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BioInterchange

Shell Tool

BioInterchange's command-line tool biointerchange can be installed as a command line tools as follows: 

gem install biointerchange

Usage

Examples: 

biointerchange --input biointerchange.gvf --rdf rdf.biointerchange.gfvo --batchsize 100 --file examples/estd176_Banerjee_et_al_2011.2012-11-29.NCBI36.gvf
biointerchange --input dbcls.catanns.json --rdf rdf.bh12.sio --file examples/pubannotation.10096561.json --annotate_name 'Peter Smith' --annotate_name_id 'peter.smith@example.com'
biointerchange --input uk.ac.man.pdfx --rdf rdf.bh12.sio --file examples/gb-2007-8-3-R40.xml --annotate_name 'Peter Smith' --annotate_name_id 'peter.smith@example.com'
biointerchange --input phylotastic.newick --rdf rdf.phylotastic.newick --file examples/tree2.new --annotate_date '1 June 2006'
Input formats: Output formats:
  • rdf.biointerchange.gfvo: RDFization of biointerchange.gff3
  • rdf.biointerchange.gfvo: RDFization of biointerchange.gvf
  • rdf.bh12.sio: RDFization of dbcls.catanns.json or uk.ac.man.pdfx
  • rdf.phylotastic.newick: RDFization of phylotastic.newick

Using a Triple Store

RDF data produced by BioInterchange can be directly loaded into a triple store. The following gives an example about loading and querying RDF data using Sesame; the commands are entered via Sesame's bin/console.sh: 

> create memory.
Please specify values for the following variables:
Repository ID [memory]: testrepo
Repository title [Memory store]: Test Repository
Persist (true|false) [true]: false
Sync delay [0]:
Repository created
> open testrepo.
testrepo> load  .
testrepo> sparql select * where { ?s ?p ?o } .
To list all seqid entries from a GFF3/GVF-file conversion in the store, the following SPARQL query can be used: 
testrepo> sparql select * where { ?s <http://www.biointerchange.org/gvf1o#GVF1_0004> ?o } .

Example Data Provenance

The following list provides information on the origin of the example-data files in the examples directory: