The DISK Ontology
type: Ontology
creator: Daniel Garijo
creator: Hernan Vargas
creator: Maximiliano Osorio
creator: Varun Ratnakar
creator: Yolanda Gil
abstract: The DISK Ontology aims to represent the components in a Line of Inquiry (e.g., hypothesis, metaworkflows, workflows, etc.), along with their relationships and main interactions. It also aims to represents hypothesis and their revisions. The ontology is aligned to the W3C PROV standard
license: http://creativecommons.org/licenses/by-nc-sa/2.0/
preferred namespace prefix: disk
label: DISK Ontology
version info: 1.2.5

created from
type: ObjectProperty
sub property of: was derived from
domain: Data
comment: Property that states from where these data have been created (e-g-, workflow, metaworkflow, line of inquiry, etc.)

has author
type: ObjectProperty
domain: Class
  union of: Hypothesis
  union of: Line of Inquiry
  union of: Triggered line of inquiry
range: Person
comment: Property to describe the author of a Line of Inquiry, Triggered Line of Inquiry or Hypothesis

has confidence report
type: ObjectProperty
domain: Class
  union of: Hypothesis
  union of: Statement
range: Confidence report
comment: Property that links the hypothesis or statement to the ConfidenceReport that supports them

has execution
type: ObjectProperty
domain: Workflow binding
range: Execution
comment: Property that links a workflow bundle to the execution results of the workflow

has hypothesis
type: ObjectProperty
domain: Triggered line of inquiry
range: Hypothesis
comment: property that links a triggered line of inquiry to the hypothesis that matched to it.

has hypothesis variable
type: ObjectProperty
domain: Class
  union of: Metaworkflow
  union of: Workflow binding
range: Class
  union of: Variable
comment: This property is used to identify which variables in the hypothesis are used in the workflows.

has input file
type: ObjectProperty
domain: Workflow binding
range: Variable binding
comment: Property that states the input files for a workflow run

has line of inquiry
type: ObjectProperty
sub property of: was derived from
domain: Triggered line of inquiry
range: Line of Inquiry
comment: Property that links a triggered line of inquiry to the original line of inquiry from which it was derived

has metaworkflow binding
type: ObjectProperty
sub property of: has workflow bindings
domain: Class
  union of: Line of Inquiry
  union of: Triggered line of inquiry
range: Workflow binding
comment: The workflow bindings associated to a metaworkflow, i.e., a workflow and a variable binding

has optional parameter
type: ObjectProperty
domain: Workflow binding
range: Variable binding
comment: Property to store the optional parameters that can be inputted to a workflow

has output file
type: ObjectProperty
domain: Workflow binding
range: Variable binding
comment: Property that states the output files for a workflow run

has parameter
type: ObjectProperty
domain: Workflow binding
range: Variable binding
comment: Property to store the parameters to be inputted to a workflow

has parent hypothesis
type: ObjectProperty
sub property of: was revision of
domain: Hypothesis
range: Hypothesis
comment: Property that links to the parent hypothesis from which the current hypothesis has been derived

has question
type: ObjectProperty
domain: Line of Inquiry
range: Question
comment: Property that links a Line of Inquiry with a question

has resulting hypothesis
type: ObjectProperty
domain: Triggered line of inquiry
range: Hypothesis
comment: Property that links a triggered line of inquiry to the hypothesis revision that resulted from its analysis

has revised hypothesis variable
type: ObjectProperty
domain: Class
  union of: Metaworkflow
  union of: Workflow binding
range: Class
  union of: Variable
comment: Property that links a metaworkflow to its revised hypothesis variable.

has step
type: ObjectProperty
domain: Execution
range: Execution information
comment: Inner step of a execution

has triggered line of inquiry
type: ObjectProperty
sub property of: has provenance
domain: Confidence report
range: Triggered line of inquiry
comment: Property that links a confidence report to the triggered line of inquiry that contains all the provenance for the report's value.

has variable
type: ObjectProperty
domain: Variable binding
range: Variable
comment: Property that links a variable binding to its corresponding variable

has variable binding
type: ObjectProperty
domain: Workflow binding
range: Variable binding
comment: Property that links a Workflow binding to it correspondent variable binding

has workflow
type: ObjectProperty
domain: Workflow binding
range: Workflow
comment: Property that links a Workflow binding to its associated workflow

has workflow bindings
type: ObjectProperty
domain: Class
  union of: Line of Inquiry
  union of: Triggered line of inquiry
range: Workflow binding
comment: Property that links a line of inquiry or executed line of inquiry to the workflow bindings present on it

has provenance
type: ObjectProperty

was derived from
type: ObjectProperty

was revision of
type: ObjectProperty
sub property of: was derived from

date created
type: DatatypeProperty
domain: Class
  union of: Hypothesis
  union of: Line of Inquiry
  union of: Triggered line of inquiry
range: date
comment: Property which describes when the hypothesis was created

date modified
type: DatatypeProperty
domain: Class
  union of: Hypothesis
  union of: Line of Inquiry
  union of: Triggered line of inquiry
range: date
comment: Property which describes when the hypothesis was modified

has binding value
type: DatatypeProperty
domain: Variable binding
range: string
comment: Property that links a binding to its associated value

has confidence type
type: DatatypeProperty
domain: Class
  union of: Confidence report
  union of: Triggered line of inquiry
range: string
comment: Property that binds a resource to its confidence type

has confidence value
type: DatatypeProperty
domain: Class
  union of: Confidence report
  union of: Triggered line of inquiry
range: double
comment: Property that binds a resource to its confidence value

has data query
type: DatatypeProperty
domain: Class
  union of: Line of Inquiry
  union of: Triggered line of inquiry
range: string
comment: Property that links a line of inquiry to the data query text associated to it

has data query description
type: DatatypeProperty
domain: Class
  union of: Line of Inquiry
  union of: Triggered line of inquiry
range: string
comment: Property to describe the data retrieved from a data query in a Line of Inquiry.

has data source
type: DatatypeProperty
domain: Class
  union of: Line of Inquiry
  union of: Triggered line of inquiry
range: string
comment: Property to configure the desired target wiki for the data query in a Line of Inquiry.

has data source URL
type: DatatypeProperty
domain: Class
  union of: Line of Inquiry
  union of: Triggered line of inquiry
range: string
comment: Property to configure the desired target wiki for the data query in a Line of Inquiry. Here we store the URL of the data source.

has datatype
type: DatatypeProperty
domain: Variable binding
range: string
comment: datatype of a binding

has email
type: DatatypeProperty
domain: Person
range: string
comment: Email of a person

has hypothesis query
type: DatatypeProperty
domain: Class
  union of: Line of Inquiry
  union of: Triggered line of inquiry
range: string
comment: Property that links a line of inquiry to the hypothesis query text

has id
type: DatatypeProperty
domain: Class
  union of: Workflow binding
  union of: Thing
range: string
comment: Property that links to the ID of the described resource

has log
type: DatatypeProperty
domain: Class
  union of: Execution information
  union of: Workflow binding
range: anyURI
comment: Log file for this run

has name
type: DatatypeProperty
domain: Person
range: string
comment: Name of a person

has query results
type: DatatypeProperty
domain: Triggered line of inquiry
range: string
comment: Results of data query execution at the moment of execution

has run end date
type: DatatypeProperty
domain: Class
  union of: Execution information
  union of: Workflow binding
range: date
comment: Date when the workflow run was finished

has run link
type: DatatypeProperty
domain: Workflow binding
range: string
comment: Link to the execution of a workflow in the corresponding workflow system

has run start date
type: DatatypeProperty
domain: Class
  union of: Execution information
  union of: Workflow binding
range: date
comment: Date when the workflow run started

has run status
type: DatatypeProperty
domain: Class
  union of: Execution information
  union of: Workflow binding
range: string
comment: Property that indicates the status of the execution (whether it has been successful or not) or the triggered line of inquiry (i.e., ongoing, finished, etc.)

has source
type: DatatypeProperty
domain: Workflow binding
range: string
comment: Identifier for the source of a Workflow

has source
type: DatatypeProperty
domain: Workflow binding
range: string
comment: URL for the source of the Workflow

has table description
type: DatatypeProperty
domain: Class
  union of: Line of Inquiry
  union of: Triggered line of inquiry
range: string
comment: Brief description of table generated

has table variables
type: DatatypeProperty
domain: Class
  union of: Line of Inquiry
  union of: Triggered line of inquiry
range: string
comment: Property that specify which variables of the data query will be used to generate a table

has triggered line of inquiry status
type: DatatypeProperty
domain: Triggered line of inquiry
range: string
comment: Property that states the status of a triggered line of inquiry.

has type
type: DatatypeProperty
domain: Variable binding
range: string
comment: Type of this binding

has usage notes
type: DatatypeProperty
domain: Class
  union of: Hypothesis
  union of: Line of Inquiry
  union of: Triggered line of inquiry
range: string
comment: Property to indicate the usage notes to consider when using a line of inquiry or hypothesis

Confidence report
type: Class
comment: A confidence report groups the confidence value and the link to the triggered line of inquiry of a given statement or hypothesis

Data
type: Class
comment: The results produced as a result of executing a workflow from a given line of inquiry

Execution information
type: Class
comment: Stores the state of an execution, start time, end time, status and log.

Hypothesis
type: Class
comment: A hypothesis h consists of: 1. A hypothesis statement, which is a set of assertions about entities in the domain. For example, they express assertions such as “The mutant form of Protein ABCD is associated with colon cancer.” 2. A hypothesis qualification (confidence report) , which qualifies the veracity of the hypothesis based on the data and the analyses done so far. A typical qualification is a numeric confidence value. For example, for the hypothesis statement above we could have a confidence value of 0.7. Each of the statements of a hypothesis may have a different confidence value. 3. A hypothesis provenance, which is a record of the analyses that were carried out in support of the hypothesis statement. For example the provenance may include an analysis of mass spectrometry data for 25 patients with colon cancer and 25 healthy controls followed by clustering, cluster metrics and binary hypothesis testing. 4. A hypothesis history, which points to a prior hypothesis h’ that was revised to generate h. In our example, a prior hypothesis could be “Protein ABCD is associated with cancer.”

Line of Inquiry
type: Class
comment: A line of inquiry represents potential analyses that can be pursued to test a type of hypothesis. A line of inquiry consists of: 1. A hypothesis pattern, which represents the type of hypotheses that can be explored with this line of inquiry. An example of a hypothesis pattern is “Protein ?p is associated with cancer ?c”. This hypothesis pattern must be expressed in the same language as hypothesis statements, so that they can be matched against a user’s hypothesis. 2. A set of query patterns, representing the kinds of data relevant to testing the hypothesis pattern as a set of templates of queries to a data repository. Several kinds of data may be relevant, so there may be several query patterns. For example, “Retrieve data of mass spectrometry experiments of tumor samples from patients with cancer ?c”. 3. A set of workflows, which capture data analysis methods that can be applied to the data retrieved by the query patterns in order to test the hypothesis pattern. For example, a workflow to analyze mass spectrometry data could include steps such as matching proteins from either a patient’s custom database or on a reference human proteomic database to tandem mass spectrometry data. 4. A set of workflow mappings, indicating how the query patterns and the datasets retrieved should be used to instantiate the workflows above to create execution-ready workflows. 5. A set of meta-workflows, which describe how to aggregate the results of the workflow executions done to analyze the data. For example, suppose that one of the workflows in the line of inquiry is for analyzing protein mass spectrometry data for n patients finding evidence for the protein ?p with a p-value p1 and another workflow is for protein fluorescence data for m patients giving a p-value p1, then the meta-workflow would indicate how to combine that evidence into a joint confidence value. 6. A set of meta-workflow mappings, which describe how the results of the workflow executions are to be used to generate b…

Metaworkflow
type: Class
subclass of: Workflow
comment: A metaworkflow is a special type of workflow which uses as inputs the results of other workflows

Person
type: Class
comment: Property to identify a person

Triggered line of inquiry
type: Class
comment: A triggered line of inquiry represents a strategy for exploring a hypothesis that is currently being explored by executing its associated workflows and metaworkflows. A triggered line of inquiry may require a long time to complete. When finished, the triggered line of inquiry will include pointers to the provenance of the workflows and metaworkflows that participated on the execution, as well as a confidence value on the original hypothesis.

Variable binding
type: Class
comment: Contains a Variable and a binding value

Workflow binding
type: Class
comment: Contains a workflow and a variable binding

Statement
type: Class

Plan
type: Class

Bundle
type: Class
comment: A bundle is a named set of provenance descriptions, and is itself an entity, so allowing provenance of provenance to be expressed.

Execution
type: Class
subclass of: Bundle
comment: An execution of a workflow

Variable
type: Class
comment: Variable of a workflow template

Workflow
type: Class
subclass of: Plan
comment: Workflows define the set of computational tasks and dependencies needed to carry out in silico experiments