The actual Research Object for the case study

ISA-tools · Apr 3, 2014 · f895f29 · f895f29
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diff --git a/ro/Galaxy-wfdesc.rdf b/ro/Galaxy-wfdesc.rdf
@@ -0,0 +1,157 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<!DOCTYPE rdf:RDF [
+    <!ENTITY rdf     "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
+    <!ENTITY rdfs    "http://www.w3.org/2000/01/rdf-schema#" >
+    <!ENTITY owl     "http://www.w3.org/2002/07/owl#" >
+    <!ENTITY xsd     "http://www.w3.org/2001/XMLSchema#" >
+    <!ENTITY xml     "http://www.w3.org/XML/1998/namespace" >
+    <!ENTITY rdfg    "http://www.w3.org/2004/03/trix/rdfg-1/" >
+    <!ENTITY ore     "http://www.openarchives.org/ore/terms/" >
+    <!ENTITY ao      "http://purl.org/ao/" >
+    <!ENTITY dcterms "http://purl.org/dc/terms/" >
+    <!ENTITY foaf    "http://xmlns.com/foaf/0.1/" >
+    <!ENTITY ro      "http://purl.org/wf4ever/ro#" >
+    <!ENTITY wfprov  "http://purl.org/wf4ever/wfprov#" >
+    <!ENTITY wfdesc  "http://purl.org/wf4ever/wfdesc#" >
+    <!ENTITY wf4ever "http://purl.org/wf4ever/wf4ever#" >
+    <!ENTITY roterms "http://purl.org/wf4ever/roterms#" >
+]>
+
+<rdf:RDF xmlns=""
+     xmlns:rdf="&rdf;"
+     xmlns:rdfs="&rdfs;"
+     xmlns:owl="&owl;"
+     xmlns:xsd="&xsd;"
+     xmlns:xml="&xml;"
+     xmlns:rdfg="&rdfg;"
+     xmlns:ore="&ore;"
+     xmlns:ao="&ao;"
+     xmlns:dcterms="&dcterms;"
+     xmlns:foaf="&foaf;"
+     xmlns:ro="&ro;"
+     xmlns:wfprov="&wfprov;"
+     xmlns:wfdesc="&wfdesc;"
+     xmlns:wf4ever="&wf4ever;"
+     xmlns:roterms="&roterms;"
+>
+
+
+  <wfprov:Artifact rdf:about="Inputs/saureus_A_L1_101bp180IS45X_1.fq">
+      <rdfs:seeAlso rdf:resource="http://w3id.org/isa/soapdenovo2/raw_data_file/18" />
+  </wfprov:Artifact>
+
+  <wfprov:Artifact rdf:about="Inputs/saureus_A_L1_101bp180IS45X_2.fq">
+    <rdfs:seeAlso rdf:resource="http://w3id.org/isa/soapdenovo2/raw_data_file/19" />
+  </wfprov:Artifact>
+
+  <wfprov:Artifact rdf:about="Inputs/saureus_B_L3_37bp3500IS45X_1.fq">
+      <rdfs:seeAlso rdf:resource="http://w3id.org/isa/soapdenovo2/raw_data_file/20" />
+  </wfprov:Artifact>
+
+<wfprov:Artifact rdf:about="Inputs/saureus_B_L3_37bp3500IS45X_2.fq">
+    <rdfs:seeAlso rdf:resource="http://w3id.org/isa/soapdenovo2/raw_data_file/21" />
+</wfprov:Artifact>
+
+<wfprov:Artifact rdf:about="Inputs/saureus.fasta">
+    <rdfs:seeAlso rdf:resource="http://w3id.org/isa/soapdenovo2/raw_data_file/17" />
+</wfprov:Artifact>
+
+
+  <wfdesc:Workflow rdf:about="Workflows/Galaxy-Workflow-Workflow_constructed_from_history__reproduce_s.aureus_pipeline_.ga">
+    <rdfs:seeAlso rdf:resource="http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/w/rluo2012-example-1-soapdenovo2-saureus" />
+    <rdfs:seeAlso rdf:resource="http://w3id.org/isa/soapdenovo2/assay_protocol_ref/14" />
+    <rdfs:label>Galaxy workflow for reproducing Table 2 of SOAPdenovo paper</rdfs:label>
+    <dcterms:title>Galaxy workflow for reproducing Table 2 of SOAPdenovo paper</dcterms:title>
+    <rdfs:comment>Galaxy workflow for reproducing Table 2 of SOAPdenovo paper</rdfs:comment>
+    <dcterms:description>
+      Galaxy workflow for reproducing Table 2 of SOAPdenovo paper
+    </dcterms:description>
+    <wfdesc:hasWorkflowDefinition rdf:resource="http://www.myexperiment.org/workflows/4078.html" />
+    <wfdesc:hasWorkflowDefinition rdf:resource="http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/w/rluo2012-example-1-soapdenovo2-saureus"/>
+
+
+    <wfdesc:hasInput>
+      <wfdesc:Input>
+        <wfdesc:hasArtifact rdf:resource="Inputs/saureus_A_L1_101bp180IS45X_1.fq" />
+        <rdfs:label>Workflow input file for KmerFreq AR</rdfs:label>
+      </wfdesc:Input>
+    </wfdesc:hasInput>
+
+    <roterms:inputValue>
+      <roterms:inputValue>
+          <roterms:portName>KmerFreq AR/Library1/Forward FASTQ file</roterms:portName>
+          <roterms:resource rdf:resource="Inputs/saureus_A_L1_101bp180IS45X_1.fq"/>
+      </roterms:inputValue>
+    </roterms:inputValue>
+
+    <wfdesc:hasInput>
+      <wfdesc:Input>
+        <wfdesc:hasArtifact rdf:resource="Inputs/saureus_A_L1_101bp180IS45X_2.fq" />
+        <rdfs:label>Workflow input file for KmerFreq AR</rdfs:label>
+      </wfdesc:Input>
+    </wfdesc:hasInput>
+
+    <roterms:inputValue>
+        <roterms:inputValue>
+            <roterms:portName>KmerFreq AR/Library1/Reverse FASTQ file</roterms:portName>
+            <roterms:resource rdf:resource="Inputs/saureus_A_L1_101bp180IS45X_2.fq"/>
+        </roterms:inputValue>
+    </roterms:inputValue>
+
+
+   <wfdesc:hasInput>
+      <wfdesc:Input>
+        <wfdesc:hasArtifact rdf:resource="Inputs/saureus_B_L3_37bp3500IS45X_1.fq" />
+        <rdfs:label>Workflow input file for SOAPdenovo2</rdfs:label>
+      </wfdesc:Input>
+    </wfdesc:hasInput>
+
+   <roterms:inputValue>
+       <roterms:inputValue>
+           <roterms:portName>SOAPdenovo2/Library2/Forward FASTQ file</roterms:portName>
+           <roterms:resource rdf:resource="Inputs/saureus_B_L3_37bp3500IS45X_1.fq"/>
+       </roterms:inputValue>
+    </roterms:inputValue>
+
+   <wfdesc:hasInput>
+      <wfdesc:Input>
+        <wfdesc:hasArtifact rdf:resource="Inputs/saureus_B_L3_37bp3500IS45X_2.fq" />
+        <rdfs:label>Workflow input file for SOAPdenovo2</rdfs:label>
+      <rdfs:comment>TODO:Upload and share the data</rdfs:comment>
+      </wfdesc:Input>
+    </wfdesc:hasInput>
+
+    <roterms:inputValue>
+        <roterms:inputValue>
+            <roterms:portName>SOAPdenovo2/Library2/Reverse FASTQ file</roterms:portName>
+            <roterms:resource rdf:resource="Inputs/saureus_B_L3_37bp3500IS45X_2.fq"/>
+        </roterms:inputValue>
+    </roterms:inputValue>
+
+
+   <wfdesc:hasInput>
+      <wfdesc:Input>
+        <wfdesc:hasArtifact rdf:resource="Inputs/saureus.fasta" />
+        <rdfs:label>Workflow input file for GAGE/Reference genome file in FASTA format</rdfs:label>
+      </wfdesc:Input>
+    </wfdesc:hasInput>
+
+    <roterms:inputValue>
+        <roterms:inputValue>
+            <roterms:portName>GAGE/Reference genome file in FASTA format</roterms:portName>
+            <roterms:resource rdf:resource="Inputs/saureus.fasta"/>
+        </roterms:inputValue>
+    </roterms:inputValue>
+
+    <wfdesc:hasOutput>
+      <wfdesc:Output>
+        <wfdesc:hasArtifact rdf:resource="Outputs/gage.out.Tabular" />
+        <rdfs:label>Workflow output file</rdfs:label>
+      </wfdesc:Output>
+    </wfdesc:hasOutput>
+
+  </wfdesc:Workflow>
+
+</rdf:RDF>
+
diff --git a/ro/NanoStm/nanopub1.trig b/ro/NanoStm/nanopub1.trig
@@ -0,0 +1,69 @@
+@prefix this: <http://purl.org/isatab/soapdenovo2/nanopub/000001> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix rdfg: <http://www.w3.org/2004/03/trix/rdfg-1/> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix dc: <http://purl.org/dc/terms/> .
+@prefix pav: <http://swan.mindinformatics.org/ontologies/1.2/pav/> .
+@prefix np: <http://www.nanopub.org/nschema#> .
+
+<http://purl.org/isatab/soapdenovo2/nanopub/000001/context> {
+	this: np:hasProvenance <http://purl.org/isatab/soapdenovo2/nanopub/000001/provenance> ;
+		a np:Nanopublication ;
+		np:hasPublicationInfo <http://purl.org/isatab/soapdenovo2/nanopub/000001/pubInfo> ;
+		np:hasAssertion <http://purl.org/isatab/soapdenovo2/nanopub/000001/assertion> .
+}
+
+<http://purl.org/isatab/soapdenovo2/nanopub/000001/assertion> {
+	<http://purl.org/isatab/soapdenovo2/nanopub/000001/genome_coverage2> <http://purl.obolibrary.org/obo/IAO_0000136> <http://purl.org/isatab/soapdenovo2/nanopub/000001/genome_coverage2> .
+
+	<http://w3id.org/isa/soapdenovo2/> <http://purl.obolibrary.org/obo/OBI_0000299> <http://purl.org/isatab/soapdenovo2/nanopub/000001/http://w3id.org/isa/soapdenovo2/> .
+
+	<http://purl.org/isatab/soapdenovo2/nanopub/000001/human_genome_YH> rdf: <http://purl.obolibrary.org/obo/SO_0001026> .
+
+	<http://purl.org/isatab/soapdenovo2/nanopub/000001/organism_YH > rdf: <http://purl.obolibrary.org/obo/NCBITaxon_9606> .
+
+	<http://w3id.org/isa/soapdenovo2/> rdf: <http://purl.obolibrary.org/obo/OBI_0001872> .
+
+	<http://purl.org/isatab/soapdenovo2/nanopub/000001/genome_assembly1> <http://purl.obolibrary.org/obo/IAO_0000136> <http://purl.org/isatab/soapdenovo2/nanopub/000001/genome_assembly1> .
+
+	<http://purl.org/isatab/soapdenovo2/nanopub/000001/human_genome_YH> <http://purl.obolibrary.org/obo/so_genome_of> <http://purl.org/isatab/soapdenovo2/nanopub/000001/human_genome_YH> .
+
+	<http://purl.org/isatab/soapdenovo2/nanopub/000001/genome_coverage1> <http://purl.obolibrary.org/obo/IAO_0000136> <http://purl.org/isatab/soapdenovo2/nanopub/000001/genome_coverage1> .
+
+	<http://purl.org/isatab/soapdenovo2/nanopub/000001/genome_assembly1> rdf: <http://purl.obolibrary.org/obo/SO_0000353> .
+
+	<http://purl.org/isatab/soapdenovo2/nanopub/000001/organism_YH > rdf: <http://purl.org/isatab/soapdenovo2/nanopub/000001/organism_YH > .
+
+	<http://purl.org/isatab/soapdenovo2/nanopub/000001/genome_assembly2> rdf: <http://purl.obolibrary.org/obo/SO_0000353> ;
+		<http://purl.obolibrary.org/obo/IAO_0000136> <http://purl.org/isatab/soapdenovo2/nanopub/000001/genome_assembly2> .
+
+	<http://purl.org/isatab/soapdenovo2/nanopub/000001/genome_coverage2> <http://semanticscience.org/resource/SIO_000734> <http://purl.org/isatab/soapdenovo2/nanopub/000001/genome_coverage2> .
+}
+
+<http://purl.org/isatab/soapdenovo2/nanopub/000001/provenance> {
+	<http://purl.org/isatab/soapdenovo2/nanopub/000001/genome coverage2> <http://purl.obolibrary.org/obo/IAO_0000039> <http://mimi.case.edu/ontologies/2009/1/UnitsOntology#percent> .
+
+	<http://purl.org/isatab/soapdenovo2/nanopub/000001/SOAPdenovo2_process> <http://purl.org/isatab/soapdenovo2/nanopub/000001/SOAPdenovo2_process> <http://purl.org/isatab/soapdenovo2/nanopub/000001/SOAPdenovo2_process> .
+
+	<http://purl.org/isatab/soapdenovo2/nanopub/000001/SOAPdenovo2_algorithm> rdf: <http://purl.obolibrary.org/obo/OBI_0001522> .
+
+	<http://purl.org/isatab/soapdenovo2/nanopub/000001/SOAPdenovo1_process> <http://purl.org/isatab/soapdenovo2/nanopub/000001/SOAPdenovo1_process> <http://purl.org/isatab/soapdenovo2/nanopub/000001/SOAPdenovo1_process> .
+
+	<http://purl.org/isatab/soapdenovo2/nanopub/000001/genome coverage_v1> <http://purl.obolibrary.org/obo/IAO_0000039> <http://mimi.case.edu/ontologies/2009/1/UnitsOntology#percent> .
+
+	<http://purl.org/isatab/soapdenovo2/nanopub/000001/genome coverage2> <http://purl.obolibrary.org/obo/IAO_0000004> <http://purl.org/isatab/soapdenovo2/nanopub/000001/genome coverage2> .
+
+	<http://purl.org/isatab/soapdenovo2/nanopub/000001/SOAPdenovo1_algorithm> rdf: <http://purl.obolibrary.org/obo/OBI_0001522> .
+
+	<http://purl.org/isatab/soapdenovo2/nanopub/000001/genome coverage_v1> <http://purl.obolibrary.org/obo/IAO_0000004> <http://purl.org/isatab/soapdenovo2/nanopub/000001/genome coverage_v1> .
+}
+
+<http://purl.org/isatab/soapdenovo2/nanopub/000001/pubInfo> {
+	<http://purl.org/isatab/soapdenovo2/nanopub/000001/<nanopubURI\>> dc:created <http://purl.org/isatab/soapdenovo2/nanopub/000001/<nanopubURI\>> ;
+		dc:rightsHolder <http://purl.org/isatab/soapdenovo2/nanopub/000001/<nanopubURI\>> ;
+		dc:bibliographicCitation <http://dx.doi.org/10.1186/2047-217X-1-18> ;
+		dc:creator <http://w3id.org/people/agbeltran> , <http://w3id.org/people/proccaserra> ;
+		dc:hasVersion <http://purl.org/isatab/soapdenovo2/nanopub/000001/<nanopubURI\>> .
+}
diff --git a/ro/Outputs/gage.out.Tabular b/ro/Outputs/gage.out.Tabular
@@ -0,0 +1 @@
+80	98.6	25	71.5	38	1086	2	1078