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ISA-TAB to RDF conversion for ToxBank
Java Web Ontology Language CSS JavaScript

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isa2rdf
README.md

README.md

toxbank

ISA-TAB to RDF conversion

Build

   isa2rdf>mvn clean package

   [INFO]
   [INFO] ------------------------------------------------------------------------
   [INFO] Reactor Summary:
   [INFO] ------------------------------------------------------------------------
   [INFO] isa2rdf ............................................... SUCCESS [2.362s]
   [INFO] isa2rdf converter ..................................... SUCCESS [17.080s]
   [INFO] isa2rdf-cli ........................................... SUCCESS [2.051s]
   [INFO] ------------------------------------------------------------------------
   [INFO] ------------------------------------------------------------------------
   [INFO] BUILD SUCCESSFUL

Download

isa2rdf-0.0.6-SNAPSHOT.jar

  • Dependency upgraded to Apache jena 2.10.1 (faster RDF input/output)
  • Multiple optimisations in RDF generation

isa2rdf-0.0.5-SNAPSHOT.jar

  • The configuration templates synchronised with the latest ISACreator 1.7.0
  • Added new study template default fields
  • New template for qHTS assays
  • Upgraded isa-tools import_layer dependency to 1.6
  • Fixed to handle multiple entries in the investigation page comments

isa2rdf-0.0.4.jar

isa2rdf-0.0.4-SNAPSHOT.jar

  • Added option -t toxbank protocol service URI, to be able to use specific instance of Toxbank protocol user,organisation,project services.
  • The deleted by mistake ISA.java class is restored and added to the isa2rdf-converter package
  • ISA tools upgraded to import-layer 1.5 (since May 2012)
  • Support for investigation authors (since May 2012)

isa2rdf-0.0.3-SNAPSHOT.jar

  • Fix for investigaton keywords not serialized (capital K).
  • More junit tests

Maven repository

Use

>java -jar isa2rdf-0.0.4-SNAPSHOT.jar
ISA-TAB to RDF conversion
usage: org.isa2rdf.cli.IsaClient
 -d,--dir <dir>                                         Directory with
                                                        ISA-TAB files
 -h,--help                                              ISA2RDF client
 -o,--output <output file>                              Output file
                                                        .n3|.rdf|.nt
 -t,--toxbankuri <ToxBank protocol service root URI >   ToxBank protocol
                                                        service root URI 
                                                        e.g. http://toxbanktest1.opentox.org:8080/toxbank
                                                        or https://services.toxbank.net/toxbank 

Example:

>java -jar isa2rdf-0.0.4-SNAPSHOT.jar -d /home/myself/sa2rdf/BII-S-11 -o /home/myself/BII-S-11/isatab.rdf -t https://services.toxbank.net/toxbank

Example: without -o argument, will write RDF/N3 to console

>java -jar isa2rdf-0.0.1-SNAPSHOT.jar -d /home/myself/sa2rdf/BII-S-11 -t https://services.toxbank.net/toxbank

@prefix :        <http://onto.toxbank.net/isa/TEST/> .
@prefix dc:      <http://purl.org/dc/elements/1.1/> .
@prefix rdfs:    <http://www.w3.org/2000/01/rdf-schema#> .
@prefix isa:     <http://onto.toxbank.net/isa/> .
@prefix owl:     <http://www.w3.org/2002/07/owl#> .
@prefix xsd:     <http://www.w3.org/2001/XMLSchema#> .
@prefix rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix dcterms:  <http://purl.org/dc/terms/> .

:M13303
      a       isa:Material ;
      isa:hasAccessionID "BII-S-11:labelled_extract:a_FP004BA-DNACHIP-transcriptome.992-biotin-labeled" .

:MN4186
      a       isa:MaterialNode ;
      isa:hasAccessionID "BII-S-11:proc:a_FP004BA-DNACHIP-transcriptome.2.4.47:out:0" ;
      isa:hasMaterial :M16232 ;
      isa:hasStudy :S4854 .

:PA20601
      a       isa:MaterialProcessing ;
      isa:hasProtocol :P_10571 .

:MN10215
      a       isa:MaterialProcessing ;
      isa:hasAccessionID "BII-S-11:proc:a_FP004BA-SELDI-MS-proteome.4.6.847" ;
      isa:hasInputNode :MN826 ;
      isa:hasOutputNode :MN3760 ;
      isa:hasProtocolApplication
              :PA21039 ;
      isa:hasStudy :S4854 .

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