DISK Ontology
type: Ontology
created: 2016-09-02
license: http://creativecommons.org/licenses/by-nc-sa/2.0/
preferred namespace uri: http://disk-project.org/ontology/disk#
creator: Varun Ratnakar
creator: Daniel Garijo
version info: 1.0.0
title: The DISK Ontology
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
creator: Yolanda Gil
preferred namespace prefix: disk

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

has provenance
type: ObjectProperty

was derived from
type: ObjectProperty

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

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

has confidence value
type: DatatypeProperty
comment: Property that binds a confidence report to its confidence value
domain: Confidence report
range: double

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

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

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

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

has status
type: DatatypeProperty
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.)
range: string
domain: Class
  union of: Triggered line of inquiry
  union of: Execution

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

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

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