SOAPdenovo2 Case Study

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Overview | Galaxy Workflows | Data Models | Queries | Contributors

Overview

The SOAPdenovo2 case study is a reproducibility study aimed at exploring how existing research objects and workflow enactment engines can help assess, record and preserve scientific workflows and associated findings by reviewing a comparison between sequence assembly algorithm performance in the light of development of the SOAPdenovo2 de novo genome assembler. The case study was a joint effort by the GigaScience journal, the Investigation/Study/Assay (ISA) infrastructure, Nanopublication (Nanopub) and Research Object (RO) communities and SOAPdenovo2 de novo genome assembler developers.

The following presentation, delivered at the International Society for Molecular Biology (ISMB) 2014 workshop on What bioinformaticians need to know about digital publishing beyond the PDF2" in Boston, USA, showcases the SOAPdenovo2 study and explores how principles derived from experimental design practice, data and computational models can greatly enhance data quality, data generation, data reporting, data publication and data review.

ISMB Workshop 2014 from Alejandra Gonzalez-Beltran

The following publication describes the SOAPdenovo2 case study and our recommendations to improving scholarly publishing using research object models.

PLOS One article
PLOS One Article
DOI: 10.1371/journal.pone.0127612

An earlier version was available as a pre-print.

Also, this work was presented at the Bionformatics Open Source Conference (BOSC) 2015 and these are the slides:

From peer-reviewed to peer-reproduced: a role for research objects in scholarly publishing in the life sciences from Alejandra Gonzalez-Beltran

Galaxy Workflows

The Galaxy workflows and corresponding histories for reproducing part of the SOAPdenovo2 study, i.e. Table 2 from the original paper, can be found at the GigaGalaxy server, and these are the specific links, classified by organism and genome assembler:

Organism / Assembler SOAPdenovo2 SOAPdenovo1 AllPathsLG
S. Aureus Workflow Workflow Workflow
History History History
R. Sphaeroides Workflow Workflow Workflow
History History History

Data Models: ISA, RO and Nanopublication

The ISA model, with its focus on experimental design, insists on the declaration of study plans (e.g., experimental factors considered) and provides cues for reviewers to assess content and suitability of the plans. Furthermore, the underlying model ensures that inputs and outputs of processes, or workflows, are declared and identified, referring to existing database identifiers when relevant. Initially intended to draw the graph of sample processing through to coarse data processing, the ISA grammar is generic enough to cover computational processing while allowing referencing to more granular forms such as Galaxy files.

ISA and RO both provide means to track experimental and computational workflows respectively, with some level of acknowledged overlap which is handled by deferring to the domain specific resources, with Research Object project recommending ISA for the biological domain. Finally, since describing how data are acquired, generated and analyzed is only part of the story, the description of the findings requires attention. The Nanopublication model tackles what used to represent the blind side of data reporting: capturing experimental conclusion.

Investigation-Study-Assay

Scope:
Experimental Design, Variable, Material Processing, Data Processing workflows.
Outcomes:
  • an tab-delimited archive presenting an overview of the SOAPdenovo2 experiment following the ISA-TAB specification: it includes a description of the experimental design (e.g. independent and response variables), the genomes and data used in SOAPdenovo2 together with stable identifiers, a description of the experimental and computational workflows for evaluation of SOAPdenovo2 with its predecessors SOAPdenovo1 and ALLPATHSLG, including their inputs and outputs, provenance and attribution information
  • an explicit OWL/RDF semantic representation generated using ISA2OWL software component and relying on mappings between the ISA syntax and ontological resources such as the Ontology for Biomedical Investigations (OBI) and the Provenance ontology (PROV-O).

Nanopublication

Scope:
Key findings, supporting evidence
Outcome:

Research Object

Scope:
Scientific workflow artifacts
Outcome:

Queries

We provide a set of queries demonstrating how the data models can be used to inspect the information about the SOAPdenovo2 study and its results. The following table summarises the queries and the model(s) used to answer them. The queries themselves and links to execute them can be found through the table and below.

Query Case RO ISA Nanopub
Who were involved in the study? See and execute query
What are the inputs and outputs for all the data transformations in the study? (for inputs) See query See and execute query
What are the Galaxy workflows related to the SOAPdenovo2 case study? See and execute query
What was the study design? See and execute query
What are the study factors (or independent variables) and their levels (or values they assumed)? See and execute query
How many study groups are there? See and execute query
Which are the study groups? See and execute query
Which are the members of the study groups? See and execute query
What are the sizes of the study groups? See and execute query
What was funding agency of the study? See and execute query
What is the licence for the metadata? See and execut query
What is the PubMed identifier for the associated publications(s) for the study? See and execute query
Find all the nanopublications related to the study See query See and execute query See and execute query
Find the authors for each assertion in the nanopublications See and execute query
Find the nanopublications and their associated authors See and execute query

Next, we list the different queries and provide links to the results of executing them in an SPARQL endpoint.

Queries over the ISA research model

Who where the people involved in creating the ISA-Tab representation and what were their roles?

contacts.sparql

25
 
1
PREFIX  rdfs: <http://www.w3.org/2000/01/rdf-schema#>
2
PREFIX  ro:   <http://purl.obolibrary.org/obo/RO_>
3
PREFIX  tax:  <http://purl.obolibrary.org/obo/NCBITaxon_>
4
PREFIX  iao:  <http://purl.obolibrary.org/obo/IAO_>
5
PREFIX  owl:  <http://www.w3.org/2002/07/owl#>
6
PREFIX  xsd:  <http://www.w3.org/2001/XMLSchema#>
7
PREFIX  isa:  <http://purl.org/isaterms/>
8
PREFIX  rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
9
PREFIX  obi:  <http://purl.obolibrary.org/obo/OBI_>
10
PREFIX  bfo:  <http://purl.obolibrary.org/obo/BFO_>
11
​
12
SELECT DISTINCT  ?person_name ?person_iri ?role
13
WHERE
14
  { ?person_iri rdf:type tax:9606 .
15
    ?person_iri rdfs:label ?person_name .
16
    ?person_iri bfo:0000056 ?study .
17
    ?study rdf:type isa:study
18
    OPTIONAL
19
      { ?role_iri rdf:type obi:0000202 .
20
        ?person_iri bfo:0000087 ?role_iri .
21
        ?role_iri rdfs:label ?role
22
      }
23
  }
24
​
25
​

Execute this SPARQL query over the SOAPdenovo2 named graph (http://w3id.org/isa/soapdenovo2).

What are the inputs and outputs for all the data transformations in the study?

data_transf_inputs_outputs.sparql

22
 
1
PREFIX iao: <http://purl.obolibrary.org/obo/IAO_>
2
PREFIX obi: <http://purl.obolibrary.org/obo/OBI_>
3
PREFIX tax: <http://purl.obolibrary.org/obo/NCBITaxon_>
4
PREFIX isa: <http://purl.org/isa-tools/ISA_>
5
PREFIX ro: <http://purl.obolibrary.org/obo/RO_>
6
​
7
SELECT DISTINCT
8
?dt, ?inputfile, ?outputfile
9
WHERE
10
{
11
    #?dt_iri rdf:type obi:data_transformation
12
    ?dt_iri rdf:type obi:0200000.
13
​
14
    ?dt_iri rdfs:label ?dt.
15
    ?dt_iri obi:0000293 ?inputfile_iri.
16
    ?dt_iri obi:0000299 ?outputfile_iri.
17
    ?inputfile_iri rdfs:label ?inputfile.
18
    ?outputfile_iri rdfs:label ?outputfile.
19
}
20
​
21
​
22
​

Execute this SPARQL query over the SOAPdenovo2 named graph (http://w3id.org/isa/soapdenovo2).

What are the Galaxy workflows related to the SOAPdenovo2 case study?

galaxy_workflows.sparql

 
1
PREFIX  isa:  <http://purl.org/isaterms/>
2
PREFIX  obi:  <http://purl.obolibrary.org/obo/OBI_>
3
PREFIX  iao:  <http://purl.obolibrary.org/obo/IAO_>
4
​
5
SELECT DISTINCT ?workflow
6
WHERE
7
{
8
#?galaxy_workflow_iri rdf:type obi:planned_process
9
?galaxy_workflow_iri rdf:type obi:0000011.
10
​
11
?galaxy_workflow_iri isa:has_parameter_value ?parameter_iri.
12
?parameter_iri rdfs:label ?parameter.
13
​
14
?galaxy_workflow_iri isa:has_parameter_value ?workflow_iri.
15
?workflow_iri rdfs:label ?workflow.
16
​
17
​
18
FILTER(regex(str(?parameter),"Galaxy") )
19
FILTER(regex(str(?workflow),"gigascience") )
20
}
21
​

Execute this SPARQL query over the SOAPdenovo2 named graph (http://w3id.org/isa/soapdenovo2).

What was the study design?

study_design_type.sparql

21
 
1
PREFIX  isa:  <http://purl.org/isaterms/>
2
PREFIX  obi:  <http://purl.obolibrary.org/obo/OBI_>
3
PREFIX  iao:  <http://purl.obolibrary.org/obo/IAO_>
4
​
5
SELECT DISTINCT ?study ?design_type ?design_type_label
6
WHERE
7
{
8
?study rdf:type isa:study.
9
​
10
#design_iri iao:denotes ?study.
11
?design_iri iao:0000219 ?study.
12
​
13
#?design_iri rdf:type obi:study_design
14
?design_iri rdf:type obi:0500000.
15
​
16
?design_iri rdf:type ?design_type.
17
OPTIONAL{
18
?design_type rdfs:label ?design_type_label.
19
}
20
}
21
​

Execute this SPARQL query over the SOAPdenovo2 named graph (http://w3id.org/isa/soapdenovo2).

What are the study factors (or independent variables) and their levels?

factors_and_levels.sparql

17
 
1
PREFIX  rdfs: <http://www.w3.org/2000/01/rdf-schema#>
2
PREFIX  ro:   <http://purl.obolibrary.org/obo/RO_>
3
PREFIX  tax:  <http://purl.obolibrary.org/obo/NCBITaxon_>
4
PREFIX  iao:  <http://purl.obolibrary.org/obo/IAO_>
5
PREFIX  isa:  <http://purl.org/isaterms/>
6
PREFIX  rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
7
PREFIX  obi:  <http://purl.obolibrary.org/obo/OBI_>
8
​
9
SELECT DISTINCT  ?factor ?factor_level
10
WHERE
11
  { ?study_design rdf:type isa:study_design .
12
    ?study_design isa:declares ?factor_iri .
13
    ?factor_iri rdfs:label ?factor .
14
    ?factor_iri isa:has_factor_level ?factor_level_iri .
15
    ?factor_level_iri rdfs:label ?factor_level
16
  }
17
​

Execute this SPARQL query over the SOAPdenovo2 named graph (http://w3id.org/isa/soapdenovo2).

How many study groups are there?

study_group_count.sparql

27
 
1
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
2
PREFIX owl: <http://www.w3.org/2002/07/owl#>
3
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
4
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
5
PREFIX bfo: <http://purl.obolibrary.org/obo/BFO_>
6
PREFIX iao: <http://purl.obolibrary.org/obo/IAO_>
7
PREFIX obi: <http://purl.obolibrary.org/obo/OBI_>
8
PREFIX tax: <http://purl.obolibrary.org/obo/NCBITaxon_>
9
PREFIX isa: <http://purl.org/isaterms/>
10
PREFIX ro: <http://purl.obolibrary.org/obo/RO_>
11
​
12
SELECT  DISTINCT (COUNT(*) AS ?count)
13
WHERE
14
{
15
    ?study rdf:type isa:study.    # could be replaced by: ?study rdf:type obi:0000066.
16
17
    #?study_design is obi:study_design
18
    ?study_design_iri rdf:type obi:0500000.
19
    #?study_design iao:denotes ?study_iri
20
    ?study_design iao:0000219 ?study.
21
22
     ?study_group_iri rdf:type isa:study_group_population.
23
     # ?study_design iao:denotes ?study_group_iri
24
     ?study_design iao:0000219 ?study_group_iri.
25
}
26
​
27
​

Execute this SPARQL query over the SOAPdenovo2 named graph (http://w3id.org/isa/soapdenovo2).

Which are the study groups?

study_groups.sparql

16
 
1
PREFIX  rdfs: <http://www.w3.org/2000/01/rdf-schema#>
2
PREFIX  iao:  <http://purl.obolibrary.org/obo/IAO_>
3
PREFIX  isa:  <http://purl.org/isaterms/>
4
PREFIX  rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
5
PREFIX  obi:  <http://purl.obolibrary.org/obo/OBI_>
6
​
7
SELECT DISTINCT  ?study_group_iri ?label
8
WHERE
9
  { ?study rdf:type obi:0000066 .
10
    ?study_design_iri rdf:type obi:0500000 .
11
    ?study_design iao:0000219 ?study .
12
    ?study_group_iri rdf:type isa:study_group_population .
13
    ?study_design iao:0000219 ?study_group_iri .
14
    ?study_group_iri rdfs:label ?label
15
  }
16
​

Execute this SPARQL query over the SOAPdenovo2 named graph (http://w3id.org/isa/soapdenovo2).

Which are the members of the study groups?

study_group_members.sparql

14
 
1
PREFIX  rdfs: <http://www.w3.org/2000/01/rdf-schema#>
2
PREFIX  isa:  <http://purl.org/isaterms/>
3
PREFIX  rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
4
PREFIX  obi:  <http://purl.obolibrary.org/obo/OBI_>
5
​
6
SELECT  ?study_group_iri ?study_group ?member
7
WHERE
8
  { ?study_group_iri rdf:type isa:study_group_population .
9
    ?study_group_iri isa:has_member ?member_iri .
10
    ?member_iri rdfs:label ?member .
11
    ?study_group_iri rdfs:label ?study_group
12
  }
13
ORDER BY DESC(?study_group_iri)
14
​

Execute this SPARQL query over the SOAPdenovo2 named graph (http://w3id.org/isa/soapdenovo2).

What are the sizes of the study groups?

study_groups_sizes.sparql

23
 
1
PREFIX  rdfs: <http://www.w3.org/2000/01/rdf-schema#>
2
PREFIX  iao:  <http://purl.obolibrary.org/obo/IAO_>
3
PREFIX  isa:  <http://purl.org/isaterms/>
4
PREFIX  rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
5
PREFIX  obi:  <http://purl.obolibrary.org/obo/OBI_>
6
​
7
SELECT DISTINCT  ?study_group (count(?member) AS ?member_count)
8
WHERE
9
  { ?study_group_iri isa:has_member ?member_iri .
10
    ?member_iri rdfs:label ?member .
11
    ?study_group_iri rdfs:label ?study_group
12
    { SELECT DISTINCT  ?study_group_iri
13
      WHERE
14
        { ?study rdf:type obi:0000066 .
15
          ?study_design_iri rdf:type obi:0500000 .
16
          ?study_design_iri iao:0000219 ?study .
17
          ?study_group_iri rdf:type isa:study_group_population .
18
          ?study_design_iri iao:0000219 ?study_group_iri
19
        }
20
    }
21
  }
22
GROUP BY ?study_group
23
​

Execute this SPARQL query over the SOAPdenovo2 named graph (http://w3id.org/isa/soapdenovo2).

What was funding agency of the study?

study_funding_agency.sparql

10
 
1
PREFIX isa: <http://purl.org/isaterms/>
2
​
3
SELECT DISTINCT ?study ?funder
4
WHERE
5
{
6
?study rdf:type isa:study.
7
?study rdfs:comment ?funder.
8
FILTER( regex(str(?funder), "Funding"))
9
}
10
​

Execute this SPARQL query over the SOAPdenovo2 named graph (http://w3id.org/isa/soapdenovo2).

What is the licence for the metadata?

study_metadata_licence.sparql

10
 
1
PREFIX  isa:  <http://purl.org/isaterms/>
2
​
3
SELECT DISTINCT  ?study ?licence
4
WHERE
5
{
6
?study rdf:type isa:study.
7
?study rdfs:comment ?licence.
8
FILTER( regex(str(?licence), "Licence"))
9
}
10
​

Execute this SPARQL query over the SOAPdenovo2 named graph (http://w3id.org/isa/soapdenovo2).

What is the PubMed identifier for the associated publications(s) for the study?

study_publication_pubmedid.sparql

22
 
1
PREFIX  isa:  <http://purl.org/isaterms/>
2
PREFIX  obi:  <http://purl.obolibrary.org/obo/OBI_>
3
PREFIX  iao:  <http://purl.obolibrary.org/obo/IAO_>
4
​
5
SELECT DISTINCT ?study ?publication_iri ?pubmedid
6
WHERE
7
{
8
?study rdf:type isa:study.
9
​
10
#publication_iri iao:denotes ?study.
11
?publication_iri iao:0000219 ?study.
12
​
13
#?publication_iri rdf:type iao:publication
14
?publication_iri rdf:type iao:0000311.
15
​
16
?pubmedid_iri iao:0000219 ?publication_iri.
17
?pubmedid_iri rdf:type obi:0001617.
18
​
19
?pubmedid_iri rdfs:label ?pubmedid.
20
​
21
}
22
​

Execute this SPARQL query over the SOAPdenovo2 named graph (http://w3id.org/isa/soapdenovo2).

What are the nanopublications genereated for the study?

isa_nanopubs.sparql

20
 
1
PREFIX iao: <http://purl.obolibrary.org/obo/IAO_>
2
PREFIX obi: <http://purl.obolibrary.org/obo/OBI_>
3
PREFIX tax: <http://purl.obolibrary.org/obo/NCBITaxon_>
4
PREFIX isa: <http://purl.org/isa-tools/ISA_>
5
PREFIX ro: <http://purl.obolibrary.org/obo/RO_>
6
​
7
SELECT DISTINCT
8
?nanopubs ?nanopub_dt, ?inputfile,
9
WHERE
10
{
11
  #?nanopub_dt rdf:type obi:data_transformation
12
  ?nanopub_dt rdf:type obi:0200000.
13
  ?nanopub_dt rdfs:label "Nanopub"^^<http://www.w3.org/2001/XMLSchema#string>.
14
  ?nanopub_dt obi:0000293 ?inputfile_iri.
15
  ?nanopub_dt obi:0000299 ?outputfile_iri.
16
  ?inputfile_iri rdfs:label ?inputfile.
17
  ?outputfile_iri rdfs:label ?nanopubs.
18
}
19
​
20
​

Execute this SPARQL query over the SOAPdenovo2 named graph (http://w3id.org/isa/soapdenovo2).

Queries over the Nanopublication research model

Find all the nanopublications related to the study

all_nanopubs.sparql

8
 
1
prefix rdfg: <http://www.w3.org/2004/03/trix/rdfg-1/>
2
​
3
SELECT ?g
4
WHERE
5
{
6
?g rdfg:subGraphOf <http://w3id.org/isa/soapdenovo2/nanopubs>.
7
}
8
​

Execute this SPARQL query.

Find the authors for each assertion in the nanopublications

assertion_author.sparql

19
 
1
prefix prov: <http://www.w3.org/ns/prov#>
2
prefix nanopub1:  <http://w3id.org/isa/soapdenovo2/nanopub/1>
3
​
4
SELECT ?assertion ?orcid
5
FROM NAMED <http://w3id.org/isa/soapdenovo2/nanopub/1/provenance>
6
FROM NAMED <http://w3id.org/isa/soapdenovo2/nanopub/2/provenance>
7
FROM NAMED <http://w3id.org/isa/soapdenovo2/nanopub/3/provenance>
8
FROM NAMED <http://w3id.org/isa/soapdenovo2/nanopub/4/provenance>
9
FROM NAMED <http://w3id.org/isa/soapdenovo2/nanopub/5/provenance>
10
FROM NAMED <http://w3id.org/isa/soapdenovo2/nanopub/6/provenance>
11
FROM NAMED <http://w3id.org/isa/soapdenovo2/nanopub/7/provenance>
12
FROM NAMED <http://w3id.org/isa/soapdenovo2/nanopub/8/provenance>
13
WHERE
14
{
15
    GRAPH ?src {
16
     ?assertion prov:wasAttributedTo ?orcid.
17
    }
18
}
19
​

Execute this SPARQL query over the SOAPdenovo2 named graph (http://w3id.org/isa/soapdenovo2).

Find the nanopublications and their associated authors

nanopub_author.sparql

18
 
1
prefix dct: <http://purl.org/dc/terms/>
2
​
3
SELECT ?nanopub ?orcid
4
FROM NAMED <http://w3id.org/isa/soapdenovo2/nanopub/1/pubInfo>
5
FROM NAMED <http://w3id.org/isa/soapdenovo2/nanopub/2/pubInfo>
6
FROM NAMED <http://w3id.org/isa/soapdenovo2/nanopub/3/pubInfo>
7
FROM NAMED <http://w3id.org/isa/soapdenovo2/nanopub/4/pubInfo>
8
FROM NAMED <http://w3id.org/isa/soapdenovo2/nanopub/5/pubInfo>
9
FROM NAMED <http://w3id.org/isa/soapdenovo2/nanopub/6/pubInfo>
10
FROM NAMED <http://w3id.org/isa/soapdenovo2/nanopub/7/pubInfo>
11
FROM NAMED <http://w3id.org/isa/soapdenovo2/nanopub/8/pubInfo>
12
WHERE
13
{
14
    GRAPH ?src {
15
     ?nanopub dct:creator ?orcid.
16
    }
17
}
18
​

Execute this SPARQL query over the SOAPdenovo2 named graph (http://w3id.org/isa/soapdenovo2).

Queries over the Research Object

hybrid_inputs_isa_provenance.sparql

15
 
1
### TODO: update RO URI
2
​
3
​
4
​
5
PREFIX roterms: <http://purl.org/wf4ever/roterms#>
6
PREFIX ore: <http://www.openarchives.org/ore/terms/>
7
PREFIX wfdesc: <http://purl.org/wf4ever/wfdesc#>
8
​
9
select ?input ?sourceData ?sourceActivities
10
where {
11
      <http://sandbox.wf4ever-project.org/rodl/ROs/soapdenovo-v1-5/> ore:aggregates ?workflow .
12
      ?workflow rdf:type wfdesc:Workflow; roterms:inputSelected ?input .
13
      ?input prov:wasDerivedFrom ?sourceData ; prov:wasGeneratedBy ?sourceActivities .
14
}
15
​

hybrid_ro_nanopub.sparql

13
 
1
### TODO update RO URI
2
### TODO: to be tested
3
​
4
PREFIX ore: <http://www.openarchives.org/ore/terms/>
5
PREFIX wfdesc: <http://purl.org/wf4ever/wfdesc#>
6
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
7
PREFIX np: <http://www.nanopub.org/nschema#>
8
​
9
select distinct ?nanopub
10
where {
11
      <http://sandbox.wf4ever-project.org/rodl/ROs/soapdenovo-v1-5/> ore:aggregates ?nanopub .
12
      ?nanopub rdf:type np:Nanopublication.}
13
​

hybrid_workflow_isa_study.sparql

14
 
1
TODO: update RO URI
2
​
3
PREFIX roterms: <http://purl.org/wf4ever/roterms#>
4
PREFIX wfdesc: <http://purl.org/wf4ever/wfdesc#>
5
PREFIX ore: <http://www.openarchives.org/ore/terms/>
6
select distinct ?study ?studyname
7
where {
8
      <http://sandbox.wf4ever-project.org/rodl/ROs/soapdenovo-v1-5/> ore:aggregates ?workflow .
9
      ?workflow rdf:type wfdesc:Workflow; rdfs:seeAlso ?soap .
10
      #?soap a ono:data_transformation; obo:part_of ?study
11
      ?soap a <http://purl.obolibrary.org/obo/OBI_0200000> ; <http://purl.obolibrary.org/obo/BFO_0000050> ?study .
12
      ?study rdfs:label ?studyname .
13
}
14
​

inputs_derived_gage_output.sparql

14
 
1
### TODO: update RO URI
2
​
3
PREFIX ore: <http://www.openarchives.org/ore/terms/>
4
PREFIX wfdesc: <http://purl.org/wf4ever/wfdesc#>
5
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
6
PREFIX prov: <http://www.w3.org/ns/prov#>
7
PREFIX roterms: <http://purl.org/wf4ever/roterms#>
8
​
9
select distinct ?input
10
where {
11
      <http://sandbox.wf4ever-project.org/rodl/ROs/soapdenovo-v1-5/> ore:aggregates ?result .
12
      ?workflow rdf:type roterms:Result ; prov:wasDerivedFrom ?input.}
13
​
14
​

inputs_role.sparql

11
 
1
### This query is final
2
​
3
PREFIX roterms: <http://purl.org/wf4ever/roterms#>
4
PREFIX wfdesc: <http://purl.org/wf4ever/wfdesc#>
5
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
6
​
7
select distinct ?role
8
where {
9
      ?workflow roterms:inputValue [roterms:resource ?data ; roterms:portName ?role] .
10
      ?data rdfs:seeAlso <http://w3id.org/isa/soapdenovo2/raw_data_file/17> .}
11
​

workflow_generated_gage_results.sparql

13
 
1
## The query is final
2
​
3
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
4
PREFIX prov: <http://www.w3.org/ns/prov#>
5
PREFIX wfprov: <http://purl.org/wf4ever/wfprov#>
6
​
7
select distinct ?workflow
8
where{
9
       ?data rdfs:seeAlso <http://w3id.org/isa/soapdenovo2/derived_data_file/3>;
10
             prov:wasGeneratedBy ?workflowrun .
11
       ?workflowrun wfprov:describedByWorkflow [rdfs:seeAlso ?workflow]
12
}
13
​

workflow_in_the_ro.sparql

10
 
1
##TODO: update the RO URI
2
​
3
PREFIX ore: <http://www.openarchives.org/ore/terms/>
4
PREFIX wfdesc: <http://purl.org/wf4ever/wfdesc#>
5
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
6
​
7
select distinct ?workflow
8
where {
9
      <http://sandbox.wf4ever-project.org/rodl/ROs/soapdenovo-v1-5/> ore:aggregates ?workflow .
10
      ?workflow rdf:type wfdesc:Workflow .}

workflow_in_the_ro.sparql

12
 
1
### TODO: update RO URI
2
​
3
PREFIX ore: <http://www.openarchives.org/ore/terms/>
4
PREFIX wfdesc: <http://purl.org/wf4ever/wfdesc#>
5
PREFIX roterms: <http://purl.org/wf4ever/roterms#>
6
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
7
​
8
select distinct ?input
9
where {
10
      <http://sandbox.wf4ever-project.org/rodl/ROs/soapdenovo-v1-5/> ore:aggregates ?workflow .
11
      ?workflow rdf:type wfdesc:Workflow; roterms:inputSelected ?input .}
12
​

Contributors

  • Alejandra Gonzalez-Beltran (@agbeltran), Oxford e-Research Centre, University of Oxford, UK
  • Peter Li (@pli888), GigaScience, BGI HK Research Institute, Hong Kong.
  • Jun Zhao, InfoLab21, Lancaster University
  • Mark Thompson, Department of Human Genetics, Leiden University Medical Center, The Netherlands
  • Maria Susana Avila-Garcia, Nuffield Department of Medicine, Experimental Medicine Division, John Radcliffe Hospital,, Oxford, UK .
  • Ruibang Luo, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory & Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong.
  • Tak-Wah Lam, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory & Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong.
  • Tin-Lap Lee, School of Biomedical Sciences and CUHK-BGI Innovation Institute of Trans-omics, The Chinese University of Hong Kong, Shatin, Hong Kong.
  • Marco Roos, Department of Human Genetics, Leiden University Medical Center, The Netherlands
  • Scott Edmunds, GigaScience, BGI HK Research Institute, Hong Kong.
  • Susanna-Assunta Sansone, Oxford e-Research Centre, University of Oxford
  • Philippe Rocca-Serra, Oxford e-Research Centre, University of Oxford

Support or Contact

For discussions about the SOAPdenovo2 case study, please contact Alejandra, Peter and Philippe.

The issue tracker is available at: SOAPdenovo2 case study GitHub site. Please, feel free to report issues or feature requests.