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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.gvf --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.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

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 } .

Data Consistency Verification

Data consistency is verifyable for the output formats rdf.biointerchange.gff3 and rdf.biointerchange.gvf using the BioInterchange ontologies GFF3O and GVF1O. The following is an example of how Jena's command line tools and the HermiT reasoner can be used for conistency verification: 

rdfcat <path-to-gff3o/gvf1o> <yourdata.n3> > merged.xml
java -d64 -Xmx4G -jar HermiT.jar -k -v merged.xml
Another approach is to load the data and its related GFF3O/GVF1O ontology into Protege, merge them, and then use the "Explain inconsistent ontology" menu item to inspect possible data inconsistencies.

Example Data Provenance

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