##Build
isa2rdf>mvn clean package
[INFO]
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[INFO] Reactor Summary:
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[INFO] isa2rdf ............................................... SUCCESS [2.362s]
[INFO] isa2rdf converter ..................................... SUCCESS [17.080s]
[INFO] isa2rdf-cli ........................................... SUCCESS [2.051s]
[INFO] ------------------------------------------------------------------------
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[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)
- Keywords namespace is now http://www.owl-ontologies.com/toxbank.owl/
- Support for N-TRIPLE output (file extension .nt)
- Expects 'Comment[Owner URI]' instead of 'Comment[Principal Investigator URI]' in i_*.txt as defined in investigation.xml. This configuration is used in ISACreator.SEURAT.
- Added TG-GATES example
- Added toxbank-config as used in ISACreator.SEURAT
[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