2018-09-12
Sheeba Samuel
Birgitta König-Ries
The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan ontology to describe a complete path of a scientific experiment. It expresses the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It provides a set of classes and properties to represent a scientific experiment including its computational and non-computational steps to track the provenance of results. It describes an experiment and its data, agents, activities, plans, steps, variables, instruments, materials and settings required for its reproducibility.
http://creativecommons.org/licenses/by-nc-sa/2.0/
2019-01-14
REPRODUCE-ME Ontology
repr
The REPRODUCE-ME ontology
1.0
1.1
Classify prov-o terms into three categories, including 'starting-point', 'qualifed', and 'extended'. This classification is used by the prov-o html document to gently introduce prov-o terms to its users.
Classify prov-o terms into six components according to prov-dm, including 'agents-responsibility', 'alternate', 'annotations', 'collections', 'derivations', and 'entities-activities'. This classification is used so that readers of prov-o specification can find its correspondence with the prov-dm specification.
A reference to the principal section of the PROV-CONSTRAINTS document that describes this concept.
A definition quoted from PROV-DM or PROV-CONSTRAINTS that describes the concept expressed with this OWL term.
A reference to the principal section of the PROV-DM document that describes this concept.
A note by the OWL development team about how this term expresses the PROV-DM concept, or how it should be used in context of semantic web or linked data.
When the prov-o term does not have a definition drawn from prov-dm, and the prov-o editor provides one.
PROV-O does not define all property inverses. The directionalities defined in PROV-O should be given preference over those not defined. However, if users wish to name the inverse of a PROV-O property, the local name given by prov:inverse should be used.
A reference to the principal section of the PROV-DM document that describes this concept.
The position that this OWL term should be listed within documentation. The scope of the documentation (e.g., among all terms, among terms within a prov:category, among properties applying to a particular class, etc.) is unspecified.
This annotation property links a subproperty of prov:wasInfluencedBy with the subclass of prov:Influence and the qualifying property that are used to qualify it.
Example annotation:
prov:wasGeneratedBy prov:qualifiedForm prov:qualifiedGeneration, prov:Generation .
Then this unqualified assertion:
:entity1 prov:wasGeneratedBy :activity1 .
can be qualified by adding:
:entity1 prov:qualifiedGeneration :entity1Gen .
:entity1Gen
a prov:Generation, prov:Influence;
prov:activity :activity1;
:customValue 1337 .
Note how the value of the unqualified influence (prov:wasGeneratedBy :activity1) is mirrored as the value of the prov:activity (or prov:entity, or prov:agent) property on the influence class.
Classes and properties used to qualify relationships are annotated with prov:unqualifiedForm to indicate the property used to assert an unqualified provenance relation.
correspondsToStep
p-plan:correspondsToStep links a p-plan:Activity to its planned p-plan:Step
correspondsToVariable
p-plan:correspondsToVariable binds a p-plan:Entity (used by a p-plan:Activity in the execution of a plan) to the p-plan:Variable it represented it in the p-plan:Plan.
hasInputVar
p-plan:hasInputVar binds a p-plan:Step to the p-plan:Variable that takes as input for the planned execution
hasOutputVar
p-plan:hasOutputVar binds a p-plan:Step to the p-plan:Variable that will be produced as output in the planned execution
isDecomposedAsPlan
The p-plan:isDecomposedAsPlan relationship binds a p-plan:MultiStep to the p-plan:Plan holding the definition of that step. That is, p-plan:isDecomposedAsPlan links the MultiStep to the Plan sptecification where it is decomposed.
isInputVarOf
p-plan:isInputVarOf links an input variable of a step to the step.
isOutputVarOf
p-plan:isOutputVarOf is intended to link an output variable of a step to the step.
Property that asserts which Step preceeds the current one.
isPrecededBy
isStepOfPlan
p-plan:isStepOfPlan links a p-plan:Step to the p-plan:Plan which it corresponds to.
isSubPlanOfPlan
A p-plan:Plan may be a subplan of another bigger p-plan:Plan. p-plan:isSubPlanOfPlan is used to state the link among the two different plans. Note that if p1 is a p-plan:subPlan of p2, p1will not necessarily be a step of p2. A multistep will represent p1 in p2, and link to p1 with the p-plan.hasStepDecomposition relationship.
isVariableofPlan
p-plan:IsVariableOfPlan binds a p-plan:Variable to the p-plan:Plan it corresponds to.
An object property to express the accountability of an agent towards another agent. The subordinate agent acted on behalf of the responsible agent in an actual activity.
actedOnBehalfOf
starting-point
agents-responsibility
hadDelegate
activity
qualified
This property behaves in spirit like rdf:object; it references the object of a prov:wasInfluencedBy triple.
The prov:activity property references an prov:Activity which influenced a resource. This property applies to an prov:ActivityInfluence, which is given by a subproperty of prov:qualifiedInfluence from the influenced prov:Entity, prov:Activity or prov:Agent.
activityOfInfluence
agent
qualified
This property behaves in spirit like rdf:object; it references the object of a prov:wasInfluencedBy triple.
The prov:agent property references an prov:Agent which influenced a resource. This property applies to an prov:AgentInfluence, which is given by a subproperty of prov:qualifiedInfluence from the influenced prov:Entity, prov:Activity or prov:Agent.
agentOfInfluence
alternateOf
expanded
alternate
http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig
Two alternate entities present aspects of the same thing. These aspects may be the same or different, and the alternate entities may or may not overlap in time.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-alternate
alternateOf
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-alternate
The Location of any resource.
This property has multiple RDFS domains to suit multiple OWL Profiles. See <a href="#owl-profile">PROV-O OWL Profile</a>.
atLocation
expanded
The naming of prov:atLocation parallels prov:atTime, and is not named prov:hadLocation to avoid conflicting with the convention that prov:had* properties are used on prov:Influence classes.
This property is not functional because the many values could be at a variety of granularies (In this building, in this room, in that chair).
locationOf
entity
qualified
This property behaves in spirit like rdf:object; it references the object of a prov:wasInfluencedBy triple.
The prov:entity property references an prov:Entity which influenced a resource. This property applies to an prov:EntityInfluence, which is given by a subproperty of prov:qualifiedInfluence from the influenced prov:Entity, prov:Activity or prov:Agent.
entityOfInfluence
generated
expanded
entities-activities
prov:generated is one of few inverse property defined, to allow Activity-oriented assertions in addition to Entity-oriented assertions.
wasGeneratedBy
The _optional_ Activity of an Influence, which used, generated, invalidated, or was the responsibility of some Entity. This property is _not_ used by ActivityInfluence (use prov:activity instead).
This property has multiple RDFS domains to suit multiple OWL Profiles. See <a href="#owl-profile">PROV-O OWL Profile</a>.
hadActivity
qualified
derivations
The multiple rdfs:domain assertions are intended. One is simpler and works for OWL-RL, the union is more specific but is not recognized by OWL-RL.
wasActivityOfInfluence
The _optional_ Generation involved in an Entity's Derivation.
hadGeneration
qualified
derivations
generatedAsDerivation
hadMember
expanded
expanded
wasMemberOf
A collection is an entity that provides a structure to some constituents, which are themselves entities. These constituents are said to be member of the collections.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-collection
The _optional_ Plan adopted by an Agent in Association with some Activity. Plan specifications are out of the scope of this specification.
hadPlan
qualified
agents-responsibility
wasPlanOf
hadPrimarySource
expanded
derivations
wasPrimarySourceOf
hadPrimarySource property is a particular case of wasDerivedFrom (see http://www.w3.org/TR/prov-dm/#term-original-source) that aims to give credit to the source that originated some information.
The _optional_ Role that an Entity assumed in the context of an Activity. For example, :baking prov:used :spoon; prov:qualified [ a prov:Usage; prov:entity :spoon; prov:hadRole roles:mixing_implement ].
This property has multiple RDFS domains to suit multiple OWL Profiles. See <a href="#owl-profile">PROV-O OWL Profile</a>.
hadRole
qualified
agents-responsibility
prov:hadRole references the Role (i.e. the function of an entity with respect to an activity), in the context of an instantaneous usage, generation, association, start, and end.
wasRoleIn
The _optional_ Usage involved in an Entity's Derivation.
hadUsage
qualified
derivations
wasUsedInDerivation
influenced
expanded
agents-responsibility
wasInfluencedBy
Subproperties of prov:influencer are used to cite the object of an unqualified PROV-O triple whose predicate is a subproperty of prov:wasInfluencedBy (e.g. prov:used, prov:wasGeneratedBy). prov:influencer is used much like rdf:object is used.
influencer
qualified
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-influence
This property and its subproperties are used in the same way as the rdf:object property, i.e. to reference the object of an unqualified prov:wasInfluencedBy or prov:influenced triple.
This property is used as part of the qualified influence pattern. Subclasses of prov:Influence use these subproperties to reference the resource (Entity, Agent, or Activity) whose influence is being qualified.
hadInfluence
invalidated
expanded
entities-activities
prov:invalidated is one of few inverse property defined, to allow Activity-oriented assertions in addition to Entity-oriented assertions.
wasInvalidatedBy
If this Activity prov:wasAssociatedWith Agent :ag, then it can qualify the Association using prov:qualifiedAssociation [ a prov:Association; prov:agent :ag; :foo :bar ].
qualifiedAssociation
qualified
agents-responsibility
qualifiedAssociationOf
If this Entity prov:wasAttributedTo Agent :ag, then it can qualify how it was influenced using prov:qualifiedAttribution [ a prov:Attribution; prov:agent :ag; :foo :bar ].
qualifiedAttribution
qualified
agents-responsibility
qualifiedAttributionOf
If this Activity prov:wasInformedBy Activity :a, then it can qualify how it was influenced using prov:qualifiedCommunication [ a prov:Communication; prov:activity :a; :foo :bar ].
qualifiedCommunication
qualified
entities-activities
qualifiedCommunicationOf
If this Agent prov:actedOnBehalfOf Agent :ag, then it can qualify how with prov:qualifiedResponsibility [ a prov:Responsibility; prov:agent :ag; :foo :bar ].
qualifiedDelegation
qualified
agents-responsibility
qualifiedDelegationOf
If this Entity prov:wasDerivedFrom Entity :e, then it can qualify how it was derived using prov:qualifiedDerivation [ a prov:Derivation; prov:entity :e; :foo :bar ].
qualifiedDerivation
qualified
derivations
qualifiedDerivationOf
If this Activity prov:wasEndedBy Entity :e1, then it can qualify how it was ended using prov:qualifiedEnd [ a prov:End; prov:entity :e1; :foo :bar ].
qualifiedEnd
qualified
entities-activities
qualifiedEndOf
If this Activity prov:generated Entity :e, then it can qualify how it performed the Generation using prov:qualifiedGeneration [ a prov:Generation; prov:entity :e; :foo :bar ].
qualifiedGeneration
qualified
entities-activities
qualifiedGenerationOf
Because prov:qualifiedInfluence is a broad relation, the more specific relations (qualifiedCommunication, qualifiedDelegation, qualifiedEnd, etc.) should be used when applicable.
qualifiedInfluence
qualified
derivations
qualifiedInfluenceOf
If this Entity prov:wasInvalidatedBy Activity :a, then it can qualify how it was invalidated using prov:qualifiedInvalidation [ a prov:Invalidation; prov:activity :a; :foo :bar ].
qualifiedInvalidation
qualified
entities-activities
qualifiedInvalidationOf
If this Entity prov:hadPrimarySource Entity :e, then it can qualify how using prov:qualifiedPrimarySource [ a prov:PrimarySource; prov:entity :e; :foo :bar ].
qualifiedPrimarySource
qualified
derivations
qualifiedSourceOf
If this Entity prov:wasQuotedFrom Entity :e, then it can qualify how using prov:qualifiedQuotation [ a prov:Quotation; prov:entity :e; :foo :bar ].
qualifiedQuotation
qualified
derivations
qualifiedQuotationOf
If this Entity prov:wasRevisionOf Entity :e, then it can qualify how it was revised using prov:qualifiedRevision [ a prov:Revision; prov:entity :e; :foo :bar ].
qualifiedRevision
qualified
derivations
revisedEntity
If this Activity prov:wasStartedBy Entity :e1, then it can qualify how it was started using prov:qualifiedStart [ a prov:Start; prov:entity :e1; :foo :bar ].
qualifiedStart
qualified
entities-activities
qualifiedStartOf
If this Activity prov:used Entity :e, then it can qualify how it used it using prov:qualifiedUsage [ a prov:Usage; prov:entity :e; :foo :bar ].
qualifiedUsage
qualified
entities-activities
qualifiedUsingActivity
A prov:Entity that was used by this prov:Activity. For example, :baking prov:used :spoon, :egg, :oven .
used
starting-point
entities-activities
wasUsedBy
An prov:Agent that had some (unspecified) responsibility for the occurrence of this prov:Activity.
wasAssociatedWith
starting-point
agents-responsibility
wasAssociateFor
Attribution is the ascribing of an entity to an agent.
wasAttributedTo
starting-point
agents-responsibility
Attribution is the ascribing of an entity to an agent.
contributed
Attribution is a particular case of trace (see http://www.w3.org/TR/prov-dm/#concept-trace), in the sense that it links an entity to the agent that ascribed it.
IF wasAttributedTo(e2,ag1,aAttr) holds, THEN wasInfluencedBy(e2,ag1) also holds.
The more specific subproperties of prov:wasDerivedFrom (i.e., prov:wasQuotedFrom, prov:wasRevisionOf, prov:hadPrimarySource) should be used when applicable.
wasDerivedFrom
starting-point
derivations
A derivation is a transformation of an entity into another, an update of an entity resulting in a new one, or the construction of a new entity based on a pre-existing entity.
hadDerivation
Derivation is a particular case of trace (see http://www.w3.org/TR/prov-dm/#term-trace), since it links an entity to another entity that contributed to its existence.
End is when an activity is deemed to have ended. An end may refer to an entity, known as trigger, that terminated the activity.
wasEndedBy
expanded
entities-activities
ended
wasGeneratedBy
starting-point
entities-activities
generated
Because prov:wasInfluencedBy is a broad relation, its more specific subproperties (e.g. prov:wasInformedBy, prov:actedOnBehalfOf, prov:wasEndedBy, etc.) should be used when applicable.
This property has multiple RDFS domains to suit multiple OWL Profiles. See <a href="#owl-profile">PROV-O OWL Profile</a>.
wasInfluencedBy
qualified
agents-responsibility
The sub-properties of prov:wasInfluencedBy can be elaborated in more detail using the Qualification Pattern. For example, the binary relation :baking prov:used :spoon can be qualified by asserting :baking prov:qualifiedUsage [ a prov:Usage; prov:entity :spoon; prov:atLocation :kitchen ] .
Subproperties of prov:wasInfluencedBy may also be asserted directly without being qualified.
prov:wasInfluencedBy should not be used without also using one of its subproperties.
influenced
influencee: an identifier (o2) for an entity, activity, or agent;
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-influence
influencer: an identifier (o1) for an ancestor entity, activity, or agent that the former depends on;
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-influence
An activity a2 is dependent on or informed by another activity a1, by way of some unspecified entity that is generated by a1 and used by a2.
wasInformedBy
starting-point
entities-activities
informed
wasInvalidatedBy
expanded
entities-activities
invalidated
An entity is derived from an original entity by copying, or 'quoting', some or all of it.
wasQuotedFrom
expanded
derivations
quotedAs
Quotation is a particular case of derivation (see http://www.w3.org/TR/prov-dm/#term-quotation) in which an entity is derived from an original entity by copying, or "quoting", some or all of it.
Revision is a derivation (see http://www.w3.org/TR/prov-dm/#term-Revision). Moreover, according to
http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#term-Revision 23 April 2012 'wasRevisionOf is a strict sub-relation of wasDerivedFrom since two entities e2 and e1 may satisfy wasDerivedFrom(e2,e1) without being a variant of each other.'
Start is when an activity is deemed to have started. A start may refer to an entity, known as trigger, that initiated the activity.
wasStartedBy
expanded
entities-activities
started
hasExperimentalMaterial binds an experiment to the data that was used in an experiment.
hasExperimentalMaterial
hasExperimentalCondition binds an experiment to its environmental condition.
hasExperimentalCondition
hasExperimentalData binds an experiment to the data that was used in an experiment.
hasExperimentalData
An entity is part of another entity if one of its part belong to the other entity.
hasPart
hasSetting binds a thing or instrument to its configurations or settings.
hasSetting
isAccessibleTo is a property which describes that an Entity is accessible or available to an Agent.
isAccessibleTo
An entity is part of another entity if one of its part belong to the other entity.
isPartOf
isSettingOf binds a thing or instrument to its configurations or settings.
isSettingOf
An entity which has used another entity as reference.
reference
The storage location of an entity.
storedAt
A process which used a method to achieve something.
usedMethod
A relationship between an entity to its creator agent.
wasCreatedBy
A relationship between an entity to its distributor agent.
wasDistributedBy
An experiment material which is extracted from another material.
wasExtractedFrom
An entity which is updated by another entity or an agent.
wasUpdatedBy
The time at which an InstantaneousEvent occurred, in the form of xsd:dateTime.
atTime
qualified
entities-activities
The time at which an activity ended. See also prov:startedAtTime.
endedAtTime
starting-point
entities-activities
It is the intent that the property chain holds: (prov:qualifiedEnd o prov:atTime) rdfs:subPropertyOf prov:endedAtTime.
The time at which an entity was completely created and is available for use.
generatedAtTime
expanded
entities-activities
It is the intent that the property chain holds: (prov:qualifiedGeneration o prov:atTime) rdfs:subPropertyOf prov:generatedAtTime.
The time at which an entity was invalidated (i.e., no longer usable).
invalidatedAtTime
expanded
entities-activities
It is the intent that the property chain holds: (prov:qualifiedInvalidation o prov:atTime) rdfs:subPropertyOf prov:invalidatedAtTime.
The time at which an activity started. See also prov:endedAtTime.
startedAtTime
starting-point
entities-activities
It is the intent that the property chain holds: (prov:qualifiedStart o prov:atTime) rdfs:subPropertyOf prov:startedAtTime.
value
expanded
entities-activities
Provides a value that is a direct representation of an entity.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-attribute-value
This property serves the same purpose as rdf:value, but has been reintroduced to avoid some of the definitional ambiguity in the RDF specification (specifically, 'may be used in describing structured values').
The editor's definition comes from http://www.w3.org/TR/rdf-primer/#rdfvalue
A standard alphanumeric code to uniquely identify scientific and other academic authors and contributors.
ORCID
Address of an Agent
Address
Textual note of an entity.
description
Publication persistent identifier
doi
A unique identifier of an entity.
Id
The time at which an entity was modified.
modifiedAtTime
The name of a thing.
Name
A standard unique PubMed Central identifier.
PubMed Central ID
A standard unique identifier for each PubMed record.
PubMed ID
The time at which an entity was received.
receivedAtTime
A p-plan:Activity represents the execution process planned in a p-plan:Step
Activity
Bundle
A p-plan:Bundle is a specific type of prov:Bundle that contains the provenance assertions of the execution of a p-plan:Plan
Entity
A p-plan:Entity represents the input of the execution of a p-plan:Activity. It corresponds to a p-plan:Variable.
MultiStep
A multi step is the representation of a plan that appears as a step of another plan.
Plan
A p-plan:Plan is a specific type of prov:Plan. It is composed of smaller steps that use and produce Variables.
Step
A p-plan:Step represents the planned execution activity
Variable
A p-plan:Variable represents a description of the input of the planned Activity (p-plan:Step)
Activity
starting-point
entities-activities
http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig
An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-Activity
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-Activity
0
ActivityInfluence provides additional descriptions of an Activity's binary influence upon any other kind of resource. Instances of ActivityInfluence use the prov:activity property to cite the influencing Activity.
It is not recommended that the type ActivityInfluence be asserted without also asserting one of its more specific subclasses.
ActivityInfluence
qualified
ActivitiyInfluence is the capacity of an activity to have an effect on the character, development, or behavior of another by means of generation, invalidation, communication, or other.
Agent
starting-point
agents-responsibility
An agent is something that bears some form of responsibility for an activity taking place, for the existence of an entity, or for another agent's activity.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-agent
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-Agent
AgentInfluence provides additional descriptions of an Agent's binary influence upon any other kind of resource. Instances of AgentInfluence use the prov:agent property to cite the influencing Agent.
It is not recommended that the type AgentInfluence be asserted without also asserting one of its more specific subclasses.
AgentInfluence
qualified
AgentInfluence is the capacity of an agent to have an effect on the character, development, or behavior of another by means of attribution, association, delegation, or other.
An instance of prov:Association provides additional descriptions about the binary prov:wasAssociatedWith relation from an prov:Activity to some prov:Agent that had some responsiblity for it. For example, :baking prov:wasAssociatedWith :baker; prov:qualifiedAssociation [ a prov:Association; prov:agent :baker; :foo :bar ].
Association
qualified
agents-responsibility
An activity association is an assignment of responsibility to an agent for an activity, indicating that the agent had a role in the activity. It further allows for a plan to be specified, which is the plan intended by the agent to achieve some goals in the context of this activity.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-Association
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-Association
An instance of prov:Attribution provides additional descriptions about the binary prov:wasAttributedTo relation from an prov:Entity to some prov:Agent that had some responsible for it. For example, :cake prov:wasAttributedTo :baker; prov:qualifiedAttribution [ a prov:Attribution; prov:entity :baker; :foo :bar ].
Attribution
qualified
agents-responsibility
http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig
Attribution is the ascribing of an entity to an agent.
When an entity e is attributed to agent ag, entity e was generated by some unspecified activity that in turn was associated to agent ag. Thus, this relation is useful when the activity is not known, or irrelevant.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-attribution
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-attribution
Note that there are kinds of bundles (e.g. handwritten letters, audio recordings, etc.) that are not expressed in PROV-O, but can be still be described by PROV-O.
Bundle
expanded
A bundle is a named set of provenance descriptions, and is itself an Entity, so allowing provenance of provenance to be expressed.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-bundle-entity
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-bundle-declaration
Collection
expanded
collections
A collection is an entity that provides a structure to some constituents, which are themselves entities. These constituents are said to be member of the collections.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-collection
An instance of prov:Communication provides additional descriptions about the binary prov:wasInformedBy relation from an informed prov:Activity to the prov:Activity that informed it. For example, :you_jumping_off_bridge prov:wasInformedBy :everyone_else_jumping_off_bridge; prov:qualifiedCommunication [ a prov:Communication; prov:activity :everyone_else_jumping_off_bridge; :foo :bar ].
Communication
qualified
entities-activities
http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig
Communication is the exchange of an entity by two activities, one activity using the entity generated by the other.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-Communication
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-wasInformedBy
An instance of prov:Delegation provides additional descriptions about the binary prov:actedOnBehalfOf relation from a performing prov:Agent to some prov:Agent for whom it was performed. For example, :mixing prov:wasAssociatedWith :toddler . :toddler prov:actedOnBehalfOf :mother; prov:qualifiedDelegation [ a prov:Delegation; prov:entity :mother; :foo :bar ].
Delegation
qualified
agents-responsibility
Delegation is the assignment of authority and responsibility to an agent (by itself or by another agent) to carry out a specific activity as a delegate or representative, while the agent it acts on behalf of retains some responsibility for the outcome of the delegated work.
For example, a student acted on behalf of his supervisor, who acted on behalf of the department chair, who acted on behalf of the university; all those agents are responsible in some way for the activity that took place but we do not say explicitly who bears responsibility and to what degree.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-delegation
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-delegation
An instance of prov:Derivation provides additional descriptions about the binary prov:wasDerivedFrom relation from some derived prov:Entity to another prov:Entity from which it was derived. For example, :chewed_bubble_gum prov:wasDerivedFrom :unwrapped_bubble_gum; prov:qualifiedDerivation [ a prov:Derivation; prov:entity :unwrapped_bubble_gum; :foo :bar ].
The more specific forms of prov:Derivation (i.e., prov:Revision, prov:Quotation, prov:PrimarySource) should be asserted if they apply.
Derivation
qualified
derivations
http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig
A derivation is a transformation of an entity into another, an update of an entity resulting in a new one, or the construction of a new entity based on a pre-existing entity.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-Derivation
http://www.w3.org/TR/2013/REC-prov-n-20130430/#Derivation-Relation
An instance of prov:End provides additional descriptions about the binary prov:wasEndedBy relation from some ended prov:Activity to an prov:Entity that ended it. For example, :ball_game prov:wasEndedBy :buzzer; prov:qualifiedEnd [ a prov:End; prov:entity :buzzer; :foo :bar; prov:atTime '2012-03-09T08:05:08-05:00'^^xsd:dateTime ].
End
qualified
entities-activities
http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig
End is when an activity is deemed to have been ended by an entity, known as trigger. The activity no longer exists after its end. Any usage, generation, or invalidation involving an activity precedes the activity's end. An end may refer to a trigger entity that terminated the activity, or to an activity, known as ender that generated the trigger.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-End
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-End
Entity
starting-point
entities-activities
http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig
An entity is a physical, digital, conceptual, or other kind of thing with some fixed aspects; entities may be real or imaginary.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-entity
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-Entity
EntityInfluence provides additional descriptions of an Entity's binary influence upon any other kind of resource. Instances of EntityInfluence use the prov:entity property to cite the influencing Entity.
It is not recommended that the type EntityInfluence be asserted without also asserting one of its more specific subclasses.
EntityInfluence
qualified
EntityInfluence is the capacity of an entity to have an effect on the character, development, or behavior of another by means of usage, start, end, derivation, or other.
An instance of prov:Generation provides additional descriptions about the binary prov:wasGeneratedBy relation from a generated prov:Entity to the prov:Activity that generated it. For example, :cake prov:wasGeneratedBy :baking; prov:qualifiedGeneration [ a prov:Generation; prov:activity :baking; :foo :bar ].
Generation
qualified
entities-activities
http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig
Generation is the completion of production of a new entity by an activity. This entity did not exist before generation and becomes available for usage after this generation.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-Generation
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-Generation
An instance of prov:Influence provides additional descriptions about the binary prov:wasInfluencedBy relation from some influenced Activity, Entity, or Agent to the influencing Activity, Entity, or Agent. For example, :stomach_ache prov:wasInfluencedBy :spoon; prov:qualifiedInfluence [ a prov:Influence; prov:entity :spoon; :foo :bar ] . Because prov:Influence is a broad relation, the more specific relations (Communication, Delegation, End, etc.) should be used when applicable.
Because prov:Influence is a broad relation, its most specific subclasses (e.g. prov:Communication, prov:Delegation, prov:End, prov:Revision, etc.) should be used when applicable.
Influence
qualified
derivations
Influence is the capacity of an entity, activity, or agent to have an effect on the character, development, or behavior of another by means of usage, start, end, generation, invalidation, communication, derivation, attribution, association, or delegation.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-influence
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-influence
An instantaneous event, or event for short, happens in the world and marks a change in the world, in its activities and in its entities. The term 'event' is commonly used in process algebra with a similar meaning. Events represent communications or interactions; they are assumed to be atomic and instantaneous.
InstantaneousEvent
qualified
entities-activities
http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#dfn-event
The PROV data model is implicitly based on a notion of instantaneous events (or just events), that mark transitions in the world. Events include generation, usage, or invalidation of entities, as well as starting or ending of activities. This notion of event is not first-class in the data model, but it is useful for explaining its other concepts and its semantics.
An instance of prov:Invalidation provides additional descriptions about the binary prov:wasInvalidatedBy relation from an invalidated prov:Entity to the prov:Activity that invalidated it. For example, :uncracked_egg prov:wasInvalidatedBy :baking; prov:qualifiedInvalidation [ a prov:Invalidation; prov:activity :baking; :foo :bar ].
Invalidation
qualified
entities-activities
http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig
Invalidation is the start of the destruction, cessation, or expiry of an existing entity by an activity. The entity is no longer available for use (or further invalidation) after invalidation. Any generation or usage of an entity precedes its invalidation.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-Invalidation
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-Invalidation
Location
expanded
A location can be an identifiable geographic place (ISO 19112), but it can also be a non-geographic place such as a directory, row, or column. As such, there are numerous ways in which location can be expressed, such as by a coordinate, address, landmark, and so forth.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-attribute-location
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-attribute
Organization
expanded
agents-responsibility
An organization is a social or legal institution such as a company, society, etc.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-agent
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-types
Person
expanded
agents-responsibility
Person agents are people.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-agent
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-types
There exist no prescriptive requirement on the nature of plans, their representation, the actions or steps they consist of, or their intended goals. Since plans may evolve over time, it may become necessary to track their provenance, so plans themselves are entities. Representing the plan explicitly in the provenance can be useful for various tasks: for example, to validate the execution as represented in the provenance record, to manage expectation failures, or to provide explanations.
Plan
expanded
qualified
agents-responsibility
A plan is an entity that represents a set of actions or steps intended by one or more agents to achieve some goals.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-Association
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-Association
An instance of prov:PrimarySource provides additional descriptions about the binary prov:hadPrimarySource relation from some secondary prov:Entity to an earlier, primary prov:Entity. For example, :blog prov:hadPrimarySource :newsArticle; prov:qualifiedPrimarySource [ a prov:PrimarySource; prov:entity :newsArticle; :foo :bar ] .
PrimarySource
qualified
derivations
A primary source for a topic refers to something produced by some agent with direct experience and knowledge about the topic, at the time of the topic's study, without benefit from hindsight.
Because of the directness of primary sources, they 'speak for themselves' in ways that cannot be captured through the filter of secondary sources. As such, it is important for secondary sources to reference those primary sources from which they were derived, so that their reliability can be investigated.
A primary source relation is a particular case of derivation of secondary materials from their primary sources. It is recognized that the determination of primary sources can be up to interpretation, and should be done according to conventions accepted within the application's domain.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-primary-source
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-original-source
An instance of prov:Quotation provides additional descriptions about the binary prov:wasQuotedFrom relation from some taken prov:Entity from an earlier, larger prov:Entity. For example, :here_is_looking_at_you_kid prov:wasQuotedFrom :casablanca_script; prov:qualifiedQuotation [ a prov:Quotation; prov:entity :casablanca_script; :foo :bar ].
Quotation
qualified
derivations
A quotation is the repeat of (some or all of) an entity, such as text or image, by someone who may or may not be its original author. Quotation is a particular case of derivation.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-quotation
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-quotation
An instance of prov:Revision provides additional descriptions about the binary prov:wasRevisionOf relation from some newer prov:Entity to an earlier prov:Entity. For example, :draft_2 prov:wasRevisionOf :draft_1; prov:qualifiedRevision [ a prov:Revision; prov:entity :draft_1; :foo :bar ].
Revision
qualified
derivations
A revision is a derivation for which the resulting entity is a revised version of some original. The implication here is that the resulting entity contains substantial content from the original. Revision is a particular case of derivation.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-revision
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-Revision
Role
qualified
agents-responsibility
A role is the function of an entity or agent with respect to an activity, in the context of a usage, generation, invalidation, association, start, and end.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-attribute-role
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-attribute
SoftwareAgent
expanded
agents-responsibility
A software agent is running software.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-agent
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-types
An instance of prov:Start provides additional descriptions about the binary prov:wasStartedBy relation from some started prov:Activity to an prov:Entity that started it. For example, :foot_race prov:wasStartedBy :bang; prov:qualifiedStart [ a prov:Start; prov:entity :bang; :foo :bar; prov:atTime '2012-03-09T08:05:08-05:00'^^xsd:dateTime ] .
Start
qualified
entities-activities
http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig
Start is when an activity is deemed to have been started by an entity, known as trigger. The activity did not exist before its start. Any usage, generation, or invalidation involving an activity follows the activity's start. A start may refer to a trigger entity that set off the activity, or to an activity, known as starter, that generated the trigger.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-Start
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-Start
An instance of prov:Usage provides additional descriptions about the binary prov:used relation from some prov:Activity to an prov:Entity that it used. For example, :keynote prov:used :podium; prov:qualifiedUsage [ a prov:Usage; prov:entity :podium; :foo :bar ].
Usage
qualified
entities-activities
http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig
Usage is the beginning of utilizing an entity by an activity. Before usage, the activity had not begun to utilize this entity and could not have been affected by the entity.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-Usage
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-Usage
Describes the type of microscopy performed for each channel
Acquistion Mode
Data that provides additional information of an experiment.
Additional Information
Air Pressure
A set of rules or steps to be followed in a problem-solving operation.
Algorithm
A person or an organisation responsible for receiving the experiment aliquots.
AliquotsReceiver
Amplification
electronic Gain applied to the detector signal.
AmplificationGain
The level of the amplification applied to a resource.
AmplificationLevel
A description added to a thing which provides comment, note or description.
Annotation
AntisenseSequence
The Arc element is used to describe various kinds of Arc lamps - Hg, Xe, HgXe.
Arc
The type of Arc Lamp.
Arc Type
A parameter.
For example, an argument of parameter of a function.
Argument
A planned procedure to investigate to qualitively assess an entity.
Assay
The Attenuation of the light source, A fraction, as a value from 0.0 to 1.0.
Attenuation
The person who authors a piece of work.
Author
The Bacterial Resistance used to transform a bacteria.
Bacterial Resistance
A subtype of a microorganism bacteria
Bacterial Strain
Bath Solution
Represents the number of pixels that are combined to form larger pixels.
Binning
BIO-Formats is an image translation library which reads and writes life sciences image file formats. It converts the proprietary microscopy data to a open standard model called OME data model, particularly into the OME-TIFF file format, which then can be used by other tools.
Bio-Formats
CAS number is a uniquely numerical identifier assigned by Chemical Abstracts Service (CAS) to every chemical substance.
CASNumber
CO2 Percent
The magnification of the lens as measured by a calibration process- i.e. '59.987' for a 60X lens.
Calibrated Magnification
The causal effects of an activity denotes the effects on an outcome because of another activity.
Causal Effect
A cell is a multiline text input field in an Interactive Notebook which can either be code cells where code can be excuted or markdown cells where a descriptive text can be provided or raw cells where output can directly be entered.
For example, a Jupyter Notebook cell.
Notebok Cell
The run of a cell of a Interactive Notebook.
Notebook Cell Execution
Cell Line
A component of an Image.
Channel
Channel Binding
The Fluor attribute is used for fluorescence images. This is the name of the fluorophore used to produce this channel
Channel Fluorophore
The settings of channel.
ChannelSetting
The method which yields the checksum from a data input for the purpose of detecting errors.
CheckSum Algorithm
A pure substance with constant chemical composition and properties used in an experiment.
Chemical
The procedure to replicate specimen.
Cloning
The column naming convention for plates.
Column Naming Convention
The number of columns in the plate.
Columns
The step or the process which uses computational resources involved in an experiment.
Computational Step
The tools that use computer-based systems for computation.
Computational Tool
Concentration
The settings or changes applied to an instrument.
Configuration
Configuration of the microscope used in the lab.
Microscope Configuration
A person who has the role of being a contact person for a certain thing.
ContactPerson
The background setting of an experiment.
Context
Describes the technique used to achieve contrast for each channel.
Contrast Method
ControlComments
The person who holds the copyright or the permission of an entity or an activity.
Copyright Holder
The correction applied to the lens.
Correction
The CorrectionCollar is normally an adjustable ring on the objective. Each has an arbitrary scale on it so the values is unit-less.
Correction Collar
CutIn is the wavelength below which there is less than 50% transmittance for a filter.
CutIn
CutIn Tolerance.
CutIn Tolerance
CutOut is the wavelength above which there is less than 50% transmittance for a filter.
CutOut
CutOut Tolerance.
CutOut Tolerance
Deoxyribonucleic acid which is carries genetic instructions for the many functions like growth, development and reproduction.
DNA
A type or format of a thing.
DataType
An element specifying a collection of images that are always processed together.
Dataset
DeltaT
The activity of describing things.
Describe
The text which is used to provide information about a thing.
Description
An instrument capture the image.
Detector
The setting applied to a detector
Detector Setting
The Type of detector. E.g. CCD, PMT, EMCCD etc.
Detector Type
The level in the developmental lifecycle of an entity.
DevelopmentalStage
The dichromatic beamsplitter or dichroic mirror used for the filter combination.
Dichroic
The order in which the individual planes of data are interleaved.
Dimension Order
Distributor is a person who is responsible for the distribution of materials.
Distributor
The detector gain.
ElectronicGain
Wavelength of emission for a particular channel.
Emission Wavelength
The attributes of the experimental execution environment.
Environment Attribute
To setup the environment to perform an experiment.
Environment Setup
The various attribute needed to setup the environment for an experiment.
Environment Setup Setting
The resistance of Eukaryotic Cells.
Eukaryotic Cell Resistance
The activity which uses or generates data.
Event
Wavelength of excitation for a particular channel
Excitation Wavelength
Experiment is an entity which describes the collective activity conducted in a science lab.
Experiment
A set of instructions to setup the environment for experiment.
Experiment Environment Setup
The materials or things used in an experiment.
For example, a specimen.
Experiment Material
A procedure to prepare experiment materials.
Experiment Material Preparation
To setup the execution environment of an experiment.
Experiment Setup
Refers to the type of an experiment.
Experiment Type
The attributes or the conditions while an experiment is performed.
Experimental Condition
Data used in an experiment.
Experimental Data
Experimenter is a person who is the owner of the Experiment and has its responsibility.
Experimenter
Configuration of an experimenter group.
Experimenter Group Config
The length of the exposure.
Exposure Time
The procedure of expression of materials.
Expression
The procedure used for the expression of experiment materials like Vectors, Protein.
Expression System
The ExternalIdentifier attribute may contain a reference to an external database.
ExternalIdentifier
Family
The index of the WellSample.
Field Index
Describe various kinds of filament bulbs such as Incadescent or Halogen.
Filament
The type of filament.
Filament Type
A storage to store data. For example, a computer file.
File
A filter is either an excitation or emission filters.
Filter
The settings of filter.
Filter Setting
The type of filter.
Filter Type
A filter 'wheel' in OME can refer to any arrangement of filters in a filter holder of any shape. It could, for example, be a filter slider.
Filter Wheel
The FilterSet
Filterset
It is the final result that is generated in an experiment which is eventually used in a publication.
Final Result
The step that is performed at the end of an experiment.
Final Step
Fixation
A protein composed of 238 amino acid residues (26.9 kDa) that exhibits bright green fluorescence when exposed to light in the blue to ultraviolet range.
Fluoroscent Protein
FrequencyMultiplication that may be specified.
Frequency Multiplication
A programming language code snippet in a script which describes a procedure or a routine.
Function
Function Activation is when a function is activated or run.
Function Activation
An organization responsible for granting funds for conducting a research project.
Funding Agency
GeneIdentifier
GeneSymbol
Generic Excitation Source
The growth condition of a specimen.
Growth Condition
Heat Inactivation
A method that is used in biological research and drug discovery to identify substances such as small molecules, peptides, or RNAi that alter the phenotype of a cell in a desired manner
https://en.wikipedia.org/wiki/High-content_screening
High Content Screening
Humidity around the sample.
Humidity
The method of illumination used to capture the channel.
Illumination
An image or picture generated in an experiment by a device.
For example, a microscopic image with metadata.
Image
The process of acquiring image from device.
Image Acquisition
The file format of an Image.
Format
The properties of an image while its acquisition.
Image Setting
The experiment environment when the image was captured.
Imaging Environment
Imaging Method
The study related to images and its acquisition.
Imaging Study
The immersion medium the lens is designed for.
Immersion
Incubation
It is the data that is used as input to an experiment.
Input Data
A device used to capture images.
Instrument
The settings of an instrument.
Instrument Setting
the number of sequential frames that get averaged, to improve the signal-to-noise ratio.
Integration
Intermediate Result
These results are obtained during the intermediate steps of an experiment.
The step which is performed during an experiment.
Intermediate Step
Records whether or not the objective was fitted with an Iris.
Iris
Isolation of Protein
A task or a piece of work.
For example, OMERO performs the task of script execution or import of metadata to the system.
Job
An Interactive Notebook computation engine that executes the code written in a programming language.
Kernel
Laser
Laser Setting
Whether or not the laser is Tuneable
Laser Tuneable
The type of the Laser.
Laser Type
The numerical aperture of the lens.
Lens Numerical Aperture
A collection of resources used for the development of software.
Library
An official permission required to perform or own something.
License
It is the document which provides official permission to use or own an entity.
License Document
The LightEmittingDiode element is used to describe various kinds of LED lamps.
Light Emitting Diode
The light path.
Light Path
The settings of the light source.
Light Settings
The lightsource for the instrument. An instrument may have several light sources. The type of lightsource is specified by one of the child-elements which are 'Laser', 'Filament', 'Arc' or 'LightEmittingDiode'.
Light Source
A log file records all the events, interactions or messages generated in a system.
Log
A component of an Image.
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Channel
Logical Channel
The properties of a logical channel.
Logical Channel Setting
The lot number of the component.
Lot Number
The attributes for recording common properties of the components such as Manufacturer name, Model etc.
ManufactuerSpec
The person who is responsible for the generation of an entity.
Manufacturer
The step where materials are prepared for the experiment.
Material Preparation Step
A Material Transfer Aggrement defines the rights that governs the transfer of materials between agents.
Material Transfer Agreement
he characteristic of an entity which is described as a numerical value which is used as a measure to compare with other entities.
Measurement
The Medium is the actual immersion medium used for the lens.
Medium
Metadata is the data about data.
Metadata
The procedure used to perform a process.
Method
Methylation Sensitivity
A microbeam operation applied to an image.
Microbeam Manipulation
The type of a microbeam operation applied to an image.
Microbeam Manipulation Type
An instrument to observe and capture images.
Microscope
The type of microscope.
Microscope Type
The model of the instrument.
Model
The changed made to an entity.
Modification
It describes the version information of an entity which tells if there is any difference from its earlier form.
Modified Version
A part of a computer program or a software.
Module
The molecular formula of a chemical substance.
Molecular Formula
The molecular weight of a chemical substance.
Molecular Weight
These results are annotated as negative. This could be because of several reasons. The results which confute the hypothesis, the changes in experimental design or execution environment can cause negative results.
Negative Result
Specifies the combined effect of any neutral density filters used. The amount of light the filter transmits at a maximum
Neutral Density Filter
The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens.
Nominal Magnification
The step or the process which does not depend on computational resources.
Non-computational Step
A comment or description of an experiment.
Note
Interactive Notebook is a notebook for interactive computation and allow users to run code.
For example, Jupyter Notebook
Notebok
The step to note the description of things.
Noting
The microscope's objective lens.
Objective
The settings of microscope's objective lens.
Objective Settings
The Detector Offset.
Offset
Short DNA or RNA molecules.
OligoNucleotide
A system software that supports and manages the hardware and the software resources and provides computer's functions.
Operating System
Specifies how different spatial frequencies are handled by the optical system such as microscope, camera etc.
OpticalTransferFunction
The specimens used in an experiment.
Organism
A step to collect original information of materials like the provenance of a thing.
Origin Information Collection
The original attribution of a thing belongs to the OriginalCreator.
Original Creator
The result obtained after an activity.
Output
A person who owns a certain thing.
Owner
A collection of programs and resources which are packed together.
Package
These values are factors which define an operation or a system which is kept constant for a particular execution of an experiment or a calculation and varied over other executions.
Parameter
It describes the observable characteristic of an individual.
Phenotype
Photometric Interpretation
Physical size of a pixel.
PhysicalSizeX
Physical size of a pixel.
PhysicalSizeY
Physical size of a pixel.
PhysicalSizeZ
PinholeSize attribute allows specifying adjustable pin hole diameters for confocal microscopes.
Pinhole Size
Pipette Solution
The Pixels element contain a list of BinData or TiffData, each containing a single plane of pixels.
Pixels
The properties of pixels element.
Pixels Setting
The variable type used to represent each pixel in the image.
Pixels Type
The Plane object holds microscope stage and image timing data for a given channel/z-section/timepoint.
Plane Information
The setting of a Plane object.
Plane Setting
A small circular DNA strand usually found in the cytoplasm.
Plasmid
Identifies microtiter plates within a screen.
Plate
The process of plate acquisition.
Plate Acquisition
The settings for plate acquiistion.
Plate Setting
The laser has a PockelCell to rotate the polarization of the beam.
PockelCell
The PockelCellSetting used for this channel. This is the amount the polarization of the beam is rotated by.
PockelCell Setting
The X position of the stage.
PositionX
The Y position of the stage.
PositionY
The Z position of the stage.
PositionZ
These results which are annotated as positive are the results that confirm the hypothesis of an experiment.
Positive Result
The light-source power.
Power
The conditions that must be fulfilled before performing an activity.
Precondition
Step of preparing something.
Preparation
An important person responsible for a ResearchProject.
Principal Investigator
The data which is modified and processed for analysis or other experiments.
Processed Data
The language used for scripting. For eg. Java, Python.
Programming Language
The provenance information of an activity that specifies its plan.
Prospective Provenance
Biomoelcules responsible for performing variety of functions in an organism.
Protein
A set of instructions needed to perform an activity.
Protocol
A description of the screen protocol; may contain very detailed information to
reproduce some of that found in a screening database.
Protocol Description
A pointer to an externally defined protocol, usually in a screening database.
Protocol Identifier
A printed work or a file describing the work of one or more agents.
Publication
The Pulse mode of the laser.
Pulse
The step for the purification of protein.
Purification of Protein
The purity of a substance.
Purity
A technique to check and control the quality of an entity.
QualityControl
Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation, and expression of genes.
RNA
RNA Injection
A four dimensional 'Region of Interest'. If they are not used, and the Image has more than one plane, the entire set of planes is assumed to be included in the ROI.
Region of Interest
The overall review provided by an agent to a thing.
Rating
The data directly generated from an experiment without any modification or processing.
Raw Data
Reaction Condition
The speed at which the detector can count pixels. This is the bytes per second that can be read from the detector
ReadOut Rate
A chemical or a physical parameter used in an experiment.
Reagent
The Pulse mode of the laser.
ReagentSet Description
ReagentSetIdentifier
The RefractiveIndex is that of the immersion medium.
Refractive Index
Rendering Def
Rendering Model
The is the rate in Hz at which the laser pulses if the Pulse type is 'Repetitive'.
Repetition Rate
Group is an organization which belongs to a department of an institution consisting of people responsible for research and education.
Research Group
A person or collaborative group working on a research plan to achieve certain goals.
Research Project
A restriction enzyme or restriction endonuclease is an enzyme that cleaves DNA into fragments at or near specific recognition sites within the molecule known as restriction sites.
Restriction Enzyme
RestrictionSite
The output of a step.
Result
The provenance information of what happened when an activity is performed.
Retrospective Provenance
The document which tells whether other scientists are allowed to use or modify the data.
Rights and Permissions Document
The Convention for Naming rows in plate.
RowNaming Convention
The number of rows in the plate.
Rows
The number of samples the detector takes to form each pixel value.
Samples Per Pixel
The Screen element is a grouping for Plates.
Screen
The properties of a High Content Screen.
Screen Setting
A computer program written to perform a task in a scripting language.
Script
SenseSequence
Sequencing
The serial number of the component.
Serial Number
A period of activity between a user is logged in and logged out of a system. For example, A OMERO session, JupyterNotebook session.
Session
A setting of a system in a session.
Session Setting
The parameters or the situation in which the experiment was performed.
Setting
The shape element contains a single specific ROI shape and links that to any channels, and a timepoint and a z-section. It also
records any transform applied to the ROI shape.
Shape
The number of bits within the type storing each pixel that are significant. For e.g. you can store 12 bit data within a 16 bit type.
Significant Bits
A dimension of a thing.
Size
Dimensional size of pixel data array
SizeC
Dimensional size of pixel data array
SizeT
Dimensional size of pixel data array
SizeX
Dimensional size of pixel data array
SizeY
Dimensional size of pixel data array
SizeZ
The computer program which performs a particular task or tasks.
Software
A homogeneous mixture of substances.
For example, a chemical solution used in an experiment.
Solution
A substance to dissolve other substances.
Solvent
The input of each cell in a Jupyter Notebook is described as Source.
Source
Specimen is a part of a thing used in an Experiment or a study to determine the character of the whole thing.
Specimen
The StageLabel is used to specify a name and position for a stage position in the microscope's reference frame.
Stage Label
A set of steb-by-step instructions to carry out a complex routine.
Standard Operating Procedure
A textual annotation of the current state of the plate with respect to the experiment work-flow; e.g. 1. Seed cell: done; 2. Transfection: done; 3. Gel doc: todo.
Plate Status
Stock Solution
The Structural Formula of a chemical substance.
Structural Formula
A process to examine and analyze a data object to answer questions and discover new facts about it.
Study
SubExperiment
The file formats supported by BIO-Format
Supported File Format
A label attached to something to identify it.
For example, an experiment tag to identify and categorize the experiments.
Tag
The process of tagging with tags.
Tagging
The temperature of the imaging environment
Temperature
The channel the plane is for.
TheC
The timepoint the plane is for.
TheT
The timepoint the plane is for.
TheZ
A short representation of an entity.
Thumbnail
TimeIncrement is used for time series that have a global timing specification instead of per-timepoint timing info.
For example in a video stream.
TimeIncrement
Transfection
The amount of light the filter transmits at a maximum [units:none] A fraction, as a value from 0.0 to 1.0.
Transmittance
The range of wavelengths that are transmitted by the filter.
Transmittance Range
Treatment
A run or execution of an activity.
For example, one execution of a script.
Trial
A standard quantity of measurement.
Unit
A DNA molecule used as a vehicle to artificially carry foreign genetic material into another cell.
Vector
Verification
A property of an entity which describes its difference with respect to its earlier form.
Version
The Voltage of the detector
Voltage
The Wavelength of the light source.
Wavelength
A Well is a component of the Well/Plate/Screen construct to describe screening applications.
A Well has a number of WellSample elements that link to the Images collected in this well.
Well
This defines the X position to use for the origin of the fields (individual images) taken in a well. It is used with the X in the WellSample to display the fields
in the correct position relative to each other. Each Well in the plate has the same well origin.
WellOriginX
This defines the Y position to use for the origin of the fields (individual images) taken in a well. It is used with the Y in the WellSample to display the fields
in the correct position relative to each other. Each Well in the plate has the same well origin.
WellOriginY
WellSample is an individual image that has been captured within a Well.
Well Sample
The working distance of the lens.
Working Distance
The fixed Zoom for a detector.
Zoom
Complementary DNA source
cDNA Source
A numerical scale used to express the acidity or alkalinity of a solution.
pH
siRNAIdentifier
siRNAPoolIdentifier
AIM
APD
Axon Raw Format (ARF)
AVI (Audio Video Interleave)
CRC-32
Alicona 3D
Amersham Biosciences Gel
Amira Mesh
Amnis FlowSight
AnalogVideo
Analyze 7.5
Andor Bio-Imaging Division (ABD) TIFF
Andor SIF
Animated PNG
Aperio AFI
Aperio SVS TIFF
Applied Precision CellWorX
BD Pathway
BMP
BandPass
BioRad
Bio-Rad Gel
Bio-Rad SCN
BrightField
BrightField
Bruker MRI
Burleigh
CCD
Canon DNG
CellH5
CellVoyager
Cellomics
Colocalization
CorrelationSpectroscopy
DIC
DICOM
Darkfield
DeltaVision
DichroicFilter
Dissection
Dye
EBCCD
ECAT7
EM-CCD
EPS (Encapsulated PostScript)
Electrophysiology
ElectrophysiologyMicroscope
Epifluorescence
Evotec/PerkinElmer Opera Flex
Excimer
FEI
FEI TIFF
FISH
FITS (Flexible Image Transport System)
FLIP
FP
FRAP
FRET
FSM
FTIR
File-Size-64
Fluorescence
Fluorescence Correlation Spectroscopy
Fluorescence Lifetime
Fluorescence Lifetime Experiment
FourDPlus
FreeElectron
GIF (Graphics Interchange Format)
Gas
Gatan Digital Micrograph
Gatan Digital Micrograph 2
Halogen
Hamamatsu Aquacosmos NAF
Hamamatsu HIS
Hamamatsu ndpi
Hamamatsu VMS
Hg
HgXe
Hitachi S-4800
HoffmanModulation
I2I
ICS (Image Cytometry Standard)
IMAGIC
IMOD
INR
IPLab
ImagePro Workspace
IVision
Imacon
ImagePro Sequence
Imaris
Immunocytochemistry
Immunofluorescence
Improvision Openlab Raw
ImprovisionTIFF
Imspector OBF
InCell 1000/2000
InCell 3000
Incandescent
IntensifiedCCD
Inveon
InverseFRAP
Inverted
IonImaging
JEOL
JPEG
JPEG 2000
JPK
JPX
Khoros VIFF (Visualization Image File Format) Bitmap
Kodak BIP
LCM
LEO
Leica LAS AF LIF (Leica Image File Format)
LIM (Laboratory Imaging/Nikon)
LaVision Imspector
Lambert Instruments FLIM
LaserScanningConfocalMicroscopy
Leica
Leica SCN
Li-Cor L2D
LifetimeImaging
LongPass
MD5-128
MIAS (Maia Scientific)
MINC MRI
MNG (Multiple-image Network Graphics)
MRC (Medical Research Council)
MetaMorph 7.5 TIFF
MetaMorph Stack (STK)
MetalVapor
Micro-Manager
MinoltaMRW
Molecular Imaging
MultiPass
MultiPhotonMicroscopy
Murmur3-128
Murmur3-32
NIfTI
NRRD (Nearly Raw Raster Data)
NearFieldScanningOpticalMicroscopy
NeutralDensity
Nikon
Nikon EZ-C1 TIFF
NEF (Nikon Electronic Format)
Nikon Elements TIFF
Nikon NIS-Elements ND2
NonLinear
OME-TIFF
OME-XML
OMERO Pyramid
Oblique
ObliqueIllumination
Olympus CellR/APL
Olympus FluoView FV1000
Olympus SIS TIFF
Olympus ScanR
OpticalTrapping
Oxford Instruments
PALM
PCORAW
PCX (PC Paintbrush)
PGIDocumentation
PGM
PICT (Macintosh Picture)
PMT
PNG (Portable Network Graphics)
Adobe Photoshop PSD
PerkinElmer Columbus
Perkin Elmer Densitometer
PerkinElmer Nuance
PerkinElmer Operetta
PerkinElmer UltraVIEW
Phase
Photoablation
Photoactivation
Photobleaching
Photodiode
Photoshop TIFF
PicoQuant Bin
PolarizedLight
Prairie Technologies TIFF
Quesant
QuickTime Movie
RHK
SBIG
Becker & Hickl SPCImage
SHA1-160
SM Camera
SPIDER
SPIM
STED
STORM
ScreenExperiment
SecondHarmonicGenerationImaging
Seiko
Semiconductor
ShortPass
SimplePCI and HCImage
SimplePCI & HCImage TIFF
SingleMoleculeImaging
3i SlideBook
SlitScanConfocal
SolidState
SpectralImaging
SpectralImagingExperiment
Spectroscopy
SpinningDiskConfocal
StructuredIllumination
SweptFieldConfocal
TCS
TIFF (Tagged Image File Format)
TIRF
Targa
Text
TillPhotonics TillVision
TimeLapse
Topometrix
TotalInternalReflection
Transmitted
Trestle
Tuneable
UBM
Uncaging
Unisoku
Upright
VG SAM
Varian FDF
Veeco AFM
VisiTech XYS
Volocity
Volocity Library Clipping
WA-TOP
WideField
Woolz
XYCTZ
XYCZT
XYTCZ
XYTZC
XYZCT
XYZTC
Xe
Zeiss AxioVision ZVI (Zeiss Vision Image)
Zeiss Axio CSM
Zeiss AxioVision TIFF
Zeiss CZI
Zeiss LSM (Laser Scanning Microscope) 510/710
cellSens VSI
EmptyCollection
expanded
collections
An empty collection is a collection without members.
specializationOf
expanded
alternate
http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig
An entity that is a specialization of another shares all aspects of the latter, and additionally presents more specific aspects of the same thing as the latter. In particular, the lifetime of the entity being specialized contains that of any specialization. Examples of aspects include a time period, an abstraction, and a context associated with the entity.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-specialization
generalizationOf
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-specialization
A revision is a derivation that revises an entity into a revised version.
wasRevisionOf
expanded
derivations
hadRevision