Provides access to chemical compounds and their features (e.g. structural, physical-chemical, biological, toxicological properties).

Documentation, Representation, Examples, Summary

An OpenTox Dataset resource is an instance of class ot:Dataset, a subclass of ot:OpentoxResource.

The concept of a Dataset of chemical compounds is central to OpenTox web services functionality. Algorithm services accept dataset URI in order to build a model, or to generate descriptor values. Model services accept dataset URI in order to apply a model and obtain predictions. Predictions are again returned as dataset URI, which could be subsequently retrieved. Search results (similarity or substructure) are also available as datasets.

The OpenTox Dataset can be thought as a file of chemical compounds, along with their properties, which however, doesn't have a filename, but unique web address and can be read and written remotely. The dataset representation in RDF format is defined in OpenTox ontology as ot:Dataset class, and can be briefly summarized as follows:

The dataset consists of data entries (or data rows);

  • Each row is associated with exactly one chemical compound, identified by its URL and available via OpenTox Compound service API;
  • One and the same compound URL can be associated with multiple dataset rows;
  • Every column is associated with a Feature URL, representation should be available via OpenTox Feature API (described above). A feature is identified by its URL and has name and source,along with other properties. Any OpenTox Dataset, Algorithm or Model can serve as feature source. If the source is an algorithm or model, this allows to exactly identify how the values in the column were generated, and run the same calculations, for new chemical compounds.

This simplified view is illustrated by Table 1.

Simplified representation of OpenTox Dataset
/feature/21591 /feature/21580 /feature/21588
/compound/413/conformer/409421 60-11-7 Solvent Yellow 2; Butter Yellow; 225.3
/compound/44497/conformer/409422 28322-02-3 4-AAF; 4-acetamidofluorene; 223.28
/compound/4480/conformer/409423 129-00-0 Benzo[def]phenanthrene; 202.26
/compound/602/conformer/409424 67-66-3 Formyl trichloride; methane trichloride 119.38

In practice, the RDF representation looks slightly more complex, because each cell in the table is represented by a separate instance of FeatureValue class, which links to the ot:Feature (column header) and holds the value itself.

Besides RDF, one can retrieve various information about the dataset by using text/uri-list mime type and following templates:

Description URI Template
Retrieve entire dataset content. If uri-list, retrieve only compound URIs http://host:port/dataset/id
Retrieve representation of features (columns) of the dataset http://host:port/dataset/id/feature
Retrieves dataset metadata (name, etc.) http://host:port/dataset/id/metadata

  • Example 1. Retrieve dataset metadata in RDF/XML
    $ curl -H "Accept:application/rdf+xml" https://apps.ideaconsult.net/ambit2/dataset/9/metadata
    <rdf:RDF
        xmlns:ac="https://apps.ideaconsult.net/ambit2/compound/"
        xmlns:ot="http://www.opentox.org/api/1.1#"
        xmlns:bx="http://purl.org/net/nknouf/ns/bibtex#"
        xmlns:otee="http://www.opentox.org/echaEndpoints.owl#"
        xmlns:dc="http://purl.org/dc/elements/1.1/"
        xmlns:ar="https://apps.ideaconsult.net/ambit2/reference/"
        xmlns="https://apps.ideaconsult.net/ambit2/"
        xmlns:am="https://apps.ideaconsult.net/ambit2/model/"
        xmlns:af="https://apps.ideaconsult.net/ambit2/feature/"
        xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
        xmlns:ad="https://apps.ideaconsult.net/ambit2/dataset/"
        xmlns:ag="https://apps.ideaconsult.net/ambit2/algorithm/"
        xmlns:owl="http://www.w3.org/2002/07/owl#"
        xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
        xmlns:ota="http://www.opentox.org/algorithmTypes.owl#"
        xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
      xml:base="https://apps.ideaconsult.net/ambit2/">
      <owl:Class rdf:about="http://www.opentox.org/api/1.1#Dataset"/>
      <owl:Class rdf:about="http://purl.org/net/nknouf/ns/bibtex#Entry"/>
      <ot:Dataset rdf:about="dataset/9">
        <dc:source>ISSCAN_v3a_1153_19Sept08.1222179139.sdf</dc:source>
        <dc:publisher>nina</dc:publisher>
        <rdfs:seeAlso>
          <bx:Entry rdf:about="reference/20117">
            <rdfs:seeAlso>http://www.epa.gov/NCCT/dsstox/sdf_isscan_external.html</rdfs:seeAlso>
            <dc:title>ISSCAN_v3a_1153_19Sept08.1222179139.sdf</dc:title>
          </bx:Entry>
        </rdfs:seeAlso>
        <dc:title>ISSCAN: Istituto Superiore di Sanita, CHEMICAL CARCINOGENS: STRUCTURES AND EXPERIMENTAL DATA</dc:title>
      </ot:Dataset>
    </rdf:RDF>
    
  • Example 2. Retrieve list of features URI, used in this dataset
    $ curl -H "Accept:text/uri-list" https://apps.ideaconsult.net/ambit2/dataset/9/feature
    https://apps.ideaconsult.net/ambit2/feature/21572
    https://apps.ideaconsult.net/ambit2/feature/21573
    https://apps.ideaconsult.net/ambit2/feature/21574
    https://apps.ideaconsult.net/ambit2/feature/21575
    https://apps.ideaconsult.net/ambit2/feature/21576
    https://apps.ideaconsult.net/ambit2/feature/21577
    https://apps.ideaconsult.net/ambit2/feature/21578
    https://apps.ideaconsult.net/ambit2/feature/21579
    https://apps.ideaconsult.net/ambit2/feature/21580
    https://apps.ideaconsult.net/ambit2/feature/21581
    https://apps.ideaconsult.net/ambit2/feature/21582
    https://apps.ideaconsult.net/ambit2/feature/21583
    https://apps.ideaconsult.net/ambit2/feature/21584
    https://apps.ideaconsult.net/ambit2/feature/21585
    https://apps.ideaconsult.net/ambit2/feature/21586
    https://apps.ideaconsult.net/ambit2/feature/21587
    https://apps.ideaconsult.net/ambit2/feature/21588
    https://apps.ideaconsult.net/ambit2/feature/21589
    https://apps.ideaconsult.net/ambit2/feature/21590
    https://apps.ideaconsult.net/ambit2/feature/21591
    https://apps.ideaconsult.net/ambit2/feature/21592
    

    Or just the compound URIs (restricted to first 3) via text/uri-list mime type:

  • Example 3. Dataset representation in N3 format
    $ curl -H "Accept:text/uri-list" "https://apps.ideaconsult.net/ambit2/dataset/9?page=0&pagesize=3"
    https://apps.ideaconsult.net/ambit2/compound/413/conformer/409421
    https://apps.ideaconsult.net/ambit2/compound/44497/conformer/409422
    https://apps.ideaconsult.net/ambit2/compound/4480/conformer/409423
    

OpenTox Dataset encapsulates compounds and their property (feature) values.

The RDF triples naturally allow to model binary relationships via Subject-Predicate-Object construct (e.g. molecular_weight has_value 200 ). In order to model higher order relationships (e.g. CompoundX hasProperty molecular_weight with value 200 and more complex statements), two more classes have been introduced in OpenTox resource ontology - namely ot:FeatureValue and ot:DataEntry. ot:FeatureValue class encapsulates the relationship Feature - hasValue - Value.

This is formally defined via object property ot:feature (links to the ot:Feature class), and data property ot:value (holds the value itself). This class can be interpreted as a cell in a table, where each cell contains not only the value, but a reference to the column header as well. This results in a flexible representation, not limited to tabular values. ot:DataEntry class encapsulates the relationship Compound - has values for - specific Features.

This can be thought as a row in a table, where the object property ot:compound specifies the ot:Compound resource, where ot:values object property specifies all the cells (ot:FeatureValue instances) , available in the data entry.

A dataset consists of multiple ot:DataEntry-ies. These classes can be represented as anonymous classes in RDF notations, or have unique URIs.

As an illustration, the content of the dataset https://apps.ideaconsult.net/ambit2/dataset/9 can be retrieved in RDF/XML and N3

  • Example 4. Dataset representation in RDF/XML or N3 format
    curl -H "Accept:application/rdf+xml" https://apps.ideaconsult.net/ambit2/dataset/9
    

    or

    curl -H "Accept:text/n3" https://apps.ideaconsult.net/ambit2/dataset/9
    
  • Example 5. Dataset comparison demo

    Datasets comparison demo

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Last Published: 2017-06-11.