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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
commit7da754f80a414810a8c4721e1e4ed9b4c2d706d7 (patch)
treed7b5422d4a7482f8d9f4f31c0cad56a36efaacdc
parent8ebb209d00fd11ccdc86bc1e695f4bb9b9300f33 (diff)
workshop presentation, enm source data added again
-rw-r--r--.gitignore3
-rw-r--r--data/marina.json3282
-rw-r--r--data/multi-walled-nano-tubes.json430
-rw-r--r--data/nanowiki.json30302
-rw-r--r--data/protein-corona.json20614
-rw-r--r--presentation/enm-workshop.rst57
6 files changed, 54687 insertions, 1 deletions
diff --git a/.gitignore b/.gitignore
index e73632d..aa39e18 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,6 @@
lib
-data
+data/*csv
+data/*yaml
papers
*tmp
*swp
diff --git a/data/marina.json b/data/marina.json
new file mode 100644
index 0000000..a615f42
--- /dev/null
+++ b/data/marina.json
@@ -0,0 +1,3282 @@
+{
+"query": {
+ "summary":"query"
+},
+"dataEntry":[
+ {
+ "compound":{
+ "URI":"https://apps.ideaconsult.net/enanomapper/substance/XLSX-7011cea0-1011-3f8b-9e8a-b3289fed836a",
+ "structype":"NA",
+ "metric":null,
+ "name":"",
+ "cas":"",
+ "einecs":""
+
+ },
+ "values":{
+ "https://apps.ideaconsult.net/enanomapper/identifier/name":"Titanium Dioxide",
+ "https://apps.ideaconsult.net/enanomapper/identifier/tradename":"NM-103 (TiO2)",
+ "https://apps.ideaconsult.net/enanomapper/identifier/uuid":"XLSX-7011cea0-1011-3f8b-9e8a-b3289fed836a",
+ "https://apps.ideaconsult.net/enanomapper/owner/name":"FP7 MARINA",
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index 0000000..93d623d
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index 0000000..ac2215c
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diff --git a/presentation/enm-workshop.rst b/presentation/enm-workshop.rst
new file mode 100644
index 0000000..7adae46
--- /dev/null
+++ b/presentation/enm-workshop.rst
@@ -0,0 +1,57 @@
+# 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