleted file mode 100644 index ec1853b..0000000 --- a/public/presentations/opentox-basel16/index.rst +++ /dev/null @@ -1,146 +0,0 @@ -.. |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Local service deployment (e.g. for in house services) - -Documentation problems -====================== - -- Scattered/outdated documentation -- Difficult to maintain for developers (no suitable cross-platform solution for code-based documentation) -- Limitations of documentation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 - |