The Workflow Motif Ontology

IRI:
http://purl.org/net/wf-motifs
Current version:
1.02
Authors:
http://delicias.dia.fi.upm.es/members/DGarijo/#me
http://semanticweb.org/wiki/Khalid_Belhajjame
http://semanticweb.org/wiki/Pinar_Alper
Contributors:
http://www.cs.man.ac.uk/~carole/
http://www.isi.edu/~gil/
http://www.oeg-upm.net/index.php/teachers/11-ocorcho
Other visualisation:
Ontology source

Abstract

Workflow Motif Ontology, created by Daniel Garijo, Pinar Alper and Khalid Belhajjame

Table of Content

  1. Classes
  2. Object Properties
  3. Annotation Properties
  4. Namespace Declarations

Classes

Atomic workflowc back to ToC or Class ToC

IRI: http://purl.org/net/wf-motifs#AtomicWorkflow

Inter-workflow motif used to characterize the workflows that perform an atomic unit of functionality, which effectively requires no sub-workflow usage. Typically these workflows are designed to be included in other workflows. Atomic workflows are the main mechanism of modularizing functionality within scientific workflows.
has super-classes
Inter-workflow motifc

Combinec back to ToC or Class ToC

IRI: http://purl.org/net/wf-motifs#Combine

Data preparation motif that refers to the step or group of steps in the workflow aggregating information from different sources. For example, the joining of two tables in a new one or the merging of three different files in a bigger one.
has super-classes
Data preparationc

Composite workflowc back to ToC or Class ToC

IRI: http://purl.org/net/wf-motifs#CompositeWorkflow

Inter-workflow motif referring to all those workflows that have one or more sub-workflows included in them (when these sub-workflows overlap they offer different views of the global workflow).
has super-classes
Inter-workflow motifc

Computational stepc back to ToC or Class ToC

IRI: http://purl.org/net/wf-motifs#ComputationalStep

Intra-workflow motif used to refer to activities performed by a computer. This motif applies to most of the steps of the workflow, except for those being human interaction steps.
has super-classes
Intra-workflow motifc

Data analysisc back to ToC or Class ToC

IRI: http://purl.org/net/wf-motifs#DataAnalysis

Data operation motif that refers to a broad category of tasks in diverse domains. An important number of workflows are designed with the purpose of analyzing different features of input data, ranging from simple comparisons between the datasets to complex protein analysis to see whether two molecules can be docked successfully or not.
has super-classes
Data operation motifc

Data cleaningc back to ToC or Class ToC

IRI: http://purl.org/net/wf-motifs#DataCleaning

Data operation motif that refers to the step or series of steps for cleaning and curating data in a workflow. Typically these steps are undertaken by sophisticated tooling/services, or by human interactions. A data cleaning step preserves and enriches the content of data (e.g., by a user’s annotation of a result with additional information, detecting and removing inconsistencies on the data, etc.).
has super-classes
Data operation motifc

Data movementc back to ToC or Class ToC

IRI: http://purl.org/net/wf-motifs#DataMovement

Certain analysis activities that are performed via external tools or services require the submission of data to a location accessible by the service/tool (i.e., a web or a local directory respectively). In such cases the workflow contains dedicated step(s) for the upload/transfer of data to these locations. The same applies to the outputs, in which case a data download/retrieval step is used to chain the data to the next steps of the workflow.
has super-classes
Data operation motifc

Data operation motifc back to ToC or Class ToC

IRI: http://purl.org/net/wf-motifs#DataOperationMotif

A data operation motif describes the data manipulation and/or transformation carried out by a step in the workflow, a collection of steps in the workflow or a sub-workflow.
has super-classes
Motifc
has sub-classes
Data analysisc, Data cleaningc, Data movementc, Data preparationc, Data retrievalc, Data visualizationc
is in range of
has data operation motifop

Data preparationc back to ToC or Class ToC

IRI: http://purl.org/net/wf-motifs#DataPreparation

Data, as it is originally retrieved, may need several transformations before being able to be used in a workflow step. These steps, typically known as ”Shims” [Duncan Hull et al. Treating shimantic web syndrome with ontologies. In AKT Workshop on Semantic Web Services, 2004.], can be annotated using the Data Preparation motif.
has super-classes
Data operation motifc
has sub-classes
Combinec, Filter c, Format transformationc, Groupc, Input augmentationc, Output extractionc, Sortc, Splitc

Data retrievalc back to ToC or Class ToC

IRI: http://purl.org/net/wf-motifs#DataRetrieval

Workflows exploit heterogeneous data sources, remote databases, repositories and other web resources mostly exposed via SOAP or REST services. Scientific data deposited in these repositories are retrieved through query and retrieval steps inside workflows. The data retrieval motif identifies those tasks within the workflow which are responsible for retrieving data from external sources into the workflow environment.
has super-classes
Data operation motifc

Data visualizationc back to ToC or Class ToC

IRI: http://purl.org/net/wf-motifs#DataVisualization

Being able to show the results is as important as producing them in some workflows. Scientists use visualizations to show the conclusions of their experiments and to take important decisions in the pipeline itself. Therefore certain steps in workflows are dedicated to generation of plots and graph outputs from input data. The data visualization motif also includes the generation of tables and files for browsing and reading the results of the workflow.
has super-classes
Data operation motifc

Filter c back to ToC or Class ToC

IRI: http://purl.org/net/wf-motifs#Filter

Data preparation motif that refers to a filtering step or set of steps. For example, A file filtered by a set of set of keywords, a table filtered by a threshold, etc.
has super-classes
Data preparationc

Format transformationc back to ToC or Class ToC

IRI: http://purl.org/net/wf-motifs#FormatTransformation

Workflows that bring together multiple access or analysis activities usually contain steps for format transformations. These steps preserve the content of the inputs while converting its representation format. An example would be a converter from CSV to VOTable format in the astronomy domain, a converter from FASTA to Swiss-Prott sequence in biology, or an Arff formating component for Weka in the text analysis domain.
has super-classes
Data preparationc

Groupc back to ToC or Class ToC

IRI: http://purl.org/net/wf-motifs#Group

Data preparation motif that refers to the step or set of steps that reorganize the input into different groups. For example, grouping a table by a certain category.
has super-classes
Data preparationc

Human interaction stepc back to ToC or Class ToC

IRI: http://purl.org/net/wf-motifs#HumanInteractionStep

Intra-workflow motif used to characterize the activities that require human inputs during their execution. For example, manual data curation of a table for a future step in the workflow, cleaning and filtering steps (such as selecting a specific dataset to continue the experiment), etc.
has super-classes
Intra-workflow motifc

Input augmentationc back to ToC or Class ToC

IRI: http://purl.org/net/wf-motifs#InputAugmentation

Data preparation motif that refers to the step or set of steps dedicated to generate an aggregation of multiple parameters and scripts for tools and external services. For example, the generation of queries for input retrieval through an aggregation of multiple parameters, the generation of scripts to be executed in further steps, etc.
has super-classes
Data preparationc

Inter-workflow motifc back to ToC or Class ToC

IRI: http://purl.org/net/wf-motifs#InterWorkflowMotif

Workflow motif that relates workflows with each other by determining whether different workflows are a composition of each other (composite workflow) or not (atomic workflow), or they have a very similar composition but work for different inputs (workflow overloading).
has super-classes
Workflow motifc
has sub-classes
Atomic workflowc, Composite workflowc, Workflow overloadc

Internal macroc back to ToC or Class ToC

IRI: http://purl.org/net/wf-motifs#InternalMacro

Intra-workflow motif that refers to those groups of steps in the workflow that correspond to repetitive patterns of combining tasks. For example, if a workflow has several branches with the same sequence of repeated steps, the sequence becomes an internal macro.
has super-classes
Intra-workflow motifc

Intra-workflow motifc back to ToC or Class ToC

IRI: http://purl.org/net/wf-motifs#IntraWorkflowMotif

Workflow motif that describes a step or a series of steps within a single workflow.
has super-classes
Workflow motifc
has sub-classes
Computational stepc, Human interaction stepc, Internal macroc, Stateful (asynchronous) invocationc, Stateless (synchronous) invocationc

Motifc back to ToC or Class ToC

IRI: http://purl.org/net/wf-motifs#Motif

A motif is a domain independent conceptual abstraction of one or more steps of a given workflow.
has sub-classes
Data operation motifc, Workflow motifc
is in range of
has motifop

Output extractionc back to ToC or Class ToC

IRI: http://purl.org/net/wf-motifs#OutputExtraction

Data preparation motif that refers to the step or set of steps in the workflow retrieving only the relevant portion from the the output of a previous step. For example, retrieving the tag value of an XML fragment.
has super-classes
Data preparationc

Sortc back to ToC or Class ToC

IRI: http://purl.org/net/wf-motifs#Sort

Data preparation motif that refers to the step or set of steps ordering the input by certain parameter. For example, a quicksort algorithm that takes an unordered vector and produces a sorted output.
has super-classes
Data preparationc

Splitc back to ToC or Class ToC

IRI: http://purl.org/net/wf-motifs#Split

Data preparation motif that refers to the step or steps in the workflow separating an input into different outputs. For example, splitting a dataset in three different subsets to be processed in parallel in a workflow.
has super-classes
Data preparationc

Stateful (asynchronous) invocationc back to ToC or Class ToC

IRI: http://purl.org/net/wf-motifs#StatefulInvocation

Certain activities such as analysis or visualizations could be performed through interaction with stateful (web) services that allow for creation of jobs over remote grid environments. These are typically performed via invocation of multiple operations at a service endpoint. An example would be a BLAST job submission where the service invoker is responsible to first create a job, then submit the data, check the status and retrieve the results once it has finished.
has super-classes
Intra-workflow motifc

Stateless (synchronous) invocationc back to ToC or Class ToC

IRI: http://purl.org/net/wf-motifs#StatelessInvocaton

Intra-workflow motif that requires a step in the workflow for performing a service call or tool invocation. All the steps of a workflow are by default stateless (synchronous) invocations unless they are explicitly declared to be stateful.
has super-classes
Intra-workflow motifc

Workflow motifc back to ToC or Class ToC

IRI: http://purl.org/net/wf-motifs#WorkflowMotif

Motif that describes how a data operation motif is realized (i.e., implemented) within a workflow. For example, a visualization step (data operation motif) can be realized in different ways: via a stateful multi-step invocation, through a single stateless invocation (depending on the environmental constraints and nature of the services), or via a sub-workflow.
has super-classes
Motifc
has sub-classes
Inter-workflow motifc, Intra-workflow motifc
is in range of
has workflow motifop

Workflow overloadc back to ToC or Class ToC

IRI: http://purl.org/net/wf-motifs#WorkflowOverload

Inter-workflow motif used to characterize workflows that are used to operate over different input parameter types. An example is performing an analysis over a String input parameter, or performing it over the contents of a specified File. Overloading is a direct response to the heterogeneity of environments in which workflows are used.
has super-classes
Inter-workflow motifc

Object Properties

has data operation motifop back to ToC or Object Property ToC

IRI: http://purl.org/net/wf-motifs#hasDataOperationMotif

Object property that binds a workflow step with its correspondent data operation motif.
has super-properties
has motifop
has range
Data operation motifc

has motifop back to ToC or Object Property ToC

IRI: http://purl.org/net/wf-motifs#hasMotif

Object property that annotates a step in the workflow, a group of steps, a subworkflow, or a workflow with a motif.
has sub-properties
has data operation motifop, has workflow motifop
has range
Motifc

has workflow motifop back to ToC or Object Property ToC

IRI: http://purl.org/net/wf-motifs#hasWorkflowMotif

Object property that relates a workflow to its correspondent workflow motif.
has super-properties
has motifop
has range
Workflow motifc

Annotation Properties

contributorap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/contributor

createdap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/created

creatorap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/creator

descriptionap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/description

preferred namespace prefixap back to ToC or Annotation Property ToC

IRI: http://purl.org/vocab/vann/preferredNamespacePrefix

preferred namespace u r iap back to ToC or Annotation Property ToC

IRI: http://purl.org/vocab/vann/preferredNamespaceURI

titleap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/title

Namespace Declarations back to ToC

default namespace
http://purl.org/net/wf-motifs#
net
http://purl.org/net/
owl
http://www.w3.org/2002/07/owl#
rdf
http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs
http://www.w3.org/2000/01/rdf-schema#
terms
http://purl.org/dc/terms/
vann
http://purl.org/vocab/vann/
xsd
http://www.w3.org/2001/XMLSchema#

This HTML document was obtained by processing the OWL ontology source code through LODE, Live OWL Documentation Environment, developed by Silvio Peroni.