Provides storage and standard SPARQL endpoint search functionality for objects, defined in OpenTox services and relevant ontologies.

Documentation, Representation, Examples

  • Query : can be sent by GET or POST, according to, or more specific the HTTP Binding
     curl -X POST -H "Content-type:application/x-www-form-urlencoded" \
             -d "query=the-sparql-query-url-encoded" \
             -H "Accept:application/rdf+xml"  -H "subjectid:SECURITY-TOKEN 
  • Resource registration - send via POST of a web form, with a field uri, containing the uri of the registered resource. The resource should return application/rdf+xml representation, otherwise it will not be registered. The security token is optional (depending on whether the resource is protected).
          curl -X POST -d "uri=http://host2:8080/ambit2/dataset/1" http://host1:8080/ontology \
                   -H "subjectid:SECURITY-TOKEN"

Results are returned in several formats, depending on the HTTP Accept header.

  • application/sparql-results+xml
  • text/html
  • text/n3
  • text/csv
  • text/plain

  • Example 1. Retrieve list of features, representing Estrogen receptor gene assay from ToxCast Phase 1 datasets:

    We will be using the predefined SPARQL query at

     curl -H "Accept:text/plain"
     | Feature                                                 | title           | OpentoxDataset                                          | assay                 | genename     |
     | <> | "NVS_NR_hER"    | <> | toxcast:NVS_NR_hER    | toxcast:ESR1 |
     | <> | "ATG_ERE_CIS"   | <>  | toxcast:ATG_ERE_CIS   | toxcast:ESR1 |
     | <> | "ATG_ERa_TRANS" | <>  | toxcast:ATG_ERa_TRANS | toxcast:ESR1 |

    There is one assay NVS_NR_hER from Novascreen ToxCast assays and two (ATG_ERE_CIS,ATG_ERa_TRANS) from Attagene ToxCast assays.

    The predefined SPARQL query looks like is as follows:

     PREFIX rdfs: <>
     PREFIX rdf:<>
     PREFIX owl:<>
     PREFIX dc:<>
     PREFIX ot:<>
     PREFIX toxcast:<>
     select ?Feature ?title ?OpentoxDataset ?assay ?genename
            where {
                ?Feature rdf:type ot:Feature.
           {?Feature ot:hasSource ?OpentoxDataset}.
               {?Feature dc:title ?title}.
               {?Feature owl:sameAs ?assay}.
               {?assay toxcast:gene <>}.
               {?assay toxcast:hasProperty ?genename}.
               {?genename rdf:type toxcast:GENE_NAME}.

    Once we know which features are representing the Estrogen receptor related studies, the three columns can be collated with the ToxCast dataset and data retrieved in various formats.

     curl -H "Accept:chemical/x-mdl-sdfile"[]=[]=[]=
     curl -H "Accept:text/n3"[]=[]=[]=

    Collating with columns from dataset gives a new dataset.

    Or it is also possible to retrieve the assay data for specific compound (e.g. Bisphenol A).

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Last Published: 2018-01-11.