OpenTox API: Lessons learnt, limitations and challenges


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A brief talk about challenges for the current OpenTox API.

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OpenTox API: Lessons learnt, limitations and challenges

  1. 1. OpenTox API Lessons Learnt, Limitations & Challenges. P. Sopasakis1 and H. Sarimveis2 1. IMT Institute for Advanced Studies Lucca, 2. National Technical University of Athens, School of Chemical Engineering. October 29, 2013 OpenTox – USA 2013 OpenTox API 1/15
  2. 2. OpenTox API Lessons learnt and perspectives for the OpenTox API. OpenTox – USA 2013 OpenTox API 2/15
  3. 3. Need for Exemplification Further testing of APIs with additional algorithm implementation, model training and validation. This procedure will reveal the shortcomings of the current OpenTox framework, OpenTox – USA 2013 OpenTox API 3/15
  4. 4. Let’s make a Standard out of OpenTox... According to RFC 6410: A “Proposed Standard” is expected to be stable (no known bugs), while it has received significant community review & enjoys enough community interest. Two seperate interoperable implementations from different code bases need to be fully documented, A “Standard” requires additionally widespread deployment and use. OpenTox – USA 2013 OpenTox API 4/15
  5. 5. Portability of Models Export the actual QSAR or QSPR model, Take into account existing formats, e.g., PMML, In-house formats such as RDF/XML, XML and JSON can serve the purpose of exporting the actual model. OpenTox – USA 2013 OpenTox API 5/15
  6. 6. Metadata for datasets and their features Datasets to be accompanied by statistics for their features (min, max, average, std and more) Datasets to be linked to other resources (if applicable), e.g., it should be clear when a dataset was created as a transformation of some other dataset. OpenTox – USA 2013 OpenTox API 6/15
  7. 7. Prediction for Mixtures It should be possible to define datasets for mixtures putting together mixturedescriptors and mixture properties, Demonstrate this functionality with relevant examples. OpenTox – USA 2013 OpenTox API 7/15
  8. 8. Stochastic DoA A stochastic/probabilistic domain of applicability (DoA) outputs a probability distribution function (histogram) for a given compound An extension of the API may be necessary (or if not, an example of how to do so will do) OpenTox – USA 2013 OpenTox API 8/15
  9. 9. Extensions for Nano-materials OpenTox – USA 2013 OpenTox API 9/15
  10. 10. Extensions for Nano-materials It should be possible to map nanomaterials to their microscopy images, Images (list of URIs) can be made available using the Accept HTTP header - This needs to be specified in the API, Feature calculation based on microscopy images (geometric and chemical characteristics), New ontological definitions (classes and properties) need to be introduced to cater for nanostructures. OpenTox – USA 2013 OpenTox API 10/15
  11. 11. Optimal Experimental Design Provide guidance to experimenters as what to measure (and under what conditions) so as to improve the predictive ability and/or the applicability of existing models Consider unsupervised and supervised approaches From the API point of view an OED can be an Algorithm that maps datasets and/or models to datasets (i.e., compounds along with experimental conditions and a feature annotated as “prediction feature”). OpenTox – USA 2013 OpenTox API 11/15
  12. 12. Laboratory Comparisons Question: Which laboratory offers more reliable measurements [There exist loads of relevant statistical tests] The OpenTox ontology needs to be extended to this direction API: An Algorithm can take up the comparison between two sets of measurements and export a Dataset where one can find various statistics and the decision. OpenTox – USA 2013 OpenTox API 12/15
  13. 13. Additional MIMEs In OpenTox we standardised the format of the RDF files, The same can be done with other well-established formats such as JSON (particularly useful for integration with applications that use Javascript), YAML or TOML. What about binary formats such as Protobuf of BSON? OpenTox – USA 2013 OpenTox API 13/15
  14. 14. Some shortcuts Make certain shortcuts part of the API: How to create a copy of an existing dataset? The method PUT /dataset/{id} is vaguely defined in the API – Explicitly state how the client can update a dataset (add/remove compounds, etc); Standardise such shortcuts. OpenTox – USA 2013 OpenTox API 14/15
  15. 15. Thank you for your attention. OpenTox – USA 2013 OpenTox API 15/15