Merge pull request #22 from junszhao/master

Pull request for updating RO queries and RO itself
ISA-tools · Nov 28, 2014 · 02efa2d · 02efa2d
2 parents 7469bc1 + 0874e23
commit 02efa2d
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diff --git a/ro-description/ro-20140403.ttl b/ro-description/ro-20140403.ttl
@@ -151,7 +151,15 @@
 <http://sandbox.wf4ever-project.org/rodl/ROs/soapdenovo-v1-5/> <http://www.openarchives.org/ore/terms/aggregates> <http://w3id.org/isa/soapdenovo2/raw_data_file/19>  .
 <http://sandbox.wf4ever-project.org/rodl/ROs/soapdenovo-v1-5/> <http://www.openarchives.org/ore/terms/aggregates> <http://w3id.org/isa/soapdenovo2/isa-owl>  .
 <http://sandbox.wf4ever-project.org/rodl/ROs/soapdenovo-v1-5/> <http://www.openarchives.org/ore/terms/aggregates> <http://w3id.org/isa/soapdenovo2/raw_data_file/20>  .
-<http://sandbox.wf4ever-project.org/rodl/ROs/soapdenovo-v1-5/> <http://www.openarchives.org/ore/terms/aggregates> <http://w3id.org/isa/soapdenovo2/nanopublication>  .
+<http://sandbox.wf4ever-project.org/rodl/ROs/soapdenovo-v1-5/> <http://www.openarchives.org/ore/terms/aggregates> <http://w3id.org/isa/soapdenovo2/nanopub/1/>  .
+<http://sandbox.wf4ever-project.org/rodl/ROs/soapdenovo-v1-5/> <http://www.openarchives.org/ore/terms/aggregates> <http://w3id.org/isa/soapdenovo2/nanopub/2/>  .
+<http://sandbox.wf4ever-project.org/rodl/ROs/soapdenovo-v1-5/> <http://www.openarchives.org/ore/terms/aggregates> <http://w3id.org/isa/soapdenovo2/nanopub/3/>  .
+<http://sandbox.wf4ever-project.org/rodl/ROs/soapdenovo-v1-5/> <http://www.openarchives.org/ore/terms/aggregates> <http://w3id.org/isa/soapdenovo2/nanopub/4/>  .
+<http://sandbox.wf4ever-project.org/rodl/ROs/soapdenovo-v1-5/> <http://www.openarchives.org/ore/terms/aggregates> <http://w3id.org/isa/soapdenovo2/nanopub/5/>  .
+<http://sandbox.wf4ever-project.org/rodl/ROs/soapdenovo-v1-5/> <http://www.openarchives.org/ore/terms/aggregates> <http://w3id.org/isa/soapdenovo2/nanopub/6/>  .
+<http://sandbox.wf4ever-project.org/rodl/ROs/soapdenovo-v1-5/> <http://www.openarchives.org/ore/terms/aggregates> <http://w3id.org/isa/soapdenovo2/nanopub/7/>  .
+<http://sandbox.wf4ever-project.org/rodl/ROs/soapdenovo-v1-5/> <http://www.openarchives.org/ore/terms/aggregates> <http://w3id.org/isa/soapdenovo2/nanopub/8/>  .
+<http://sandbox.wf4ever-project.org/rodl/ROs/soapdenovo-v1-5/> <http://www.openarchives.org/ore/terms/aggregates> <http://w3id.org/isa/soapdenovo2/nanopub/9/>  .
 <http://sandbox.wf4ever-project.org/rodl/ROs/soapdenovo-v1-5/> <http://www.openarchives.org/ore/terms/aggregates> <http://w3id.org/isa/soapdenovo2/raw_data_file/21>  .
 <http://sandbox.wf4ever-project.org/rodl/ROs/soapdenovo-v1-5/> <http://www.openarchives.org/ore/terms/aggregates> <http://w3id.org/isa/soapdenovo2/derived_data_file/3>  .
 <http://sandbox.wf4ever-project.org/rodl/ROs/soapdenovo-v1-5/> <http://www.openarchives.org/ore/terms/aggregates> <http://sandbox.wf4ever-project.org/rodl/ROs/soapdenovo-v1-5/.ro/annotations/41a99b7b-fa20-445d-abab-8c6e63b94840>  .

diff --git a/ro/make.sh b/ro/make.sh
@@ -55,7 +55,16 @@ ro annotate . dcterms:descriptions "RO that aggregates the ISA documents, the na
 ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/isatab_distribution/1
 ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/isaowl_distribution/1
 ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/study/1
-ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/nanopubs
+ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/nanopub/1/
+ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/nanopub/2/
+ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/nanopub/3/
+ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/nanopub/4/
+ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/nanopub/5/
+ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/nanopub/6/
+ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/nanopub/7/
+ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/nanopub/8/
+ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/nanopub/9/
+
 
 
 ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/derived_data_file/3
@@ -90,7 +99,7 @@ ro annotations
 
 # publish an RO
 
-ro push -d . -r "http://sandbox.wf4ever-project.org/rodl/ROs/" -t "73975122-9503-4000-ba52-d2c2d2bfccbb"
+#ro push -d . -r "http://sandbox.wf4ever-project.org/rodl/ROs/" -t "73975122-9503-4000-ba52-d2c2d2bfccbb"
 
 # End.
 
diff --git a/ro/ro.rdf b/ro/ro.rdf
diff --git a/sparql/ro/hybrid_inputs_isa_provenance.sparql b/sparql/ro/hybrid_inputs_isa_provenance.sparql
@@ -1,10 +1,23 @@
-### TODO: update RO URI
+### Query 6 (Demonstrate querying across the models): Find out more provenance information about the inputs used to generate the results
 
+### Expected results
 
+# input	     sourceData	sourceActivities
+# http://w3id.org/isa/soapdenovo2/raw_data_file/21	http://w3id.org/isa/soapdenovo2/extract/6	http://w3id.org/isa/soapdenovo2/assay_protocol_ref/5
+# http://w3id.org/isa/soapdenovo2/raw_data_file/17	http://w3id.org/isa/soapdenovo2/extract/4	http://w3id.org/isa/soapdenovo2/assay_protocol_ref/5
+# http://w3id.org/isa/soapdenovo2/raw_data_file/19	http://w3id.org/isa/soapdenovo2/extract/5	http://w3id.org/isa/soapdenovo2/assay_protocol_ref/5
+# http://w3id.org/isa/soapdenovo2/raw_data_file/18	http://w3id.org/isa/soapdenovo2/extract/5	http://w3id.org/isa/soapdenovo2/assay_protocol_ref/5
+# http://w3id.org/isa/soapdenovo2/raw_data_file/20	http://w3id.org/isa/soapdenovo2/extract/6	http://w3id.org/isa/soapdenovo2/assay_protocol_ref/5
 
+
+
+
+
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 PREFIX roterms: <http://purl.org/wf4ever/roterms#>
 PREFIX ore: <http://www.openarchives.org/ore/terms/>
 PREFIX wfdesc: <http://purl.org/wf4ever/wfdesc#>
+PREFIX prov: <http://www.w3.org/ns/prov#>
 
 select ?input ?sourceData ?sourceActivities
 where { 

diff --git a/sparql/ro/hybrid_ro_nanopub.sparql b/sparql/ro/hybrid_ro_nanopub.sparql
@@ -1,5 +1,16 @@
-### TODO update RO URI
-### TODO: to be tested
+### Query 7 (Demonstrate querying across the models): Find out the nanopublication statements aggregated in the RO
+
+### Expected results
+
+# http://w3id.org/isa/soapdenovo2/nanopub/1/
+# http://w3id.org/isa/soapdenovo2/nanopub/9/
+# http://w3id.org/isa/soapdenovo2/nanopub/2/
+# http://w3id.org/isa/soapdenovo2/nanopub/3/
+# http://w3id.org/isa/soapdenovo2/nanopub/4/
+# http://w3id.org/isa/soapdenovo2/nanopub/5/
+# http://w3id.org/isa/soapdenovo2/nanopub/6/
+# http://w3id.org/isa/soapdenovo2/nanopub/7/
+# http://w3id.org/isa/soapdenovo2/nanopub/8/
 
 PREFIX ore: <http://www.openarchives.org/ore/terms/>
 PREFIX wfdesc: <http://purl.org/wf4ever/wfdesc#>

diff --git a/sparql/ro/hybrid_workflow_isa_study.sparql b/sparql/ro/hybrid_workflow_isa_study.sparql
@@ -1,8 +1,15 @@
-TODO: update RO URI
+### Query 8 (Demonstrate querying across the models): Find out the study that the workflow in the RO is part of
 
+### Expected results:
+# http://w3id.org/isa/soapdenovo2/study/1	"SOAPdenovo2"
+
+PREFIX ore: <http://www.openarchives.org/ore/terms/>
 PREFIX roterms: <http://purl.org/wf4ever/roterms#>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX prov: <http://www.w3.org/ns/prov#>
 PREFIX wfdesc: <http://purl.org/wf4ever/wfdesc#>
-PREFIX ore: <http://www.openarchives.org/ore/terms/>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
 select distinct ?study ?studyname
 where { 
       <http://sandbox.wf4ever-project.org/rodl/ROs/soapdenovo-v1-5/> ore:aggregates ?workflow .

diff --git a/sparql/ro/inputs_derived_gage_output.sparql b/sparql/ro/inputs_derived_gage_output.sparql
@@ -1,5 +1,9 @@
 ### TODO: update RO URI
 
+### Query 4: Find out the original inputs data used to derive the outputs that are aggregated in this RO
+
+### Expected results: http://w3id.org/isa/soapdenovo2/raw_data_file/17, http://w3id.org/isa/soapdenovo2/raw_data_file/18, http://w3id.org/isa/soapdenovo2/raw_data_file/19, http://w3id.org/isa/soapdenovo2/raw_data_file/20, http://w3id.org/isa/soapdenovo2/raw_data_file/21
+
 PREFIX ore: <http://www.openarchives.org/ore/terms/>
 PREFIX wfdesc: <http://purl.org/wf4ever/wfdesc#>
 PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>

diff --git a/sparql/ro/inputs_role.sparql b/sparql/ro/inputs_role.sparql
@@ -1,5 +1,9 @@
 ### This query is final
 
+### Query 5: Find out the exact role of the inputs <http://w3id.org/isa/soapdenovo2/raw_data_file/17> in the execution of the Galaxy workflow
+
+### Expected result: "GAGE/Reference genome file in FASTA format"
+
 PREFIX roterms: <http://purl.org/wf4ever/roterms#>
 PREFIX wfdesc: <http://purl.org/wf4ever/wfdesc#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

diff --git a/sparql/ro/workflow_generated_gage_results.sparql b/sparql/ro/workflow_generated_gage_results.sparql
@@ -1,4 +1,6 @@
-## The query is final
+## Query1: Find out the workflow used to generate the GAGE result
+
+### Expected results: http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/w/rluo2012-example-1-soapdenovo2-saureus
 
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 PREFIX prov: <http://www.w3.org/ns/prov#>

diff --git a/sparql/ro/workflow_in_the_ro.sparql b/sparql/ro/workflow_in_the_ro.sparql
@@ -1,4 +1,6 @@
-##TODO: update the RO URI
+## Query 2: Find out the workflow(s) aggregated in the RO
+
+### Expected results: http://sandbox.wf4ever-project.org/rodl/ROs/soapdenovo-v1-5/Workflows/Galaxy-Workflow-Workflow_constructed_from_history__reproduce_s.aureus_pipeline_.ga
 
 PREFIX ore: <http://www.openarchives.org/ore/terms/>
 PREFIX wfdesc: <http://purl.org/wf4ever/wfdesc#>

diff --git a/sparql/ro/workflow_inputs.sparql b/sparql/ro/workflow_inputs.sparql
@@ -1,4 +1,13 @@
-### TODO: update RO URI
+### Query 3: Find out the original inputs data used to execute this workflow that is aggregated in this RO
+
+### Expected results: 
+
+### http://w3id.org/isa/soapdenovo2/raw_data_file/17
+### http://w3id.org/isa/soapdenovo2/raw_data_file/18
+### http://w3id.org/isa/soapdenovo2/raw_data_file/19
+### http://w3id.org/isa/soapdenovo2/raw_data_file/20
+### http://w3id.org/isa/soapdenovo2/raw_data_file/21
+
 
 PREFIX ore: <http://www.openarchives.org/ore/terms/>
 PREFIX wfdesc: <http://purl.org/wf4ever/wfdesc#>