Dr. Nina Jeliazkova Ideaconsult Ltd. Sofia,...
Transcript of Dr. Nina Jeliazkova Ideaconsult Ltd. Sofia,...
OpenTox
Dr Nina Jeliazkova
Ideaconsult Ltd Sofia Bulgaria
Why integration framework for predictive
toxicology
March 17 2011
bull Challengesndash Chemical structures
bull Might be ambiguous
bull Might be error prone or time consuming to reproduce from publications
ndash Data bull Multiple formats
bull Implicit semantics often buried in human readable documentation only
ndash Modelsbull Tens of thousands available in software or in publications
bull Multiple software solutions mostly incompatible
bull Predictions reproducibility is time consuming and often hard to achieve
bull Automatic comparison of prediction results difficult
Why integration framework for predictive
toxicology
March 17 2011 Ideaconsult Ltd3
OpenTox Framework approach
4Ideaconsult LtdMarch 17
2011
User Requirements Software Requirements
Umambiguous data formal way of representing information about data
Unambiguous access well-defined interfaces
Transparency of
computational tools
formal way of representing information about
methods well-defined interfaces
Variety of user groups simplicity and modularity of design
Need to integrate various
resources (eg databases
prediction methods
models hellip) to make
meaningful predictions
distributed architecture interoperability
Need to integrate
biological information
again modularity of design extensibility
bull Distributed Web Services for predictive toxicology
bull Several types of Web Services (using REST Web service technology )
bull Service types corresponds to following building blocks
ndash Chemical compound
ndash Dataset of chemical compounds and their properties (calculated or measured)
ndash Algorithm (descriptor calculation regression classification structural alerts
QC etc)
ndash Predictive model
ndash Report validation applicability domain etc
bull Every object (compound dataset algorithm model etc) has an
unique web address ( eg httpmyhostcommodelbestpredictivemodel )
bull These objects can be created read deleted and updated
bull Every object has RDF (W3C Resource Description Framework)
representation defined in OpenTox ontology (opentoxowl)
OpenTox framework
5Ideaconsult LtdMarch 17 2011
OpenTox components
Overview of OpenTox API (Application Programming Interface)
7
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Ontology
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
AppDomain
GET
POST
PUT
DELETEValidation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETE
bullThe way applications talk to each other
bullThe way developers talk to applications
CompoundData
httpmyhostcomfeature21580
httpmyhostcomfeature21589
httpmyhostcomfeature21573
httpmyhostcomfeature21576
httpmyhostcomfeature21588
httpmyhostcomfeature21858
httpmyhostcomfeature22114
httpmyhostcomcompound413
NN-dimethyl-4-aminoazobenzene
CN(C1=CC=C(C=C1)N=NC2=CC=CC=C2)C
3 331 2253 YES 3123
httpmyhostcomcompound44497
4-
acetamidofl
uorene O=C(Nc3c2c1ccccc1Cc2ccc3)C
1 NP 22328 YES 2085
hellip hellip hellip hellip hellip hellip hellip hellip
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
All columns have explicit and machine readable pointers to
originating algorithms models or data
Everything described by W3C RDF (Resource Description framework)
representation
OpenTox datasets Unified access to data
8Ideaconsult LtdMarch 17 2011
httpmyhostcomfeature21573af21573
a otFeature otNumericFeature otNominalFeature
dccreator
httpwwwepagovNCCTdsstoxsdf_isscan_externalhtml
dctitle Canc
othasSource ISSCAN_v3a_1153_19Sept081222179139sdf
= oteeCarcinogenicity
httpmyhostcomfeature21858dctitle Structural Alert for genotoxic carcinogenicity
othasSource
lthttpmyhostcomalgorithmBenigni+2F+Bossa+rul
ebase+28for+mutagenicity+and+carcinogenicitygt
httpmyhostcomfeature22114a otFeature otNumericFeature
dccreator
httpwwwblueobeliskorgontologieschemoinformatics-
algorithmsxlogP
dctitle XLogP
othasSource
lthttpmyhostcomalgorithmorgopensciencecdkqsardescriptors
molecularXLogPDescriptorgt
= oteeOctanol-water_partition_coefficient_Kow
bull Ontologies are critical to unambiguously describe data ndash Opentoxowl
ndash Blue Obelisk algorithm ontology (cheminformatics algorithms)
ndash OpenTox algotihm types ontology
ndash OpenTox endpoints ontology based on ECHA endpoints classification
ndash Specific endpoints ontologies developed by OpenTox partners with toxicology
expertise
ndash Existing biomedical ontologies
bull Datasets can be easily merged compared and calculations
reproduced regardless of their physical place
bull OWL sameAs construct can be used to denote two links point to the
same object
bull Authentication and authorization to protect sensitive data
Uniform access to the data
9Ideaconsult LtdMarch 17 2011
bull Datasets can be easily merged compared and calculations
reproduced regardless of their physical place
bull The dataset service offers property compound substructure and
similarity searches via uniform OpenTox Application Programming
Interface
Uniform access to the data
10Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset2344 (the dataset)
bull httpappsideaconsultnet8080ambit2dataset2344metadata
(metadata obviously)
Example mutagenicity dataset
11Ideaconsult LtdMarch 17 2011
Example mutagenicity dataset
12Ideaconsult LtdMarch 17 2011
bull Activity column (httpappsideaconsultnet8080ambit2feature28958)prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
hellip
prefix af lthttpappsideaconsultnet8080ambit2featuregt
af28958
a otFeature otNumericFeature
dccreator 1941410136
dctitle Activity
othasSource tox_benchmark_N6512sdf
otunits
= oteeMutagenicity
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
Query Is there other mutagenicity data
available
13Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2featuresameas=http3A2F2Fwww
opentoxorg2FechaEndpointsowl23Mutagenicity
httpappsideaconsultnet8080ambit2feature21611
httpappsideaconsultnet8080ambit2feature26221
httpappsideaconsultnet8080ambit2feature28958
httpappsideaconsultnet8080ambit2feature21590
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[]=
httpappsideaconsultnet8080ambit2feature28958ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature21611ampfeature_uri
s[]=httpappsideaconsultnet8080ambit2feature26221ampfeature_u
ris[]= httpappsideaconsultnet8080ambit2feature21590
Merge mutagenicity data
14Ideaconsult LtdMarch 17 2011
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
15Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
List available models
16Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model
Apply ToxTree module for carcinogenicity
and mutagenicity prediction
17Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model8
bull The benchmatk dataset web address
bull httpappsideaconsultnet8080ambit2dataset2344
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the model URL with parameter
the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset2344rdquo
httpappsideaconsultnet8080ambit2model8
Long running calculations ndash web address
again
18Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2taske75057a0-b005-4c74-
949f-0be9304a3c422model
And the results (a dataset web address)
19Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[
]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2
F82Fpredicted httpappsideaconsultnet8080ambit2
chartpiedataset_uri=httpappsideac
onsultnet8080ambit2dataset2344ampfe
ature_uris[]=httpappsideaconsultnet
8080ambit2feature21858
Building blocks for model creation
20Ideaconsult LtdMarch 17 2011
bull A Datasetndash Datasets can be uploaded (SDF CSV SMI MOL)
bull via HTTP POST to the dataset service
bull Web browser file upload
ndash Existing datasets (uploaded by others) can be used
ndash Dataset Web address assigned
bull Descriptor calculation
bull Learning algorithm
bull Perform predictions
bull Make the model available
The dataset (Caco-2 dataset from a JCIM
publication)
21Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54
bull httpappsideaconsultnet8080ambit2dataset54metadata
bull The endpoint (caco2 column)
httpappsideaconsultnet8080ambit2feature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to data processing (eg
Descriptors calculation)
22Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
+ =
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
=
httpmyhostcomdatasetresults
The algorithms (including descriptors
calculation)
23Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithm
Descriptors calculation
24Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmorgopenscience
cdkqsardescriptorsmolecularXLogPDescriptor
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset
2344rdquo
httpappsideaconsultnet8080ambit2algorithmorgopensci
encecdkqsardescriptorsmolecularXLogPDescriptor
Results from descriptors calculation (a
dataset web address)
25Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttp3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F92
Fpredicted
The descriptors are stored under the web address
httpappsideaconsultnet8080ambit2feature22114
prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
prefix ar lthttpappsideaconsultnet8080ambit2referencegt
prefix bx lthttppurlorgnetnknoufnsbibtexgt
prefix rdfs lthttpwwww3org200001rdf-schemagt
prefix am lthttpappsideaconsultnet8080ambit2modelgt
prefix owl lthttpwwww3org200207owlgt
prefix xsd lthttpwwww3org2001XMLSchemagt
prefix ac lthttpappsideaconsultnet8080ambit2compoundgt
prefix ad lthttpappsideaconsultnet8080ambit2datasetgt
prefix rdf lthttpwwww3org19990222-rdf-syntax-nsgt
prefix ag lthttpappsideaconsultnet8080ambit2algorithmgt
prefix af lthttpappsideaconsultnet8080ambit2featuregt
otAlgorithm
a owlClass
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
af22114
a otFeature otNumericFeature
dccreator httpwwwblueobeliskorgontologieschemoinformatics-algorithmsxlogP
dctitle XLogP
othasSource lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
otunits
= oteeOctanol-water_partition_coefficient_Kow
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
a otAlgorithm
Merge descriptor with activity ndash dataset
with a web address again
26Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=httpap
psideaconsultnet8080ambit2feature22213ampfeature_uris[]=httpappside
aconsultnet8080ambit2feature22200
httpappsideaconsultnet8080ambit2
chartxydataset_uri=httpappsideaco
nsultnet8080ambit2dataset54ampfeatur
e_uris[]=httpappsideaconsultnet8080
ambit2feature22213ampfeature_uris[]=ht
tpappsideaconsultnet8080ambit2f
eature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to models creation
27Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+=
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
httpmyhostcommodelpredictivemodel1
Build a regression model
28Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmLR
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset54rdquo ndashd
ldquoprediction_feature=
httpappsideaconsultnet8080ambit2feature22200 ldquo
httpappsideaconsultnet8080ambit2algorithmLR
The model
29Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2model57
Web address of results could be retrieved
httpappsideaconsultnet8080ambit2model57predicted in
this case it is a the web address
httpappsideaconsultnet8080ambit2feature28963
Web address of X variables could be retrieved
viahttpappsideaconsultnet8080ambit2model57independent
in this case it is a the web address of
httpappsideaconsultnet8080ambit2feature22213
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
Why integration framework for predictive
toxicology
March 17 2011
bull Challengesndash Chemical structures
bull Might be ambiguous
bull Might be error prone or time consuming to reproduce from publications
ndash Data bull Multiple formats
bull Implicit semantics often buried in human readable documentation only
ndash Modelsbull Tens of thousands available in software or in publications
bull Multiple software solutions mostly incompatible
bull Predictions reproducibility is time consuming and often hard to achieve
bull Automatic comparison of prediction results difficult
Why integration framework for predictive
toxicology
March 17 2011 Ideaconsult Ltd3
OpenTox Framework approach
4Ideaconsult LtdMarch 17
2011
User Requirements Software Requirements
Umambiguous data formal way of representing information about data
Unambiguous access well-defined interfaces
Transparency of
computational tools
formal way of representing information about
methods well-defined interfaces
Variety of user groups simplicity and modularity of design
Need to integrate various
resources (eg databases
prediction methods
models hellip) to make
meaningful predictions
distributed architecture interoperability
Need to integrate
biological information
again modularity of design extensibility
bull Distributed Web Services for predictive toxicology
bull Several types of Web Services (using REST Web service technology )
bull Service types corresponds to following building blocks
ndash Chemical compound
ndash Dataset of chemical compounds and their properties (calculated or measured)
ndash Algorithm (descriptor calculation regression classification structural alerts
QC etc)
ndash Predictive model
ndash Report validation applicability domain etc
bull Every object (compound dataset algorithm model etc) has an
unique web address ( eg httpmyhostcommodelbestpredictivemodel )
bull These objects can be created read deleted and updated
bull Every object has RDF (W3C Resource Description Framework)
representation defined in OpenTox ontology (opentoxowl)
OpenTox framework
5Ideaconsult LtdMarch 17 2011
OpenTox components
Overview of OpenTox API (Application Programming Interface)
7
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Ontology
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
AppDomain
GET
POST
PUT
DELETEValidation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETE
bullThe way applications talk to each other
bullThe way developers talk to applications
CompoundData
httpmyhostcomfeature21580
httpmyhostcomfeature21589
httpmyhostcomfeature21573
httpmyhostcomfeature21576
httpmyhostcomfeature21588
httpmyhostcomfeature21858
httpmyhostcomfeature22114
httpmyhostcomcompound413
NN-dimethyl-4-aminoazobenzene
CN(C1=CC=C(C=C1)N=NC2=CC=CC=C2)C
3 331 2253 YES 3123
httpmyhostcomcompound44497
4-
acetamidofl
uorene O=C(Nc3c2c1ccccc1Cc2ccc3)C
1 NP 22328 YES 2085
hellip hellip hellip hellip hellip hellip hellip hellip
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
All columns have explicit and machine readable pointers to
originating algorithms models or data
Everything described by W3C RDF (Resource Description framework)
representation
OpenTox datasets Unified access to data
8Ideaconsult LtdMarch 17 2011
httpmyhostcomfeature21573af21573
a otFeature otNumericFeature otNominalFeature
dccreator
httpwwwepagovNCCTdsstoxsdf_isscan_externalhtml
dctitle Canc
othasSource ISSCAN_v3a_1153_19Sept081222179139sdf
= oteeCarcinogenicity
httpmyhostcomfeature21858dctitle Structural Alert for genotoxic carcinogenicity
othasSource
lthttpmyhostcomalgorithmBenigni+2F+Bossa+rul
ebase+28for+mutagenicity+and+carcinogenicitygt
httpmyhostcomfeature22114a otFeature otNumericFeature
dccreator
httpwwwblueobeliskorgontologieschemoinformatics-
algorithmsxlogP
dctitle XLogP
othasSource
lthttpmyhostcomalgorithmorgopensciencecdkqsardescriptors
molecularXLogPDescriptorgt
= oteeOctanol-water_partition_coefficient_Kow
bull Ontologies are critical to unambiguously describe data ndash Opentoxowl
ndash Blue Obelisk algorithm ontology (cheminformatics algorithms)
ndash OpenTox algotihm types ontology
ndash OpenTox endpoints ontology based on ECHA endpoints classification
ndash Specific endpoints ontologies developed by OpenTox partners with toxicology
expertise
ndash Existing biomedical ontologies
bull Datasets can be easily merged compared and calculations
reproduced regardless of their physical place
bull OWL sameAs construct can be used to denote two links point to the
same object
bull Authentication and authorization to protect sensitive data
Uniform access to the data
9Ideaconsult LtdMarch 17 2011
bull Datasets can be easily merged compared and calculations
reproduced regardless of their physical place
bull The dataset service offers property compound substructure and
similarity searches via uniform OpenTox Application Programming
Interface
Uniform access to the data
10Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset2344 (the dataset)
bull httpappsideaconsultnet8080ambit2dataset2344metadata
(metadata obviously)
Example mutagenicity dataset
11Ideaconsult LtdMarch 17 2011
Example mutagenicity dataset
12Ideaconsult LtdMarch 17 2011
bull Activity column (httpappsideaconsultnet8080ambit2feature28958)prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
hellip
prefix af lthttpappsideaconsultnet8080ambit2featuregt
af28958
a otFeature otNumericFeature
dccreator 1941410136
dctitle Activity
othasSource tox_benchmark_N6512sdf
otunits
= oteeMutagenicity
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
Query Is there other mutagenicity data
available
13Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2featuresameas=http3A2F2Fwww
opentoxorg2FechaEndpointsowl23Mutagenicity
httpappsideaconsultnet8080ambit2feature21611
httpappsideaconsultnet8080ambit2feature26221
httpappsideaconsultnet8080ambit2feature28958
httpappsideaconsultnet8080ambit2feature21590
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[]=
httpappsideaconsultnet8080ambit2feature28958ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature21611ampfeature_uri
s[]=httpappsideaconsultnet8080ambit2feature26221ampfeature_u
ris[]= httpappsideaconsultnet8080ambit2feature21590
Merge mutagenicity data
14Ideaconsult LtdMarch 17 2011
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
15Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
List available models
16Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model
Apply ToxTree module for carcinogenicity
and mutagenicity prediction
17Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model8
bull The benchmatk dataset web address
bull httpappsideaconsultnet8080ambit2dataset2344
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the model URL with parameter
the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset2344rdquo
httpappsideaconsultnet8080ambit2model8
Long running calculations ndash web address
again
18Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2taske75057a0-b005-4c74-
949f-0be9304a3c422model
And the results (a dataset web address)
19Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[
]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2
F82Fpredicted httpappsideaconsultnet8080ambit2
chartpiedataset_uri=httpappsideac
onsultnet8080ambit2dataset2344ampfe
ature_uris[]=httpappsideaconsultnet
8080ambit2feature21858
Building blocks for model creation
20Ideaconsult LtdMarch 17 2011
bull A Datasetndash Datasets can be uploaded (SDF CSV SMI MOL)
bull via HTTP POST to the dataset service
bull Web browser file upload
ndash Existing datasets (uploaded by others) can be used
ndash Dataset Web address assigned
bull Descriptor calculation
bull Learning algorithm
bull Perform predictions
bull Make the model available
The dataset (Caco-2 dataset from a JCIM
publication)
21Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54
bull httpappsideaconsultnet8080ambit2dataset54metadata
bull The endpoint (caco2 column)
httpappsideaconsultnet8080ambit2feature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to data processing (eg
Descriptors calculation)
22Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
+ =
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
=
httpmyhostcomdatasetresults
The algorithms (including descriptors
calculation)
23Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithm
Descriptors calculation
24Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmorgopenscience
cdkqsardescriptorsmolecularXLogPDescriptor
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset
2344rdquo
httpappsideaconsultnet8080ambit2algorithmorgopensci
encecdkqsardescriptorsmolecularXLogPDescriptor
Results from descriptors calculation (a
dataset web address)
25Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttp3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F92
Fpredicted
The descriptors are stored under the web address
httpappsideaconsultnet8080ambit2feature22114
prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
prefix ar lthttpappsideaconsultnet8080ambit2referencegt
prefix bx lthttppurlorgnetnknoufnsbibtexgt
prefix rdfs lthttpwwww3org200001rdf-schemagt
prefix am lthttpappsideaconsultnet8080ambit2modelgt
prefix owl lthttpwwww3org200207owlgt
prefix xsd lthttpwwww3org2001XMLSchemagt
prefix ac lthttpappsideaconsultnet8080ambit2compoundgt
prefix ad lthttpappsideaconsultnet8080ambit2datasetgt
prefix rdf lthttpwwww3org19990222-rdf-syntax-nsgt
prefix ag lthttpappsideaconsultnet8080ambit2algorithmgt
prefix af lthttpappsideaconsultnet8080ambit2featuregt
otAlgorithm
a owlClass
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
af22114
a otFeature otNumericFeature
dccreator httpwwwblueobeliskorgontologieschemoinformatics-algorithmsxlogP
dctitle XLogP
othasSource lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
otunits
= oteeOctanol-water_partition_coefficient_Kow
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
a otAlgorithm
Merge descriptor with activity ndash dataset
with a web address again
26Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=httpap
psideaconsultnet8080ambit2feature22213ampfeature_uris[]=httpappside
aconsultnet8080ambit2feature22200
httpappsideaconsultnet8080ambit2
chartxydataset_uri=httpappsideaco
nsultnet8080ambit2dataset54ampfeatur
e_uris[]=httpappsideaconsultnet8080
ambit2feature22213ampfeature_uris[]=ht
tpappsideaconsultnet8080ambit2f
eature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to models creation
27Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+=
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
httpmyhostcommodelpredictivemodel1
Build a regression model
28Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmLR
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset54rdquo ndashd
ldquoprediction_feature=
httpappsideaconsultnet8080ambit2feature22200 ldquo
httpappsideaconsultnet8080ambit2algorithmLR
The model
29Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2model57
Web address of results could be retrieved
httpappsideaconsultnet8080ambit2model57predicted in
this case it is a the web address
httpappsideaconsultnet8080ambit2feature28963
Web address of X variables could be retrieved
viahttpappsideaconsultnet8080ambit2model57independent
in this case it is a the web address of
httpappsideaconsultnet8080ambit2feature22213
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
bull Challengesndash Chemical structures
bull Might be ambiguous
bull Might be error prone or time consuming to reproduce from publications
ndash Data bull Multiple formats
bull Implicit semantics often buried in human readable documentation only
ndash Modelsbull Tens of thousands available in software or in publications
bull Multiple software solutions mostly incompatible
bull Predictions reproducibility is time consuming and often hard to achieve
bull Automatic comparison of prediction results difficult
Why integration framework for predictive
toxicology
March 17 2011 Ideaconsult Ltd3
OpenTox Framework approach
4Ideaconsult LtdMarch 17
2011
User Requirements Software Requirements
Umambiguous data formal way of representing information about data
Unambiguous access well-defined interfaces
Transparency of
computational tools
formal way of representing information about
methods well-defined interfaces
Variety of user groups simplicity and modularity of design
Need to integrate various
resources (eg databases
prediction methods
models hellip) to make
meaningful predictions
distributed architecture interoperability
Need to integrate
biological information
again modularity of design extensibility
bull Distributed Web Services for predictive toxicology
bull Several types of Web Services (using REST Web service technology )
bull Service types corresponds to following building blocks
ndash Chemical compound
ndash Dataset of chemical compounds and their properties (calculated or measured)
ndash Algorithm (descriptor calculation regression classification structural alerts
QC etc)
ndash Predictive model
ndash Report validation applicability domain etc
bull Every object (compound dataset algorithm model etc) has an
unique web address ( eg httpmyhostcommodelbestpredictivemodel )
bull These objects can be created read deleted and updated
bull Every object has RDF (W3C Resource Description Framework)
representation defined in OpenTox ontology (opentoxowl)
OpenTox framework
5Ideaconsult LtdMarch 17 2011
OpenTox components
Overview of OpenTox API (Application Programming Interface)
7
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Ontology
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
AppDomain
GET
POST
PUT
DELETEValidation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETE
bullThe way applications talk to each other
bullThe way developers talk to applications
CompoundData
httpmyhostcomfeature21580
httpmyhostcomfeature21589
httpmyhostcomfeature21573
httpmyhostcomfeature21576
httpmyhostcomfeature21588
httpmyhostcomfeature21858
httpmyhostcomfeature22114
httpmyhostcomcompound413
NN-dimethyl-4-aminoazobenzene
CN(C1=CC=C(C=C1)N=NC2=CC=CC=C2)C
3 331 2253 YES 3123
httpmyhostcomcompound44497
4-
acetamidofl
uorene O=C(Nc3c2c1ccccc1Cc2ccc3)C
1 NP 22328 YES 2085
hellip hellip hellip hellip hellip hellip hellip hellip
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
All columns have explicit and machine readable pointers to
originating algorithms models or data
Everything described by W3C RDF (Resource Description framework)
representation
OpenTox datasets Unified access to data
8Ideaconsult LtdMarch 17 2011
httpmyhostcomfeature21573af21573
a otFeature otNumericFeature otNominalFeature
dccreator
httpwwwepagovNCCTdsstoxsdf_isscan_externalhtml
dctitle Canc
othasSource ISSCAN_v3a_1153_19Sept081222179139sdf
= oteeCarcinogenicity
httpmyhostcomfeature21858dctitle Structural Alert for genotoxic carcinogenicity
othasSource
lthttpmyhostcomalgorithmBenigni+2F+Bossa+rul
ebase+28for+mutagenicity+and+carcinogenicitygt
httpmyhostcomfeature22114a otFeature otNumericFeature
dccreator
httpwwwblueobeliskorgontologieschemoinformatics-
algorithmsxlogP
dctitle XLogP
othasSource
lthttpmyhostcomalgorithmorgopensciencecdkqsardescriptors
molecularXLogPDescriptorgt
= oteeOctanol-water_partition_coefficient_Kow
bull Ontologies are critical to unambiguously describe data ndash Opentoxowl
ndash Blue Obelisk algorithm ontology (cheminformatics algorithms)
ndash OpenTox algotihm types ontology
ndash OpenTox endpoints ontology based on ECHA endpoints classification
ndash Specific endpoints ontologies developed by OpenTox partners with toxicology
expertise
ndash Existing biomedical ontologies
bull Datasets can be easily merged compared and calculations
reproduced regardless of their physical place
bull OWL sameAs construct can be used to denote two links point to the
same object
bull Authentication and authorization to protect sensitive data
Uniform access to the data
9Ideaconsult LtdMarch 17 2011
bull Datasets can be easily merged compared and calculations
reproduced regardless of their physical place
bull The dataset service offers property compound substructure and
similarity searches via uniform OpenTox Application Programming
Interface
Uniform access to the data
10Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset2344 (the dataset)
bull httpappsideaconsultnet8080ambit2dataset2344metadata
(metadata obviously)
Example mutagenicity dataset
11Ideaconsult LtdMarch 17 2011
Example mutagenicity dataset
12Ideaconsult LtdMarch 17 2011
bull Activity column (httpappsideaconsultnet8080ambit2feature28958)prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
hellip
prefix af lthttpappsideaconsultnet8080ambit2featuregt
af28958
a otFeature otNumericFeature
dccreator 1941410136
dctitle Activity
othasSource tox_benchmark_N6512sdf
otunits
= oteeMutagenicity
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
Query Is there other mutagenicity data
available
13Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2featuresameas=http3A2F2Fwww
opentoxorg2FechaEndpointsowl23Mutagenicity
httpappsideaconsultnet8080ambit2feature21611
httpappsideaconsultnet8080ambit2feature26221
httpappsideaconsultnet8080ambit2feature28958
httpappsideaconsultnet8080ambit2feature21590
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[]=
httpappsideaconsultnet8080ambit2feature28958ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature21611ampfeature_uri
s[]=httpappsideaconsultnet8080ambit2feature26221ampfeature_u
ris[]= httpappsideaconsultnet8080ambit2feature21590
Merge mutagenicity data
14Ideaconsult LtdMarch 17 2011
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
15Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
List available models
16Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model
Apply ToxTree module for carcinogenicity
and mutagenicity prediction
17Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model8
bull The benchmatk dataset web address
bull httpappsideaconsultnet8080ambit2dataset2344
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the model URL with parameter
the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset2344rdquo
httpappsideaconsultnet8080ambit2model8
Long running calculations ndash web address
again
18Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2taske75057a0-b005-4c74-
949f-0be9304a3c422model
And the results (a dataset web address)
19Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[
]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2
F82Fpredicted httpappsideaconsultnet8080ambit2
chartpiedataset_uri=httpappsideac
onsultnet8080ambit2dataset2344ampfe
ature_uris[]=httpappsideaconsultnet
8080ambit2feature21858
Building blocks for model creation
20Ideaconsult LtdMarch 17 2011
bull A Datasetndash Datasets can be uploaded (SDF CSV SMI MOL)
bull via HTTP POST to the dataset service
bull Web browser file upload
ndash Existing datasets (uploaded by others) can be used
ndash Dataset Web address assigned
bull Descriptor calculation
bull Learning algorithm
bull Perform predictions
bull Make the model available
The dataset (Caco-2 dataset from a JCIM
publication)
21Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54
bull httpappsideaconsultnet8080ambit2dataset54metadata
bull The endpoint (caco2 column)
httpappsideaconsultnet8080ambit2feature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to data processing (eg
Descriptors calculation)
22Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
+ =
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
=
httpmyhostcomdatasetresults
The algorithms (including descriptors
calculation)
23Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithm
Descriptors calculation
24Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmorgopenscience
cdkqsardescriptorsmolecularXLogPDescriptor
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset
2344rdquo
httpappsideaconsultnet8080ambit2algorithmorgopensci
encecdkqsardescriptorsmolecularXLogPDescriptor
Results from descriptors calculation (a
dataset web address)
25Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttp3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F92
Fpredicted
The descriptors are stored under the web address
httpappsideaconsultnet8080ambit2feature22114
prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
prefix ar lthttpappsideaconsultnet8080ambit2referencegt
prefix bx lthttppurlorgnetnknoufnsbibtexgt
prefix rdfs lthttpwwww3org200001rdf-schemagt
prefix am lthttpappsideaconsultnet8080ambit2modelgt
prefix owl lthttpwwww3org200207owlgt
prefix xsd lthttpwwww3org2001XMLSchemagt
prefix ac lthttpappsideaconsultnet8080ambit2compoundgt
prefix ad lthttpappsideaconsultnet8080ambit2datasetgt
prefix rdf lthttpwwww3org19990222-rdf-syntax-nsgt
prefix ag lthttpappsideaconsultnet8080ambit2algorithmgt
prefix af lthttpappsideaconsultnet8080ambit2featuregt
otAlgorithm
a owlClass
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
af22114
a otFeature otNumericFeature
dccreator httpwwwblueobeliskorgontologieschemoinformatics-algorithmsxlogP
dctitle XLogP
othasSource lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
otunits
= oteeOctanol-water_partition_coefficient_Kow
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
a otAlgorithm
Merge descriptor with activity ndash dataset
with a web address again
26Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=httpap
psideaconsultnet8080ambit2feature22213ampfeature_uris[]=httpappside
aconsultnet8080ambit2feature22200
httpappsideaconsultnet8080ambit2
chartxydataset_uri=httpappsideaco
nsultnet8080ambit2dataset54ampfeatur
e_uris[]=httpappsideaconsultnet8080
ambit2feature22213ampfeature_uris[]=ht
tpappsideaconsultnet8080ambit2f
eature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to models creation
27Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+=
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
httpmyhostcommodelpredictivemodel1
Build a regression model
28Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmLR
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset54rdquo ndashd
ldquoprediction_feature=
httpappsideaconsultnet8080ambit2feature22200 ldquo
httpappsideaconsultnet8080ambit2algorithmLR
The model
29Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2model57
Web address of results could be retrieved
httpappsideaconsultnet8080ambit2model57predicted in
this case it is a the web address
httpappsideaconsultnet8080ambit2feature28963
Web address of X variables could be retrieved
viahttpappsideaconsultnet8080ambit2model57independent
in this case it is a the web address of
httpappsideaconsultnet8080ambit2feature22213
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
OpenTox Framework approach
4Ideaconsult LtdMarch 17
2011
User Requirements Software Requirements
Umambiguous data formal way of representing information about data
Unambiguous access well-defined interfaces
Transparency of
computational tools
formal way of representing information about
methods well-defined interfaces
Variety of user groups simplicity and modularity of design
Need to integrate various
resources (eg databases
prediction methods
models hellip) to make
meaningful predictions
distributed architecture interoperability
Need to integrate
biological information
again modularity of design extensibility
bull Distributed Web Services for predictive toxicology
bull Several types of Web Services (using REST Web service technology )
bull Service types corresponds to following building blocks
ndash Chemical compound
ndash Dataset of chemical compounds and their properties (calculated or measured)
ndash Algorithm (descriptor calculation regression classification structural alerts
QC etc)
ndash Predictive model
ndash Report validation applicability domain etc
bull Every object (compound dataset algorithm model etc) has an
unique web address ( eg httpmyhostcommodelbestpredictivemodel )
bull These objects can be created read deleted and updated
bull Every object has RDF (W3C Resource Description Framework)
representation defined in OpenTox ontology (opentoxowl)
OpenTox framework
5Ideaconsult LtdMarch 17 2011
OpenTox components
Overview of OpenTox API (Application Programming Interface)
7
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Ontology
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
AppDomain
GET
POST
PUT
DELETEValidation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETE
bullThe way applications talk to each other
bullThe way developers talk to applications
CompoundData
httpmyhostcomfeature21580
httpmyhostcomfeature21589
httpmyhostcomfeature21573
httpmyhostcomfeature21576
httpmyhostcomfeature21588
httpmyhostcomfeature21858
httpmyhostcomfeature22114
httpmyhostcomcompound413
NN-dimethyl-4-aminoazobenzene
CN(C1=CC=C(C=C1)N=NC2=CC=CC=C2)C
3 331 2253 YES 3123
httpmyhostcomcompound44497
4-
acetamidofl
uorene O=C(Nc3c2c1ccccc1Cc2ccc3)C
1 NP 22328 YES 2085
hellip hellip hellip hellip hellip hellip hellip hellip
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
All columns have explicit and machine readable pointers to
originating algorithms models or data
Everything described by W3C RDF (Resource Description framework)
representation
OpenTox datasets Unified access to data
8Ideaconsult LtdMarch 17 2011
httpmyhostcomfeature21573af21573
a otFeature otNumericFeature otNominalFeature
dccreator
httpwwwepagovNCCTdsstoxsdf_isscan_externalhtml
dctitle Canc
othasSource ISSCAN_v3a_1153_19Sept081222179139sdf
= oteeCarcinogenicity
httpmyhostcomfeature21858dctitle Structural Alert for genotoxic carcinogenicity
othasSource
lthttpmyhostcomalgorithmBenigni+2F+Bossa+rul
ebase+28for+mutagenicity+and+carcinogenicitygt
httpmyhostcomfeature22114a otFeature otNumericFeature
dccreator
httpwwwblueobeliskorgontologieschemoinformatics-
algorithmsxlogP
dctitle XLogP
othasSource
lthttpmyhostcomalgorithmorgopensciencecdkqsardescriptors
molecularXLogPDescriptorgt
= oteeOctanol-water_partition_coefficient_Kow
bull Ontologies are critical to unambiguously describe data ndash Opentoxowl
ndash Blue Obelisk algorithm ontology (cheminformatics algorithms)
ndash OpenTox algotihm types ontology
ndash OpenTox endpoints ontology based on ECHA endpoints classification
ndash Specific endpoints ontologies developed by OpenTox partners with toxicology
expertise
ndash Existing biomedical ontologies
bull Datasets can be easily merged compared and calculations
reproduced regardless of their physical place
bull OWL sameAs construct can be used to denote two links point to the
same object
bull Authentication and authorization to protect sensitive data
Uniform access to the data
9Ideaconsult LtdMarch 17 2011
bull Datasets can be easily merged compared and calculations
reproduced regardless of their physical place
bull The dataset service offers property compound substructure and
similarity searches via uniform OpenTox Application Programming
Interface
Uniform access to the data
10Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset2344 (the dataset)
bull httpappsideaconsultnet8080ambit2dataset2344metadata
(metadata obviously)
Example mutagenicity dataset
11Ideaconsult LtdMarch 17 2011
Example mutagenicity dataset
12Ideaconsult LtdMarch 17 2011
bull Activity column (httpappsideaconsultnet8080ambit2feature28958)prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
hellip
prefix af lthttpappsideaconsultnet8080ambit2featuregt
af28958
a otFeature otNumericFeature
dccreator 1941410136
dctitle Activity
othasSource tox_benchmark_N6512sdf
otunits
= oteeMutagenicity
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
Query Is there other mutagenicity data
available
13Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2featuresameas=http3A2F2Fwww
opentoxorg2FechaEndpointsowl23Mutagenicity
httpappsideaconsultnet8080ambit2feature21611
httpappsideaconsultnet8080ambit2feature26221
httpappsideaconsultnet8080ambit2feature28958
httpappsideaconsultnet8080ambit2feature21590
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[]=
httpappsideaconsultnet8080ambit2feature28958ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature21611ampfeature_uri
s[]=httpappsideaconsultnet8080ambit2feature26221ampfeature_u
ris[]= httpappsideaconsultnet8080ambit2feature21590
Merge mutagenicity data
14Ideaconsult LtdMarch 17 2011
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
15Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
List available models
16Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model
Apply ToxTree module for carcinogenicity
and mutagenicity prediction
17Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model8
bull The benchmatk dataset web address
bull httpappsideaconsultnet8080ambit2dataset2344
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the model URL with parameter
the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset2344rdquo
httpappsideaconsultnet8080ambit2model8
Long running calculations ndash web address
again
18Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2taske75057a0-b005-4c74-
949f-0be9304a3c422model
And the results (a dataset web address)
19Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[
]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2
F82Fpredicted httpappsideaconsultnet8080ambit2
chartpiedataset_uri=httpappsideac
onsultnet8080ambit2dataset2344ampfe
ature_uris[]=httpappsideaconsultnet
8080ambit2feature21858
Building blocks for model creation
20Ideaconsult LtdMarch 17 2011
bull A Datasetndash Datasets can be uploaded (SDF CSV SMI MOL)
bull via HTTP POST to the dataset service
bull Web browser file upload
ndash Existing datasets (uploaded by others) can be used
ndash Dataset Web address assigned
bull Descriptor calculation
bull Learning algorithm
bull Perform predictions
bull Make the model available
The dataset (Caco-2 dataset from a JCIM
publication)
21Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54
bull httpappsideaconsultnet8080ambit2dataset54metadata
bull The endpoint (caco2 column)
httpappsideaconsultnet8080ambit2feature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to data processing (eg
Descriptors calculation)
22Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
+ =
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
=
httpmyhostcomdatasetresults
The algorithms (including descriptors
calculation)
23Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithm
Descriptors calculation
24Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmorgopenscience
cdkqsardescriptorsmolecularXLogPDescriptor
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset
2344rdquo
httpappsideaconsultnet8080ambit2algorithmorgopensci
encecdkqsardescriptorsmolecularXLogPDescriptor
Results from descriptors calculation (a
dataset web address)
25Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttp3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F92
Fpredicted
The descriptors are stored under the web address
httpappsideaconsultnet8080ambit2feature22114
prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
prefix ar lthttpappsideaconsultnet8080ambit2referencegt
prefix bx lthttppurlorgnetnknoufnsbibtexgt
prefix rdfs lthttpwwww3org200001rdf-schemagt
prefix am lthttpappsideaconsultnet8080ambit2modelgt
prefix owl lthttpwwww3org200207owlgt
prefix xsd lthttpwwww3org2001XMLSchemagt
prefix ac lthttpappsideaconsultnet8080ambit2compoundgt
prefix ad lthttpappsideaconsultnet8080ambit2datasetgt
prefix rdf lthttpwwww3org19990222-rdf-syntax-nsgt
prefix ag lthttpappsideaconsultnet8080ambit2algorithmgt
prefix af lthttpappsideaconsultnet8080ambit2featuregt
otAlgorithm
a owlClass
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
af22114
a otFeature otNumericFeature
dccreator httpwwwblueobeliskorgontologieschemoinformatics-algorithmsxlogP
dctitle XLogP
othasSource lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
otunits
= oteeOctanol-water_partition_coefficient_Kow
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
a otAlgorithm
Merge descriptor with activity ndash dataset
with a web address again
26Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=httpap
psideaconsultnet8080ambit2feature22213ampfeature_uris[]=httpappside
aconsultnet8080ambit2feature22200
httpappsideaconsultnet8080ambit2
chartxydataset_uri=httpappsideaco
nsultnet8080ambit2dataset54ampfeatur
e_uris[]=httpappsideaconsultnet8080
ambit2feature22213ampfeature_uris[]=ht
tpappsideaconsultnet8080ambit2f
eature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to models creation
27Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+=
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
httpmyhostcommodelpredictivemodel1
Build a regression model
28Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmLR
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset54rdquo ndashd
ldquoprediction_feature=
httpappsideaconsultnet8080ambit2feature22200 ldquo
httpappsideaconsultnet8080ambit2algorithmLR
The model
29Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2model57
Web address of results could be retrieved
httpappsideaconsultnet8080ambit2model57predicted in
this case it is a the web address
httpappsideaconsultnet8080ambit2feature28963
Web address of X variables could be retrieved
viahttpappsideaconsultnet8080ambit2model57independent
in this case it is a the web address of
httpappsideaconsultnet8080ambit2feature22213
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
bull Distributed Web Services for predictive toxicology
bull Several types of Web Services (using REST Web service technology )
bull Service types corresponds to following building blocks
ndash Chemical compound
ndash Dataset of chemical compounds and their properties (calculated or measured)
ndash Algorithm (descriptor calculation regression classification structural alerts
QC etc)
ndash Predictive model
ndash Report validation applicability domain etc
bull Every object (compound dataset algorithm model etc) has an
unique web address ( eg httpmyhostcommodelbestpredictivemodel )
bull These objects can be created read deleted and updated
bull Every object has RDF (W3C Resource Description Framework)
representation defined in OpenTox ontology (opentoxowl)
OpenTox framework
5Ideaconsult LtdMarch 17 2011
OpenTox components
Overview of OpenTox API (Application Programming Interface)
7
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Ontology
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
AppDomain
GET
POST
PUT
DELETEValidation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETE
bullThe way applications talk to each other
bullThe way developers talk to applications
CompoundData
httpmyhostcomfeature21580
httpmyhostcomfeature21589
httpmyhostcomfeature21573
httpmyhostcomfeature21576
httpmyhostcomfeature21588
httpmyhostcomfeature21858
httpmyhostcomfeature22114
httpmyhostcomcompound413
NN-dimethyl-4-aminoazobenzene
CN(C1=CC=C(C=C1)N=NC2=CC=CC=C2)C
3 331 2253 YES 3123
httpmyhostcomcompound44497
4-
acetamidofl
uorene O=C(Nc3c2c1ccccc1Cc2ccc3)C
1 NP 22328 YES 2085
hellip hellip hellip hellip hellip hellip hellip hellip
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
All columns have explicit and machine readable pointers to
originating algorithms models or data
Everything described by W3C RDF (Resource Description framework)
representation
OpenTox datasets Unified access to data
8Ideaconsult LtdMarch 17 2011
httpmyhostcomfeature21573af21573
a otFeature otNumericFeature otNominalFeature
dccreator
httpwwwepagovNCCTdsstoxsdf_isscan_externalhtml
dctitle Canc
othasSource ISSCAN_v3a_1153_19Sept081222179139sdf
= oteeCarcinogenicity
httpmyhostcomfeature21858dctitle Structural Alert for genotoxic carcinogenicity
othasSource
lthttpmyhostcomalgorithmBenigni+2F+Bossa+rul
ebase+28for+mutagenicity+and+carcinogenicitygt
httpmyhostcomfeature22114a otFeature otNumericFeature
dccreator
httpwwwblueobeliskorgontologieschemoinformatics-
algorithmsxlogP
dctitle XLogP
othasSource
lthttpmyhostcomalgorithmorgopensciencecdkqsardescriptors
molecularXLogPDescriptorgt
= oteeOctanol-water_partition_coefficient_Kow
bull Ontologies are critical to unambiguously describe data ndash Opentoxowl
ndash Blue Obelisk algorithm ontology (cheminformatics algorithms)
ndash OpenTox algotihm types ontology
ndash OpenTox endpoints ontology based on ECHA endpoints classification
ndash Specific endpoints ontologies developed by OpenTox partners with toxicology
expertise
ndash Existing biomedical ontologies
bull Datasets can be easily merged compared and calculations
reproduced regardless of their physical place
bull OWL sameAs construct can be used to denote two links point to the
same object
bull Authentication and authorization to protect sensitive data
Uniform access to the data
9Ideaconsult LtdMarch 17 2011
bull Datasets can be easily merged compared and calculations
reproduced regardless of their physical place
bull The dataset service offers property compound substructure and
similarity searches via uniform OpenTox Application Programming
Interface
Uniform access to the data
10Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset2344 (the dataset)
bull httpappsideaconsultnet8080ambit2dataset2344metadata
(metadata obviously)
Example mutagenicity dataset
11Ideaconsult LtdMarch 17 2011
Example mutagenicity dataset
12Ideaconsult LtdMarch 17 2011
bull Activity column (httpappsideaconsultnet8080ambit2feature28958)prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
hellip
prefix af lthttpappsideaconsultnet8080ambit2featuregt
af28958
a otFeature otNumericFeature
dccreator 1941410136
dctitle Activity
othasSource tox_benchmark_N6512sdf
otunits
= oteeMutagenicity
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
Query Is there other mutagenicity data
available
13Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2featuresameas=http3A2F2Fwww
opentoxorg2FechaEndpointsowl23Mutagenicity
httpappsideaconsultnet8080ambit2feature21611
httpappsideaconsultnet8080ambit2feature26221
httpappsideaconsultnet8080ambit2feature28958
httpappsideaconsultnet8080ambit2feature21590
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[]=
httpappsideaconsultnet8080ambit2feature28958ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature21611ampfeature_uri
s[]=httpappsideaconsultnet8080ambit2feature26221ampfeature_u
ris[]= httpappsideaconsultnet8080ambit2feature21590
Merge mutagenicity data
14Ideaconsult LtdMarch 17 2011
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
15Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
List available models
16Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model
Apply ToxTree module for carcinogenicity
and mutagenicity prediction
17Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model8
bull The benchmatk dataset web address
bull httpappsideaconsultnet8080ambit2dataset2344
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the model URL with parameter
the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset2344rdquo
httpappsideaconsultnet8080ambit2model8
Long running calculations ndash web address
again
18Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2taske75057a0-b005-4c74-
949f-0be9304a3c422model
And the results (a dataset web address)
19Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[
]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2
F82Fpredicted httpappsideaconsultnet8080ambit2
chartpiedataset_uri=httpappsideac
onsultnet8080ambit2dataset2344ampfe
ature_uris[]=httpappsideaconsultnet
8080ambit2feature21858
Building blocks for model creation
20Ideaconsult LtdMarch 17 2011
bull A Datasetndash Datasets can be uploaded (SDF CSV SMI MOL)
bull via HTTP POST to the dataset service
bull Web browser file upload
ndash Existing datasets (uploaded by others) can be used
ndash Dataset Web address assigned
bull Descriptor calculation
bull Learning algorithm
bull Perform predictions
bull Make the model available
The dataset (Caco-2 dataset from a JCIM
publication)
21Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54
bull httpappsideaconsultnet8080ambit2dataset54metadata
bull The endpoint (caco2 column)
httpappsideaconsultnet8080ambit2feature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to data processing (eg
Descriptors calculation)
22Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
+ =
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
=
httpmyhostcomdatasetresults
The algorithms (including descriptors
calculation)
23Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithm
Descriptors calculation
24Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmorgopenscience
cdkqsardescriptorsmolecularXLogPDescriptor
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset
2344rdquo
httpappsideaconsultnet8080ambit2algorithmorgopensci
encecdkqsardescriptorsmolecularXLogPDescriptor
Results from descriptors calculation (a
dataset web address)
25Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttp3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F92
Fpredicted
The descriptors are stored under the web address
httpappsideaconsultnet8080ambit2feature22114
prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
prefix ar lthttpappsideaconsultnet8080ambit2referencegt
prefix bx lthttppurlorgnetnknoufnsbibtexgt
prefix rdfs lthttpwwww3org200001rdf-schemagt
prefix am lthttpappsideaconsultnet8080ambit2modelgt
prefix owl lthttpwwww3org200207owlgt
prefix xsd lthttpwwww3org2001XMLSchemagt
prefix ac lthttpappsideaconsultnet8080ambit2compoundgt
prefix ad lthttpappsideaconsultnet8080ambit2datasetgt
prefix rdf lthttpwwww3org19990222-rdf-syntax-nsgt
prefix ag lthttpappsideaconsultnet8080ambit2algorithmgt
prefix af lthttpappsideaconsultnet8080ambit2featuregt
otAlgorithm
a owlClass
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
af22114
a otFeature otNumericFeature
dccreator httpwwwblueobeliskorgontologieschemoinformatics-algorithmsxlogP
dctitle XLogP
othasSource lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
otunits
= oteeOctanol-water_partition_coefficient_Kow
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
a otAlgorithm
Merge descriptor with activity ndash dataset
with a web address again
26Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=httpap
psideaconsultnet8080ambit2feature22213ampfeature_uris[]=httpappside
aconsultnet8080ambit2feature22200
httpappsideaconsultnet8080ambit2
chartxydataset_uri=httpappsideaco
nsultnet8080ambit2dataset54ampfeatur
e_uris[]=httpappsideaconsultnet8080
ambit2feature22213ampfeature_uris[]=ht
tpappsideaconsultnet8080ambit2f
eature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to models creation
27Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+=
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
httpmyhostcommodelpredictivemodel1
Build a regression model
28Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmLR
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset54rdquo ndashd
ldquoprediction_feature=
httpappsideaconsultnet8080ambit2feature22200 ldquo
httpappsideaconsultnet8080ambit2algorithmLR
The model
29Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2model57
Web address of results could be retrieved
httpappsideaconsultnet8080ambit2model57predicted in
this case it is a the web address
httpappsideaconsultnet8080ambit2feature28963
Web address of X variables could be retrieved
viahttpappsideaconsultnet8080ambit2model57independent
in this case it is a the web address of
httpappsideaconsultnet8080ambit2feature22213
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
OpenTox components
Overview of OpenTox API (Application Programming Interface)
7
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Ontology
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
AppDomain
GET
POST
PUT
DELETEValidation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETE
bullThe way applications talk to each other
bullThe way developers talk to applications
CompoundData
httpmyhostcomfeature21580
httpmyhostcomfeature21589
httpmyhostcomfeature21573
httpmyhostcomfeature21576
httpmyhostcomfeature21588
httpmyhostcomfeature21858
httpmyhostcomfeature22114
httpmyhostcomcompound413
NN-dimethyl-4-aminoazobenzene
CN(C1=CC=C(C=C1)N=NC2=CC=CC=C2)C
3 331 2253 YES 3123
httpmyhostcomcompound44497
4-
acetamidofl
uorene O=C(Nc3c2c1ccccc1Cc2ccc3)C
1 NP 22328 YES 2085
hellip hellip hellip hellip hellip hellip hellip hellip
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
All columns have explicit and machine readable pointers to
originating algorithms models or data
Everything described by W3C RDF (Resource Description framework)
representation
OpenTox datasets Unified access to data
8Ideaconsult LtdMarch 17 2011
httpmyhostcomfeature21573af21573
a otFeature otNumericFeature otNominalFeature
dccreator
httpwwwepagovNCCTdsstoxsdf_isscan_externalhtml
dctitle Canc
othasSource ISSCAN_v3a_1153_19Sept081222179139sdf
= oteeCarcinogenicity
httpmyhostcomfeature21858dctitle Structural Alert for genotoxic carcinogenicity
othasSource
lthttpmyhostcomalgorithmBenigni+2F+Bossa+rul
ebase+28for+mutagenicity+and+carcinogenicitygt
httpmyhostcomfeature22114a otFeature otNumericFeature
dccreator
httpwwwblueobeliskorgontologieschemoinformatics-
algorithmsxlogP
dctitle XLogP
othasSource
lthttpmyhostcomalgorithmorgopensciencecdkqsardescriptors
molecularXLogPDescriptorgt
= oteeOctanol-water_partition_coefficient_Kow
bull Ontologies are critical to unambiguously describe data ndash Opentoxowl
ndash Blue Obelisk algorithm ontology (cheminformatics algorithms)
ndash OpenTox algotihm types ontology
ndash OpenTox endpoints ontology based on ECHA endpoints classification
ndash Specific endpoints ontologies developed by OpenTox partners with toxicology
expertise
ndash Existing biomedical ontologies
bull Datasets can be easily merged compared and calculations
reproduced regardless of their physical place
bull OWL sameAs construct can be used to denote two links point to the
same object
bull Authentication and authorization to protect sensitive data
Uniform access to the data
9Ideaconsult LtdMarch 17 2011
bull Datasets can be easily merged compared and calculations
reproduced regardless of their physical place
bull The dataset service offers property compound substructure and
similarity searches via uniform OpenTox Application Programming
Interface
Uniform access to the data
10Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset2344 (the dataset)
bull httpappsideaconsultnet8080ambit2dataset2344metadata
(metadata obviously)
Example mutagenicity dataset
11Ideaconsult LtdMarch 17 2011
Example mutagenicity dataset
12Ideaconsult LtdMarch 17 2011
bull Activity column (httpappsideaconsultnet8080ambit2feature28958)prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
hellip
prefix af lthttpappsideaconsultnet8080ambit2featuregt
af28958
a otFeature otNumericFeature
dccreator 1941410136
dctitle Activity
othasSource tox_benchmark_N6512sdf
otunits
= oteeMutagenicity
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
Query Is there other mutagenicity data
available
13Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2featuresameas=http3A2F2Fwww
opentoxorg2FechaEndpointsowl23Mutagenicity
httpappsideaconsultnet8080ambit2feature21611
httpappsideaconsultnet8080ambit2feature26221
httpappsideaconsultnet8080ambit2feature28958
httpappsideaconsultnet8080ambit2feature21590
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[]=
httpappsideaconsultnet8080ambit2feature28958ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature21611ampfeature_uri
s[]=httpappsideaconsultnet8080ambit2feature26221ampfeature_u
ris[]= httpappsideaconsultnet8080ambit2feature21590
Merge mutagenicity data
14Ideaconsult LtdMarch 17 2011
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
15Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
List available models
16Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model
Apply ToxTree module for carcinogenicity
and mutagenicity prediction
17Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model8
bull The benchmatk dataset web address
bull httpappsideaconsultnet8080ambit2dataset2344
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the model URL with parameter
the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset2344rdquo
httpappsideaconsultnet8080ambit2model8
Long running calculations ndash web address
again
18Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2taske75057a0-b005-4c74-
949f-0be9304a3c422model
And the results (a dataset web address)
19Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[
]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2
F82Fpredicted httpappsideaconsultnet8080ambit2
chartpiedataset_uri=httpappsideac
onsultnet8080ambit2dataset2344ampfe
ature_uris[]=httpappsideaconsultnet
8080ambit2feature21858
Building blocks for model creation
20Ideaconsult LtdMarch 17 2011
bull A Datasetndash Datasets can be uploaded (SDF CSV SMI MOL)
bull via HTTP POST to the dataset service
bull Web browser file upload
ndash Existing datasets (uploaded by others) can be used
ndash Dataset Web address assigned
bull Descriptor calculation
bull Learning algorithm
bull Perform predictions
bull Make the model available
The dataset (Caco-2 dataset from a JCIM
publication)
21Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54
bull httpappsideaconsultnet8080ambit2dataset54metadata
bull The endpoint (caco2 column)
httpappsideaconsultnet8080ambit2feature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to data processing (eg
Descriptors calculation)
22Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
+ =
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
=
httpmyhostcomdatasetresults
The algorithms (including descriptors
calculation)
23Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithm
Descriptors calculation
24Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmorgopenscience
cdkqsardescriptorsmolecularXLogPDescriptor
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset
2344rdquo
httpappsideaconsultnet8080ambit2algorithmorgopensci
encecdkqsardescriptorsmolecularXLogPDescriptor
Results from descriptors calculation (a
dataset web address)
25Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttp3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F92
Fpredicted
The descriptors are stored under the web address
httpappsideaconsultnet8080ambit2feature22114
prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
prefix ar lthttpappsideaconsultnet8080ambit2referencegt
prefix bx lthttppurlorgnetnknoufnsbibtexgt
prefix rdfs lthttpwwww3org200001rdf-schemagt
prefix am lthttpappsideaconsultnet8080ambit2modelgt
prefix owl lthttpwwww3org200207owlgt
prefix xsd lthttpwwww3org2001XMLSchemagt
prefix ac lthttpappsideaconsultnet8080ambit2compoundgt
prefix ad lthttpappsideaconsultnet8080ambit2datasetgt
prefix rdf lthttpwwww3org19990222-rdf-syntax-nsgt
prefix ag lthttpappsideaconsultnet8080ambit2algorithmgt
prefix af lthttpappsideaconsultnet8080ambit2featuregt
otAlgorithm
a owlClass
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
af22114
a otFeature otNumericFeature
dccreator httpwwwblueobeliskorgontologieschemoinformatics-algorithmsxlogP
dctitle XLogP
othasSource lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
otunits
= oteeOctanol-water_partition_coefficient_Kow
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
a otAlgorithm
Merge descriptor with activity ndash dataset
with a web address again
26Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=httpap
psideaconsultnet8080ambit2feature22213ampfeature_uris[]=httpappside
aconsultnet8080ambit2feature22200
httpappsideaconsultnet8080ambit2
chartxydataset_uri=httpappsideaco
nsultnet8080ambit2dataset54ampfeatur
e_uris[]=httpappsideaconsultnet8080
ambit2feature22213ampfeature_uris[]=ht
tpappsideaconsultnet8080ambit2f
eature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to models creation
27Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+=
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
httpmyhostcommodelpredictivemodel1
Build a regression model
28Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmLR
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset54rdquo ndashd
ldquoprediction_feature=
httpappsideaconsultnet8080ambit2feature22200 ldquo
httpappsideaconsultnet8080ambit2algorithmLR
The model
29Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2model57
Web address of results could be retrieved
httpappsideaconsultnet8080ambit2model57predicted in
this case it is a the web address
httpappsideaconsultnet8080ambit2feature28963
Web address of X variables could be retrieved
viahttpappsideaconsultnet8080ambit2model57independent
in this case it is a the web address of
httpappsideaconsultnet8080ambit2feature22213
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
Overview of OpenTox API (Application Programming Interface)
7
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Ontology
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
AppDomain
GET
POST
PUT
DELETEValidation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETE
bullThe way applications talk to each other
bullThe way developers talk to applications
CompoundData
httpmyhostcomfeature21580
httpmyhostcomfeature21589
httpmyhostcomfeature21573
httpmyhostcomfeature21576
httpmyhostcomfeature21588
httpmyhostcomfeature21858
httpmyhostcomfeature22114
httpmyhostcomcompound413
NN-dimethyl-4-aminoazobenzene
CN(C1=CC=C(C=C1)N=NC2=CC=CC=C2)C
3 331 2253 YES 3123
httpmyhostcomcompound44497
4-
acetamidofl
uorene O=C(Nc3c2c1ccccc1Cc2ccc3)C
1 NP 22328 YES 2085
hellip hellip hellip hellip hellip hellip hellip hellip
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
All columns have explicit and machine readable pointers to
originating algorithms models or data
Everything described by W3C RDF (Resource Description framework)
representation
OpenTox datasets Unified access to data
8Ideaconsult LtdMarch 17 2011
httpmyhostcomfeature21573af21573
a otFeature otNumericFeature otNominalFeature
dccreator
httpwwwepagovNCCTdsstoxsdf_isscan_externalhtml
dctitle Canc
othasSource ISSCAN_v3a_1153_19Sept081222179139sdf
= oteeCarcinogenicity
httpmyhostcomfeature21858dctitle Structural Alert for genotoxic carcinogenicity
othasSource
lthttpmyhostcomalgorithmBenigni+2F+Bossa+rul
ebase+28for+mutagenicity+and+carcinogenicitygt
httpmyhostcomfeature22114a otFeature otNumericFeature
dccreator
httpwwwblueobeliskorgontologieschemoinformatics-
algorithmsxlogP
dctitle XLogP
othasSource
lthttpmyhostcomalgorithmorgopensciencecdkqsardescriptors
molecularXLogPDescriptorgt
= oteeOctanol-water_partition_coefficient_Kow
bull Ontologies are critical to unambiguously describe data ndash Opentoxowl
ndash Blue Obelisk algorithm ontology (cheminformatics algorithms)
ndash OpenTox algotihm types ontology
ndash OpenTox endpoints ontology based on ECHA endpoints classification
ndash Specific endpoints ontologies developed by OpenTox partners with toxicology
expertise
ndash Existing biomedical ontologies
bull Datasets can be easily merged compared and calculations
reproduced regardless of their physical place
bull OWL sameAs construct can be used to denote two links point to the
same object
bull Authentication and authorization to protect sensitive data
Uniform access to the data
9Ideaconsult LtdMarch 17 2011
bull Datasets can be easily merged compared and calculations
reproduced regardless of their physical place
bull The dataset service offers property compound substructure and
similarity searches via uniform OpenTox Application Programming
Interface
Uniform access to the data
10Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset2344 (the dataset)
bull httpappsideaconsultnet8080ambit2dataset2344metadata
(metadata obviously)
Example mutagenicity dataset
11Ideaconsult LtdMarch 17 2011
Example mutagenicity dataset
12Ideaconsult LtdMarch 17 2011
bull Activity column (httpappsideaconsultnet8080ambit2feature28958)prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
hellip
prefix af lthttpappsideaconsultnet8080ambit2featuregt
af28958
a otFeature otNumericFeature
dccreator 1941410136
dctitle Activity
othasSource tox_benchmark_N6512sdf
otunits
= oteeMutagenicity
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
Query Is there other mutagenicity data
available
13Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2featuresameas=http3A2F2Fwww
opentoxorg2FechaEndpointsowl23Mutagenicity
httpappsideaconsultnet8080ambit2feature21611
httpappsideaconsultnet8080ambit2feature26221
httpappsideaconsultnet8080ambit2feature28958
httpappsideaconsultnet8080ambit2feature21590
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[]=
httpappsideaconsultnet8080ambit2feature28958ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature21611ampfeature_uri
s[]=httpappsideaconsultnet8080ambit2feature26221ampfeature_u
ris[]= httpappsideaconsultnet8080ambit2feature21590
Merge mutagenicity data
14Ideaconsult LtdMarch 17 2011
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
15Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
List available models
16Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model
Apply ToxTree module for carcinogenicity
and mutagenicity prediction
17Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model8
bull The benchmatk dataset web address
bull httpappsideaconsultnet8080ambit2dataset2344
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the model URL with parameter
the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset2344rdquo
httpappsideaconsultnet8080ambit2model8
Long running calculations ndash web address
again
18Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2taske75057a0-b005-4c74-
949f-0be9304a3c422model
And the results (a dataset web address)
19Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[
]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2
F82Fpredicted httpappsideaconsultnet8080ambit2
chartpiedataset_uri=httpappsideac
onsultnet8080ambit2dataset2344ampfe
ature_uris[]=httpappsideaconsultnet
8080ambit2feature21858
Building blocks for model creation
20Ideaconsult LtdMarch 17 2011
bull A Datasetndash Datasets can be uploaded (SDF CSV SMI MOL)
bull via HTTP POST to the dataset service
bull Web browser file upload
ndash Existing datasets (uploaded by others) can be used
ndash Dataset Web address assigned
bull Descriptor calculation
bull Learning algorithm
bull Perform predictions
bull Make the model available
The dataset (Caco-2 dataset from a JCIM
publication)
21Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54
bull httpappsideaconsultnet8080ambit2dataset54metadata
bull The endpoint (caco2 column)
httpappsideaconsultnet8080ambit2feature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to data processing (eg
Descriptors calculation)
22Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
+ =
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
=
httpmyhostcomdatasetresults
The algorithms (including descriptors
calculation)
23Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithm
Descriptors calculation
24Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmorgopenscience
cdkqsardescriptorsmolecularXLogPDescriptor
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset
2344rdquo
httpappsideaconsultnet8080ambit2algorithmorgopensci
encecdkqsardescriptorsmolecularXLogPDescriptor
Results from descriptors calculation (a
dataset web address)
25Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttp3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F92
Fpredicted
The descriptors are stored under the web address
httpappsideaconsultnet8080ambit2feature22114
prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
prefix ar lthttpappsideaconsultnet8080ambit2referencegt
prefix bx lthttppurlorgnetnknoufnsbibtexgt
prefix rdfs lthttpwwww3org200001rdf-schemagt
prefix am lthttpappsideaconsultnet8080ambit2modelgt
prefix owl lthttpwwww3org200207owlgt
prefix xsd lthttpwwww3org2001XMLSchemagt
prefix ac lthttpappsideaconsultnet8080ambit2compoundgt
prefix ad lthttpappsideaconsultnet8080ambit2datasetgt
prefix rdf lthttpwwww3org19990222-rdf-syntax-nsgt
prefix ag lthttpappsideaconsultnet8080ambit2algorithmgt
prefix af lthttpappsideaconsultnet8080ambit2featuregt
otAlgorithm
a owlClass
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
af22114
a otFeature otNumericFeature
dccreator httpwwwblueobeliskorgontologieschemoinformatics-algorithmsxlogP
dctitle XLogP
othasSource lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
otunits
= oteeOctanol-water_partition_coefficient_Kow
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
a otAlgorithm
Merge descriptor with activity ndash dataset
with a web address again
26Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=httpap
psideaconsultnet8080ambit2feature22213ampfeature_uris[]=httpappside
aconsultnet8080ambit2feature22200
httpappsideaconsultnet8080ambit2
chartxydataset_uri=httpappsideaco
nsultnet8080ambit2dataset54ampfeatur
e_uris[]=httpappsideaconsultnet8080
ambit2feature22213ampfeature_uris[]=ht
tpappsideaconsultnet8080ambit2f
eature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to models creation
27Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+=
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
httpmyhostcommodelpredictivemodel1
Build a regression model
28Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmLR
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset54rdquo ndashd
ldquoprediction_feature=
httpappsideaconsultnet8080ambit2feature22200 ldquo
httpappsideaconsultnet8080ambit2algorithmLR
The model
29Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2model57
Web address of results could be retrieved
httpappsideaconsultnet8080ambit2model57predicted in
this case it is a the web address
httpappsideaconsultnet8080ambit2feature28963
Web address of X variables could be retrieved
viahttpappsideaconsultnet8080ambit2model57independent
in this case it is a the web address of
httpappsideaconsultnet8080ambit2feature22213
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
CompoundData
httpmyhostcomfeature21580
httpmyhostcomfeature21589
httpmyhostcomfeature21573
httpmyhostcomfeature21576
httpmyhostcomfeature21588
httpmyhostcomfeature21858
httpmyhostcomfeature22114
httpmyhostcomcompound413
NN-dimethyl-4-aminoazobenzene
CN(C1=CC=C(C=C1)N=NC2=CC=CC=C2)C
3 331 2253 YES 3123
httpmyhostcomcompound44497
4-
acetamidofl
uorene O=C(Nc3c2c1ccccc1Cc2ccc3)C
1 NP 22328 YES 2085
hellip hellip hellip hellip hellip hellip hellip hellip
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
All columns have explicit and machine readable pointers to
originating algorithms models or data
Everything described by W3C RDF (Resource Description framework)
representation
OpenTox datasets Unified access to data
8Ideaconsult LtdMarch 17 2011
httpmyhostcomfeature21573af21573
a otFeature otNumericFeature otNominalFeature
dccreator
httpwwwepagovNCCTdsstoxsdf_isscan_externalhtml
dctitle Canc
othasSource ISSCAN_v3a_1153_19Sept081222179139sdf
= oteeCarcinogenicity
httpmyhostcomfeature21858dctitle Structural Alert for genotoxic carcinogenicity
othasSource
lthttpmyhostcomalgorithmBenigni+2F+Bossa+rul
ebase+28for+mutagenicity+and+carcinogenicitygt
httpmyhostcomfeature22114a otFeature otNumericFeature
dccreator
httpwwwblueobeliskorgontologieschemoinformatics-
algorithmsxlogP
dctitle XLogP
othasSource
lthttpmyhostcomalgorithmorgopensciencecdkqsardescriptors
molecularXLogPDescriptorgt
= oteeOctanol-water_partition_coefficient_Kow
bull Ontologies are critical to unambiguously describe data ndash Opentoxowl
ndash Blue Obelisk algorithm ontology (cheminformatics algorithms)
ndash OpenTox algotihm types ontology
ndash OpenTox endpoints ontology based on ECHA endpoints classification
ndash Specific endpoints ontologies developed by OpenTox partners with toxicology
expertise
ndash Existing biomedical ontologies
bull Datasets can be easily merged compared and calculations
reproduced regardless of their physical place
bull OWL sameAs construct can be used to denote two links point to the
same object
bull Authentication and authorization to protect sensitive data
Uniform access to the data
9Ideaconsult LtdMarch 17 2011
bull Datasets can be easily merged compared and calculations
reproduced regardless of their physical place
bull The dataset service offers property compound substructure and
similarity searches via uniform OpenTox Application Programming
Interface
Uniform access to the data
10Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset2344 (the dataset)
bull httpappsideaconsultnet8080ambit2dataset2344metadata
(metadata obviously)
Example mutagenicity dataset
11Ideaconsult LtdMarch 17 2011
Example mutagenicity dataset
12Ideaconsult LtdMarch 17 2011
bull Activity column (httpappsideaconsultnet8080ambit2feature28958)prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
hellip
prefix af lthttpappsideaconsultnet8080ambit2featuregt
af28958
a otFeature otNumericFeature
dccreator 1941410136
dctitle Activity
othasSource tox_benchmark_N6512sdf
otunits
= oteeMutagenicity
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
Query Is there other mutagenicity data
available
13Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2featuresameas=http3A2F2Fwww
opentoxorg2FechaEndpointsowl23Mutagenicity
httpappsideaconsultnet8080ambit2feature21611
httpappsideaconsultnet8080ambit2feature26221
httpappsideaconsultnet8080ambit2feature28958
httpappsideaconsultnet8080ambit2feature21590
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[]=
httpappsideaconsultnet8080ambit2feature28958ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature21611ampfeature_uri
s[]=httpappsideaconsultnet8080ambit2feature26221ampfeature_u
ris[]= httpappsideaconsultnet8080ambit2feature21590
Merge mutagenicity data
14Ideaconsult LtdMarch 17 2011
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
15Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
List available models
16Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model
Apply ToxTree module for carcinogenicity
and mutagenicity prediction
17Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model8
bull The benchmatk dataset web address
bull httpappsideaconsultnet8080ambit2dataset2344
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the model URL with parameter
the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset2344rdquo
httpappsideaconsultnet8080ambit2model8
Long running calculations ndash web address
again
18Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2taske75057a0-b005-4c74-
949f-0be9304a3c422model
And the results (a dataset web address)
19Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[
]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2
F82Fpredicted httpappsideaconsultnet8080ambit2
chartpiedataset_uri=httpappsideac
onsultnet8080ambit2dataset2344ampfe
ature_uris[]=httpappsideaconsultnet
8080ambit2feature21858
Building blocks for model creation
20Ideaconsult LtdMarch 17 2011
bull A Datasetndash Datasets can be uploaded (SDF CSV SMI MOL)
bull via HTTP POST to the dataset service
bull Web browser file upload
ndash Existing datasets (uploaded by others) can be used
ndash Dataset Web address assigned
bull Descriptor calculation
bull Learning algorithm
bull Perform predictions
bull Make the model available
The dataset (Caco-2 dataset from a JCIM
publication)
21Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54
bull httpappsideaconsultnet8080ambit2dataset54metadata
bull The endpoint (caco2 column)
httpappsideaconsultnet8080ambit2feature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to data processing (eg
Descriptors calculation)
22Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
+ =
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
=
httpmyhostcomdatasetresults
The algorithms (including descriptors
calculation)
23Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithm
Descriptors calculation
24Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmorgopenscience
cdkqsardescriptorsmolecularXLogPDescriptor
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset
2344rdquo
httpappsideaconsultnet8080ambit2algorithmorgopensci
encecdkqsardescriptorsmolecularXLogPDescriptor
Results from descriptors calculation (a
dataset web address)
25Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttp3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F92
Fpredicted
The descriptors are stored under the web address
httpappsideaconsultnet8080ambit2feature22114
prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
prefix ar lthttpappsideaconsultnet8080ambit2referencegt
prefix bx lthttppurlorgnetnknoufnsbibtexgt
prefix rdfs lthttpwwww3org200001rdf-schemagt
prefix am lthttpappsideaconsultnet8080ambit2modelgt
prefix owl lthttpwwww3org200207owlgt
prefix xsd lthttpwwww3org2001XMLSchemagt
prefix ac lthttpappsideaconsultnet8080ambit2compoundgt
prefix ad lthttpappsideaconsultnet8080ambit2datasetgt
prefix rdf lthttpwwww3org19990222-rdf-syntax-nsgt
prefix ag lthttpappsideaconsultnet8080ambit2algorithmgt
prefix af lthttpappsideaconsultnet8080ambit2featuregt
otAlgorithm
a owlClass
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
af22114
a otFeature otNumericFeature
dccreator httpwwwblueobeliskorgontologieschemoinformatics-algorithmsxlogP
dctitle XLogP
othasSource lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
otunits
= oteeOctanol-water_partition_coefficient_Kow
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
a otAlgorithm
Merge descriptor with activity ndash dataset
with a web address again
26Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=httpap
psideaconsultnet8080ambit2feature22213ampfeature_uris[]=httpappside
aconsultnet8080ambit2feature22200
httpappsideaconsultnet8080ambit2
chartxydataset_uri=httpappsideaco
nsultnet8080ambit2dataset54ampfeatur
e_uris[]=httpappsideaconsultnet8080
ambit2feature22213ampfeature_uris[]=ht
tpappsideaconsultnet8080ambit2f
eature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to models creation
27Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+=
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
httpmyhostcommodelpredictivemodel1
Build a regression model
28Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmLR
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset54rdquo ndashd
ldquoprediction_feature=
httpappsideaconsultnet8080ambit2feature22200 ldquo
httpappsideaconsultnet8080ambit2algorithmLR
The model
29Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2model57
Web address of results could be retrieved
httpappsideaconsultnet8080ambit2model57predicted in
this case it is a the web address
httpappsideaconsultnet8080ambit2feature28963
Web address of X variables could be retrieved
viahttpappsideaconsultnet8080ambit2model57independent
in this case it is a the web address of
httpappsideaconsultnet8080ambit2feature22213
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
bull Ontologies are critical to unambiguously describe data ndash Opentoxowl
ndash Blue Obelisk algorithm ontology (cheminformatics algorithms)
ndash OpenTox algotihm types ontology
ndash OpenTox endpoints ontology based on ECHA endpoints classification
ndash Specific endpoints ontologies developed by OpenTox partners with toxicology
expertise
ndash Existing biomedical ontologies
bull Datasets can be easily merged compared and calculations
reproduced regardless of their physical place
bull OWL sameAs construct can be used to denote two links point to the
same object
bull Authentication and authorization to protect sensitive data
Uniform access to the data
9Ideaconsult LtdMarch 17 2011
bull Datasets can be easily merged compared and calculations
reproduced regardless of their physical place
bull The dataset service offers property compound substructure and
similarity searches via uniform OpenTox Application Programming
Interface
Uniform access to the data
10Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset2344 (the dataset)
bull httpappsideaconsultnet8080ambit2dataset2344metadata
(metadata obviously)
Example mutagenicity dataset
11Ideaconsult LtdMarch 17 2011
Example mutagenicity dataset
12Ideaconsult LtdMarch 17 2011
bull Activity column (httpappsideaconsultnet8080ambit2feature28958)prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
hellip
prefix af lthttpappsideaconsultnet8080ambit2featuregt
af28958
a otFeature otNumericFeature
dccreator 1941410136
dctitle Activity
othasSource tox_benchmark_N6512sdf
otunits
= oteeMutagenicity
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
Query Is there other mutagenicity data
available
13Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2featuresameas=http3A2F2Fwww
opentoxorg2FechaEndpointsowl23Mutagenicity
httpappsideaconsultnet8080ambit2feature21611
httpappsideaconsultnet8080ambit2feature26221
httpappsideaconsultnet8080ambit2feature28958
httpappsideaconsultnet8080ambit2feature21590
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[]=
httpappsideaconsultnet8080ambit2feature28958ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature21611ampfeature_uri
s[]=httpappsideaconsultnet8080ambit2feature26221ampfeature_u
ris[]= httpappsideaconsultnet8080ambit2feature21590
Merge mutagenicity data
14Ideaconsult LtdMarch 17 2011
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
15Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
List available models
16Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model
Apply ToxTree module for carcinogenicity
and mutagenicity prediction
17Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model8
bull The benchmatk dataset web address
bull httpappsideaconsultnet8080ambit2dataset2344
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the model URL with parameter
the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset2344rdquo
httpappsideaconsultnet8080ambit2model8
Long running calculations ndash web address
again
18Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2taske75057a0-b005-4c74-
949f-0be9304a3c422model
And the results (a dataset web address)
19Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[
]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2
F82Fpredicted httpappsideaconsultnet8080ambit2
chartpiedataset_uri=httpappsideac
onsultnet8080ambit2dataset2344ampfe
ature_uris[]=httpappsideaconsultnet
8080ambit2feature21858
Building blocks for model creation
20Ideaconsult LtdMarch 17 2011
bull A Datasetndash Datasets can be uploaded (SDF CSV SMI MOL)
bull via HTTP POST to the dataset service
bull Web browser file upload
ndash Existing datasets (uploaded by others) can be used
ndash Dataset Web address assigned
bull Descriptor calculation
bull Learning algorithm
bull Perform predictions
bull Make the model available
The dataset (Caco-2 dataset from a JCIM
publication)
21Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54
bull httpappsideaconsultnet8080ambit2dataset54metadata
bull The endpoint (caco2 column)
httpappsideaconsultnet8080ambit2feature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to data processing (eg
Descriptors calculation)
22Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
+ =
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
=
httpmyhostcomdatasetresults
The algorithms (including descriptors
calculation)
23Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithm
Descriptors calculation
24Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmorgopenscience
cdkqsardescriptorsmolecularXLogPDescriptor
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset
2344rdquo
httpappsideaconsultnet8080ambit2algorithmorgopensci
encecdkqsardescriptorsmolecularXLogPDescriptor
Results from descriptors calculation (a
dataset web address)
25Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttp3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F92
Fpredicted
The descriptors are stored under the web address
httpappsideaconsultnet8080ambit2feature22114
prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
prefix ar lthttpappsideaconsultnet8080ambit2referencegt
prefix bx lthttppurlorgnetnknoufnsbibtexgt
prefix rdfs lthttpwwww3org200001rdf-schemagt
prefix am lthttpappsideaconsultnet8080ambit2modelgt
prefix owl lthttpwwww3org200207owlgt
prefix xsd lthttpwwww3org2001XMLSchemagt
prefix ac lthttpappsideaconsultnet8080ambit2compoundgt
prefix ad lthttpappsideaconsultnet8080ambit2datasetgt
prefix rdf lthttpwwww3org19990222-rdf-syntax-nsgt
prefix ag lthttpappsideaconsultnet8080ambit2algorithmgt
prefix af lthttpappsideaconsultnet8080ambit2featuregt
otAlgorithm
a owlClass
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
af22114
a otFeature otNumericFeature
dccreator httpwwwblueobeliskorgontologieschemoinformatics-algorithmsxlogP
dctitle XLogP
othasSource lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
otunits
= oteeOctanol-water_partition_coefficient_Kow
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
a otAlgorithm
Merge descriptor with activity ndash dataset
with a web address again
26Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=httpap
psideaconsultnet8080ambit2feature22213ampfeature_uris[]=httpappside
aconsultnet8080ambit2feature22200
httpappsideaconsultnet8080ambit2
chartxydataset_uri=httpappsideaco
nsultnet8080ambit2dataset54ampfeatur
e_uris[]=httpappsideaconsultnet8080
ambit2feature22213ampfeature_uris[]=ht
tpappsideaconsultnet8080ambit2f
eature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to models creation
27Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+=
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
httpmyhostcommodelpredictivemodel1
Build a regression model
28Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmLR
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset54rdquo ndashd
ldquoprediction_feature=
httpappsideaconsultnet8080ambit2feature22200 ldquo
httpappsideaconsultnet8080ambit2algorithmLR
The model
29Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2model57
Web address of results could be retrieved
httpappsideaconsultnet8080ambit2model57predicted in
this case it is a the web address
httpappsideaconsultnet8080ambit2feature28963
Web address of X variables could be retrieved
viahttpappsideaconsultnet8080ambit2model57independent
in this case it is a the web address of
httpappsideaconsultnet8080ambit2feature22213
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
bull Datasets can be easily merged compared and calculations
reproduced regardless of their physical place
bull The dataset service offers property compound substructure and
similarity searches via uniform OpenTox Application Programming
Interface
Uniform access to the data
10Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset2344 (the dataset)
bull httpappsideaconsultnet8080ambit2dataset2344metadata
(metadata obviously)
Example mutagenicity dataset
11Ideaconsult LtdMarch 17 2011
Example mutagenicity dataset
12Ideaconsult LtdMarch 17 2011
bull Activity column (httpappsideaconsultnet8080ambit2feature28958)prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
hellip
prefix af lthttpappsideaconsultnet8080ambit2featuregt
af28958
a otFeature otNumericFeature
dccreator 1941410136
dctitle Activity
othasSource tox_benchmark_N6512sdf
otunits
= oteeMutagenicity
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
Query Is there other mutagenicity data
available
13Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2featuresameas=http3A2F2Fwww
opentoxorg2FechaEndpointsowl23Mutagenicity
httpappsideaconsultnet8080ambit2feature21611
httpappsideaconsultnet8080ambit2feature26221
httpappsideaconsultnet8080ambit2feature28958
httpappsideaconsultnet8080ambit2feature21590
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[]=
httpappsideaconsultnet8080ambit2feature28958ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature21611ampfeature_uri
s[]=httpappsideaconsultnet8080ambit2feature26221ampfeature_u
ris[]= httpappsideaconsultnet8080ambit2feature21590
Merge mutagenicity data
14Ideaconsult LtdMarch 17 2011
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
15Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
List available models
16Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model
Apply ToxTree module for carcinogenicity
and mutagenicity prediction
17Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model8
bull The benchmatk dataset web address
bull httpappsideaconsultnet8080ambit2dataset2344
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the model URL with parameter
the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset2344rdquo
httpappsideaconsultnet8080ambit2model8
Long running calculations ndash web address
again
18Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2taske75057a0-b005-4c74-
949f-0be9304a3c422model
And the results (a dataset web address)
19Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[
]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2
F82Fpredicted httpappsideaconsultnet8080ambit2
chartpiedataset_uri=httpappsideac
onsultnet8080ambit2dataset2344ampfe
ature_uris[]=httpappsideaconsultnet
8080ambit2feature21858
Building blocks for model creation
20Ideaconsult LtdMarch 17 2011
bull A Datasetndash Datasets can be uploaded (SDF CSV SMI MOL)
bull via HTTP POST to the dataset service
bull Web browser file upload
ndash Existing datasets (uploaded by others) can be used
ndash Dataset Web address assigned
bull Descriptor calculation
bull Learning algorithm
bull Perform predictions
bull Make the model available
The dataset (Caco-2 dataset from a JCIM
publication)
21Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54
bull httpappsideaconsultnet8080ambit2dataset54metadata
bull The endpoint (caco2 column)
httpappsideaconsultnet8080ambit2feature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to data processing (eg
Descriptors calculation)
22Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
+ =
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
=
httpmyhostcomdatasetresults
The algorithms (including descriptors
calculation)
23Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithm
Descriptors calculation
24Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmorgopenscience
cdkqsardescriptorsmolecularXLogPDescriptor
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset
2344rdquo
httpappsideaconsultnet8080ambit2algorithmorgopensci
encecdkqsardescriptorsmolecularXLogPDescriptor
Results from descriptors calculation (a
dataset web address)
25Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttp3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F92
Fpredicted
The descriptors are stored under the web address
httpappsideaconsultnet8080ambit2feature22114
prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
prefix ar lthttpappsideaconsultnet8080ambit2referencegt
prefix bx lthttppurlorgnetnknoufnsbibtexgt
prefix rdfs lthttpwwww3org200001rdf-schemagt
prefix am lthttpappsideaconsultnet8080ambit2modelgt
prefix owl lthttpwwww3org200207owlgt
prefix xsd lthttpwwww3org2001XMLSchemagt
prefix ac lthttpappsideaconsultnet8080ambit2compoundgt
prefix ad lthttpappsideaconsultnet8080ambit2datasetgt
prefix rdf lthttpwwww3org19990222-rdf-syntax-nsgt
prefix ag lthttpappsideaconsultnet8080ambit2algorithmgt
prefix af lthttpappsideaconsultnet8080ambit2featuregt
otAlgorithm
a owlClass
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
af22114
a otFeature otNumericFeature
dccreator httpwwwblueobeliskorgontologieschemoinformatics-algorithmsxlogP
dctitle XLogP
othasSource lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
otunits
= oteeOctanol-water_partition_coefficient_Kow
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
a otAlgorithm
Merge descriptor with activity ndash dataset
with a web address again
26Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=httpap
psideaconsultnet8080ambit2feature22213ampfeature_uris[]=httpappside
aconsultnet8080ambit2feature22200
httpappsideaconsultnet8080ambit2
chartxydataset_uri=httpappsideaco
nsultnet8080ambit2dataset54ampfeatur
e_uris[]=httpappsideaconsultnet8080
ambit2feature22213ampfeature_uris[]=ht
tpappsideaconsultnet8080ambit2f
eature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to models creation
27Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+=
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
httpmyhostcommodelpredictivemodel1
Build a regression model
28Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmLR
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset54rdquo ndashd
ldquoprediction_feature=
httpappsideaconsultnet8080ambit2feature22200 ldquo
httpappsideaconsultnet8080ambit2algorithmLR
The model
29Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2model57
Web address of results could be retrieved
httpappsideaconsultnet8080ambit2model57predicted in
this case it is a the web address
httpappsideaconsultnet8080ambit2feature28963
Web address of X variables could be retrieved
viahttpappsideaconsultnet8080ambit2model57independent
in this case it is a the web address of
httpappsideaconsultnet8080ambit2feature22213
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
bull httpappsideaconsultnet8080ambit2dataset2344 (the dataset)
bull httpappsideaconsultnet8080ambit2dataset2344metadata
(metadata obviously)
Example mutagenicity dataset
11Ideaconsult LtdMarch 17 2011
Example mutagenicity dataset
12Ideaconsult LtdMarch 17 2011
bull Activity column (httpappsideaconsultnet8080ambit2feature28958)prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
hellip
prefix af lthttpappsideaconsultnet8080ambit2featuregt
af28958
a otFeature otNumericFeature
dccreator 1941410136
dctitle Activity
othasSource tox_benchmark_N6512sdf
otunits
= oteeMutagenicity
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
Query Is there other mutagenicity data
available
13Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2featuresameas=http3A2F2Fwww
opentoxorg2FechaEndpointsowl23Mutagenicity
httpappsideaconsultnet8080ambit2feature21611
httpappsideaconsultnet8080ambit2feature26221
httpappsideaconsultnet8080ambit2feature28958
httpappsideaconsultnet8080ambit2feature21590
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[]=
httpappsideaconsultnet8080ambit2feature28958ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature21611ampfeature_uri
s[]=httpappsideaconsultnet8080ambit2feature26221ampfeature_u
ris[]= httpappsideaconsultnet8080ambit2feature21590
Merge mutagenicity data
14Ideaconsult LtdMarch 17 2011
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
15Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
List available models
16Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model
Apply ToxTree module for carcinogenicity
and mutagenicity prediction
17Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model8
bull The benchmatk dataset web address
bull httpappsideaconsultnet8080ambit2dataset2344
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the model URL with parameter
the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset2344rdquo
httpappsideaconsultnet8080ambit2model8
Long running calculations ndash web address
again
18Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2taske75057a0-b005-4c74-
949f-0be9304a3c422model
And the results (a dataset web address)
19Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[
]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2
F82Fpredicted httpappsideaconsultnet8080ambit2
chartpiedataset_uri=httpappsideac
onsultnet8080ambit2dataset2344ampfe
ature_uris[]=httpappsideaconsultnet
8080ambit2feature21858
Building blocks for model creation
20Ideaconsult LtdMarch 17 2011
bull A Datasetndash Datasets can be uploaded (SDF CSV SMI MOL)
bull via HTTP POST to the dataset service
bull Web browser file upload
ndash Existing datasets (uploaded by others) can be used
ndash Dataset Web address assigned
bull Descriptor calculation
bull Learning algorithm
bull Perform predictions
bull Make the model available
The dataset (Caco-2 dataset from a JCIM
publication)
21Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54
bull httpappsideaconsultnet8080ambit2dataset54metadata
bull The endpoint (caco2 column)
httpappsideaconsultnet8080ambit2feature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to data processing (eg
Descriptors calculation)
22Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
+ =
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
=
httpmyhostcomdatasetresults
The algorithms (including descriptors
calculation)
23Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithm
Descriptors calculation
24Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmorgopenscience
cdkqsardescriptorsmolecularXLogPDescriptor
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset
2344rdquo
httpappsideaconsultnet8080ambit2algorithmorgopensci
encecdkqsardescriptorsmolecularXLogPDescriptor
Results from descriptors calculation (a
dataset web address)
25Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttp3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F92
Fpredicted
The descriptors are stored under the web address
httpappsideaconsultnet8080ambit2feature22114
prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
prefix ar lthttpappsideaconsultnet8080ambit2referencegt
prefix bx lthttppurlorgnetnknoufnsbibtexgt
prefix rdfs lthttpwwww3org200001rdf-schemagt
prefix am lthttpappsideaconsultnet8080ambit2modelgt
prefix owl lthttpwwww3org200207owlgt
prefix xsd lthttpwwww3org2001XMLSchemagt
prefix ac lthttpappsideaconsultnet8080ambit2compoundgt
prefix ad lthttpappsideaconsultnet8080ambit2datasetgt
prefix rdf lthttpwwww3org19990222-rdf-syntax-nsgt
prefix ag lthttpappsideaconsultnet8080ambit2algorithmgt
prefix af lthttpappsideaconsultnet8080ambit2featuregt
otAlgorithm
a owlClass
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
af22114
a otFeature otNumericFeature
dccreator httpwwwblueobeliskorgontologieschemoinformatics-algorithmsxlogP
dctitle XLogP
othasSource lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
otunits
= oteeOctanol-water_partition_coefficient_Kow
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
a otAlgorithm
Merge descriptor with activity ndash dataset
with a web address again
26Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=httpap
psideaconsultnet8080ambit2feature22213ampfeature_uris[]=httpappside
aconsultnet8080ambit2feature22200
httpappsideaconsultnet8080ambit2
chartxydataset_uri=httpappsideaco
nsultnet8080ambit2dataset54ampfeatur
e_uris[]=httpappsideaconsultnet8080
ambit2feature22213ampfeature_uris[]=ht
tpappsideaconsultnet8080ambit2f
eature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to models creation
27Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+=
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
httpmyhostcommodelpredictivemodel1
Build a regression model
28Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmLR
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset54rdquo ndashd
ldquoprediction_feature=
httpappsideaconsultnet8080ambit2feature22200 ldquo
httpappsideaconsultnet8080ambit2algorithmLR
The model
29Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2model57
Web address of results could be retrieved
httpappsideaconsultnet8080ambit2model57predicted in
this case it is a the web address
httpappsideaconsultnet8080ambit2feature28963
Web address of X variables could be retrieved
viahttpappsideaconsultnet8080ambit2model57independent
in this case it is a the web address of
httpappsideaconsultnet8080ambit2feature22213
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
Example mutagenicity dataset
12Ideaconsult LtdMarch 17 2011
bull Activity column (httpappsideaconsultnet8080ambit2feature28958)prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
hellip
prefix af lthttpappsideaconsultnet8080ambit2featuregt
af28958
a otFeature otNumericFeature
dccreator 1941410136
dctitle Activity
othasSource tox_benchmark_N6512sdf
otunits
= oteeMutagenicity
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
Query Is there other mutagenicity data
available
13Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2featuresameas=http3A2F2Fwww
opentoxorg2FechaEndpointsowl23Mutagenicity
httpappsideaconsultnet8080ambit2feature21611
httpappsideaconsultnet8080ambit2feature26221
httpappsideaconsultnet8080ambit2feature28958
httpappsideaconsultnet8080ambit2feature21590
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[]=
httpappsideaconsultnet8080ambit2feature28958ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature21611ampfeature_uri
s[]=httpappsideaconsultnet8080ambit2feature26221ampfeature_u
ris[]= httpappsideaconsultnet8080ambit2feature21590
Merge mutagenicity data
14Ideaconsult LtdMarch 17 2011
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
15Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
List available models
16Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model
Apply ToxTree module for carcinogenicity
and mutagenicity prediction
17Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model8
bull The benchmatk dataset web address
bull httpappsideaconsultnet8080ambit2dataset2344
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the model URL with parameter
the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset2344rdquo
httpappsideaconsultnet8080ambit2model8
Long running calculations ndash web address
again
18Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2taske75057a0-b005-4c74-
949f-0be9304a3c422model
And the results (a dataset web address)
19Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[
]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2
F82Fpredicted httpappsideaconsultnet8080ambit2
chartpiedataset_uri=httpappsideac
onsultnet8080ambit2dataset2344ampfe
ature_uris[]=httpappsideaconsultnet
8080ambit2feature21858
Building blocks for model creation
20Ideaconsult LtdMarch 17 2011
bull A Datasetndash Datasets can be uploaded (SDF CSV SMI MOL)
bull via HTTP POST to the dataset service
bull Web browser file upload
ndash Existing datasets (uploaded by others) can be used
ndash Dataset Web address assigned
bull Descriptor calculation
bull Learning algorithm
bull Perform predictions
bull Make the model available
The dataset (Caco-2 dataset from a JCIM
publication)
21Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54
bull httpappsideaconsultnet8080ambit2dataset54metadata
bull The endpoint (caco2 column)
httpappsideaconsultnet8080ambit2feature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to data processing (eg
Descriptors calculation)
22Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
+ =
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
=
httpmyhostcomdatasetresults
The algorithms (including descriptors
calculation)
23Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithm
Descriptors calculation
24Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmorgopenscience
cdkqsardescriptorsmolecularXLogPDescriptor
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset
2344rdquo
httpappsideaconsultnet8080ambit2algorithmorgopensci
encecdkqsardescriptorsmolecularXLogPDescriptor
Results from descriptors calculation (a
dataset web address)
25Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttp3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F92
Fpredicted
The descriptors are stored under the web address
httpappsideaconsultnet8080ambit2feature22114
prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
prefix ar lthttpappsideaconsultnet8080ambit2referencegt
prefix bx lthttppurlorgnetnknoufnsbibtexgt
prefix rdfs lthttpwwww3org200001rdf-schemagt
prefix am lthttpappsideaconsultnet8080ambit2modelgt
prefix owl lthttpwwww3org200207owlgt
prefix xsd lthttpwwww3org2001XMLSchemagt
prefix ac lthttpappsideaconsultnet8080ambit2compoundgt
prefix ad lthttpappsideaconsultnet8080ambit2datasetgt
prefix rdf lthttpwwww3org19990222-rdf-syntax-nsgt
prefix ag lthttpappsideaconsultnet8080ambit2algorithmgt
prefix af lthttpappsideaconsultnet8080ambit2featuregt
otAlgorithm
a owlClass
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
af22114
a otFeature otNumericFeature
dccreator httpwwwblueobeliskorgontologieschemoinformatics-algorithmsxlogP
dctitle XLogP
othasSource lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
otunits
= oteeOctanol-water_partition_coefficient_Kow
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
a otAlgorithm
Merge descriptor with activity ndash dataset
with a web address again
26Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=httpap
psideaconsultnet8080ambit2feature22213ampfeature_uris[]=httpappside
aconsultnet8080ambit2feature22200
httpappsideaconsultnet8080ambit2
chartxydataset_uri=httpappsideaco
nsultnet8080ambit2dataset54ampfeatur
e_uris[]=httpappsideaconsultnet8080
ambit2feature22213ampfeature_uris[]=ht
tpappsideaconsultnet8080ambit2f
eature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to models creation
27Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+=
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
httpmyhostcommodelpredictivemodel1
Build a regression model
28Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmLR
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset54rdquo ndashd
ldquoprediction_feature=
httpappsideaconsultnet8080ambit2feature22200 ldquo
httpappsideaconsultnet8080ambit2algorithmLR
The model
29Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2model57
Web address of results could be retrieved
httpappsideaconsultnet8080ambit2model57predicted in
this case it is a the web address
httpappsideaconsultnet8080ambit2feature28963
Web address of X variables could be retrieved
viahttpappsideaconsultnet8080ambit2model57independent
in this case it is a the web address of
httpappsideaconsultnet8080ambit2feature22213
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
Query Is there other mutagenicity data
available
13Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2featuresameas=http3A2F2Fwww
opentoxorg2FechaEndpointsowl23Mutagenicity
httpappsideaconsultnet8080ambit2feature21611
httpappsideaconsultnet8080ambit2feature26221
httpappsideaconsultnet8080ambit2feature28958
httpappsideaconsultnet8080ambit2feature21590
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[]=
httpappsideaconsultnet8080ambit2feature28958ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature21611ampfeature_uri
s[]=httpappsideaconsultnet8080ambit2feature26221ampfeature_u
ris[]= httpappsideaconsultnet8080ambit2feature21590
Merge mutagenicity data
14Ideaconsult LtdMarch 17 2011
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
15Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
List available models
16Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model
Apply ToxTree module for carcinogenicity
and mutagenicity prediction
17Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model8
bull The benchmatk dataset web address
bull httpappsideaconsultnet8080ambit2dataset2344
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the model URL with parameter
the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset2344rdquo
httpappsideaconsultnet8080ambit2model8
Long running calculations ndash web address
again
18Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2taske75057a0-b005-4c74-
949f-0be9304a3c422model
And the results (a dataset web address)
19Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[
]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2
F82Fpredicted httpappsideaconsultnet8080ambit2
chartpiedataset_uri=httpappsideac
onsultnet8080ambit2dataset2344ampfe
ature_uris[]=httpappsideaconsultnet
8080ambit2feature21858
Building blocks for model creation
20Ideaconsult LtdMarch 17 2011
bull A Datasetndash Datasets can be uploaded (SDF CSV SMI MOL)
bull via HTTP POST to the dataset service
bull Web browser file upload
ndash Existing datasets (uploaded by others) can be used
ndash Dataset Web address assigned
bull Descriptor calculation
bull Learning algorithm
bull Perform predictions
bull Make the model available
The dataset (Caco-2 dataset from a JCIM
publication)
21Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54
bull httpappsideaconsultnet8080ambit2dataset54metadata
bull The endpoint (caco2 column)
httpappsideaconsultnet8080ambit2feature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to data processing (eg
Descriptors calculation)
22Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
+ =
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
=
httpmyhostcomdatasetresults
The algorithms (including descriptors
calculation)
23Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithm
Descriptors calculation
24Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmorgopenscience
cdkqsardescriptorsmolecularXLogPDescriptor
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset
2344rdquo
httpappsideaconsultnet8080ambit2algorithmorgopensci
encecdkqsardescriptorsmolecularXLogPDescriptor
Results from descriptors calculation (a
dataset web address)
25Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttp3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F92
Fpredicted
The descriptors are stored under the web address
httpappsideaconsultnet8080ambit2feature22114
prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
prefix ar lthttpappsideaconsultnet8080ambit2referencegt
prefix bx lthttppurlorgnetnknoufnsbibtexgt
prefix rdfs lthttpwwww3org200001rdf-schemagt
prefix am lthttpappsideaconsultnet8080ambit2modelgt
prefix owl lthttpwwww3org200207owlgt
prefix xsd lthttpwwww3org2001XMLSchemagt
prefix ac lthttpappsideaconsultnet8080ambit2compoundgt
prefix ad lthttpappsideaconsultnet8080ambit2datasetgt
prefix rdf lthttpwwww3org19990222-rdf-syntax-nsgt
prefix ag lthttpappsideaconsultnet8080ambit2algorithmgt
prefix af lthttpappsideaconsultnet8080ambit2featuregt
otAlgorithm
a owlClass
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
af22114
a otFeature otNumericFeature
dccreator httpwwwblueobeliskorgontologieschemoinformatics-algorithmsxlogP
dctitle XLogP
othasSource lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
otunits
= oteeOctanol-water_partition_coefficient_Kow
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
a otAlgorithm
Merge descriptor with activity ndash dataset
with a web address again
26Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=httpap
psideaconsultnet8080ambit2feature22213ampfeature_uris[]=httpappside
aconsultnet8080ambit2feature22200
httpappsideaconsultnet8080ambit2
chartxydataset_uri=httpappsideaco
nsultnet8080ambit2dataset54ampfeatur
e_uris[]=httpappsideaconsultnet8080
ambit2feature22213ampfeature_uris[]=ht
tpappsideaconsultnet8080ambit2f
eature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to models creation
27Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+=
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
httpmyhostcommodelpredictivemodel1
Build a regression model
28Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmLR
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset54rdquo ndashd
ldquoprediction_feature=
httpappsideaconsultnet8080ambit2feature22200 ldquo
httpappsideaconsultnet8080ambit2algorithmLR
The model
29Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2model57
Web address of results could be retrieved
httpappsideaconsultnet8080ambit2model57predicted in
this case it is a the web address
httpappsideaconsultnet8080ambit2feature28963
Web address of X variables could be retrieved
viahttpappsideaconsultnet8080ambit2model57independent
in this case it is a the web address of
httpappsideaconsultnet8080ambit2feature22213
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[]=
httpappsideaconsultnet8080ambit2feature28958ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature21611ampfeature_uri
s[]=httpappsideaconsultnet8080ambit2feature26221ampfeature_u
ris[]= httpappsideaconsultnet8080ambit2feature21590
Merge mutagenicity data
14Ideaconsult LtdMarch 17 2011
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
15Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
List available models
16Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model
Apply ToxTree module for carcinogenicity
and mutagenicity prediction
17Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model8
bull The benchmatk dataset web address
bull httpappsideaconsultnet8080ambit2dataset2344
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the model URL with parameter
the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset2344rdquo
httpappsideaconsultnet8080ambit2model8
Long running calculations ndash web address
again
18Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2taske75057a0-b005-4c74-
949f-0be9304a3c422model
And the results (a dataset web address)
19Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[
]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2
F82Fpredicted httpappsideaconsultnet8080ambit2
chartpiedataset_uri=httpappsideac
onsultnet8080ambit2dataset2344ampfe
ature_uris[]=httpappsideaconsultnet
8080ambit2feature21858
Building blocks for model creation
20Ideaconsult LtdMarch 17 2011
bull A Datasetndash Datasets can be uploaded (SDF CSV SMI MOL)
bull via HTTP POST to the dataset service
bull Web browser file upload
ndash Existing datasets (uploaded by others) can be used
ndash Dataset Web address assigned
bull Descriptor calculation
bull Learning algorithm
bull Perform predictions
bull Make the model available
The dataset (Caco-2 dataset from a JCIM
publication)
21Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54
bull httpappsideaconsultnet8080ambit2dataset54metadata
bull The endpoint (caco2 column)
httpappsideaconsultnet8080ambit2feature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to data processing (eg
Descriptors calculation)
22Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
+ =
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
=
httpmyhostcomdatasetresults
The algorithms (including descriptors
calculation)
23Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithm
Descriptors calculation
24Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmorgopenscience
cdkqsardescriptorsmolecularXLogPDescriptor
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset
2344rdquo
httpappsideaconsultnet8080ambit2algorithmorgopensci
encecdkqsardescriptorsmolecularXLogPDescriptor
Results from descriptors calculation (a
dataset web address)
25Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttp3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F92
Fpredicted
The descriptors are stored under the web address
httpappsideaconsultnet8080ambit2feature22114
prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
prefix ar lthttpappsideaconsultnet8080ambit2referencegt
prefix bx lthttppurlorgnetnknoufnsbibtexgt
prefix rdfs lthttpwwww3org200001rdf-schemagt
prefix am lthttpappsideaconsultnet8080ambit2modelgt
prefix owl lthttpwwww3org200207owlgt
prefix xsd lthttpwwww3org2001XMLSchemagt
prefix ac lthttpappsideaconsultnet8080ambit2compoundgt
prefix ad lthttpappsideaconsultnet8080ambit2datasetgt
prefix rdf lthttpwwww3org19990222-rdf-syntax-nsgt
prefix ag lthttpappsideaconsultnet8080ambit2algorithmgt
prefix af lthttpappsideaconsultnet8080ambit2featuregt
otAlgorithm
a owlClass
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
af22114
a otFeature otNumericFeature
dccreator httpwwwblueobeliskorgontologieschemoinformatics-algorithmsxlogP
dctitle XLogP
othasSource lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
otunits
= oteeOctanol-water_partition_coefficient_Kow
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
a otAlgorithm
Merge descriptor with activity ndash dataset
with a web address again
26Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=httpap
psideaconsultnet8080ambit2feature22213ampfeature_uris[]=httpappside
aconsultnet8080ambit2feature22200
httpappsideaconsultnet8080ambit2
chartxydataset_uri=httpappsideaco
nsultnet8080ambit2dataset54ampfeatur
e_uris[]=httpappsideaconsultnet8080
ambit2feature22213ampfeature_uris[]=ht
tpappsideaconsultnet8080ambit2f
eature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to models creation
27Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+=
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
httpmyhostcommodelpredictivemodel1
Build a regression model
28Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmLR
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset54rdquo ndashd
ldquoprediction_feature=
httpappsideaconsultnet8080ambit2feature22200 ldquo
httpappsideaconsultnet8080ambit2algorithmLR
The model
29Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2model57
Web address of results could be retrieved
httpappsideaconsultnet8080ambit2model57predicted in
this case it is a the web address
httpappsideaconsultnet8080ambit2feature28963
Web address of X variables could be retrieved
viahttpappsideaconsultnet8080ambit2model57independent
in this case it is a the web address of
httpappsideaconsultnet8080ambit2feature22213
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
15Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
List available models
16Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model
Apply ToxTree module for carcinogenicity
and mutagenicity prediction
17Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model8
bull The benchmatk dataset web address
bull httpappsideaconsultnet8080ambit2dataset2344
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the model URL with parameter
the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset2344rdquo
httpappsideaconsultnet8080ambit2model8
Long running calculations ndash web address
again
18Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2taske75057a0-b005-4c74-
949f-0be9304a3c422model
And the results (a dataset web address)
19Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[
]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2
F82Fpredicted httpappsideaconsultnet8080ambit2
chartpiedataset_uri=httpappsideac
onsultnet8080ambit2dataset2344ampfe
ature_uris[]=httpappsideaconsultnet
8080ambit2feature21858
Building blocks for model creation
20Ideaconsult LtdMarch 17 2011
bull A Datasetndash Datasets can be uploaded (SDF CSV SMI MOL)
bull via HTTP POST to the dataset service
bull Web browser file upload
ndash Existing datasets (uploaded by others) can be used
ndash Dataset Web address assigned
bull Descriptor calculation
bull Learning algorithm
bull Perform predictions
bull Make the model available
The dataset (Caco-2 dataset from a JCIM
publication)
21Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54
bull httpappsideaconsultnet8080ambit2dataset54metadata
bull The endpoint (caco2 column)
httpappsideaconsultnet8080ambit2feature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to data processing (eg
Descriptors calculation)
22Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
+ =
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
=
httpmyhostcomdatasetresults
The algorithms (including descriptors
calculation)
23Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithm
Descriptors calculation
24Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmorgopenscience
cdkqsardescriptorsmolecularXLogPDescriptor
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset
2344rdquo
httpappsideaconsultnet8080ambit2algorithmorgopensci
encecdkqsardescriptorsmolecularXLogPDescriptor
Results from descriptors calculation (a
dataset web address)
25Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttp3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F92
Fpredicted
The descriptors are stored under the web address
httpappsideaconsultnet8080ambit2feature22114
prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
prefix ar lthttpappsideaconsultnet8080ambit2referencegt
prefix bx lthttppurlorgnetnknoufnsbibtexgt
prefix rdfs lthttpwwww3org200001rdf-schemagt
prefix am lthttpappsideaconsultnet8080ambit2modelgt
prefix owl lthttpwwww3org200207owlgt
prefix xsd lthttpwwww3org2001XMLSchemagt
prefix ac lthttpappsideaconsultnet8080ambit2compoundgt
prefix ad lthttpappsideaconsultnet8080ambit2datasetgt
prefix rdf lthttpwwww3org19990222-rdf-syntax-nsgt
prefix ag lthttpappsideaconsultnet8080ambit2algorithmgt
prefix af lthttpappsideaconsultnet8080ambit2featuregt
otAlgorithm
a owlClass
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
af22114
a otFeature otNumericFeature
dccreator httpwwwblueobeliskorgontologieschemoinformatics-algorithmsxlogP
dctitle XLogP
othasSource lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
otunits
= oteeOctanol-water_partition_coefficient_Kow
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
a otAlgorithm
Merge descriptor with activity ndash dataset
with a web address again
26Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=httpap
psideaconsultnet8080ambit2feature22213ampfeature_uris[]=httpappside
aconsultnet8080ambit2feature22200
httpappsideaconsultnet8080ambit2
chartxydataset_uri=httpappsideaco
nsultnet8080ambit2dataset54ampfeatur
e_uris[]=httpappsideaconsultnet8080
ambit2feature22213ampfeature_uris[]=ht
tpappsideaconsultnet8080ambit2f
eature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to models creation
27Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+=
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
httpmyhostcommodelpredictivemodel1
Build a regression model
28Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmLR
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset54rdquo ndashd
ldquoprediction_feature=
httpappsideaconsultnet8080ambit2feature22200 ldquo
httpappsideaconsultnet8080ambit2algorithmLR
The model
29Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2model57
Web address of results could be retrieved
httpappsideaconsultnet8080ambit2model57predicted in
this case it is a the web address
httpappsideaconsultnet8080ambit2feature28963
Web address of X variables could be retrieved
viahttpappsideaconsultnet8080ambit2model57independent
in this case it is a the web address of
httpappsideaconsultnet8080ambit2feature22213
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
List available models
16Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model
Apply ToxTree module for carcinogenicity
and mutagenicity prediction
17Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model8
bull The benchmatk dataset web address
bull httpappsideaconsultnet8080ambit2dataset2344
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the model URL with parameter
the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset2344rdquo
httpappsideaconsultnet8080ambit2model8
Long running calculations ndash web address
again
18Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2taske75057a0-b005-4c74-
949f-0be9304a3c422model
And the results (a dataset web address)
19Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[
]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2
F82Fpredicted httpappsideaconsultnet8080ambit2
chartpiedataset_uri=httpappsideac
onsultnet8080ambit2dataset2344ampfe
ature_uris[]=httpappsideaconsultnet
8080ambit2feature21858
Building blocks for model creation
20Ideaconsult LtdMarch 17 2011
bull A Datasetndash Datasets can be uploaded (SDF CSV SMI MOL)
bull via HTTP POST to the dataset service
bull Web browser file upload
ndash Existing datasets (uploaded by others) can be used
ndash Dataset Web address assigned
bull Descriptor calculation
bull Learning algorithm
bull Perform predictions
bull Make the model available
The dataset (Caco-2 dataset from a JCIM
publication)
21Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54
bull httpappsideaconsultnet8080ambit2dataset54metadata
bull The endpoint (caco2 column)
httpappsideaconsultnet8080ambit2feature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to data processing (eg
Descriptors calculation)
22Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
+ =
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
=
httpmyhostcomdatasetresults
The algorithms (including descriptors
calculation)
23Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithm
Descriptors calculation
24Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmorgopenscience
cdkqsardescriptorsmolecularXLogPDescriptor
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset
2344rdquo
httpappsideaconsultnet8080ambit2algorithmorgopensci
encecdkqsardescriptorsmolecularXLogPDescriptor
Results from descriptors calculation (a
dataset web address)
25Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttp3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F92
Fpredicted
The descriptors are stored under the web address
httpappsideaconsultnet8080ambit2feature22114
prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
prefix ar lthttpappsideaconsultnet8080ambit2referencegt
prefix bx lthttppurlorgnetnknoufnsbibtexgt
prefix rdfs lthttpwwww3org200001rdf-schemagt
prefix am lthttpappsideaconsultnet8080ambit2modelgt
prefix owl lthttpwwww3org200207owlgt
prefix xsd lthttpwwww3org2001XMLSchemagt
prefix ac lthttpappsideaconsultnet8080ambit2compoundgt
prefix ad lthttpappsideaconsultnet8080ambit2datasetgt
prefix rdf lthttpwwww3org19990222-rdf-syntax-nsgt
prefix ag lthttpappsideaconsultnet8080ambit2algorithmgt
prefix af lthttpappsideaconsultnet8080ambit2featuregt
otAlgorithm
a owlClass
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
af22114
a otFeature otNumericFeature
dccreator httpwwwblueobeliskorgontologieschemoinformatics-algorithmsxlogP
dctitle XLogP
othasSource lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
otunits
= oteeOctanol-water_partition_coefficient_Kow
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
a otAlgorithm
Merge descriptor with activity ndash dataset
with a web address again
26Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=httpap
psideaconsultnet8080ambit2feature22213ampfeature_uris[]=httpappside
aconsultnet8080ambit2feature22200
httpappsideaconsultnet8080ambit2
chartxydataset_uri=httpappsideaco
nsultnet8080ambit2dataset54ampfeatur
e_uris[]=httpappsideaconsultnet8080
ambit2feature22213ampfeature_uris[]=ht
tpappsideaconsultnet8080ambit2f
eature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to models creation
27Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+=
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
httpmyhostcommodelpredictivemodel1
Build a regression model
28Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmLR
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset54rdquo ndashd
ldquoprediction_feature=
httpappsideaconsultnet8080ambit2feature22200 ldquo
httpappsideaconsultnet8080ambit2algorithmLR
The model
29Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2model57
Web address of results could be retrieved
httpappsideaconsultnet8080ambit2model57predicted in
this case it is a the web address
httpappsideaconsultnet8080ambit2feature28963
Web address of X variables could be retrieved
viahttpappsideaconsultnet8080ambit2model57independent
in this case it is a the web address of
httpappsideaconsultnet8080ambit2feature22213
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
Apply ToxTree module for carcinogenicity
and mutagenicity prediction
17Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model8
bull The benchmatk dataset web address
bull httpappsideaconsultnet8080ambit2dataset2344
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the model URL with parameter
the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset2344rdquo
httpappsideaconsultnet8080ambit2model8
Long running calculations ndash web address
again
18Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2taske75057a0-b005-4c74-
949f-0be9304a3c422model
And the results (a dataset web address)
19Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[
]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2
F82Fpredicted httpappsideaconsultnet8080ambit2
chartpiedataset_uri=httpappsideac
onsultnet8080ambit2dataset2344ampfe
ature_uris[]=httpappsideaconsultnet
8080ambit2feature21858
Building blocks for model creation
20Ideaconsult LtdMarch 17 2011
bull A Datasetndash Datasets can be uploaded (SDF CSV SMI MOL)
bull via HTTP POST to the dataset service
bull Web browser file upload
ndash Existing datasets (uploaded by others) can be used
ndash Dataset Web address assigned
bull Descriptor calculation
bull Learning algorithm
bull Perform predictions
bull Make the model available
The dataset (Caco-2 dataset from a JCIM
publication)
21Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54
bull httpappsideaconsultnet8080ambit2dataset54metadata
bull The endpoint (caco2 column)
httpappsideaconsultnet8080ambit2feature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to data processing (eg
Descriptors calculation)
22Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
+ =
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
=
httpmyhostcomdatasetresults
The algorithms (including descriptors
calculation)
23Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithm
Descriptors calculation
24Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmorgopenscience
cdkqsardescriptorsmolecularXLogPDescriptor
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset
2344rdquo
httpappsideaconsultnet8080ambit2algorithmorgopensci
encecdkqsardescriptorsmolecularXLogPDescriptor
Results from descriptors calculation (a
dataset web address)
25Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttp3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F92
Fpredicted
The descriptors are stored under the web address
httpappsideaconsultnet8080ambit2feature22114
prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
prefix ar lthttpappsideaconsultnet8080ambit2referencegt
prefix bx lthttppurlorgnetnknoufnsbibtexgt
prefix rdfs lthttpwwww3org200001rdf-schemagt
prefix am lthttpappsideaconsultnet8080ambit2modelgt
prefix owl lthttpwwww3org200207owlgt
prefix xsd lthttpwwww3org2001XMLSchemagt
prefix ac lthttpappsideaconsultnet8080ambit2compoundgt
prefix ad lthttpappsideaconsultnet8080ambit2datasetgt
prefix rdf lthttpwwww3org19990222-rdf-syntax-nsgt
prefix ag lthttpappsideaconsultnet8080ambit2algorithmgt
prefix af lthttpappsideaconsultnet8080ambit2featuregt
otAlgorithm
a owlClass
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
af22114
a otFeature otNumericFeature
dccreator httpwwwblueobeliskorgontologieschemoinformatics-algorithmsxlogP
dctitle XLogP
othasSource lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
otunits
= oteeOctanol-water_partition_coefficient_Kow
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
a otAlgorithm
Merge descriptor with activity ndash dataset
with a web address again
26Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=httpap
psideaconsultnet8080ambit2feature22213ampfeature_uris[]=httpappside
aconsultnet8080ambit2feature22200
httpappsideaconsultnet8080ambit2
chartxydataset_uri=httpappsideaco
nsultnet8080ambit2dataset54ampfeatur
e_uris[]=httpappsideaconsultnet8080
ambit2feature22213ampfeature_uris[]=ht
tpappsideaconsultnet8080ambit2f
eature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to models creation
27Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+=
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
httpmyhostcommodelpredictivemodel1
Build a regression model
28Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmLR
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset54rdquo ndashd
ldquoprediction_feature=
httpappsideaconsultnet8080ambit2feature22200 ldquo
httpappsideaconsultnet8080ambit2algorithmLR
The model
29Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2model57
Web address of results could be retrieved
httpappsideaconsultnet8080ambit2model57predicted in
this case it is a the web address
httpappsideaconsultnet8080ambit2feature28963
Web address of X variables could be retrieved
viahttpappsideaconsultnet8080ambit2model57independent
in this case it is a the web address of
httpappsideaconsultnet8080ambit2feature22213
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
Long running calculations ndash web address
again
18Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2taske75057a0-b005-4c74-
949f-0be9304a3c422model
And the results (a dataset web address)
19Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[
]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2
F82Fpredicted httpappsideaconsultnet8080ambit2
chartpiedataset_uri=httpappsideac
onsultnet8080ambit2dataset2344ampfe
ature_uris[]=httpappsideaconsultnet
8080ambit2feature21858
Building blocks for model creation
20Ideaconsult LtdMarch 17 2011
bull A Datasetndash Datasets can be uploaded (SDF CSV SMI MOL)
bull via HTTP POST to the dataset service
bull Web browser file upload
ndash Existing datasets (uploaded by others) can be used
ndash Dataset Web address assigned
bull Descriptor calculation
bull Learning algorithm
bull Perform predictions
bull Make the model available
The dataset (Caco-2 dataset from a JCIM
publication)
21Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54
bull httpappsideaconsultnet8080ambit2dataset54metadata
bull The endpoint (caco2 column)
httpappsideaconsultnet8080ambit2feature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to data processing (eg
Descriptors calculation)
22Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
+ =
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
=
httpmyhostcomdatasetresults
The algorithms (including descriptors
calculation)
23Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithm
Descriptors calculation
24Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmorgopenscience
cdkqsardescriptorsmolecularXLogPDescriptor
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset
2344rdquo
httpappsideaconsultnet8080ambit2algorithmorgopensci
encecdkqsardescriptorsmolecularXLogPDescriptor
Results from descriptors calculation (a
dataset web address)
25Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttp3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F92
Fpredicted
The descriptors are stored under the web address
httpappsideaconsultnet8080ambit2feature22114
prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
prefix ar lthttpappsideaconsultnet8080ambit2referencegt
prefix bx lthttppurlorgnetnknoufnsbibtexgt
prefix rdfs lthttpwwww3org200001rdf-schemagt
prefix am lthttpappsideaconsultnet8080ambit2modelgt
prefix owl lthttpwwww3org200207owlgt
prefix xsd lthttpwwww3org2001XMLSchemagt
prefix ac lthttpappsideaconsultnet8080ambit2compoundgt
prefix ad lthttpappsideaconsultnet8080ambit2datasetgt
prefix rdf lthttpwwww3org19990222-rdf-syntax-nsgt
prefix ag lthttpappsideaconsultnet8080ambit2algorithmgt
prefix af lthttpappsideaconsultnet8080ambit2featuregt
otAlgorithm
a owlClass
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
af22114
a otFeature otNumericFeature
dccreator httpwwwblueobeliskorgontologieschemoinformatics-algorithmsxlogP
dctitle XLogP
othasSource lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
otunits
= oteeOctanol-water_partition_coefficient_Kow
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
a otAlgorithm
Merge descriptor with activity ndash dataset
with a web address again
26Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=httpap
psideaconsultnet8080ambit2feature22213ampfeature_uris[]=httpappside
aconsultnet8080ambit2feature22200
httpappsideaconsultnet8080ambit2
chartxydataset_uri=httpappsideaco
nsultnet8080ambit2dataset54ampfeatur
e_uris[]=httpappsideaconsultnet8080
ambit2feature22213ampfeature_uris[]=ht
tpappsideaconsultnet8080ambit2f
eature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to models creation
27Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+=
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
httpmyhostcommodelpredictivemodel1
Build a regression model
28Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmLR
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset54rdquo ndashd
ldquoprediction_feature=
httpappsideaconsultnet8080ambit2feature22200 ldquo
httpappsideaconsultnet8080ambit2algorithmLR
The model
29Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2model57
Web address of results could be retrieved
httpappsideaconsultnet8080ambit2model57predicted in
this case it is a the web address
httpappsideaconsultnet8080ambit2feature28963
Web address of X variables could be retrieved
viahttpappsideaconsultnet8080ambit2model57independent
in this case it is a the web address of
httpappsideaconsultnet8080ambit2feature22213
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
And the results (a dataset web address)
19Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset2344feature_uris[
]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2
F82Fpredicted httpappsideaconsultnet8080ambit2
chartpiedataset_uri=httpappsideac
onsultnet8080ambit2dataset2344ampfe
ature_uris[]=httpappsideaconsultnet
8080ambit2feature21858
Building blocks for model creation
20Ideaconsult LtdMarch 17 2011
bull A Datasetndash Datasets can be uploaded (SDF CSV SMI MOL)
bull via HTTP POST to the dataset service
bull Web browser file upload
ndash Existing datasets (uploaded by others) can be used
ndash Dataset Web address assigned
bull Descriptor calculation
bull Learning algorithm
bull Perform predictions
bull Make the model available
The dataset (Caco-2 dataset from a JCIM
publication)
21Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54
bull httpappsideaconsultnet8080ambit2dataset54metadata
bull The endpoint (caco2 column)
httpappsideaconsultnet8080ambit2feature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to data processing (eg
Descriptors calculation)
22Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
+ =
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
=
httpmyhostcomdatasetresults
The algorithms (including descriptors
calculation)
23Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithm
Descriptors calculation
24Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmorgopenscience
cdkqsardescriptorsmolecularXLogPDescriptor
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset
2344rdquo
httpappsideaconsultnet8080ambit2algorithmorgopensci
encecdkqsardescriptorsmolecularXLogPDescriptor
Results from descriptors calculation (a
dataset web address)
25Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttp3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F92
Fpredicted
The descriptors are stored under the web address
httpappsideaconsultnet8080ambit2feature22114
prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
prefix ar lthttpappsideaconsultnet8080ambit2referencegt
prefix bx lthttppurlorgnetnknoufnsbibtexgt
prefix rdfs lthttpwwww3org200001rdf-schemagt
prefix am lthttpappsideaconsultnet8080ambit2modelgt
prefix owl lthttpwwww3org200207owlgt
prefix xsd lthttpwwww3org2001XMLSchemagt
prefix ac lthttpappsideaconsultnet8080ambit2compoundgt
prefix ad lthttpappsideaconsultnet8080ambit2datasetgt
prefix rdf lthttpwwww3org19990222-rdf-syntax-nsgt
prefix ag lthttpappsideaconsultnet8080ambit2algorithmgt
prefix af lthttpappsideaconsultnet8080ambit2featuregt
otAlgorithm
a owlClass
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
af22114
a otFeature otNumericFeature
dccreator httpwwwblueobeliskorgontologieschemoinformatics-algorithmsxlogP
dctitle XLogP
othasSource lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
otunits
= oteeOctanol-water_partition_coefficient_Kow
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
a otAlgorithm
Merge descriptor with activity ndash dataset
with a web address again
26Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=httpap
psideaconsultnet8080ambit2feature22213ampfeature_uris[]=httpappside
aconsultnet8080ambit2feature22200
httpappsideaconsultnet8080ambit2
chartxydataset_uri=httpappsideaco
nsultnet8080ambit2dataset54ampfeatur
e_uris[]=httpappsideaconsultnet8080
ambit2feature22213ampfeature_uris[]=ht
tpappsideaconsultnet8080ambit2f
eature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to models creation
27Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+=
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
httpmyhostcommodelpredictivemodel1
Build a regression model
28Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmLR
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset54rdquo ndashd
ldquoprediction_feature=
httpappsideaconsultnet8080ambit2feature22200 ldquo
httpappsideaconsultnet8080ambit2algorithmLR
The model
29Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2model57
Web address of results could be retrieved
httpappsideaconsultnet8080ambit2model57predicted in
this case it is a the web address
httpappsideaconsultnet8080ambit2feature28963
Web address of X variables could be retrieved
viahttpappsideaconsultnet8080ambit2model57independent
in this case it is a the web address of
httpappsideaconsultnet8080ambit2feature22213
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
Building blocks for model creation
20Ideaconsult LtdMarch 17 2011
bull A Datasetndash Datasets can be uploaded (SDF CSV SMI MOL)
bull via HTTP POST to the dataset service
bull Web browser file upload
ndash Existing datasets (uploaded by others) can be used
ndash Dataset Web address assigned
bull Descriptor calculation
bull Learning algorithm
bull Perform predictions
bull Make the model available
The dataset (Caco-2 dataset from a JCIM
publication)
21Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54
bull httpappsideaconsultnet8080ambit2dataset54metadata
bull The endpoint (caco2 column)
httpappsideaconsultnet8080ambit2feature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to data processing (eg
Descriptors calculation)
22Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
+ =
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
=
httpmyhostcomdatasetresults
The algorithms (including descriptors
calculation)
23Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithm
Descriptors calculation
24Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmorgopenscience
cdkqsardescriptorsmolecularXLogPDescriptor
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset
2344rdquo
httpappsideaconsultnet8080ambit2algorithmorgopensci
encecdkqsardescriptorsmolecularXLogPDescriptor
Results from descriptors calculation (a
dataset web address)
25Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttp3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F92
Fpredicted
The descriptors are stored under the web address
httpappsideaconsultnet8080ambit2feature22114
prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
prefix ar lthttpappsideaconsultnet8080ambit2referencegt
prefix bx lthttppurlorgnetnknoufnsbibtexgt
prefix rdfs lthttpwwww3org200001rdf-schemagt
prefix am lthttpappsideaconsultnet8080ambit2modelgt
prefix owl lthttpwwww3org200207owlgt
prefix xsd lthttpwwww3org2001XMLSchemagt
prefix ac lthttpappsideaconsultnet8080ambit2compoundgt
prefix ad lthttpappsideaconsultnet8080ambit2datasetgt
prefix rdf lthttpwwww3org19990222-rdf-syntax-nsgt
prefix ag lthttpappsideaconsultnet8080ambit2algorithmgt
prefix af lthttpappsideaconsultnet8080ambit2featuregt
otAlgorithm
a owlClass
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
af22114
a otFeature otNumericFeature
dccreator httpwwwblueobeliskorgontologieschemoinformatics-algorithmsxlogP
dctitle XLogP
othasSource lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
otunits
= oteeOctanol-water_partition_coefficient_Kow
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
a otAlgorithm
Merge descriptor with activity ndash dataset
with a web address again
26Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=httpap
psideaconsultnet8080ambit2feature22213ampfeature_uris[]=httpappside
aconsultnet8080ambit2feature22200
httpappsideaconsultnet8080ambit2
chartxydataset_uri=httpappsideaco
nsultnet8080ambit2dataset54ampfeatur
e_uris[]=httpappsideaconsultnet8080
ambit2feature22213ampfeature_uris[]=ht
tpappsideaconsultnet8080ambit2f
eature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to models creation
27Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+=
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
httpmyhostcommodelpredictivemodel1
Build a regression model
28Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmLR
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset54rdquo ndashd
ldquoprediction_feature=
httpappsideaconsultnet8080ambit2feature22200 ldquo
httpappsideaconsultnet8080ambit2algorithmLR
The model
29Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2model57
Web address of results could be retrieved
httpappsideaconsultnet8080ambit2model57predicted in
this case it is a the web address
httpappsideaconsultnet8080ambit2feature28963
Web address of X variables could be retrieved
viahttpappsideaconsultnet8080ambit2model57independent
in this case it is a the web address of
httpappsideaconsultnet8080ambit2feature22213
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
The dataset (Caco-2 dataset from a JCIM
publication)
21Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54
bull httpappsideaconsultnet8080ambit2dataset54metadata
bull The endpoint (caco2 column)
httpappsideaconsultnet8080ambit2feature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to data processing (eg
Descriptors calculation)
22Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
+ =
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
=
httpmyhostcomdatasetresults
The algorithms (including descriptors
calculation)
23Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithm
Descriptors calculation
24Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmorgopenscience
cdkqsardescriptorsmolecularXLogPDescriptor
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset
2344rdquo
httpappsideaconsultnet8080ambit2algorithmorgopensci
encecdkqsardescriptorsmolecularXLogPDescriptor
Results from descriptors calculation (a
dataset web address)
25Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttp3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F92
Fpredicted
The descriptors are stored under the web address
httpappsideaconsultnet8080ambit2feature22114
prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
prefix ar lthttpappsideaconsultnet8080ambit2referencegt
prefix bx lthttppurlorgnetnknoufnsbibtexgt
prefix rdfs lthttpwwww3org200001rdf-schemagt
prefix am lthttpappsideaconsultnet8080ambit2modelgt
prefix owl lthttpwwww3org200207owlgt
prefix xsd lthttpwwww3org2001XMLSchemagt
prefix ac lthttpappsideaconsultnet8080ambit2compoundgt
prefix ad lthttpappsideaconsultnet8080ambit2datasetgt
prefix rdf lthttpwwww3org19990222-rdf-syntax-nsgt
prefix ag lthttpappsideaconsultnet8080ambit2algorithmgt
prefix af lthttpappsideaconsultnet8080ambit2featuregt
otAlgorithm
a owlClass
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
af22114
a otFeature otNumericFeature
dccreator httpwwwblueobeliskorgontologieschemoinformatics-algorithmsxlogP
dctitle XLogP
othasSource lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
otunits
= oteeOctanol-water_partition_coefficient_Kow
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
a otAlgorithm
Merge descriptor with activity ndash dataset
with a web address again
26Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=httpap
psideaconsultnet8080ambit2feature22213ampfeature_uris[]=httpappside
aconsultnet8080ambit2feature22200
httpappsideaconsultnet8080ambit2
chartxydataset_uri=httpappsideaco
nsultnet8080ambit2dataset54ampfeatur
e_uris[]=httpappsideaconsultnet8080
ambit2feature22213ampfeature_uris[]=ht
tpappsideaconsultnet8080ambit2f
eature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to models creation
27Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+=
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
httpmyhostcommodelpredictivemodel1
Build a regression model
28Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmLR
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset54rdquo ndashd
ldquoprediction_feature=
httpappsideaconsultnet8080ambit2feature22200 ldquo
httpappsideaconsultnet8080ambit2algorithmLR
The model
29Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2model57
Web address of results could be retrieved
httpappsideaconsultnet8080ambit2model57predicted in
this case it is a the web address
httpappsideaconsultnet8080ambit2feature28963
Web address of X variables could be retrieved
viahttpappsideaconsultnet8080ambit2model57independent
in this case it is a the web address of
httpappsideaconsultnet8080ambit2feature22213
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
Read data from a web address ndash process ndash write to a web address
Uniform approach to data processing (eg
Descriptors calculation)
22Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
+ =
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
=
httpmyhostcomdatasetresults
The algorithms (including descriptors
calculation)
23Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithm
Descriptors calculation
24Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmorgopenscience
cdkqsardescriptorsmolecularXLogPDescriptor
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset
2344rdquo
httpappsideaconsultnet8080ambit2algorithmorgopensci
encecdkqsardescriptorsmolecularXLogPDescriptor
Results from descriptors calculation (a
dataset web address)
25Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttp3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F92
Fpredicted
The descriptors are stored under the web address
httpappsideaconsultnet8080ambit2feature22114
prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
prefix ar lthttpappsideaconsultnet8080ambit2referencegt
prefix bx lthttppurlorgnetnknoufnsbibtexgt
prefix rdfs lthttpwwww3org200001rdf-schemagt
prefix am lthttpappsideaconsultnet8080ambit2modelgt
prefix owl lthttpwwww3org200207owlgt
prefix xsd lthttpwwww3org2001XMLSchemagt
prefix ac lthttpappsideaconsultnet8080ambit2compoundgt
prefix ad lthttpappsideaconsultnet8080ambit2datasetgt
prefix rdf lthttpwwww3org19990222-rdf-syntax-nsgt
prefix ag lthttpappsideaconsultnet8080ambit2algorithmgt
prefix af lthttpappsideaconsultnet8080ambit2featuregt
otAlgorithm
a owlClass
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
af22114
a otFeature otNumericFeature
dccreator httpwwwblueobeliskorgontologieschemoinformatics-algorithmsxlogP
dctitle XLogP
othasSource lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
otunits
= oteeOctanol-water_partition_coefficient_Kow
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
a otAlgorithm
Merge descriptor with activity ndash dataset
with a web address again
26Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=httpap
psideaconsultnet8080ambit2feature22213ampfeature_uris[]=httpappside
aconsultnet8080ambit2feature22200
httpappsideaconsultnet8080ambit2
chartxydataset_uri=httpappsideaco
nsultnet8080ambit2dataset54ampfeatur
e_uris[]=httpappsideaconsultnet8080
ambit2feature22213ampfeature_uris[]=ht
tpappsideaconsultnet8080ambit2f
eature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to models creation
27Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+=
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
httpmyhostcommodelpredictivemodel1
Build a regression model
28Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmLR
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset54rdquo ndashd
ldquoprediction_feature=
httpappsideaconsultnet8080ambit2feature22200 ldquo
httpappsideaconsultnet8080ambit2algorithmLR
The model
29Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2model57
Web address of results could be retrieved
httpappsideaconsultnet8080ambit2model57predicted in
this case it is a the web address
httpappsideaconsultnet8080ambit2feature28963
Web address of X variables could be retrieved
viahttpappsideaconsultnet8080ambit2model57independent
in this case it is a the web address of
httpappsideaconsultnet8080ambit2feature22213
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
The algorithms (including descriptors
calculation)
23Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithm
Descriptors calculation
24Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmorgopenscience
cdkqsardescriptorsmolecularXLogPDescriptor
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset
2344rdquo
httpappsideaconsultnet8080ambit2algorithmorgopensci
encecdkqsardescriptorsmolecularXLogPDescriptor
Results from descriptors calculation (a
dataset web address)
25Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttp3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F92
Fpredicted
The descriptors are stored under the web address
httpappsideaconsultnet8080ambit2feature22114
prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
prefix ar lthttpappsideaconsultnet8080ambit2referencegt
prefix bx lthttppurlorgnetnknoufnsbibtexgt
prefix rdfs lthttpwwww3org200001rdf-schemagt
prefix am lthttpappsideaconsultnet8080ambit2modelgt
prefix owl lthttpwwww3org200207owlgt
prefix xsd lthttpwwww3org2001XMLSchemagt
prefix ac lthttpappsideaconsultnet8080ambit2compoundgt
prefix ad lthttpappsideaconsultnet8080ambit2datasetgt
prefix rdf lthttpwwww3org19990222-rdf-syntax-nsgt
prefix ag lthttpappsideaconsultnet8080ambit2algorithmgt
prefix af lthttpappsideaconsultnet8080ambit2featuregt
otAlgorithm
a owlClass
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
af22114
a otFeature otNumericFeature
dccreator httpwwwblueobeliskorgontologieschemoinformatics-algorithmsxlogP
dctitle XLogP
othasSource lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
otunits
= oteeOctanol-water_partition_coefficient_Kow
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
a otAlgorithm
Merge descriptor with activity ndash dataset
with a web address again
26Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=httpap
psideaconsultnet8080ambit2feature22213ampfeature_uris[]=httpappside
aconsultnet8080ambit2feature22200
httpappsideaconsultnet8080ambit2
chartxydataset_uri=httpappsideaco
nsultnet8080ambit2dataset54ampfeatur
e_uris[]=httpappsideaconsultnet8080
ambit2feature22213ampfeature_uris[]=ht
tpappsideaconsultnet8080ambit2f
eature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to models creation
27Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+=
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
httpmyhostcommodelpredictivemodel1
Build a regression model
28Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmLR
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset54rdquo ndashd
ldquoprediction_feature=
httpappsideaconsultnet8080ambit2feature22200 ldquo
httpappsideaconsultnet8080ambit2algorithmLR
The model
29Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2model57
Web address of results could be retrieved
httpappsideaconsultnet8080ambit2model57predicted in
this case it is a the web address
httpappsideaconsultnet8080ambit2feature28963
Web address of X variables could be retrieved
viahttpappsideaconsultnet8080ambit2model57independent
in this case it is a the web address of
httpappsideaconsultnet8080ambit2feature22213
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
Descriptors calculation
24Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmorgopenscience
cdkqsardescriptorsmolecularXLogPDescriptor
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset
2344rdquo
httpappsideaconsultnet8080ambit2algorithmorgopensci
encecdkqsardescriptorsmolecularXLogPDescriptor
Results from descriptors calculation (a
dataset web address)
25Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttp3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F92
Fpredicted
The descriptors are stored under the web address
httpappsideaconsultnet8080ambit2feature22114
prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
prefix ar lthttpappsideaconsultnet8080ambit2referencegt
prefix bx lthttppurlorgnetnknoufnsbibtexgt
prefix rdfs lthttpwwww3org200001rdf-schemagt
prefix am lthttpappsideaconsultnet8080ambit2modelgt
prefix owl lthttpwwww3org200207owlgt
prefix xsd lthttpwwww3org2001XMLSchemagt
prefix ac lthttpappsideaconsultnet8080ambit2compoundgt
prefix ad lthttpappsideaconsultnet8080ambit2datasetgt
prefix rdf lthttpwwww3org19990222-rdf-syntax-nsgt
prefix ag lthttpappsideaconsultnet8080ambit2algorithmgt
prefix af lthttpappsideaconsultnet8080ambit2featuregt
otAlgorithm
a owlClass
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
af22114
a otFeature otNumericFeature
dccreator httpwwwblueobeliskorgontologieschemoinformatics-algorithmsxlogP
dctitle XLogP
othasSource lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
otunits
= oteeOctanol-water_partition_coefficient_Kow
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
a otAlgorithm
Merge descriptor with activity ndash dataset
with a web address again
26Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=httpap
psideaconsultnet8080ambit2feature22213ampfeature_uris[]=httpappside
aconsultnet8080ambit2feature22200
httpappsideaconsultnet8080ambit2
chartxydataset_uri=httpappsideaco
nsultnet8080ambit2dataset54ampfeatur
e_uris[]=httpappsideaconsultnet8080
ambit2feature22213ampfeature_uris[]=ht
tpappsideaconsultnet8080ambit2f
eature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to models creation
27Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+=
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
httpmyhostcommodelpredictivemodel1
Build a regression model
28Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmLR
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset54rdquo ndashd
ldquoprediction_feature=
httpappsideaconsultnet8080ambit2feature22200 ldquo
httpappsideaconsultnet8080ambit2algorithmLR
The model
29Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2model57
Web address of results could be retrieved
httpappsideaconsultnet8080ambit2model57predicted in
this case it is a the web address
httpappsideaconsultnet8080ambit2feature28963
Web address of X variables could be retrieved
viahttpappsideaconsultnet8080ambit2model57independent
in this case it is a the web address of
httpappsideaconsultnet8080ambit2feature22213
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
Results from descriptors calculation (a
dataset web address)
25Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttp3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F92
Fpredicted
The descriptors are stored under the web address
httpappsideaconsultnet8080ambit2feature22114
prefix ot lthttpwwwopentoxorgapi11gt
prefix dc lthttppurlorgdcelements11gt
prefix lthttpappsideaconsultnet8080ambit2gt
prefix ota lthttpwwwopentoxorgalgorithmTypesowlgt
prefix otee lthttpwwwopentoxorgechaEndpointsowlgt
prefix ar lthttpappsideaconsultnet8080ambit2referencegt
prefix bx lthttppurlorgnetnknoufnsbibtexgt
prefix rdfs lthttpwwww3org200001rdf-schemagt
prefix am lthttpappsideaconsultnet8080ambit2modelgt
prefix owl lthttpwwww3org200207owlgt
prefix xsd lthttpwwww3org2001XMLSchemagt
prefix ac lthttpappsideaconsultnet8080ambit2compoundgt
prefix ad lthttpappsideaconsultnet8080ambit2datasetgt
prefix rdf lthttpwwww3org19990222-rdf-syntax-nsgt
prefix ag lthttpappsideaconsultnet8080ambit2algorithmgt
prefix af lthttpappsideaconsultnet8080ambit2featuregt
otAlgorithm
a owlClass
othasSource
a owlObjectProperty
otunits
a owlDatatypeProperty
af22114
a otFeature otNumericFeature
dccreator httpwwwblueobeliskorgontologieschemoinformatics-algorithmsxlogP
dctitle XLogP
othasSource lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
otunits
= oteeOctanol-water_partition_coefficient_Kow
otFeature
a owlClass
otNumericFeature
a owlClass
rdfssubClassOf otFeature
lthttpappsideaconsultnet8080ambit2algorithmorgopensciencecdkqsardescriptorsmolecularXLogPDescriptorgt
a otAlgorithm
Merge descriptor with activity ndash dataset
with a web address again
26Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=httpap
psideaconsultnet8080ambit2feature22213ampfeature_uris[]=httpappside
aconsultnet8080ambit2feature22200
httpappsideaconsultnet8080ambit2
chartxydataset_uri=httpappsideaco
nsultnet8080ambit2dataset54ampfeatur
e_uris[]=httpappsideaconsultnet8080
ambit2feature22213ampfeature_uris[]=ht
tpappsideaconsultnet8080ambit2f
eature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to models creation
27Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+=
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
httpmyhostcommodelpredictivemodel1
Build a regression model
28Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmLR
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset54rdquo ndashd
ldquoprediction_feature=
httpappsideaconsultnet8080ambit2feature22200 ldquo
httpappsideaconsultnet8080ambit2algorithmLR
The model
29Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2model57
Web address of results could be retrieved
httpappsideaconsultnet8080ambit2model57predicted in
this case it is a the web address
httpappsideaconsultnet8080ambit2feature28963
Web address of X variables could be retrieved
viahttpappsideaconsultnet8080ambit2model57independent
in this case it is a the web address of
httpappsideaconsultnet8080ambit2feature22213
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
Merge descriptor with activity ndash dataset
with a web address again
26Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=httpap
psideaconsultnet8080ambit2feature22213ampfeature_uris[]=httpappside
aconsultnet8080ambit2feature22200
httpappsideaconsultnet8080ambit2
chartxydataset_uri=httpappsideaco
nsultnet8080ambit2dataset54ampfeatur
e_uris[]=httpappsideaconsultnet8080
ambit2feature22213ampfeature_uris[]=ht
tpappsideaconsultnet8080ambit2f
eature22200
Read data from a web address ndash process ndash write to a web address
Uniform approach to models creation
27Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+=
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
httpmyhostcommodelpredictivemodel1
Build a regression model
28Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmLR
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset54rdquo ndashd
ldquoprediction_feature=
httpappsideaconsultnet8080ambit2feature22200 ldquo
httpappsideaconsultnet8080ambit2algorithmLR
The model
29Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2model57
Web address of results could be retrieved
httpappsideaconsultnet8080ambit2model57predicted in
this case it is a the web address
httpappsideaconsultnet8080ambit2feature28963
Web address of X variables could be retrieved
viahttpappsideaconsultnet8080ambit2model57independent
in this case it is a the web address of
httpappsideaconsultnet8080ambit2feature22213
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
Read data from a web address ndash process ndash write to a web address
Uniform approach to models creation
27Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Algorithm
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+=
httpmyhostcomdatasettrainingset1
httpmyhostcomalgorithmneuralnetwork
httpmyhostcommodelpredictivemodel1
Build a regression model
28Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmLR
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset54rdquo ndashd
ldquoprediction_feature=
httpappsideaconsultnet8080ambit2feature22200 ldquo
httpappsideaconsultnet8080ambit2algorithmLR
The model
29Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2model57
Web address of results could be retrieved
httpappsideaconsultnet8080ambit2model57predicted in
this case it is a the web address
httpappsideaconsultnet8080ambit2feature28963
Web address of X variables could be retrieved
viahttpappsideaconsultnet8080ambit2model57independent
in this case it is a the web address of
httpappsideaconsultnet8080ambit2feature22213
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
Build a regression model
28Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2algorithmLR
bull The demo dataset web address
bull httpappsideaconsultnet8080ambit2dataset54
bull Clicking bdquoPredict‟ button initiates calculations
bull It actually sends HTTP POST command to the algorithm URL with
parameter the dataset URL
bull curl ndashX POST ndashd
ldquodataset_uri=httpappsideaconsultnet8080ambit2dataset54rdquo ndashd
ldquoprediction_feature=
httpappsideaconsultnet8080ambit2feature22200 ldquo
httpappsideaconsultnet8080ambit2algorithmLR
The model
29Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2model57
Web address of results could be retrieved
httpappsideaconsultnet8080ambit2model57predicted in
this case it is a the web address
httpappsideaconsultnet8080ambit2feature28963
Web address of X variables could be retrieved
viahttpappsideaconsultnet8080ambit2model57independent
in this case it is a the web address of
httpappsideaconsultnet8080ambit2feature22213
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
The model
29Ideaconsult LtdMarch 17 2011
httpappsideaconsultnet8080ambit2model57
Web address of results could be retrieved
httpappsideaconsultnet8080ambit2model57predicted in
this case it is a the web address
httpappsideaconsultnet8080ambit2feature28963
Web address of X variables could be retrieved
viahttpappsideaconsultnet8080ambit2model57independent
in this case it is a the web address of
httpappsideaconsultnet8080ambit2feature22213
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
Read data from a web address ndash process ndash write to a web address
Uniform access to calculations
30Ideaconsult LtdMarch 17 2011
Feature
GET
POST
PUT
DELETE
Compound
GET
POST
PUT
DELETE
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+ = Dataset
GET
POST
PUT
DELETE
Predicted results
httpmyhostcomdatasetnewcompounds
httpmyhostcommodelpredictivemodel1
httpmyhostcomdatasetpredictedresults1
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
Apply the new regression model
31Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2model57 (Model)
bull The demo dataset web address
httpappsideaconsultnet8080ambit2dataset54feature_uris[]=ht
tpappsideaconsultnet8080ambit2feature22213ampfeature_uris[]=
httpappsideaconsultnet8080ambit2feature22200
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
Predictions finally (at a dataset web
address)
32Ideaconsult LtdMarch 17 2011
bull httpappsideaconsultnet8080ambit2dataset54feature_uris[]=h
ttpappsideaconsultnet8080ambit2feature22213ampfeature_uris[
]=httpappsideaconsultnet8080ambit2feature22200ampfeature_u
ris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel
2F572Fpredicted
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
Advanced options
(a bit of command line no web browser)
33Ideaconsult LtdMarch 17 2011
bull httpcurlhaxxse
bull curl is a command line tool for transferring data with URL syntax
bull Copy the dataset to a new onecurl -X POST -d
dataset_uri=httpappsideaconsultnet3A80802Fambit22Fdataset2F543Ffeature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2221326feature_uris5B5D3Dhttp3A2F2Fappsideaconsultnet3A80802Fambit22Ffeature2F2220026feature_uris5B5D3Dhttp253A252F252Fappsideaconsultnet253A8080252Fambit2252Fmodel252F57252Fpredictedrdquo httpappsideaconsultnet8080ambit2dataset
The new URL returned is
httpappsideaconsultnet8080ambit2datasetR3940
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
Read data from a web address ndash process ndash write to a web address
Uniform approach to models validation and
report generation
34Ideaconsult LtdMarch 17 2011
Dataset
GET
POST
PUT
DELETE
Model
GET
POST
PUT
DELETE
+
=Validation
GET
POST
PUT
DELETE
Report
GET
POST
PUT
DELETEModel generating
predictions
Validation report
httpmyhostcomreport1
httpmyhostcomdatasettrainingset1
httpmyhostcomdatasetpredictedresults1
httpmyhostcommodelpredictivemodel1
httpmyhostcomvalidation
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
Ask the Validation service at Freiburg
to validate the model
35Ideaconsult LtdMarch 17 2011
bull curl -d
test_dataset_uri=httpappsideaconsultnet8080ambit2datasetR3940
-d
prediction_feature=httpappsideaconsultnet8080ambit2feature222
00 -d model_uri=httpappsideaconsultnet8080ambit2model57
httpopentoxinformatikuni-freiburgdevalidation
Task URL returned httpopentoxinformatikuni-
freiburgdetask4062
Query if the task is completed
bull curl -H Accepttexturi-list httpopentoxinformatikuni-
freiburgdetask4062
bull Yes it is here is the address of the validation object
httpopentoxinformatikuni-freiburgdevalidation18920
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
The validation resource
36Ideaconsult LtdMarch 17 2011
curl httpopentoxinformatikuni-freiburgdevalidation18920
---
regression_statistics
sum_squared_error 664592554978574
sample_correlation_coefficient 042022542118295
root_mean_squared_error 0929035636699631
mean_absolute_error 0752657632127617
r_square 0176589404608387
target_variance_actual 106200222895221
target_variance_predicted 0187523074000816
date 2010-08-03 094148 +0200
test_target_dataset_uri
real_runtime 1
prediction_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940feature_uris[]=http3A2F2Fappsideaconsultnet3A80802Fambit22Fmodel2F572Fpredicted
algorithm_uri httpappsideaconsultnet8080ambit2algorithmLR
percent_without_class 00
num_without_class 0
prediction_feature httpappsideaconsultnet8080ambit2feature22200
percent_unpredicted 00
num_instances 77
training_dataset_uri
model_uri httpappsideaconsultnet8080ambit2model57
num_unpredicted 0
test_dataset_uri httpappsideaconsultnet8080ambit2datasetR3940
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
The validation report
37Ideaconsult LtdMarch 17 2011
curl -d validation_uris=httpopentoxinformatikuni-freiburgdevalidation18920 httpopentoxinformatikuni-freiburgdevalidationreportvalidation
httpopentoxinformatikuni-freiburgdetask4063 lt---- Task URI
curl httpopentoxinformatikuni-freiburgdetask4063 - Ask if completed
---
description
date 2010-08-03T094831+0200
uri httpopentoxinformatikuni-freiburgdetask4063
hasStatus Completed
title
percentageCompleted 00
resultURI
httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
due_to_time 2010-08-03T104831+0200
creator
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
The validation report (human readable this time)httpopentoxinformatikuni-freiburgdevalidationreportvalidation160
38Ideaconsult LtdMarch 17 2011
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
bull Could be hosted on a single computer (even a laptop or netbook would do) o
bull Could be transparently distributed on multiple servers in various physical locations in particular for better reliability resilience and scalability
bull OpenTox webservices could be deployed behind firewalls in Intranets (or even offline) when very tight security policies would have to be met
bull Third parties willing to deploy OpenTox webservices could select a relevant subset of services to run tailored to their specific needs
OpenTox web services implementation
39Ideaconsult LtdMarch 17
2011
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
Make the model available
40Ideaconsult LtdMarch 17 2011
Register at OpenTox ontology service
ndash RDF tripple storage
ndash Accepts HTTP POST
ndash SPARQL endpoint
Curl ndashX POST ndashd
rdquouri=httpappsideaconsultnet8080ambit2model57
rdquo httpappsideaconsultnet8080ontology
Becomes visible for applications
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
OpenTox Is A Framework
Framework
Unified Access
Open Source
bull Toxicity data
bull QSAR models
bull Validation support
bull Interpretation aids
bull Toxicologists
bull QSAR Modelers
bull API for new QSAR algorithmdevelopment amp integration
bull To optimise impact
bull To allow inspection review
bull To attract external contributors
OpenTox services can be used to develop specific applications or embedded in
workflow systems
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
bull Two end user oriented demo applications making use of OpenTox
webservices have been developed deployed and are available for
testing ndash httptoxcreateorg and httptoxpredictorg
bull ToxCreate creates models from user supplied datasets
bull ToxPredict uses existing OpenTox models to estimate
chemicalcompound properties
Demo applications
42Ideaconsult LtdMarch 17
2011
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
bull Interested in applying predictive models but not in
OpenTox implementation details
bull Interested in building predictive models but not in
OpenTox implementation details
bull End users interested in learning implementation details of
OpenTox web services
bull
bull Developers
43
Exercises (4 options)
httpwwwideaconsultnetdownloadsecheminfo
Thank you
March 17
2011
44Ideaconsult Ltd
Thank you
March 17
2011
44Ideaconsult Ltd