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Web-Services

Two query points to access BioInterchange are provided on the internet:

  1. an interactive web-interface
  2. a RESTful web-service

The interactive web-interfaces makes use of the RESTful web-service.

Interactive Web-Interface

Select the input format of the data:

Select the RDF serialization method (output format):
Not all output format are supported for a given input format. Invalid choices are disabled automatically here.

Paste Input-Specific Example

Input format specific parameters:
These parameters add meta-data to the data below. This meta-data says something about the data that is not represented in the data structure itself. For example, it could be a version number or date of when the data was created.
Paste data for RDFization below:

RDF output:
Generate RDF Clear RDF

RDF output will be concatenated here...

RESTful Web-Service

A RESTful web-service is available via the URI: http://www.biointerchange.org/service/rdfizer.biocgi

RDFization parameters and data are send as a single HTTP POST requests containing a JSON object. The JSON object has to be formatted as follows:

{
  "parameters" : {
    "input" : "INPUT_FORMAT",
    "output": "OUTPUT_METHOD"
  },
  "data" : "URL_ENCODED_DATA"
}
  • INPUT_FORMAT: determines the input data type; available input formats are
  • OUTPUT_METHOD: determines the RDFization method that should be used, output will always be RDF N-Triples; available output formats are
    • rdf.biointerchange.gff3: RDFization of biointerchange.gff3
    • rdf.biointerchange.gvf: RDFization of biointerchange.gvf
    • rdf.bh12.sio: RDFization of dbcls.catanns.json or uk.ac.man.pdfx
    • rdf.phylotastic.newick: RDFization of phylotastic.newick
  • URL_ENCODED_DATA: data for RDFization as URL encoded string

Example

A query example is part of BioInterchange's source repository. The file webservice_example.json contains the following query:

{
    "parameters" : {
      "input" : "biointerchange.gff3",
      "output": "rdf.biointerchange.gff3"
    },
    "data" : "ChrX.38%09bovine_complete_cds_gmap_perfect%09gene%0915870%0916254%09.%09+%09.%09ID%3DBC109609_ChrX.38%0AChrX.38%09bovine_complete_cds_gmap_perfect%09mRNA%0915870%0916254%09.%09+%09.%09ID%3Dbovine_complete_cds_gmap_perfect_BC109609_ChrX.38%3BParent%3DBC109609_ChrX.38%0AChrX.38%09bovine_complete_cds_gmap_perfect%09CDS%0915870%0916254%09.%09+%090%09Parent%3Dbovine_complete_cds_gmap_perfect_BC109609_ChrX.38%0AChrX.38%09bovine_complete_cds_gmap_perfect%09exon%0915870%0916254%09.%09+%090%09Parent%3Dbovine_complete_cds_gmap_perfect_BC109609_ChrX.38%0A"
}

The query can be run using the popular [cURL](http://en.wikipedia.org/wiki/CURL) tool:

curl -d '@webservice_example.json' http://www.biointerchange.org/service/rdfizer.biocgi