From 2813d3c1688e6a178fe814d32bfd5d6a8613f39f Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Fri, 11 Sep 2020 23:40:47 +0200 Subject: static, single page --- public/presentations/opentox-dublin/api.html | 512 --------------------------- 1 file changed, 512 deletions(-) delete mode 100644 public/presentations/opentox-dublin/api.html (limited to 'public/presentations/opentox-dublin/api.html') diff --git a/public/presentations/opentox-dublin/api.html b/public/presentations/opentox-dublin/api.html deleted file mode 100644 index 5a386a8..0000000 --- a/public/presentations/opentox-dublin/api.html +++ /dev/null @@ -1,512 +0,0 @@ - - - - - - - -OpenTox API Working Group - - - - - - - - - - - - - - -
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OpenTox API Working Group

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Workshop Objectives

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Capture
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  • service provider (developer) experiences
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  • service consumer (client) experiences
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Identify open issues

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Resolve open issues

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Unify and update API documentation

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OpenTox

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http://opentox.org/dev/apis/api-1.2

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Focus on predictive toxicology

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REST interfaces for: Compound, Feature, Dataset, Algorithm, Model, Validation, Report, Ontology, Task, Authentication and Authorisation

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RDF representation

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ToxBank

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http://api.toxbank.net

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Extensions for capturing bioassay data

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Additional objects: Alert, Data, Index, Investigation, Organisation, Project, Protocol, Search, Session, Template, User.

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RDF representation, ISA-Tab (http://isatab.sourceforge.net/format.html)

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eNanoMapper

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IDEA: http://enanomapper.github.io/API

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NTUA: http://app.jaqpot.org:8080/jaqpot/swagger

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IST: https://enm.in-silico.ch/api/dist

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Extensions for capturing nanomaterial data

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Additional objects: Bundle, Myaccount, Property, Query, Substance, Substanceowner, Pmml, Bibtex

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JSON representation

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Developer experiences

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(De)Serialisation of large datasets/investigations

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  • system/infrastructure limitations (time, memory, database/webserver size limits, ...)
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  • impossible for RDF (performance of RDF parsers/serializers, markup size)
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  • even JSON markup can cause problems
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  • we propose CSV/TSV as data exchange format for datasets
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Complexity of the one webservice/class model

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  • code separation, maintenance
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  • performance penalties caused by suboptimal data structures
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  • performance penalties of webservices (data (de)serialisation)
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  • complicated server infrastructure
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Communication with external services

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  • ad hoc requests for features that deviate from official API
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  • reliablity/availability of external services
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  • undocumented API details
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  • undocumented/silent API/data format changes
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  • no common strategy for conflict resolution, API or data representation updates
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Local service deployment (e.g. for in house services)

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  • installation far from straightforward
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  • management of additional server instances
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  • duplication of functionality, bloat
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  • update strategy
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Documentation

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  • scattered/outdated documentation
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  • maintenance -- too many places to consider (error prone) -- ideally autogenerated from code
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  • ideally combined with tests (availability, API coverage, API compliance)
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Client experiences

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Open issues

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Workflow for
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  • API unification and updates
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Documentation
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  • location
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  • format (Swagger, Wiki, ...)
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  • maintenance
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  • link to inventories, tests
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...

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Next steps

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