Permalink
Fetching contributors…
Cannot retrieve contributors at this time
196 lines (137 sloc) 9.4 KB

toxbank

ISA-TAB to RDF conversion

ISA-TAB RDF classes and properties PDF or N3 or SVG

##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-1.0.2.jar] (http://ambit.uni-plovdiv.bg:8083/nexus/index.html#nexus-search;gav~~isa2rdf-cli~1.0.2~~)

java -jar isa2rdf-1.0.2.jar

  • The data file conversion generates .nt files (N-TRIPLES) as well
  • Converts Comment[Investigation licence] field (investigation.txt file into dcterms:license triple.

[isa2rdf-1.0.1.jar] (http://ambit.uni-plovdiv.bg:8083/nexus/index.html#nexus-search;gav~~isa2rdf-cli~1.0.1~~)

java -jar isa2rdf-1.0.1.jar

  • Converts metabolite profiling files (as generated by the Metabolights database ISACreator plugin) to RDF/XML
  • The data file conversion is triggered by specifying the output directory for converted data files (option -a )
  • The data RDF is an OpenTox Dataset RDF, where features are samples metabolite intensities, as defined by ISA-TAB metadata.
  • Support for ordering Investigation contacts.

[isa2rdf-1.0.0.jar] (http://ambit.uni-plovdiv.bg:8083/nexus/index.html#nexus-search;gav~~isa2rdf-cli~1.0.0~~)

java -jar isa2rdf-1.0.0.jar

  • Converts microarray, mass spec and protein assignment data files to RDF/XML
  • The data file conversion is triggered by specifying the output directory for converted data files (option -a )
  • The investigation URI to be assigned (option -i)
  • The data RDF is an extension of OpenTox Dataset RDF, defined by OpenTox ontology.
ISA-TAB to RDF conversion
usage: org.isa2rdf.cli.IsaClient
 -a,--outdatafilesdir <dir>                             Directory to write
                                                        the data files converted to RDF/XML
 -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 
 -i,--investigationuri <URI>                            URI to be assigned
                                                        to this investigation e.g. http://services.toxbank.net/investigation/12345

[isa2rdf-0.0.8.jar] (http://ambit.uni-plovdiv.bg:8083/nexus/index.html#nexus-search;gav~~isa2rdf-cli~0.0.8~~)

  • Fixed parsing Investigation author URIs as generated by ISACreator 1.7.x

[isa2rdf-0.0.7.jar] (http://ambit.uni-plovdiv.bg:8083/nexus/index.html#nexus-search;gav~~isa2rdf-cli~0.0.7~~)

  • Fixed NPE when an ontology source is incomplete

[isa2rdf-0.0.6.jar] (http://ambit.uni-plovdiv.bg:8083/nexus/index.html#nexus-search;gav~~isa2rdf-cli~0.0.6~~)

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

[isa2rdf-0.0.5-SNAPSHOT.jar] (http://ambit.uni-plovdiv.bg:8083/nexus/index.html#nexus-search;gav~~isa2rdf-cli~0.0.5-SNAPSHOT~~)

  • 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] (https://www.ideaconsult.net/downloads/ISAcreator.SEURAT/isa2rdf-0.0.4.jar)

[isa2rdf-0.0.4-SNAPSHOT.jar] (https://www.ideaconsult.net/downloads/ISAcreator.SEURAT/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] (https://github.com/ToxBank/isa2rdf/downloads)

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

[Maven repository ] (http://ambit.uni-plovdiv.bg:8083/nexus/index.html#nexus-search;gav~~isa2rdf-cli~~~)

##Use

>java -jar isa2rdf-0.0.8.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-0.0.8.jar -d /home/myself/isa2rdf/BII-I-1 -o /home/myself/qHTS/isatab.rdf -t https://services.toxbank.net/toxbank

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

>java -jar isa2rdf-0.0.8.jar -d /home/myself/isa2rdf/qHTS -t https://services.toxbank.net/toxbank

@prefix :      <http://onto.toxbank.net/isa/qHTS/> .
@prefix dc:    <http://purl.org/dc/elements/1.1/> .
@prefix kw:    <http://www.owl-ontologies.com/toxbank.owl/> .
@prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
@prefix tb:    <http://onto.toxbank.net/api/> .
@prefix foaf:  <http://xmlns.com/foaf/0.1/> .
@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/> .

:MN4    a                isa:MaterialNode ;
        isa:hasMaterial  :source76 ;
        isa:hasStudy     :S36 .

<https://services.toxbank.net/toxbank/organisation/G27>
        a       tb:Organization .

isa:hasParameterValue
        a            owl:ObjectProperty ;
        rdfs:domain  isa:ProtocolApplication ;
        rdfs:range   isa:ParameterValue .

:DAN42  a                  isa:DataAcquisition ;
        isa:hasInputNode   :MN16 ;
        isa:hasOutputNode  :DN17 ;
        isa:hasStudy       :S36 .

:CV6    a                isa:CharacteristicValue ;
        isa:hasProperty  :C6 ;
        isa:hasValue     "1"^^xsd:int .

:MN11   a                isa:MaterialNode ;
        isa:hasMaterial  :generic_assay66 ;
        isa:hasStudy     :S36 .

isa:Node  rdfs:subClassOf  isa:GraphElement .

:PRM2   a              isa:Parameter ;
        dcterms:title  "dye" .

:sample73  a                isa:Material ;
        isa:hasAccessionID  "exp1-A1-C2" ;
        isa:hasFactorValue  :FV4 , :FV2 , :FV1 .

See the full output in N3