Merge pull request #57 from SciDAP/master

DOI and corresponding README

README.md

@@ -31,18 +31,77 @@ Incomplete descriptions are welcome as long as they are usable. Generally sharin
 
 For your convinience [Apache Jena Fuseki](https://jena.apache.org/documentation/fuseki2/) SPARQL server is provided. It automaticaly downloads new CWL tool descriptions converts them into XML/RDF format and makes available at https://sparql-test.commonwl.org. Each CWL tool becomes a graph that can be queried. 
 Provided sample queries all the graphs where foaf:name **"Dobin"** is present. 
+
+To run a simple query that searches for all graphs(cwl files) where foaf:name is "Dobin":
+```SPARQL
+    PREFIX foaf: <http://xmlns.com/foaf/0.1/>
+    PREFIX doap: <http://usefulinc.com/ns/doap#>
+        SELECT distinct ?file ?name
+    WHERE {
+      graph ?file {
+      ?P foaf:name ?name  .
+      FILTER (regex(?name, "Dobin","i"))
+      }
+    }
+    LIMIT 25
+```
+
+If you use different ontologies like schema and foaf you can join them in one query using union: 
+```SPARQL
+    PREFIX schema: <http://schema.org/>
+    PREFIX foaf: <http://xmlns.com/foaf/0.1/>
+    PREFIX adms: <http://www.w3.org/ns/adms#>    
+    SELECT ?file ?name 
+    WHERE {
+      graph ?file {
+      {
+       ?P a foaf:Person;
+            foaf:name ?name.
+       ?x adms:includedAsset ?SSC .
+       ?SSC !schema:Thing+ ?P .
+       FILTER (regex(?name, "Dobin","i"))
+       }
+     union {
+       ?P a schema:Person;
+            schema:name ?name.
+       ?SSC a schema:SoftwareSourceCode .
+       ?file ?direct ?SSC .
+       ?SSC !schema:Thing+ ?P .
+       FILTER (regex(?name, "Karimi","i"))
+       }
+      }
+    }
+```
+
+If you provide DOI url and use it as id for a class, it will be automaticaly pulled into default graph. You can query DOI information to find corresponding CWL:
+```SPARQL
+    PREFIX foaf: <http://xmlns.com/foaf/0.1/>
+	PREFIX schema: <http://schema.org/>
+    SELECT distinct ?file ?DOI ?name
+    WHERE {
+       ?DOI ?direct0 ?P .
+       ?P foaf:name ?name  .    
+       FILTER (regex(?name, "Lorincz","i"))
+    GRAPH ?file {
+        ?SSC a schema:SoftwareSourceCode .
+        ?file ?direct1 ?SSC .
+        ?SSC !schema:Thing+ ?DOI .
+        } 
+    }
+```
+
+Another one:
 ```SPARQL
-PREFIX foaf: <http://xmlns.com/foaf/0.1/>
-PREFIX doap: <http://usefulinc.com/ns/doap#>
-
-SELECT distinct ?file ?name
-WHERE {
-  graph ?file {
-  ?P foaf:name ?name  .
-  FILTER (regex(?name, "Dobin","i"))
-  }
-}
-LIMIT 25
+    PREFIX schema: <http://schema.org/>
+    PREFIX foaf: <http://xmlns.com/foaf/0.1/>
+    select distinct ?file ?name
+    where {
+    ?pub !schema:Thing+ ?Person .
+    ?Person foaf:name ?name .
+    graph ?file {
+        ?SSC schema:publication ?pub .
+     } 
+    }
 ```
 
 

tools/GATK-FastaAlternateReferenceMaker.cwl

@@ -1,7 +1,4 @@
 #!/usr/bin/env cwl-runner
-#
-# Author: [email protected] (http://orcid.org/0000-0001-9102-5681) / Cincinnati Children’s Hospital Medical Center / Dr. Barski Lab
-# Developed for CWL consortium http://commonwl.org/
 
 cwlVersion: "cwl:draft-3.dev3"
 
@@ -85,32 +82,27 @@ $namespaces:
   doap: http://usefulinc.com/ns/doap#
   adms: http://www.w3.org/ns/adms#
   dcat: http://www.w3.org/ns/dcat#
+  schema: http://schema.org/
 
 $schemas:
-- http://schema.rdfs.org/all.rdf
+- https://sparql-test.commonwl.org/schema.rdf
 - http://dublincore.org/2012/06/14/dcterms.rdf
 - http://xmlns.com/foaf/spec/20140114.rdf
 - http://usefulinc.com/ns/doap#
 - http://www.w3.org/ns/adms#
 - http://www.w3.org/ns/dcat.rdf
 
-adms:includedAsset:
-  $include: GATK-ontology.yaml
-
-doap:name: "GATK-FastaAlternateReferenceMaker.cwl"
-dcat:downloadURL: "https://github.com/common-workflow-language/workflows/blob/master/tools/GATK-FastaAlternateReferenceMaker.cwl"
-doap:repository:
-- class: doap:GitRepository
-  doap:location: "https://github.com/common-workflow-language/workflows"
-doap:homepage: "http://commonwl.org/"
-doap:license: "Apache2"
-
-doap:maintainer:
-- class: foaf:Organization
-  foaf:name: "Barski Lab, Cincinnati Children's Hospital Medical Center"
-  foaf:member:
-  - class: foaf:Person
-    id: "http://orcid.org/0000-0001-9102-5681"
-    foaf:openid: "http://orcid.org/0000-0001-9102-5681"
-    foaf:name: "Andrey Kartashov"
-    foaf:mbox: "mailto:Andrey.Kartashov@cchmc.org"
+schema:mainEntity:
+  $import: https://scidap.com/description/tools/GATK.yaml
+
+schema:downloadUrl: https://github.com/common-workflow-language/workflows/blob/master/tools/GATK-FastaAlternateReferenceMaker.cwl
+schema:codeRepository: https://github.com/common-workflow-language/workflows
+schema:license: http://www.apache.org/licenses/LICENSE-2.0
+schema:isPartOf:
+  class: schema:CreativeWork
+  schema:name: "Common Workflow Language"
+  schema:url: http://commonwl.org/
+
+schema:author:
+  $import: https://scidap.com/description/porter.yaml
+

tools/GATK-RealignTargetCreator.cwl

@@ -143,7 +143,6 @@ doap:maintainer:
 
 requirements:
 - $import: envvar-global.cwl
-- $import: envvar-global.cwl
 - $import: GATK-docker.cwl
 
 inputs:

tools/alea-alignReads.cwl

@@ -150,7 +150,7 @@ $schemas:
 - https://sparql-test.commonwl.org/schema.rdf
 
 schema:mainEntity:
-  $import: alea-ontology.inc
+  $import: https://scidap.com/description/tools/alea.yaml
 
 schema:downloadUrl: https://github.com/common-workflow-language/workflows/blob/master/tools/alea-alignReads.cwl
 schema:codeRepository: https://github.com/common-workflow-language/workflows
@@ -161,4 +161,4 @@ schema:isPartOf:
   schema:url: http://commonwl.org/
 
 schema:author:
-  $import: https://scidap.com/porter.yaml
+  $import: https://scidap.com/description/porter.yaml

tools/alea-createGenome.cwl

@@ -158,7 +158,7 @@ $schemas:
 - https://sparql-test.commonwl.org/schema.rdf
 
 schema:mainEntity:
-  $import: alea-ontology.inc
+  $import: https://scidap.com/description/tools/alea.yaml
 
 schema:downloadUrl: https://github.com/common-workflow-language/workflows/blob/master/tools/alea-createGenome.cwl
 schema:codeRepository: https://github.com/common-workflow-language/workflows
@@ -169,4 +169,4 @@ schema:isPartOf:
   schema:url: http://commonwl.org/
 
 schema:author:
-  $import: https://scidap.com/porter.yaml
+  $import: https://scidap.com/description/porter.yaml

tools/alea-insilico.cwl

@@ -104,7 +104,7 @@ $schemas:
 #- http://topbraid.org/schema/schema.rdf
 
 schema:mainEntity:
-  $import: alea-ontology.inc
+  $import: https://scidap.com/description/tools/alea.yaml
 
 schema:downloadUrl: https://github.com/common-workflow-language/workflows/blob/master/tools/alea-insilico.cwl
 schema:codeRepository: https://github.com/common-workflow-language/workflows
@@ -115,5 +115,5 @@ schema:isPartOf:
   schema:url: http://commonwl.org/
 
 schema:author:
-  $import: https://scidap.com/porter.yaml
+  $import: https://scidap.com/description/porter.yaml
 

tools/alea-phaseVCF.cwl

@@ -47,7 +47,7 @@ $schemas:
 - https://sparql-test.commonwl.org/schema.rdf
 
 schema:mainEntity:
-  $import: alea-ontology.inc
+  $import: https://scidap.com/description/tools/alea.yaml
 
 schema:downloadUrl: https://github.com/common-workflow-language/workflows/blob/master/tools/alea-phaseVCF.cwl
 schema:codeRepository: https://github.com/common-workflow-language/workflows
@@ -58,4 +58,4 @@ schema:isPartOf:
   schema:url: http://commonwl.org/
 
 schema:author:
-  $import: https://scidap.com/porter.yaml
+  $import: https://scidap.com/description/porter.yaml

tools/cwl-credentials.inc

@@ -0,0 +1,65 @@
+class: schema:CreativeWork
+
+schema:name: "Common Workflow Language"
+schema:url: http://commonwl.org/
+schema:license: http://www.apache.org/licenses/LICENSE-2.0
+
+schema:workExample:
+- class: schema:SoftwareSourceCode
+  schema:codeRepository: https://github.com/common-workflow-language/workflows
+
+schema:schemaVersion: http://common-workflow-language.github.io/draft-3/
+
+schema:author:
+- class: schema:Organization
+  schema:name: "Curoverse"
+  schema:member:
+  - class: schema:Person
+    id: "http://orcid.org/0000-0003-3566-7705"
+    schema:name: "Peter Amstutz"
+    schema:email: "mailto:[email protected]"
+- class: schema:Organization
+  schema:name: "Seven Bridges Genomics"
+  schema:member:
+  - class: schema:Person
+    id: "mailto:[email protected]"
+    schema:name: "Nebojša Tijanić"
+    schema:email: "mailto:[email protected]"
+
+schema:contributor:
+- class: schema:Organization
+  schema:name: "Seven Bridges Genomics"
+  schema:member:
+  - class: schema:Person
+    schema:name: "Luka Stojanovic"
+    schema:email: "mailto:[email protected]"
+- class: schema:Organization
+  schema:name: "Galaxy Project, Pennsylvania State University"
+  schema:member:
+  - class: schema:Person
+    schema:name: "John Chilton"
+    schema:email: "mailto:[email protected]"
+- class: schema:Organization
+  schema:name: "University of California, Davis"
+  schema:member:
+  - class: schema:Person
+    schema:name: "Michael R. Crusoe"
+    schema:email: "mailto:[email protected]"
+- class: schema:Organization
+  schema:name: "Institut Pasteur"
+  schema:member:
+  - class: schema:Person
+    schema:name: "Hervé Ménager"
+    schema:email: "mailto:[email protected]"
+- class: schema:Organization
+  schema:name: "BioDatomics"
+  schema:member:
+  - class: schema:Person
+    schema:name: "Maxim Mikheev"
+    schema:email: "mailto:[email protected]"
+- class: schema:Organization
+  schema:name: "University of Manchester"
+  schema:member:
+  - class: schema:Person
+    schema:name: "Stian Soiland-Reyes"
+    schema:email: "mailto:[email protected]"

tools/samtools-faidx.cwl

@@ -53,7 +53,7 @@ $schemas:
 - https://sparql-test.commonwl.org/schema.rdf
 
 schema:mainEntity:
-  $import: samtools-ontology.inc
+  $import: https://scidap.com/description/tools/samtools.yaml
 
 description: |
   samtools-faidx.cwl is developed for CWL consortium
@@ -68,4 +68,4 @@ schema:isPartOf:
   schema:url: http://commonwl.org/
 
 schema:author:
-  $import: https://scidap.com/porter.yaml
+  $import: https://scidap.com/description/porter.yaml