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-rw-r--r--example/example.rb70
1 files changed, 38 insertions, 32 deletions
diff --git a/example/example.rb b/example/example.rb
index e268a5c..df26aa3 100644
--- a/example/example.rb
+++ b/example/example.rb
@@ -10,7 +10,7 @@ prediction_model = Model::Prediction.find_by :model_id => params[:id]
validation_template = File.join(File.dirname(__FILE__),"../views/model_details.haml") #detailed validation results from lazar-rest
-# Start filling the QMRF report
+# Start filling the QMRF report
# QSAR identifier (title) 1.1
report.value "QSAR_title", "Model for #{prediction_model.species} #{prediction_model.endpoint}"
@@ -22,10 +22,16 @@ report.ref_catalog :QSAR_software, :software_catalog, :firstsoftware
# Date of QMRF 2.1
report.value "qmrf_date", "#{Time.now.strftime('%d %B %Y')}"
-# QMRF author(s) and contact details 2.1
+# QMRF author(s) and contact details 2.2
report.change_catalog :authors_catalog, :firstauthor, {:name => "Christoph Helma", :affiliation => "in silico toxicology gmbh", :contact => "Contact Address", :email => "Contact Email", :number => "1", :url => "Web Page"}
report.ref_catalog :qmrf_authors, :authors_catalog, :firstauthor
+# Date of QMRF update(s) 2.3
+report.value "qmrf_date_revision", ""
+
+# QMRF update(s) 2.4
+report.value "qmrf_revision", ""
+
# Model developer(s) and contact details 2.5
report.change_catalog :authors_catalog, :modelauthor, {:name => "Christoph Helma", :affiliation => "in silico toxicology gmbh", :contact => "Contact Address", :email => "Contact Email", :number => "1", :url => "Web Page"}
report.ref_catalog :model_authors, :authors_catalog, :modelauthor
@@ -42,9 +48,9 @@ report.change_catalog :publications_catalog, :publications_catalog_2, {:title =>
report.ref_catalog :references, :publications_catalog, :publications_catalog_2
# Species 3.1
-report.value "model_species", prediction_model.species
+report.value "model_species", prediction_model.species
-# Endpoint 3.2
+# Endpoint 3.2
report.change_catalog :endpoints_catalog, :endpoints_catalog_1, {:name => prediction_model.endpoint, :group => ""}
report.ref_catalog :model_endpoint, :endpoints_catalog, :endpoints_catalog_1
@@ -75,23 +81,23 @@ report.ref_catalog :descriptors_generation_software, :software_catalog, :softwar
# Chemicals/Descriptors ratio 4.7
report.value "descriptors_chemicals_ratio", "not applicable (classification based on activities of neighbors, descriptors are used for similarity calculation)"
-# Some QMRF fields (tag contents) can have formatted HTML contents.
-# These contents have to have a complete HTML document structure with basic surrounding tags like <html><body>.
-# see Example below
+# Some QMRF fields (tag contents) can have formatted HTML contents.
+# These contents have to have a complete HTML document structure with basic surrounding tags like <html><body>.
+# see Example below
# Description of the applicability domain of the model 5.1
report.value "app_domain_description", "<html><head></head><body>
<p>
- The applicability domain (AD) of the training set is characterized by
- the confidence index of a prediction (high confidence index: close to
- the applicability domain of the training set/reliable prediction, low
- confidence: far from the applicability domain of the
- trainingset/unreliable prediction). The confidence index considers (i)
- the similarity and number of neighbors and (ii) contradictory examples
+ The applicability domain (AD) of the training set is characterized by
+ the confidence index of a prediction (high confidence index: close to
+ the applicability domain of the training set/reliable prediction, low
+ confidence: far from the applicability domain of the
+ trainingset/unreliable prediction). The confidence index considers (i)
+ the similarity and number of neighbors and (ii) contradictory examples
within the neighbors. A formal definition can be found in Helma 2006.
</p>
<p>
- The reliability of predictions decreases gradually with increasing
+ The reliability of predictions decreases gradually with increasing
distance from the applicability domain (i.e. decreasing confidence index)
</p>
</body>
@@ -100,7 +106,7 @@ report.value "app_domain_description", "<html><head></head><body>
# Method used to assess the applicability domain 5.2
report.value "app_domain_method", "see Helma 2006 and Maunz 2008"
-# Software name and version for applicability domain assessment 5.3
+# Software name and version for applicability domain assessment 5.3
report.change_catalog :software_catalog, :software_catalog_3, {:name => "lazar, submitted version: #{lazar_commit}", :description => "integrated into main lazar algorithm", :number => "3", :url => "https://lazar.in-silico.ch", :contact => "Contact Email"}
report.ref_catalog :app_domain_software, :software_catalog, :software_catalog_3
@@ -135,10 +141,10 @@ end
# Mechanistic basis of the model 8.1
report.value "mechanistic_basis","<html><head></head><body>
<p>
- Compounds with similar structures (neighbors) are assumed to have
- similar activities as the query compound. For the determination of
- activity specific similarities only statistically relevant subtructures
- (paths) are used. For this reason there is a priori no bias towards
+ Compounds with similar structures (neighbors) are assumed to have
+ similar activities as the query compound. For the determination of
+ activity specific similarities only statistically relevant subtructures
+ (paths) are used. For this reason there is a priori no bias towards
specific mechanistic hypothesis.
</p>
</body>
@@ -148,22 +154,22 @@ report.value "mechanistic_basis","<html><head></head><body>
report.value "mechanistic_basis_comments","a posteriori for individual predictions"
# Other information about the mechanistic interpretation 8.3
-report.value "mechanistic_basis_info","<html><head></head><body><p>Hypothesis about biochemical mechanisms can be derived from individual
+report.value "mechanistic_basis_info","<html><head></head><body><p>Hypothesis about biochemical mechanisms can be derived from individual
predictions by inspecting neighbors and relevant fragments.</p>
- <p>Neighbors are compounds that are similar in respect to a certain
- endpoint and it is likely that compounds with high similarity act by
- similar mechanisms as the query compound. Links at the webinterface
- prove an easy access to additional experimental data and literature
+ <p>Neighbors are compounds that are similar in respect to a certain
+ endpoint and it is likely that compounds with high similarity act by
+ similar mechanisms as the query compound. Links at the webinterface
+ prove an easy access to additional experimental data and literature
citations for the neighbors and the query structure.</p>
- <p>Activating and deactivating parts of the query compound are highlighted
- in red and green on the webinterface. Fragments that are unknown (or too
- infrequent for statistical evaluation are marked in yellow and
- additional statistical information about the individual fragments can be
- retrieved. Please note that lazar predictions are based on neighbors and
- not on fragments. Fragments and their statistical significance are used
+ <p>Activating and deactivating parts of the query compound are highlighted
+ in red and green on the webinterface. Fragments that are unknown (or too
+ infrequent for statistical evaluation are marked in yellow and
+ additional statistical information about the individual fragments can be
+ retrieved. Please note that lazar predictions are based on neighbors and
+ not on fragments. Fragments and their statistical significance are used
for the calculation of activity specific similarities.</p>"
-# Reference all publications to the bibliography
+# Reference all publications to the bibliography
# Bibliography 9.2
report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_1
report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_2
@@ -172,4 +178,4 @@ report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_3
# output
response['Content-Type'] = "application/xml"
-return report.to_xml \ No newline at end of file
+return report.to_xml