Development of Predictive Toxicology

Applications

Data management and integration

presented by Nina Jeliazkova

(Ideaconsult Ltd Bulgaria)

An OpenTox Workshop

19 Sep 2010 Rhodes Greece

bull Ontology Server

bull Using the Dataset API

bull Dataset Integration

bull Data quality and accuracy

Outline

2

Component Description URL Template (example)

Compound Representations of chemical compounds httphostportcompoundcompoundid

Feature Properties and identifiers httphostportfeaturefeatureid

Dataset Encapsulates set of chemical compounds and their property

values

httphostportdatasetdatasetid

Model OpenTox model services httphostportmodelmodeld

Algorithm OpenTox algorithm services httphostportalgorithmalgorithmid

Validation

Report

A validation corresponds to the validation of a model on a test

dataset

httphostportvalidationvalidationid

httphostportreportreportid

Task Asynchronous jobs are handled via an intermediate Task

resource A resource submitting an asynchronous job should

return the URI of the task

httphostporttasktaskid

Ontology service Provides storage and SPARQL search functionality for objects

defined in OpenTox services and relevant ontologies

httphostportontology

Authentication and

authorisation

Granting access to protected resources for authorised users httphostportopensso

httphostportopensso-pol

bull Distributed Web services for predictive toxicology

bull REST technology

ndash Every object has an unique URI

ndash URIs are dereferensable

ndash Multiple representation of an object is encouraged (eg RDF but also others)

ndash Fixed operations ndash GET PUT POST DELETE

bull Every object has RDF representationndash Compounds

ndash Datasets

ndash Compound properties

ndash Prediction algorithms

ndash Models

ndash Validation statistics

ndash Reports

bull Ontologies Opentoxowl Blue Obelisk algorithm ontology OpenTox

algotihm types ontology OpenTox endpoints ontology based on ECHA

endpoints classification specific endpoints ontologies developed by ISS amp

ITEM

OpenTox

3

Ontology service

4

bullRDF triple storage

bullREST interface for

registration of OpenTox

objects

bullHTTP POST

bullSPARQL

bullquery

Build a predictive model

Create a model

Run calculations with

dataset

httphost1datasetid

Structures

descriptors

endpoints

Dataset service

Returns the model URL

httphost1modelid

HTTP POST

Build a predictive model

Regression

Classification

Quantum Chemistry

Descriptors etc

validationid

Algorithm service

Validation service

modelid

Published models

Algorithms

Ontologies

metadata

Ontology service

HTTP POST

Model service

Apply predictive models

Returns the results

dataset URL

httphostdatasetid

Retrieve available

endpoints and model

URLs eg

httphost1modelid

Published models

Algorithms

Ontologies

metadata

Ontology

service

HTTP POST

SPARQL

HTTP POST

modelidApply the model

httphost1modelid

to dataset

httphost2datasetid

Model service

OpenTox API (Application Programming Interface)

bullThe way applications talk to each other

bullThe way developers talk to applications

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

DELETE

Validation

GET

POST

PUT

DELETE

Report

GET

POST

PUT

DELETE

RDF - Resources representation

bull The opentoxowl ontology

ndash A common OWL data model of all

OpenTox resources

ndash Describes OpenTox resources

ndash Describes relationships between them

ndash Generates objects RDF representations

bull RDFXML representation is mandatory for

OpenTox resources

bull Uniform approach to data representation

ndash Calculated and measured properties of

chemical compounds are represented in an

uniform way

ndash Linked to the resource used for data

generation

ndash Annotated via ontology entries

ndash Model representations link to algorithms

and data used

bull

8

All OpenTox components are defined by

OWL ontology

httpopentoxorgapi11opentoxowl

All resources are subclasses of

otOpenToxResource

bull Ontology Server

bull Using the Dataset API

bull Dataset Integration

bull Data quality and accuracy

Outline

2

Component Description URL Template (example)

Compound Representations of chemical compounds httphostportcompoundcompoundid

Feature Properties and identifiers httphostportfeaturefeatureid

Dataset Encapsulates set of chemical compounds and their property

values

httphostportdatasetdatasetid

Model OpenTox model services httphostportmodelmodeld

Algorithm OpenTox algorithm services httphostportalgorithmalgorithmid

Validation

Report

A validation corresponds to the validation of a model on a test

dataset

httphostportvalidationvalidationid

httphostportreportreportid

Task Asynchronous jobs are handled via an intermediate Task

resource A resource submitting an asynchronous job should

return the URI of the task

httphostporttasktaskid

Ontology service Provides storage and SPARQL search functionality for objects

defined in OpenTox services and relevant ontologies

httphostportontology

Authentication and

authorisation

Granting access to protected resources for authorised users httphostportopensso

httphostportopensso-pol

bull Distributed Web services for predictive toxicology

bull REST technology

ndash Every object has an unique URI

ndash URIs are dereferensable

ndash Multiple representation of an object is encouraged (eg RDF but also others)

ndash Fixed operations ndash GET PUT POST DELETE

bull Every object has RDF representationndash Compounds

ndash Datasets

ndash Compound properties

ndash Prediction algorithms

ndash Models

ndash Validation statistics

ndash Reports

bull Ontologies Opentoxowl Blue Obelisk algorithm ontology OpenTox

algotihm types ontology OpenTox endpoints ontology based on ECHA

endpoints classification specific endpoints ontologies developed by ISS amp

ITEM

OpenTox

3

Ontology service

4

bullRDF triple storage

bullREST interface for

registration of OpenTox

objects

bullHTTP POST

bullSPARQL

bullquery

Build a predictive model

Create a model

Run calculations with

dataset

httphost1datasetid

Structures

descriptors

endpoints

Dataset service

Returns the model URL

httphost1modelid

HTTP POST

Build a predictive model

Regression

Classification

Quantum Chemistry

Descriptors etc

validationid

Algorithm service

Validation service

modelid

Published models

Algorithms

Ontologies

metadata

Ontology service

HTTP POST

Model service

Apply predictive models

Returns the results

dataset URL

httphostdatasetid

Retrieve available

endpoints and model

URLs eg

httphost1modelid

Published models

Algorithms

Ontologies

metadata

Ontology

service

HTTP POST

SPARQL

HTTP POST

modelidApply the model

httphost1modelid

to dataset

httphost2datasetid

Model service

OpenTox API (Application Programming Interface)

bullThe way applications talk to each other

bullThe way developers talk to applications

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

DELETE

Validation

GET

POST

PUT

DELETE

Report

GET

POST

PUT

DELETE

RDF - Resources representation

bull The opentoxowl ontology

ndash A common OWL data model of all

OpenTox resources

ndash Describes OpenTox resources

ndash Describes relationships between them

ndash Generates objects RDF representations

bull RDFXML representation is mandatory for

OpenTox resources

bull Uniform approach to data representation

ndash Calculated and measured properties of

chemical compounds are represented in an

uniform way

ndash Linked to the resource used for data

generation

ndash Annotated via ontology entries

ndash Model representations link to algorithms

and data used

bull

8

All OpenTox components are defined by

OWL ontology

httpopentoxorgapi11opentoxowl

All resources are subclasses of

otOpenToxResource

bull Distributed Web services for predictive toxicology

bull REST technology

ndash Every object has an unique URI

ndash URIs are dereferensable

ndash Multiple representation of an object is encouraged (eg RDF but also others)

ndash Fixed operations ndash GET PUT POST DELETE

bull Every object has RDF representationndash Compounds

ndash Datasets

ndash Compound properties

ndash Prediction algorithms

ndash Models

ndash Validation statistics

ndash Reports

bull Ontologies Opentoxowl Blue Obelisk algorithm ontology OpenTox

algotihm types ontology OpenTox endpoints ontology based on ECHA

endpoints classification specific endpoints ontologies developed by ISS amp

ITEM

OpenTox

3

Ontology service

4

bullRDF triple storage

bullREST interface for

registration of OpenTox

objects

bullHTTP POST

bullSPARQL

bullquery

Build a predictive model

Create a model

Run calculations with

dataset

httphost1datasetid

Structures

descriptors

endpoints

Dataset service

Returns the model URL

httphost1modelid

HTTP POST

Build a predictive model

Regression

Classification

Quantum Chemistry

Descriptors etc

validationid

Algorithm service

Validation service

modelid

Published models

Algorithms

Ontologies

metadata

Ontology service

HTTP POST

Model service

Apply predictive models

Returns the results

dataset URL

httphostdatasetid

Retrieve available

endpoints and model

URLs eg

httphost1modelid

Published models

Algorithms

Ontologies

metadata

Ontology

service

HTTP POST

SPARQL

HTTP POST

modelidApply the model

httphost1modelid

to dataset

httphost2datasetid

Model service

OpenTox API (Application Programming Interface)

bullThe way applications talk to each other

bullThe way developers talk to applications

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

DELETE

Validation

GET

POST

PUT

DELETE

Report

GET

POST

PUT

DELETE

RDF - Resources representation

bull The opentoxowl ontology

ndash A common OWL data model of all

OpenTox resources

ndash Describes OpenTox resources

ndash Describes relationships between them

ndash Generates objects RDF representations

bull RDFXML representation is mandatory for

OpenTox resources

bull Uniform approach to data representation

ndash Calculated and measured properties of

chemical compounds are represented in an

uniform way

ndash Linked to the resource used for data

generation

ndash Annotated via ontology entries

ndash Model representations link to algorithms

and data used

bull

8

All OpenTox components are defined by

OWL ontology

httpopentoxorgapi11opentoxowl

All resources are subclasses of

otOpenToxResource

Ontology service

4

bullRDF triple storage

bullREST interface for

registration of OpenTox

objects

bullHTTP POST

bullSPARQL

bullquery

Build a predictive model

Create a model

Run calculations with

dataset

httphost1datasetid

Structures

descriptors

endpoints

Dataset service

Returns the model URL

httphost1modelid

HTTP POST

Build a predictive model

Regression

Classification

Quantum Chemistry

Descriptors etc

validationid

Algorithm service

Validation service

modelid

Published models

Algorithms

Ontologies

metadata

Ontology service

HTTP POST

Model service

Apply predictive models

Returns the results

dataset URL

httphostdatasetid

Retrieve available

endpoints and model

URLs eg

httphost1modelid

Published models

Algorithms

Ontologies

metadata

Ontology

service

HTTP POST

SPARQL

HTTP POST

modelidApply the model

httphost1modelid

to dataset

httphost2datasetid

Model service

OpenTox API (Application Programming Interface)

bullThe way applications talk to each other

bullThe way developers talk to applications

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

DELETE

Validation

GET

POST

PUT

DELETE

Report

GET

POST

PUT

DELETE

RDF - Resources representation

bull The opentoxowl ontology

ndash A common OWL data model of all

OpenTox resources

ndash Describes OpenTox resources

ndash Describes relationships between them

ndash Generates objects RDF representations

bull RDFXML representation is mandatory for

OpenTox resources

bull Uniform approach to data representation

ndash Calculated and measured properties of

chemical compounds are represented in an

uniform way

ndash Linked to the resource used for data

generation

ndash Annotated via ontology entries

ndash Model representations link to algorithms

and data used

bull

8

All OpenTox components are defined by

OWL ontology

httpopentoxorgapi11opentoxowl

All resources are subclasses of

otOpenToxResource

Build a predictive model

Create a model

Run calculations with

dataset

httphost1datasetid

Structures

descriptors

endpoints

Dataset service

Returns the model URL

httphost1modelid

HTTP POST

Build a predictive model

Regression

Classification

Quantum Chemistry

Descriptors etc

validationid

Algorithm service

Validation service

modelid

Published models

Algorithms

Ontologies

metadata

Ontology service

HTTP POST

Model service

Apply predictive models

Returns the results

dataset URL

httphostdatasetid

Retrieve available

endpoints and model

URLs eg

httphost1modelid

Published models

Algorithms

Ontologies

metadata

Ontology

service

HTTP POST

SPARQL

HTTP POST

modelidApply the model

httphost1modelid

to dataset

httphost2datasetid

Model service

OpenTox API (Application Programming Interface)

bullThe way applications talk to each other

bullThe way developers talk to applications

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

DELETE

Validation

GET

POST

PUT

DELETE

Report

GET

POST

PUT

DELETE

RDF - Resources representation

bull The opentoxowl ontology

ndash A common OWL data model of all

OpenTox resources

ndash Describes OpenTox resources

ndash Describes relationships between them

ndash Generates objects RDF representations

bull RDFXML representation is mandatory for

OpenTox resources

bull Uniform approach to data representation

ndash Calculated and measured properties of

chemical compounds are represented in an

uniform way

ndash Linked to the resource used for data

generation

ndash Annotated via ontology entries

ndash Model representations link to algorithms

and data used

bull

8

All OpenTox components are defined by

OWL ontology

httpopentoxorgapi11opentoxowl

All resources are subclasses of

otOpenToxResource

Apply predictive models

Returns the results

dataset URL

httphostdatasetid

Retrieve available

endpoints and model

URLs eg

httphost1modelid

Published models

Algorithms

Ontologies

metadata

Ontology

service

HTTP POST

SPARQL

HTTP POST

modelidApply the model

httphost1modelid

to dataset

httphost2datasetid

Model service

OpenTox API (Application Programming Interface)

bullThe way applications talk to each other

bullThe way developers talk to applications

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

DELETE

Validation

GET

POST

PUT

DELETE

Report

GET

POST

PUT

DELETE

RDF - Resources representation

bull The opentoxowl ontology

ndash A common OWL data model of all

OpenTox resources

ndash Describes OpenTox resources

ndash Describes relationships between them

ndash Generates objects RDF representations

bull RDFXML representation is mandatory for

OpenTox resources

bull Uniform approach to data representation

ndash Calculated and measured properties of

chemical compounds are represented in an

uniform way

ndash Linked to the resource used for data

generation

ndash Annotated via ontology entries

ndash Model representations link to algorithms

and data used

bull

8

All OpenTox components are defined by

OWL ontology

httpopentoxorgapi11opentoxowl

All resources are subclasses of

otOpenToxResource

OpenTox API (Application Programming Interface)

bullThe way applications talk to each other

bullThe way developers talk to applications

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

DELETE

Validation

GET

POST

PUT

DELETE

Report

GET

POST

PUT

DELETE

RDF - Resources representation

bull The opentoxowl ontology

ndash A common OWL data model of all

OpenTox resources

ndash Describes OpenTox resources

ndash Describes relationships between them

ndash Generates objects RDF representations

bull RDFXML representation is mandatory for

OpenTox resources

bull Uniform approach to data representation

ndash Calculated and measured properties of

chemical compounds are represented in an

uniform way

ndash Linked to the resource used for data

generation

ndash Annotated via ontology entries

ndash Model representations link to algorithms

and data used

bull

8

All OpenTox components are defined by

OWL ontology

httpopentoxorgapi11opentoxowl

All resources are subclasses of

otOpenToxResource

RDF - Resources representation

bull The opentoxowl ontology

ndash A common OWL data model of all

OpenTox resources

ndash Describes OpenTox resources

ndash Describes relationships between them

ndash Generates objects RDF representations

bull RDFXML representation is mandatory for

OpenTox resources

bull Uniform approach to data representation

ndash Calculated and measured properties of

chemical compounds are represented in an

uniform way

ndash Linked to the resource used for data

generation

ndash Annotated via ontology entries

ndash Model representations link to algorithms

and data used

bull

8

All OpenTox components are defined by

OWL ontology

httpopentoxorgapi11opentoxowl

All resources are subclasses of

otOpenToxResource

Resources Chemical compound

9

$ curl -H Acceptchemicalx-daylight-smiles

httpappsideaconsultnet8080ambit2compound1

O=C

$ curl -H Acceptchemicalx-mdl-molfile

httpappsideaconsultnet8080ambit2compound1

CH2O

APtclcactv09040902283D 0 000000 000000

4 3 0 0 0 0 0 0 0 0999 V2000

-06004 00000 00001 O 0 0 0 0 0 0 0 0 0 0 0 0

06072 00000 -00004 C 0 0 0 0 0 0 0 0 0 0 0 0

11472 09353 00016 H 0 0 0 0 0 0 0 0 0 0 0 0

11472 -09353 00016 H 0 0 0 0 0 0 0 0 0 0 0 0

1 2 2 0 0 0 0

2 3 1 0 0 0 0

2 4 1 0 0 0 0

CompoundProvides different representations for

chemical compounds with a unique and

defined chemical structurecompoundid

Conformercompoundidconformerid

Documentationhttpopentoxorgdevapisapi-11structure

RepresentationA subclass of otOpenToxResource

Supports different Chemical MIME

formats

RDF representation only for specifying

owlsameAs links to external resources

Example 1 Retrieve compound as MOL

Example 2 Retrieve compound as SMILES

Example 3 Query compounds

$ curl ndashH Acceptchemical-mime ldquo

httpappsideaconsultnet8080ambit2querycompoundany-identifier-or-keyword

$ curl ndashH Acceptchemical-mime ldquo

httpappsideaconsultnet8080ambit2querysmartssearch=smarts

Compound

GET

POST

PUT

DELETE

Resources Dataset

OperationsbullPOST ndash Upload a dataset

bullPUT ndash Update the dataset content

bullDELETE ndash Remove the dataset

RepresentationRDFXML (mandatory) MOL SDF CSV TXT

ARFF (optional)

bullThe dataset consists of data entries

bullEach entry is associated with exactly one

chemical compound identified by its

URI and available via OpenTox

Compound service API

bullOne and the same compound can be

associated with multiple dataset entries

bullEvery ldquocolumnrdquo is associated with a

Feature its representation should be

available via OpenTox Feature API

10

DatasetProvides access to chemical compounds and their

features (eg structural physical-chemical

biological toxicological properties) prefix ad lthttpappsideaconsultnet8080ambit2datasetgt

prefix af lthttpappsideaconsultnet8080ambit2featuregt

prefix ot lthttpwwwopentoxorgapi11gt

hellip

ad9 a otDataset

otdataEntry

[ a otDataEntry

otcompound

lthttpappsideaconsultnet8080ambit2compound413conformer4094

21gt

otvalues

[ a otFeatureValue

otfeature af21576

otvalue 3309999942779541^^xsddouble

]

otvalues

[ a otFeatureValue

otfeature af21573

otvalue 30^^xsddouble

]

]

Feature

GET

POST

PUT

DELETE

Dataset

GET

POST

PUT

DELETE

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 Uniform access to data

11

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

Resources Dataset

OperationsbullPOST ndash Upload a dataset

bullPUT ndash Update the dataset content

bullDELETE ndash Remove the dataset

RepresentationRDFXML (mandatory) MOL SDF CSV TXT

ARFF (optional)

bullThe dataset consists of data entries

bullEach entry is associated with exactly one

chemical compound identified by its

URI and available via OpenTox

Compound service API

bullOne and the same compound can be

associated with multiple dataset entries

bullEvery ldquocolumnrdquo is associated with a

Feature its representation should be

available via OpenTox Feature API

10

DatasetProvides access to chemical compounds and their

features (eg structural physical-chemical

biological toxicological properties) prefix ad lthttpappsideaconsultnet8080ambit2datasetgt

prefix af lthttpappsideaconsultnet8080ambit2featuregt

prefix ot lthttpwwwopentoxorgapi11gt

hellip

ad9 a otDataset

otdataEntry

[ a otDataEntry

otcompound

lthttpappsideaconsultnet8080ambit2compound413conformer4094

21gt

otvalues

[ a otFeatureValue

otfeature af21576

otvalue 3309999942779541^^xsddouble

]

otvalues

[ a otFeatureValue

otfeature af21573

otvalue 30^^xsddouble

]

]

Feature

GET

POST

PUT

DELETE

Dataset

GET

POST

PUT

DELETE

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 Uniform access to data

11

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

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 Uniform access to data

11

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 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

12Ideaconsult LtdMarch 17 2011

bull httpappsideaconsultnet8080ambit2dataset2344 (the dataset)

bull httpappsideaconsultnet8080ambit2dataset2344metadata

(metadata obviously)

Example mutagenicity dataset

13Ideaconsult Ltd

bull httpappsideaconsultnet8080ambit2dataset2344 (the dataset)

bull httpappsideaconsultnet8080ambit2dataset2344metadata

(metadata obviously)

Example mutagenicity dataset

13Ideaconsult Ltd

Example mutagenicity dataset

14Ideaconsult 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

15Ideaconsult LtdMarch 17 2011

bull httpappsideaconsultnet8080ambit2featuresameas=http3A2F2Fwww

opentoxorg2FechaEndpointsowl23Mutagenicity

httpappsideaconsultnet8080ambit2feature21611

httpappsideaconsultnet8080ambit2feature26221

httpappsideaconsultnet8080ambit2feature28958

httpappsideaconsultnet8080ambit2feature21590

Query Is there other mutagenicity data

available

15Ideaconsult 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

16March 17 2011

Dataset metadata and features

17

Description URI Template

Retrieve entire dataset content If uri-list

retrieve only compound URIs

httphostportdatasetid

Retrieve representation of features (columns)

of the dataset

httphostportdatasetidfeature

Retrieves dataset metadata (name etc) httphostportdatasetidmetadata

$ curl -H Acceptapplicationrdf+xml httpappsideaconsultnet8080ambit2dataset9metadata

ltrdfRDF

xmlnsot=httpwwwopentoxorgapi11

helliphellip

xmlnsrdfs=httpwwww3org200001rdf-schema

xmlbase=httpappsideaconsultnet8080ambit2gt

ltotDataset rdfabout=dataset9gt

ltdcsourcegtISSCAN_v3a_1153_19Sept081222179139sdfltdcsourcegt

ltdcpublishergtsomebodyltdcpublishergt

ltrdfsseeAlsogt

ltbxEntry rdfabout=reference20117gt

ltrdfsseeAlsogthttpwwwepagovNCCTdsstoxsdf_isscan_externalhtmlltrdfsseeAlsogt

ltdctitlegtISSCAN_v3a_1153_19Sept081222179139sdfltdctitlegt

ltbxEntrygt

ltrdfsseeAlsogt

ltdctitlegtISSCAN Istituto Superiore di Sanita CHEMICAL CARCINOGENS STRUCTURES AND EXPERIMENTAL DATAltdctitlegt

ltotDatasetgt

ltrdfRDFgt

Dataset metadata and features

17

Description URI Template

Retrieve entire dataset content If uri-list

retrieve only compound URIs

httphostportdatasetid

Retrieve representation of features (columns)

of the dataset

httphostportdatasetidfeature

Retrieves dataset metadata (name etc) httphostportdatasetidmetadata

$ curl -H Acceptapplicationrdf+xml httpappsideaconsultnet8080ambit2dataset9metadata

ltrdfRDF

xmlnsot=httpwwwopentoxorgapi11

helliphellip

xmlnsrdfs=httpwwww3org200001rdf-schema

xmlbase=httpappsideaconsultnet8080ambit2gt

ltotDataset rdfabout=dataset9gt

ltdcsourcegtISSCAN_v3a_1153_19Sept081222179139sdfltdcsourcegt

ltdcpublishergtsomebodyltdcpublishergt

ltrdfsseeAlsogt

ltbxEntry rdfabout=reference20117gt

ltrdfsseeAlsogthttpwwwepagovNCCTdsstoxsdf_isscan_externalhtmlltrdfsseeAlsogt

ltdctitlegtISSCAN_v3a_1153_19Sept081222179139sdfltdctitlegt

ltbxEntrygt

ltrdfsseeAlsogt

ltdctitlegtISSCAN Istituto Superiore di Sanita CHEMICAL CARCINOGENS STRUCTURES AND EXPERIMENTAL DATAltdctitlegt

ltotDatasetgt

ltrdfRDFgt

Published models

Algorithms

Ontologies

metadata

Ontology service

Data publishing

Upload data receive

dataset URL

httphost2datasetid

AnnotationFind chemical compounds

return dataset URL

httphost2compoundid

HTTP GET POST

Dataset service

Structures

endpoints

amppredictions

1)POST a file with chemical structures and properties to

OpenTox dataset servicebullThe structures and data are assigned a dataset URL and

become available by multiple formats (RDF Chemical

MIME CSV Weka ARFF)

2)Assign metadata

bullPUT datasetidmetadata

3)Annotate any of dataset features

datasetidfeature by assigning links to relevant

ontologies

bullPUT featureid

Toxiciology related

ontologies

Algorithms

ontologies

Dataset and Ontology ndash find an

assay linked to specific genePREFIX otlthttpwwwopentoxorgapi11gt

PREFIX otalthttpwwwopentoxorgalgorithmsowlgt

PREFIX owllthttpwwww3org200207owlgt

PREFIX dclthttppurlorgdcelements11gt

PREFIX rdfs lthttpwwww3org200001rdf-schemagt

PREFIX rdflthttpwwww3org19990222-rdf-syntax-nsgt

PREFIX oteelthttpwwwopentoxorgechaEndpointsowlgt

PREFIX toxcastlthttpwwwopentoxorgtoxcastgt

select Feature title id assay geneid genename

where

Feature rdftype otFeature

Feature dctitle title

Feature owlsameAs assay

assay toxcastgene geneid

assay toxcasthasProperty genename

genename rdftype toxcastGENE_NAME

Query an OpenTox ontology service at

httpambituni-plovdivbg8082ontology

httpambituni-

plovdivbg8080ambit2dataset961feat

ure_uris[]=httpambituni-

plovdivbg8080ambit2feature335126

Read data from a web address ndash process ndash write to a web address

OpenTox dataset create a model

20

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

Read data from a web address ndash process ndash write to a web address

OpenTox dataset descriptor calculation

21

Feature

GET

POST

PUT

DELETE

Compound

GET

POST

PUT

DELETE

Dataset

GET

POST

PUT

DELETE

Algorithm

GET

POST

PUT

DELETE

+ =

httpmyhostcomdatasettrainingset1

httpmyhostcomalgorithmdescriptorX

Feature

GET

POST

PUT

DELETE

Compound

GET

POST

PUT

DELETE

Dataset

GET

POST

PUT

DELETE

=

httpmyhostcomdatasetresults

Read data from a web address ndash process ndash write to a web address

OpenTox dataset apply a model

22

Feature

GET

POST

PUT

DELETE

Compound

GET

POST

PUT

DELETE

Dataset

GET

POST

PUT

DELETE

+=

httpmyhostcomdatasetid1

Feature

GET

POST

PUT

DELETE

Compound

GET

POST

PUT

DELETE

Dataset

GET

POST

PUT

DELETE

=

httpmyhostcomdatasetresults1

Model

GET

POST

PUT

DELETE

httpmyhostcommodelpredictivemodel1

OpenTox datasets Substructure and

similarity search

23

httpappsideaconsultnet8080ambit2querysma

rtssearch=c1ccccc1[ClBrFI]

REST web service interface

Datasets Structure and quality labels

24

Linked resources Compound Algorithm Model Dataset Features

Ideaconsult Ltd25

Dataset

Resource

Descriptor

resource

Assay

resource

Chemical

compound

Regression

Classification

Quantum

Chemistry

Descriptorsetc

Blue Obelisk

algorithms

ontology

OpenTox

algorithm types

ontology

Toxiciology related

ontologies

Algorithm

service

Linked resources Compound Algorithm Model Dataset Features

26

Model

resourceDataset

Resource

Descriptor

resource

Assay

resource

Chemical

compound

Feature

service

Feature

service

Compound

service

Thank you

Ideaconsult Ltd27

Dataset and Ontology ndash find an

assay linked to specific genePREFIX otlthttpwwwopentoxorgapi11gt

PREFIX otalthttpwwwopentoxorgalgorithmsowlgt

PREFIX owllthttpwwww3org200207owlgt

PREFIX dclthttppurlorgdcelements11gt

PREFIX rdfs lthttpwwww3org200001rdf-schemagt

PREFIX rdflthttpwwww3org19990222-rdf-syntax-nsgt

PREFIX oteelthttpwwwopentoxorgechaEndpointsowlgt

PREFIX toxcastlthttpwwwopentoxorgtoxcastgt

select Feature title id assay geneid genename

where

Feature rdftype otFeature

Feature dctitle title

Feature owlsameAs assay

assay toxcastgene geneid

assay toxcasthasProperty genename

genename rdftype toxcastGENE_NAME

Query an OpenTox ontology service at

httpambituni-plovdivbg8082ontology

httpambituni-

plovdivbg8080ambit2dataset961feat

ure_uris[]=httpambituni-

plovdivbg8080ambit2feature335126

Read data from a web address ndash process ndash write to a web address

OpenTox dataset create a model

20

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

Read data from a web address ndash process ndash write to a web address

OpenTox dataset descriptor calculation

21

Feature

GET

POST

PUT

DELETE

Compound

GET

POST

PUT

DELETE

Dataset

GET

POST

PUT

DELETE

Algorithm

GET

POST

PUT

DELETE

+ =

httpmyhostcomdatasettrainingset1

httpmyhostcomalgorithmdescriptorX

Feature

GET

POST

PUT

DELETE

Compound

GET

POST

PUT

DELETE

Dataset

GET

POST

PUT

DELETE

=

httpmyhostcomdatasetresults

Read data from a web address ndash process ndash write to a web address

OpenTox dataset apply a model

22

Feature

GET

POST

PUT

DELETE

Compound

GET

POST

PUT

DELETE

Dataset

GET

POST

PUT

DELETE

+=

httpmyhostcomdatasetid1

Feature

GET

POST

PUT

DELETE

Compound

GET

POST

PUT

DELETE

Dataset

GET

POST

PUT

DELETE

=

httpmyhostcomdatasetresults1

Model

GET

POST

PUT

DELETE

httpmyhostcommodelpredictivemodel1

OpenTox datasets Substructure and

similarity search

23

httpappsideaconsultnet8080ambit2querysma

rtssearch=c1ccccc1[ClBrFI]

REST web service interface

Datasets Structure and quality labels

24

Linked resources Compound Algorithm Model Dataset Features

Ideaconsult Ltd25

Dataset

Resource

Descriptor

resource

Assay

resource

Chemical

compound

Regression

Classification

Quantum

Chemistry

Descriptorsetc

Blue Obelisk

algorithms

ontology

OpenTox

algorithm types

ontology

Toxiciology related

ontologies

Algorithm

service

Linked resources Compound Algorithm Model Dataset Features

26

Model

resourceDataset

Resource

Descriptor

resource

Assay

resource

Chemical

compound

Feature

service

Feature

service

Compound

service

Thank you

Ideaconsult Ltd27

Read data from a web address ndash process ndash write to a web address

OpenTox dataset create a model

20

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

Read data from a web address ndash process ndash write to a web address

OpenTox dataset descriptor calculation

21

Feature

GET

POST

PUT

DELETE

Compound

GET

POST

PUT

DELETE

Dataset

GET

POST

PUT

DELETE

Algorithm

GET

POST

PUT

DELETE

+ =

httpmyhostcomdatasettrainingset1

httpmyhostcomalgorithmdescriptorX

Feature

GET

POST

PUT

DELETE

Compound

GET

POST

PUT

DELETE

Dataset

GET

POST

PUT

DELETE

=

httpmyhostcomdatasetresults

Read data from a web address ndash process ndash write to a web address

OpenTox dataset apply a model

22

Feature

GET

POST

PUT

DELETE

Compound

GET

POST

PUT

DELETE

Dataset

GET

POST

PUT

DELETE

+=

httpmyhostcomdatasetid1

Feature

GET

POST

PUT

DELETE

Compound

GET

POST

PUT

DELETE

Dataset

GET

POST

PUT

DELETE

=

httpmyhostcomdatasetresults1

Model

GET

POST

PUT

DELETE

httpmyhostcommodelpredictivemodel1

OpenTox datasets Substructure and

similarity search

23

httpappsideaconsultnet8080ambit2querysma

rtssearch=c1ccccc1[ClBrFI]

REST web service interface

Datasets Structure and quality labels

24

Linked resources Compound Algorithm Model Dataset Features

Ideaconsult Ltd25

Dataset

Resource

Descriptor

resource

Assay

resource

Chemical

compound

Regression

Classification

Quantum

Chemistry

Descriptorsetc

Blue Obelisk

algorithms

ontology

OpenTox

algorithm types

ontology

Toxiciology related

ontologies

Algorithm

service

Linked resources Compound Algorithm Model Dataset Features

26

Model

resourceDataset

Resource

Descriptor

resource

Assay

resource

Chemical

compound

Feature

service

Feature

service

Compound

service

Thank you

Ideaconsult Ltd27

Read data from a web address ndash process ndash write to a web address

OpenTox dataset descriptor calculation

21

Feature

GET

POST

PUT

DELETE

Compound

GET

POST

PUT

DELETE

Dataset

GET

POST

PUT

DELETE

Algorithm

GET

POST

PUT

DELETE

+ =

httpmyhostcomdatasettrainingset1

httpmyhostcomalgorithmdescriptorX

Feature

GET

POST

PUT

DELETE

Compound

GET

POST

PUT

DELETE

Dataset

GET

POST

PUT

DELETE

=

httpmyhostcomdatasetresults

Read data from a web address ndash process ndash write to a web address

OpenTox dataset apply a model

22

Feature

GET

POST

PUT

DELETE

Compound

GET

POST

PUT

DELETE

Dataset

GET

POST

PUT

DELETE

+=

httpmyhostcomdatasetid1

Feature

GET

POST

PUT

DELETE

Compound

GET

POST

PUT

DELETE

Dataset

GET

POST

PUT

DELETE

=

httpmyhostcomdatasetresults1

Model

GET

POST

PUT

DELETE

httpmyhostcommodelpredictivemodel1

OpenTox datasets Substructure and

similarity search

23

httpappsideaconsultnet8080ambit2querysma

rtssearch=c1ccccc1[ClBrFI]

REST web service interface

Datasets Structure and quality labels

24

Linked resources Compound Algorithm Model Dataset Features

Ideaconsult Ltd25

Dataset

Resource

Descriptor

resource

Assay

resource

Chemical

compound

Regression

Classification

Quantum

Chemistry

Descriptorsetc

Blue Obelisk

algorithms

ontology

OpenTox

algorithm types

ontology

Toxiciology related

ontologies

Algorithm

service

Linked resources Compound Algorithm Model Dataset Features

26

Model

resourceDataset

Resource

Descriptor

resource

Assay

resource

Chemical

compound

Feature

service

Feature

service

Compound

service

Thank you

Ideaconsult Ltd27

Read data from a web address ndash process ndash write to a web address

OpenTox dataset apply a model

22

Feature

GET

POST

PUT

DELETE

Compound

GET

POST

PUT

DELETE

Dataset

GET

POST

PUT

DELETE

+=

httpmyhostcomdatasetid1

Feature

GET

POST

PUT

DELETE

Compound

GET

POST

PUT

DELETE

Dataset

GET

POST

PUT

DELETE

=

httpmyhostcomdatasetresults1

Model

GET

POST

PUT

DELETE

httpmyhostcommodelpredictivemodel1

OpenTox datasets Substructure and

similarity search

23

httpappsideaconsultnet8080ambit2querysma

rtssearch=c1ccccc1[ClBrFI]

REST web service interface

Datasets Structure and quality labels

24

Linked resources Compound Algorithm Model Dataset Features

Ideaconsult Ltd25

Dataset

Resource

Descriptor

resource

Assay

resource

Chemical

compound

Regression

Classification

Quantum

Chemistry

Descriptorsetc

Blue Obelisk

algorithms

ontology

OpenTox

algorithm types

ontology

Toxiciology related

ontologies

Algorithm

service

Linked resources Compound Algorithm Model Dataset Features

26

Model

resourceDataset

Resource

Descriptor

resource

Assay

resource

Chemical

compound

Feature

service

Feature

service

Compound

service

Thank you

Ideaconsult Ltd27

OpenTox datasets Substructure and

similarity search

23

httpappsideaconsultnet8080ambit2querysma

rtssearch=c1ccccc1[ClBrFI]

REST web service interface

Datasets Structure and quality labels

24

Linked resources Compound Algorithm Model Dataset Features

Ideaconsult Ltd25

Dataset

Resource

Descriptor

resource

Assay

resource

Chemical

compound

Regression

Classification

Quantum

Chemistry

Descriptorsetc

Blue Obelisk

algorithms

ontology

OpenTox

algorithm types

ontology

Toxiciology related

ontologies

Algorithm

service

Linked resources Compound Algorithm Model Dataset Features

26

Model

resourceDataset

Resource

Descriptor

resource

Assay

resource

Chemical

compound

Feature

service

Feature

service

Compound

service

Thank you

Ideaconsult Ltd27

Datasets Structure and quality labels

24

Linked resources Compound Algorithm Model Dataset Features

Ideaconsult Ltd25

Dataset

Resource

Descriptor

resource

Assay

resource

Chemical

compound

Regression

Classification

Quantum

Chemistry

Descriptorsetc

Blue Obelisk

algorithms

ontology

OpenTox

algorithm types

ontology

Toxiciology related

ontologies

Algorithm

service

Linked resources Compound Algorithm Model Dataset Features

26

Model

resourceDataset

Resource

Descriptor

resource

Assay

resource

Chemical

compound

Feature

service

Feature

service

Compound

service

Thank you

Ideaconsult Ltd27

Linked resources Compound Algorithm Model Dataset Features

Ideaconsult Ltd25

Dataset

Resource

Descriptor

resource

Assay

resource

Chemical

compound

Regression

Classification

Quantum

Chemistry

Descriptorsetc

Blue Obelisk

algorithms

ontology

OpenTox

algorithm types

ontology

Toxiciology related

ontologies

Algorithm

service

Linked resources Compound Algorithm Model Dataset Features

26

Model

resourceDataset

Resource

Descriptor

resource

Assay

resource

Chemical

compound

Feature

service

Feature

service

Compound

service

Thank you

Ideaconsult Ltd27

Algorithm

service

Linked resources Compound Algorithm Model Dataset Features

26

Model

resourceDataset

Resource

Descriptor

resource

Assay

resource

Chemical

compound

Feature

service

Feature

service

Compound

service

Thank you

Ideaconsult Ltd27

Thank you

Ideaconsult Ltd27