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authorChristoph Helma <helma@in-silico.ch>2016-01-22 13:36:01 +0100
committerChristoph Helma <helma@in-silico.ch>2016-01-22 13:36:01 +0100
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+# Nanoparticle read across toxicity predictions with nano-lazar
+
+# Requirements
+
+- Nanoparticle characterisation
+- Toxicity measurements
+
+# eNanoMapper data import
+
+Nanoparticles imported: 464
+Nanoparticles with particle characterisation: 394
+Nanoparticles with toxicity data: 167
+Nanoparticles with toxicity data and particle characterisation: 160
+
+# eNanoMapper toxicity endpoints
+
+.. alles ohne falsch? zugewiesene protein corona tox endpoints
+Toxicity endpoints: 41
+Toxicity endpoints with more than one measurement value: 22
+Toxicity endpoints with more than 10 measurements: 2
+
+# Selected data
+
+Protein corona dataset Au particles (106 particles)
+Toxicity endpoint:
+
+# Read across procedure
+
+- Identify relevant fragments (significant correlation with toxicity)
+ TODO list of fragments, number
+- Calculate similarities (weighted cosine similarity, correlation coefficients = weights)
+- Identify neighbors (particles with more than 0.95 similarity)
+- Calculate prediction (weighted average from neighbors, similarities = weights)
+
+# Future development
+
+- Validation of predictions
+- Applicability domain/reliability of predictions
+
+- Accuracy improvements:
+ - additional data
+ - feature selection
+ - similarity calculation
+ - predictions (local regression models)
+
+- Usability improvements:
+ - additional data (extension of applicability domain, additional endpoints and chemistries)
+ - inclusion of ontologies
+ - Descriptor calculation directly from core and coating chemistries
+
+# Webinterface
+
+Your recommendations?
+
+# Source code
+
+https://github.com/opentox/nano-lazar