The YesWorkflow conceptual model is illustrated by the UML diagram of Figure 1.
Figure 1: YesWorkflow Conceptual Model UML Diagram
The following namespaces and prefixes are used in YesWorkflow RDF Turtle facts and SPARQL queries.
Table 1: Prefix and Namespaces used in this specification
| Prefix | Namespace IRI | Definition |
|---|---|---|
| yw | http://yesworkflow.org/ns/yesworkflow | The YesWorkflow namespace |
| p1 | http://purl.dataone.org/provone/2015/01/15/ontology# | The ProvONE namespace |
| rdf | http://www.w3.org/1999/02/22-rdf-syntax-ns# | The RDF namespace |
| rdfs | http://www.w3.org/2000/01/rdf-schema# | The RDFS namespace |
| owl | http://www.w3.org/2002/07/owl# | The OWL Full namespace |
The YesWorkflow constructs are summarized in Table 2 below.
Table 2: YesWorkflow Constructs
| YW Provenance | Construct Type | Name | Specification |
|---|---|---|---|
| Prospective | Class | Block | Section 2.1 |
| Workflow | Section 2.2 | ||
| Port | Section 2.3 | ||
| InPort | Section 2.4 | ||
| ParamPort | Section 2.5 | ||
| OutPort | Section 2.6 | ||
| Data | Section 2.7 | ||
| Association | hasSubBlock | Section 2.8 | |
| hasInPort | Section 2.9 | ||
| hasOutPort | Section 2.10 | ||
| receives | Section 2.11 | ||
| sends | Section 2.12 | ||
| hasVariableSource | Section 2.13 | ||
| Retrospective | Class | Resource | Section 2.14 |
| URIVariable | Section 2.15 | ||
| Association | wasReadFrom | Section 2.16 | |
| wasWrittenTo | Section 2.17 | ||
| hasURIVariable | Section 2.18 |
This section presents the specification of the various components of the YesWorkflow model outlined in the previous section.
A Block represents a computational task that consumes and produces data through its input and output ports, respectively. It can be atomic or composite, the latter case represented by a possibly nested Block.
is in domain of
- yw:hasSubBlock, yw:hasInPort, yw:hasOutPort
is in range of
- yw:hasSubBlock
Example:
The following RDF Turtle fragment specifies a Block.
BASE <http://yesworkflow.org/0000000000/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX p1: <http://purl.dataone.org/provone/2015/01/15/ontology#>
PREFIX yw: <http://yesworkflow.org/ns/yesworkflow>
yw:Block rdf:type rdfs:Class .
<simulate_data_collection/load_screening_results>
rdf:type yw:Block ;
rdfs:label "load_screening_results" ; # The name of the program block
rdfs:comment "Load sample information from spreadsheet." ; # The description of the program block
yw:hasInPort <simulate_data_collection/load_screening_results#cassette_id_port> ,
<simulate_data_collection/load_screening_results#sample_spreadsheet_port> ;
yw:hasOutPort <simulate_data_collection/load_screening_results#sample_name_port> ,
<simulate_data_collection/load_screening_results#sample_quality_port> .
yw:hasSubBlock <...> . # (Optional) The sub-blocks of current block
A Workflow is a distinguished Block, representing an enire computational experiment for a source script. It has super-class Block.
has super-class
- yw:Block
has self-attribute
- yw:sourceScript
is in domain of
- yw:hasSubBlock, yw:hasInPort, yw:hasOutPort
Example:
The following RDF Turtle fragment specifies a Workflow.
yw:Workflow rdf:type rdfs:Class ;
rdfs:subClassOf yw:Block .
<simulate_data_collection>
rdf:type yw:Workflow ;
rdfs:label "simulate_data_collection" ; # The name of the workflow
rdfs:comment "Workflow for collecting diffraction data from high quality crystals in a cassette." ; # The description of the workflow
yw:sourceScript "simulate_data_collection.py" ; # The source script that the workflow is annotated for.
yw:hasInPort <simulate_data_collection#cassette_id_port> ,
<...> , <...> ;
yw:hasOutPort <simulate_data_collection#corrected_image_port> ,
<...> , <...> ;
yw:hasSubBlock <simulate_data_collection/initialize_run> ,
<...> , <...> .
A Port enables a Block to send or receive data items (as class Data). There are two main types of ports used as inputs and outputs. For input ports, they include both ports as input data and ports as input parameters. Therefore, Port is the super-class of class InPort and OutPort, and InPort is the super-class of ParamPort.
has self-attribute
- yw:filePathTemplate
is in domain of
- yw:receives, yw:sends, yw:hasVariableSource
is in range of
- yw:hasInPort, yw:hasOutPort
Example:
The following RDF Turtle fragment specifies a Port.
yw:Port rdf:type rdfs:Class .
yw:InPort rdf:type rdfs:Class ;
rdfs:subClassOf yw:Port .
yw:OutPort rdf:type rdfs:Class ;
rdfs:subClassOf yw:Port .
yw:ParamPort rdf:type rdfs:Class ;
rdfs:subClassOf yw:InPort .
<simulate_data_collection/load_screening_results#sample_spreadsheet_port>
rdf:type yw:InPort ; # InPort is a sub-class of Port
rdfs:label "sample_spreadsheet_file" ; # The port name (not the alias)
yw:receives <simulate_data_collection#sample_spreadsheet_data> ; # The Data that the in-port receives
yw:filePathTemplate "file:cassette_{cassette_id}_spreadsheet.csv" ; # (Optional) The URI file path template of the port
yw:hasVariableSource <simulate_data_collection#cassette_id_data> . # (Optional) The referred Data in the URI file path template
<simulate_data_collection/log_rejected_sample#rejection_log_port>
rdf:type yw:OutPort ; # OutPort is a sub-class of Port
rdfs:label "rejection_log" ;
yw:sends <simulate_data_collection#rejection_log_data> ; # The Data that the out-port sends
yw:filePathTemplate "file:run/rejected_samples.txt" . # (Optional)
<simulate_data_collection/log_average_image_intensity#cassette_id_port>
rdf:type yw:ParamPort ; # ParamPort is a sub-class of InPort
rdfs:label "cassette_id" ;
yw:receives <simulate_data_collection#cassette_id_data> .
An InPort is a sub-class of Port. It means the port is used as an input data or parameter port of its Block or Workflow.
has self-attribute
- yw:filePathTemplate
is in domain of
- yw:receives, yw:hasVariableSource
is in range of
- yw:hasInPort
Example:
The same as Port.
A ParamPort is a sub-class of InPort. It means the port is used as an input parameter port of its Block or Workflow.
has self-attribute
- yw:filePathTemplate
is in domain of
- yw:receives, yw:hasVariableSource
is in range of
- yw:hasInPort
Example:
The same as Port.
An OutPort is a sub-class of Port. It means the port is used as an output port of its Block or Workflow.
has self-attribute
- yw:filePathTemplate
is in domain of
- yw:sends, yw:hasVariableSource
is in range of
- yw:hasOutPort
Example:
The same as Port.
A Data is a data item that multiple ports from different blocks or workflows receive or send. The ports which connect to the same Data share the same actual data. In other words, ports with the same alias name connect to the same Data.
is in domain of
- yw:wasReadFrom, yw:wasWrittenTo
is in range of
- yw:receives, yw:sends, yw:hasVariableSource
Example:
The following RDF Turtle fragment specifies a Data.
yw:Data rdf:type rdfs:Class .
<simulate_data_collection#raw_image_data>
rdf:type yw:Data ;
rdfs:label "raw_image" ; # The alias name of ports connected to the same Data
rdfs:comment "Path of file storing the raw diffraction image." . # The description of the Data
##### Relation between Data and Resource #####
<simulate_data_collection#sample_spreadsheet_data>
yw:wasReadFrom <simulate_data_collection#sample_spreadsheet_resource/001> .
<simulate_data_collection#run_log_data>
yw:wasWrittenTo <simulate_data_collection#run_log_resource/001> .
The association hasSubBlock specifies the recursive composition of Blocks, a parent Block includes a child Block as part of its specification.
has domain
- yw:Block, yw:Workflow
has range
- yw:Block
Example:
It is shown in class Block and Workflow.
The association hasInPort specifies the InPorts (including ParamPorts) of a particular Block or Workflow that are used as input data or parameter ports.
has domain
- yw:Block, yw:Workflow
has range
- yw:InPort, yw:ParamPort
Example:
It is shown in class Block and Workflow.
The association hasOutPort specifies the OutPorts of a particular Block or Workflow that are used as output ports.
has domain
- yw:Block, yw:Workflow
has range
- yw:OutPort
Example:
It is shown in class Block and Workflow.
The association receives specifies that an InPort receives a Data. Ports with the same alias names connect to the same Data.
has domain
- yw:InPort, yw:ParamPort
has range
- yw:Data
Example:
It is shown in class Port.
The association sends specifies that an OutPort sends a Data. Ports with the same alias names connect to the same Data.
has domain
- yw:OutPort
has range
- yw:Data
Example:
It is shown in class Port.
The association hasVariableSource specifies that a Port with filePathTemplate can have its corresponding URI variable names inside the string of filePathTemplate. The URI variable names are Data names indeed.
has domain
- yw:InPort, yw:ParamPort, yw:OutPort
has range
- yw:Data
Example:
It is shown in class Port.
A Resource is an actual file (with its path) generated after running the source script. The Resource is named according to the filePathTemplate of its connected port. Resource files are associated with retrospective provenance.
has self-attribute
- yw:actualFilePath
is in domain of
- yw:hasURIVariable
is in range of
- yw:wasReadFrom, yw:wasWrittenTo
Example:
The following RDF Turtle fragment specifies a Resource.
yw:Resource rdf:type rdfs:Class .
<simulate_data_collection#sample_spreadsheet_resource/001>
rdf:type yw:Resource ;
yw:actualFilePath "cassette_q55_spreadsheet.csv" ; # The actual file name (with its path) of the resource
yw:hasURIVariable <simulate_data_collection#sample_spreadsheet_resource/001/v1> , <...> . # The referred URI variables in the resource file name (with its path)
An URIVariable is a variable referred in the resource file name (with its path). URIVariables have variable names between "{" and "}" in corresponding port's filePathTemplate. URIVariables have variable values in the actualFilePath string.
has self-attribute
- yw:variableName, yw:variableValue
is in range of
- yw:hasURIVariable
Example:
The following RDF Turtle fragment specifies an URIVariable.
yw:URIVariable rdf:type rdfs:Class .
<simulate_data_collection#sample_spreadsheet_resource/001/v1>
rdf:type yw:URIVariable ;
yw:variableName "cassette_id" ; # The name of the URIVariable
yw:variableValue "q55" . # The value of the URIVariable
The association wasReadFrom specifies that a Data was read from a Resource file. The Data is received by an InPort with a URI file path template. The association wasReadFrom is a bridge property between prospective model and retrospective model.
has domain
- yw:Data
has range
- yw:Resource
Example:
It is shown in class Data.
The association wasWrittenTo specifies that a Data was written to a Resource file. The Data is sent by an OutPort with a URI file path template. The association wasWrittenTo is a bridge property between prospective model and retrospective model.
has domain
- yw:Data
has range
- yw:Resource
Example:
It is shown in class Data.
The association hasURIVariable specifies that a Resource may have some URI variables in its actual file path. The URI variables are corresponding to the Port's filePathTemplate that the Resource is generated by.
has domain
- yw:Resource
has range
- yw:URIVariable
Example:
It is shown in class Resource.
The comparison between YesWorkflow Model and ProvONE Model is shown in the following figure.
Figure 2: ProvONE Model and YesWorkflow Model UML Diagrams
The built-in OWL property owl:sameAs is used for connecting equivalent classes and associations when mapping from YesWorkflow Model to ProvONE Model. Only some concepts are the same between YesWorkflow (yw) and ProvONE (p1) namespaces. The following is the code in the RDF Turtle file.
##### Class Equality #####
yw:Block rdf:type rdfs:Class ;
owl:sameAs p1:Program .
yw:Workflow rdf:type rdfs:Class ;
rdfs:subClassOf yw:Block ;
owl:sameAs p1:Workflow .
yw:InPort rdf:type rdfs:Class ;
rdfs:subClassOf yw:Port .
yw:OutPort rdf:type rdfs:Class ;
rdfs:subClassOf yw:Port .
yw:ParamPort rdf:type rdfs:Class ;
rdfs:subClassOf yw:InPort .
yw:Port rdf:type rdfs:Class ;
owl:sameAs p1:Port .
yw:Data rdf:type rdfs:Class .
yw:Resource rdf:type rdfs:Class .
yw:URIVariable rdf:type rdfs:Class .
##### Property Equality #####
yw:hasSubBlock owl:sameAs p1:hasSubProgram .
yw:hasInPort owl:sameAs p1:hasInPort .
yw:hasOutPort owl:sameAs p1:hasOutPort .
The following table describes the mapping rules from YesWorkflow (yw) to ProvONE (p1) namespace.
Table 3: YesWorkflow (yw) Data Model Mapping to ProvONE (p1) Data Model
| YW Provenance | Construct Type | YesWorkflow Namespace | ProvONE Namespace |
|---|---|---|---|
| Prospective | Class | yw:Block | p1:Program |
| yw:Workflow | p1:Workflow | ||
| yw:Port | p1:Port | ||
| yw:InPort | n/a | ||
| yw:ParamPort | n/a | ||
| yw:OutPort | n/a | ||
| yw:Data | n/a | ||
| Association | yw:hasSubBlock | p1:hasSubProgram | |
| yw:hasInPort | p1:hasInPort | ||
| yw:hasOutPort | p1:hasOutPort | ||
| yw:receives | n/a | ||
| yw:sends | n/a | ||
| yw:hasVariableSource | n/a | ||
| Retrospective | Class | yw:Resource | n/a |
| yw:URIVariable | n/a | ||
| Association | yw:wasReadFrom | n/a | |
| yw:wasWrittenTo | n/a | ||
| yw:hasURIVariable | n/a |