ToxBank/isa2rdf

Name: isa2rdf

Owner: ToxBank

Description: ISA-TAB to RDF conversion for ToxBank

Created: 2011-11-17 06:55:57.0

Updated: 2014-09-25 16:37:41.0

Pushed: 2015-08-20 17:20:52.0

Homepage: http://toxbank.github.com/isa2rdf

Size: 47966

Language: Java

GitHub Committers

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README

ISA-TAB to RDF conversion

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

Build

sa2rdf>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

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

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

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.

TAB to RDF conversion
e: org.isa2rdf.cli.IsaClient
--outdatafilesdir <dir>                             Directory to write
                                                    the data files converted to RDF/XML
--dir <dir>                                         Directory with  ISA-TAB files
--help                                              ISA2RDF client
--output <output file>                              Output file
                                                    .n3|.rdf|.nt
--toxbankuri <ToxBank protocol service root URI >   ToxBank protocol service root URI 
--investigationuri <URI>                            URI to be assigned
                                                    to this investigation e.g. http://services.toxbank.net/investigation/12345

isa2rdf-0.0.8.jar

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

isa2rdf-0.0.7.jar

• Fixed NPE when an ontology source is incomplete

isa2rdf-0.0.6.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

• 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

• 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

a -jar isa2rdf-0.0.8.jar
TAB to RDF conversion
e: org.isa2rdf.cli.IsaClient
--dir <dir>                                         Directory with
                                                    ISA-TAB files
--help                                              ISA2RDF client
--output <output file>                              Output file
                                                    .n3|.rdf|.nt
--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:

a -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

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

fix :      <http://onto.toxbank.net/isa/qHTS/> .
fix dc:    <http://purl.org/dc/elements/1.1/> .
fix kw:    <http://www.owl-ontologies.com/toxbank.owl/> .
fix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
fix tb:    <http://onto.toxbank.net/api/> .
fix foaf:  <http://xmlns.com/foaf/0.1/> .
fix isa:   <http://onto.toxbank.net/isa/> .
fix owl:   <http://www.w3.org/2002/07/owl#> .
fix xsd:   <http://www.w3.org/2001/XMLSchema#> .
fix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
fix dcterms: <http://purl.org/dc/terms/> .

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

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

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

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

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

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

Node  rdfs:subClassOf  isa:GraphElement .

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

ple73  a                isa:Material ;
    isa:hasAccessionID  "exp1-A1-C2" ;
    isa:hasFactorValue  :FV4 , :FV2 , :FV1 .

See the full output in N3