Two query points to access BioInterchange are provided on the internet:
The interactive web-interfaces makes use of the RESTful web-service.
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...
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 arebiointerchange.gff3
: Generic Feature Format Version 3biointerchange.gvf
: Genome Variation Formatdbcls.catanns.json
: PubAnnotation categorical annotationsphylotastic.newick
: Newick tree file formatuk.ac.man.pdfx
: PDFxOUTPUT_METHOD
: determines the RDFization method that should be used, output will always be RDF N-Triples; available output formats arerdf.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 stringA 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