This document is published by the Provenance Working Group (http://www.w3.org/2011/prov/wiki/Main_Page).
If you wish to make comments regarding this document, please send them to public-prov-comments@w3.org (subscribe public-prov-comments-request@w3.org, archives http://lists.w3.org/Archives/Public/public-prov-comments/). All feedback is welcome.
W3C PROVenance Interchange Ontology (PROV-O)
Recommendation version 2013-04-30
Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
Really of interest to developers only
BFO OWL specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
Person:Alan Ruttenberg
Really of interest to developers only
BFO CLIF specification label
editor preferred label
editor preferred term
editor preferred term
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
editor preferred label
editor preferred term
editor preferred term
example
example of usage
A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
example of usage
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
OBI_0000281
has curation status
definition
definition
definition
textual definition
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition
definition
definition
textual definition
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
editor note
term editor
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
alternative term
definition source
formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
PERSON:Daniel Schober
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source
curator note
An administrative note of use for a curator but of no use for a user
PERSON:Alan Ruttenberg
curator note
imported from
For external terms/classes, the ontology from which the term was imported
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
imported from
elucidation
person:Alan Ruttenberg
Person:Barry Smith
Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms
elucidation
Contributor
Date may be used to express temporal information at any level of granularity. Recommended best practice is to use an encoding scheme, such as the W3CDTF profile of ISO 8601 [W3CDTF].
1999-07-02
2008-01-14
A point or period of time associated with an event in the lifecycle of the resource.
Date
Date
A second property with the same name as this property has been declared in the dcterms: namespace (http://purl.org/dc/terms/). See the Introduction to the document "DCMI Metadata Terms" (http://dublincore.org/documents/dcmi-terms/) for an explanation.
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:
prov:entity1 prov:wasGeneratedBy prov:activity1 .
can be qualified by adding:
prov:entity1 prov:qualifiedGeneration prov:entity1Gen .
prov:entity1Gen
a prov:Generation, prov:Influence;
prov:activity prov:activity1;
prov:customValue 1337 .
Note how the value of the unqualified influence (prov:wasGeneratedBy prov: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.
A property that associates a 'Drift Model' to a 'Design Matrix' (only used for first-level fMRI experiments).
Discussed at https://github.com/incf-nidash/nidm/issues/298
has Drift Model
Property that associates an 'Error Parameter Map-Wise Dependence' to the dependence of an 'Error Model'.
Discussed at https://github.com/incf-nidash/nidm/issues/194
dependence Map-Wise Dependence
Discussed in https://github.com/incf-nidash/nidm/pull/81
has Alternative Hypothesis
http://purl.obolibrary.org/obo/STATO_0000208
A property that associates a clusters label map to the excursion set.
Discussed at https://github.com/incf-nidash/nidm/issues/282
has Cluster Labels Map
Property that associates a 'Connectivity Criterion' with a 'Cluster Definition Criteria'.
Discussed in https://github.com/incf-nidash/nidm/pull/201
has Connectivity Criterion
Property that associates a covariance structure representing the dependence structure of the error, used as part of model estimation with an 'Error Model'.
has Error Dependence
Property that associates a Probability distribution used to model the error with an ErrorModel.
has Error Distribution
A property that associates a set of functions that, when convolved with the anticipated neural responses, yields a set of regressors to model the anticipated hemodynamic responses in a 'Design Matrix'.
Discussed at https://github.com/incf-nidash/nidm/issues/281
has HRF Basis
A Property that associates an additional file containing the 'Map Header' with a map
Discussed at https://github.com/incf-nidash/nidm/issues/289
has Map Header
Property of a DataArray to associate a 'Coordinate Space' with a physical file.
Discussed in https://github.com/incf-nidash/nidm/pull/171 by NN JT CM SG KH TN.
in Coordinate Space
Under discussion at https://github.com/incf-nidash/nidm/pull/137
object Model
Property that associates a [stato:"statistic"](http://purl.obolibrary.org/obo/STATO_0000039) with a StatisticMap or a ContrastWeights entity.
Discussed at https://github.com/incf-nidash/nidm/issues/293
statistic Type
Property that associates an 'Error Parameter Map-Wise Dependence' to the variance of an 'Error Model'
Discussed at https://github.com/incf-nidash/nidm/issues/194
variance Map-Wise Dependence
Property that associates a [stato:"model parameter estimation"](http://purl.obolibrary.org/obo/STATO_0000119) method with a model parameter estimation
Discussed at https://github.com/incf-nidash/nidm/issues/293
with Estimation Method
Property that associates an image of the maximum intensity projection with an 'Excursion Set Map'.
Discussed at https://github.com/incf-nidash/nidm/issues/293
has Maximum Intensity Projection
Property that associates another 'Threshold' that is equivalent (e.g. if the user specified a 'Threshold' in terms of FWE-corrected p-value, this property can be used to associate the corresponding uncorrected p-value).
Discussed in https://github.com/incf-nidash/nidm/issues/329
equivalent Threshold
'MRI Protocol' used to acquire these 'Data'.
has MRI Protocol
Relates to the property of the reification class, which relates to the object of the "shortcut relation".
has object property
testing
Relates to the reification class, which can be related to the object and subject property to be able to associate the
object and subject of the "shortcut relation". The reification class should provide detailed descriptions of the relationship that is
described in a simple form by the "shortcut relation".
has reification class
testing
Relates to the property of the "shortcut relation" (its predicate).
has shortcut
testing
Relates to the property of the reification class, which relates to the predicate of the "shortcut relation". So
that the specific property reification can be "verified" (the property of the prv:shortcut relation and this one associated by the
referred shortcut property should be equal).
has shortcut property
testing
Relates to the property of the reification class, which relates to the subject of the "shortcut relation".
has subject property
testing
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.
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 Location of any resource
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, prov:baking prov:used prov:spoon; prov:qualified [ a prov:Usage; prov:entity prov: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 prov:ag, then it can qualify the Association using prov:qualifiedAssociation [ a prov:Association; prov:agent prov:ag; prov:foo prov:bar ].
qualifiedAssociation
qualified
agents-responsibility
qualifiedAssociationOf
If this Entity prov:wasAttributedTo Agent prov:ag, then it can qualify how it was influenced using prov:qualifiedAttribution [ a prov:Attribution; prov:agent prov:ag; prov:foo prov:bar ].
qualifiedAttribution
qualified
agents-responsibility
qualifiedAttributionOf
If this Activity prov:wasInformedBy Activity prov:a, then it can qualify how it was influenced using prov:qualifiedCommunication [ a prov:Communication; prov:activity prov:a; prov:foo prov:bar ].
qualifiedCommunication
qualified
entities-activities
qualifiedCommunicationOf
If this Agent prov:actedOnBehalfOf Agent prov:ag, then it can qualify how with prov:qualifiedResponsibility [ a prov:Responsibility; prov:agent prov:ag; prov:foo prov:bar ].
qualifiedDelegation
qualified
agents-responsibility
qualifiedDelegationOf
If this Entity prov:wasDerivedFrom Entity prov:e, then it can qualify how it was derived using prov:qualifiedDerivation [ a prov:Derivation; prov:entity prov:e; prov:foo prov:bar ].
qualifiedDerivation
qualified
derivations
qualifiedDerivationOf
If this Activity prov:wasEndedBy Entity prov:e1, then it can qualify how it was ended using prov:qualifiedEnd [ a prov:End; prov:entity prov:e1; prov:foo prov:bar ].
qualifiedEnd
qualified
entities-activities
qualifiedEndOf
If this Activity prov:generated Entity prov:e, then it can qualify how it performed the Generation using prov:qualifiedGeneration [ a prov:Generation; prov:entity prov:e; prov:foo prov: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 prov:a, then it can qualify how it was invalidated using prov:qualifiedInvalidation [ a prov:Invalidation; prov:activity prov:a; prov:foo prov:bar ].
qualifiedInvalidation
qualified
entities-activities
qualifiedInvalidationOf
If this Entity prov:hadPrimarySource Entity prov:e, then it can qualify how using prov:qualifiedPrimarySource [ a prov:PrimarySource; prov:entity prov:e; prov:foo prov:bar ].
qualifiedPrimarySource
qualified
derivations
qualifiedSourceOf
If this Entity prov:wasQuotedFrom Entity prov:e, then it can qualify how using prov:qualifiedQuotation [ a prov:Quotation; prov:entity prov:e; prov:foo prov:bar ].
qualifiedQuotation
qualified
derivations
qualifiedQuotationOf
If this Entity prov:wasRevisionOf Entity prov:e, then it can qualify how it was revised using prov:qualifiedRevision [ a prov:Revision; prov:entity prov:e; prov:foo prov:bar ].
qualifiedRevision
qualified
derivations
revisedEntity
If this Activity prov:wasStartedBy Entity prov:e1, then it can qualify how it was started using prov:qualifiedStart [ a prov:Start; prov:entity prov:e1; prov:foo prov:bar ].
qualifiedStart
qualified
entities-activities
qualifiedStartOf
If this Activity prov:used Entity prov:e, then it can qualify how it used it using prov:qualifiedUsage [ a prov:Usage; prov:entity prov:e; prov:foo prov:bar ].
qualifiedUsage
qualified
entities-activities
qualifiedUsingActivity
A prov:Entity that was used by this prov:Activity. For example, prov:baking prov:used prov:spoon, prov:egg, prov: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 prov:baking prov:used prov:spoon can be qualified by asserting prov:baking prov:qualifiedUsage [ a prov:Usage; prov:entity prov:spoon; prov:atLocation prov: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
Secure Hash Algorithm 512.
SHA stands for Secure Hash Algorithm. Hash algorithms compute a fixed-length digital representation (known as a message digest) of an input data sequence (the message) of any length.
The file format, physical medium, or dimensions of the resource.
Examples of dimensions include size and duration. Recommended best practice is to use a controlled vocabulary such as the list of Internet Media Types [MIME].
Doubled standard deviation in seconds of the Gaussian weight function used in the running line smoother.
Discussed at https://github.com/incf-nidash/nidm/issues/298
drift Cutoff Period
Version of the FEAT software.
Discussed at https://github.com/incf-nidash/nidm/issues/291
feat Version
A list of abstract names associated with each column of the 'Design Matrix' (e.g. ["motor_left", "motor_right"]).
Discussed at https://github.com/incf-nidash/nidm/issues/299
regressor Names
5
Integer value used in the cluster label map to identify the location of the cluster within the excursion set.
Discussed at https://github.com/incf-nidash/nidm/pull/271
cluster Label Id
18
Number of voxels that make up the cluster.
cluster Size In Voxels
"Listening > Rest"
Name of the contrast.
contrast Name
[-60, 32, 54]
A vector with one number per dimension. The first element corresponds to the 'Coordinate' along the first dimension measured in map elements (e.g., pixels, voxels, vertices, or faces), the second element to the 'Coordinate' along the second dimension etc.
Under discussion at: https://github.com/incf-nidash/nidm/pull/270 and https://github.com/incf-nidash/nidm/issues/145
coordinate Vector
[64, 64, 20]
Number of voxels in each of the dimensions of the data array. For example, "[91, 109, 91]" indicates there are 91 voxels in the first dimension, 109 in the second dimension, and 91 in the third dimension.
Discussed at: https://github.com/incf-nidash/nidm/issues/146
dimensions In Voxels
0.0
1
In the context of a general linear model, the effect degrees of freedom is the rank of the contrast. For example, a contrast comprising of a vector has effect degrees of freedom of 1 and can be tested with a F-test with numerator degrees of freedom of 1.
Under discussion at https://github.com/incf-nidash/nidm/issues/277
effect Degrees Of Freedom
3.5
Statistic value transformed into Z units; the output of a process which takes a non-normal statistic and transforms it to an equivalent z score.
equivalent ZStatistic
0.0
72.999999
In the context of a general linear model, the error degrees of freedom are the number of observations less the rank of the 'Design Matrix'.
Under discussion at https://github.com/incf-nidash/nidm/issues/277
error Degrees Of Freedom
A boolean value reflecting how the variance of the error is modeled during parameter estimation; TRUE for constant variance over all observations in the model, FALSE for heterogeneous variance.
error Variance Homogeneous
The number of non-null effects permitted in a partial conjunction null, as part of a 'Partial Conjunction Inference'
Discussed at https://github.com/incf-nidash/nidm/issues/294
partial Conjunction Degree
true
TRUE
Binary flag defining whether the data was scaled (true for scaled). Specifically, "grand mean scaling" refers to multiplication of every voxel in every scan by a common (or session-specific) value.
Discussed at https://github.com/incf-nidash/nidm/issues/285
grand Mean Scaling
A binary flag defining whether the mask was specified by the user (true) or automatically generated during the analysis (false)
Under discussion at https://github.com/incf-nidash/nidm/pull/258
is User Defined
155.23
Median value considering only in-mask voxels. Useful diagnostic when computed on grand mean image when grandMeanScaling is TRUE, as the median should be close to targetIntensity.
Discussed at https://github.com/incf-nidash/nidm/issues/288, naming previously discussed at: https://github.com/incf-nidash/nidm/issues/70
masked Median
http://purl.obolibrary.org/obo/OBI_0200119
Maximum number of 'Peak's to be reported after 'Inference' within a cluster.
Discussed in https://github.com/incf-nidash/nidm/pull/200
max Number Of Peaks Per Cluster
Minimum distance between two 'Peak's to be reported after 'Inference'.
Discussed in https://github.com/incf-nidash/nidm/pull/200
min Distance Between Peaks
Number of 'Supra-Threshold Clusters' found by the 'Inference' activity. This is SPM's set level statistic.
Discussed at https://github.com/incf-nidash/nidm/issues/292
number Of Supra-Threshold Clusters
3
Number of dimensions of the data matrix (e.g. 3 for volumetric data)
Discussed at https://github.com/incf-nidash/nidm/issues/295
number Of Dimensions
0.0
1.0
8.95E-14
Under discussion at https://github.com/ISA-tools/stato/issues/38
p Value
http://purl.obolibrary.org/obo/IAO_0000121
http://purl.obolibrary.org/obo/OBI_0000175
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P-Value
http://purl.obolibrary.org/obo/OBI_0000175
0.0
1.0
0.05
"A quantitative confidence value resulting from a multiple testing error correction method which adjusts the p-value used as input to control for Type I error in the context of multiple pairwise tests"
Under discussion at https://github.com/ISA-tools/stato/issues/38
p Value FWER
Synonym of "nidm:pFWE"
This definition is from OBI. Please update this note if the definition is modified.
0.0
1.0
0.0542
A p-value reported without correction for multiple testing.
Under discussion at https://github.com/ISA-tools/stato/issues/38
p Value Uncorrected
http://purl.obolibrary.org/obo/IAO_0000121
0.0
1.0
0.000154
A quantitative confidence value that measures the minimum false discovery rate that is incurred when calling that test significant. To compute q-values, it is necessary to know the p-value produced by a test and possibly set a false discovery rate level (same as OBI_0001442).
Under discussion at https://github.com/ISA-tools/stato/issues/38
q Value FDR
http://purl.obolibrary.org/obo/OBI_0001442
A binary flag that indicates whether Random Field Theory methods assumed smoothness that was homogeneous over the map (true), or allowed for smoothness that varies over the map (false).
Discussed at https://github.com/incf-nidash/nidm/issues/130
random Field Stationarity
68656
Total number of voxels within the search volume.
search Volume In Voxels
Synonyms of nidm:volumeInVoxels
8.6225
Name and number that specifies the software version. For SPM, this includes the main software version followed by the revision number (e.g. 8.6225 for SPM8 revision 6225).
Discussed at https://github.com/incf-nidash/nidm/issues/291
software Version
0.0
100
Value to which the grand mean of the Data was scaled (applies only if 'grand Mean Scaling' is true).
Discussed at https://github.com/incf-nidash/nidm/issues/285
target Intensity
nidm:pValueFWER
Type of method used to define a 'Threshold' (e.g. statistic value, uncorrected P-value or corrected P-value).
Discussed in https://github.com/incf-nidash/nidm/pull/150
Range is currently string but should be limited to {'nidm:pValueFWER' not found'nidm:pValueFDR' not found'nidm:pValueUncorrected';'nidm:statistic'}?
user Specified Threshold Type
true
Version of NIDM in use in the document.
Discussed at https://github.com/incf-nidash/nidm/pull/137
version
[2, 2, 4]
3D size of a voxel measured in 'voxel Units' (e.g. [2, 2, 4])
Discussed at https://github.com/incf-nidash/nidm/issues/295
voxel Size
[3 0 0 0;0 3 0 0;0 0 3 0; 0 0 0 1]
Homogeneous transformation matrix to map from voxel coordinate system to 'World Coordinate System'.
Range: Matrix of float.
Discussed in https://github.com/incf-nidash/nidm/pull/148
voxel To World Mapping
'["mm", "mm", "s"]'
Set of units associated with the dimensions of some N-dimensional data (e.g. '["mm", "mm", "mm"]')
Discussed at https://github.com/incf-nidash/nidm/issues/295 and https://github.com/incf-nidash/nidm/issues/147
Range: Vector of strings.
voxel Units
0.0
1771011
The volume of the searched region in units determined by the current 'Coordinate Space' units (e.g., mm^3 for axis units of mm in a three dimensional image, sec.Hz for a time by frequency two dimensional image).
Context: volumeInVoxels nidm_0025. Range: Positivefloat not found.
Discussed at https://github.com/incf-nidash/nidm/pull/131
search Volume In Units
[12 51 48]
Coordinate along the first dimension in voxels. (This definition needs to be re-worked as this term was renamed from coordinate1 to coordinate in https://github.com/incf-nidash/nidm/issues/270)
Under discussion at: https://github.com/incf-nidash/nidm/pull/270
coordinate Vector In Voxels
0.0
9.51
Expected number of clusters in an excursion set under the null hypothesis.
expected Number Of Clusters
0.0
60.632
Expected number of voxels in a cluster under the null hypothesis.
expected Number Of Voxels Per Cluster
Estimated spatial roughness of the noise process in 'voxel Units', as measured by the square-root determinant of the variance-covariance matrix of spatial derivatives of the noise process (Lambda matrix).
Discussed at https://github.com/incf-nidash/nidm/pull/214 and https://github.com/incf-nidash/nidm/issues/275
noise Roughness In Voxels
5.896
'Peak' statistic 'Threshold' corrected for false discovery rate at a level of alpha = 0.05.
height Critical Threshold FDR 05
4.913
'Peak' statistic 'Threshold' corrected for family-wise error at a level of alpha = 0.05.
height Critical Threshold FWE 05
0.0
22.325
Size of one resel in elements (e.g., pixels, voxels or vertices).
Discussed at https://github.com/incf-nidash/nidm/issues/275
resel Size In Voxels
0.0
151.3
Size of search volume measured in resels.
Discussed at https://github.com/incf-nidash/nidm/issues/275
search Volume In Resels
0.0
13
Size of cluster measured in resels.
Under discussion at: https://github.com/incf-nidash/nidm/issues/127
cluster Size In Resels
[8.87, 8.89, 7.83]
Estimated Full Width at Half Maximum of the spatial smoothness of the noise process in world units (e.g. mm^2 or mm^3, in subject or atlas space).
Discussed at: https://github.com/incf-nidash/nidm/pull/214
Range: Vector of positive floats.
noise FWHM In Units
[3.7 3.7 3.1]
Estimated Full Width at Half Maximum of the spatial smoothness of the noise process in voxels.
Discussed at: https://github.com/incf-nidash/nidm/pull/214
Range: Vector of positive floats.
noise FWHM In Voxels
Synonyms of or close match with nidm:NoiseFWHM
Name of the group
group Name
Number of subjects in the group.
Linked with http://purl.obolibrary.org/obo/STATO_0000088 to be discussed.
number Of Subjects
Discrete Cosine Transform basis cut-off, specified as period length in seconds and ensures that all basis elements will have period of this duration or longer.
Discussed at https://github.com/incf-nidash/nidm/issues/298
SPM's Drift Cut-off Period
[8.87, 8.89, 7.83]
Estimated Full Width at Half Maximum of the spatial smoothness of the noise process in world units (e.g. mm^2 or mm^3, in subject or atlas space).
Discussed at: https://github.com/incf-nidash/nidm/pull/214
Range: Vector of positive floats.
noise FWHM In Units
true
[2.95, 2.96, 2.61]
Estimated Full Width at Half Maximum of the spatial smoothness of the noise process in vertices.
Discussed at: https://github.com/incf-nidash/nidm/pull/214
Range: Vector of positive floats.
noise FWHM In Vertices
true
[3.7 3.7 3.1]
Estimated Full Width at Half Maximum of the spatial smoothness of the noise process in voxels.
Discussed at: https://github.com/incf-nidash/nidm/pull/214
Range: Vector of positive floats.
noise FWHM In Voxels
Synonyms of or close match with nidm:NoiseFWHM
true
[6 68.8 589.1 1475.5]
Description of geometry of search volume. As per Worsley et al. [ http://www.ncbi.nlm.nih.gov/pubmed/20408186 ], for space dimension 3 the first element is the Euler Characteristic of the search volume, the second element is twice the average caliper diameter, the third element is half the surface area, and the fourth element is the volume. With the exception of the first element (which is a unitless integer) all quantities are in units of Resels.
Discussed at https://github.com/incf-nidash/nidm/issues/310
Range: Vector of 1 positive integer and 3 positive floats.
search Volume Resels Geometry
http://www.ncbi.nlm.nih.gov/pubmed/20408186
3
Smallest cluster size in voxels that is significant at the false discovery rate of 0.05.
Discussed at https://github.com/incf-nidash/nidm/issues/310
smallest Significant Cluster Size In Voxels FDR 05
1
Smallest cluster size in voxels that is significant at the family-wise error corrected type I error rate (alpha value) of 0.05.
Discussed at https://github.com/incf-nidash/nidm/issues/310
smallest Significant Cluster Size In Voxels FWE 05
The number of non-null effects permitted in a partial conjunction null, as part of a 'Partial Conjunction Inference'
Discussed at https://github.com/incf-nidash/nidm/issues/294
partial Conjunction Degree
con_0001.img
Name of the file, together with the extension
1
fileName
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
The editor's definition comes from http://www.w3.org/TR/rdf-primer/#rdfvalue
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').
OBI:0000251
cluster
Cluster of the lymphocytes population.
A data set which is a subset of data that are a similar to each other in some way.
person:Allyson
person:Chris Stoeckert
group:OBI
cluster
OBI:0001265
A quantitative confidence value resulting from a multiple testing error correction method which adjusts the p-value used as input to control for Type I error in the context of multiple pairwise tests.
FWER adjusted p-value
OBI:0001442
A quantitative confidence value that measures the minimum false discovery rate that is incurred when calling that test significant. To compute q-values, it is necessary to know the p-value produced by a test and possibly set a false discovery rate level.
q-value
STATO:0000030
Chi-squared statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a Chi-Squared distribution.
Alejandra Gonzalez-Beltran
Orlaith Burke
Philippe Rocca-Serra
STATO
Chi-Squared statistic
STATO:0000039
a statistic is a measurement datum to describe a dataset or a variable. It is generated by a calculation on set of observed data.
Alejandra Gonzalez-Beltran
Orlaith Burke
Philippe Rocca-Serra
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Statistic).
statistic
statistic
STATO:0000051
Poisson distribution is a probability distribution used to model the number of events occurring within a given time interval. It is defined by a real number (Î») and an integer k representing the number of events and a function.
The expected value of a Poisson-distributed random variable is equal to Î» and so is its variance.
Alejandra Gonzalez-Beltran
Orlaith Burke
Philippe Rocca-Serra
dpois(x, lambda, log = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Poisson.html
NIST: http://www.itl.nist.gov/div898/handbook/eda/section3/eda366j.htm
Poisson distribution
STATO:0000067
a continuousprobability distribution is a probability distribution which is defined by a probability density function
Alejandra Gonzalez-Beltran
Orlaith Burke
Philippe Rocca-Serra
adapted from Wikipedia
http://en.wikipedia.org/wiki/Probability_distribution#Continuous_probability_distribution
last accessed:
14/01/2014
continuous probability distribution
STATO:0000117
a discrete probability distribution is a probability distribution which is defined by a probability mass function where the random variable can only assume a finite number of values or infinitely countable values
Alejandra Gonzalez-Beltran
Orlaith Burke
Philippe Rocca-Serra
adapted from Wikipedia
http://en.wikipedia.org/wiki/Probability_distribution#Discrete_probability_distribution
last accessed:
14/01/2014
discrete probability distribution
STATO:0000119
model parameter estimation is a data transformation that finds parameter values (the model parameter estimates) most compatible with the data as judged by the model.
textual definition modified following contributiong by Thomas Nichols:
https://github.com/ISA-tools/stato/issues/18
Alejandra Gonzalez-Beltran
Orlaith Burke
Philippe Rocca-Serra
model parameter estimation
STATO:0000176
t-statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a Student's t distribution.
Alejandra Gonzalez-Beltran
Orlaith Burke
Philippe Rocca-Serra
STATO
t-statistic
STATO:0000193
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/Group.txt
is a population whose individual members realize (may be expressed as) a combination of inclusion rule values specifications or resulting from a sampling process (e.g. recruitment followed by randomization to group) on which a number of measurements will be carried out, which may be used as input to statistical tests and statistical inference.
Alejandra Gonzalez-Beltran
Orlaith Burke
Philippe Rocca-Serra
STATO
statistical sample
study group population
STATO:0000225
A probability distribution is a information content entity specifies the probability of the value of a random variable.
For a discrete random variable, a mathematical formula that gives the probability of each value of the variable. For a continuous random variable, a curve described by a mathematical formula which specifies, by way of areas under the curve, the probability that the variable falls within a particular interval.
Alejandra Gonzalez-Beltran
Orlaith Burke
Philippe Rocca-Serra
probability distribution
STATO:0000227
a normal distribution is a continuous probability distribution described by a probability distribution function described here:
http://mathworld.wolfram.com/NormalDistribution.html
Alejandra Gonzalez-Beltran
Orlaith Burke
Philippe Rocca-Serra
Gaussian distribution
http://mathworld.wolfram.com/NormalDistribution.html
normal distribution
STATO:0000276
The binomial distribution is a discrete probability distribution which describes the probability of k successes in n draws with replacement from a finite population of size N.
The binomial distribution is frequently used to model the number of successes in a sample of size n drawn with replacement from a population of size N.
The binomial distribution gives the discrete probability distribution of obtaining exactly n successes out of N Bernoulli trials (where the result of each Bernoulli trial is true with probability p and false with probability q=1-p )
notation: B(n,p)
The mean is N*p
The variance is N*p*q
Alejandra Gonzalez-Beltran
Orlaith Burke
Philippe Rocca-Serra
http://en.wikipedia.org/wiki/Binomial_distribution
dbinom(x, size, prob, log = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Binomial.html
binomial distribution
STATO:0000282
F statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a F distribution. the F statistic is the ratio of two scaled sums of squares reflecting different sources of variability
Alejandra Gonzalez-Beltran
Orlaith Burke
Philippe Rocca-Serra
STATO
F-statistic
STATO:0000323
[1,0,0]
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ContrastWeights.txt
a contrast weight matrix is a information content entity which holds a set of contrast weight, coefficient used in a weighting sum of means defining a contrast
Alejandra Gonzalez-Beltran
Camille Maumet
Orlaith Burke
Philippe Rocca-Serra
Tom Nichols
STATO
contrast weights
contrast weight matrix
STATO:0000346
a covariance structure is a data item which is part of a regression model and which indicates a pattern in the covariance matrix. The nature of covariance structure is specified before the regression analysis and various covariance structure may be tested and evaluated using information criteria to help choose the most suiteable model
Alejandra Gonzalez-Beltran
Camille Maumet
Orlaith Burke
Philippe Rocca-Serra
Tom Nichols
http://www3.nd.edu/~kyuan/courses/sem/readpapers/benter.pdf
covariance structure
STATO:0000357
Alejandra Gonzalez-Beltran
Camille Maumet
Orlaith Burke
Philippe Rocca-Serra
Tom Nichols
TOEP
http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
Toeplitz covariance structure
STATO:0000362
compound symmetry covariance structure is a covariance structure which means that all the variances are equal and all the covariances are equal.
Alejandra Gonzalez-Beltran
Camille Maumet
Orlaith Burke
Philippe Rocca-Serra
Tom Nichols
CS
http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/corCompSymm.html
compound symmetry covariance structure
STATO:0000370
the ordinary least squares estimation is a model parameter estimation for a linear regression model when the errors are uncorrelated and equal in variance. Is the Best Linear Unbiased Estimation (BLUE) method under these assumptions, Uniformly Minimum-Variance Unbiased Estimator (UMVUE) with addition of a Gaussian assumption.
Alejandra Gonzalez-Beltran
Camille Maumet
Philippe Rocca-Serra
Tom Nichols
http://en.wikipedia.org/wiki/Ordinary_least_squares and Tom Nichols
OLS estimation
https://stat.ethz.ch/R-manual/R-patched/library/stats/html/lm.html
ordinary least squares estimation
STATO:0000371
the weighted least squares estimation is a model parameter estimation for a linear regression model with errors that independent but have heterogeneous variance. Difficult to use use in practice, as weights must be set based on the variance which is usually unknown. If true variance is known, it is the Best Linear Unbiased Estimation (BLUE) method under these assumptions, Uniformly Minimum-Variance Unbiased Estimator (UMVUE) with addition of a Gaussian assumption.
Alejandra Gonzalez-Beltran
Camille Maumet
Orlaith Burke
Philippe Rocca-Serra
Tom Nichols
http://en.wikipedia.org/wiki/Least_squares#Weighted_least_squares and Tom Nichols
WLS estimation
https://stat.ethz.ch/R-manual/R-patched/library/stats/html/lm.html
weighted least squares estimation
STATO:0000372
the generalized least squares estimation is a model parameter estimation for a linear regression model with errors that are dependent and (possibly) have heterogeneous variance. Difficult to use use in practice, as covariance matrix of the errors must known to "whiten" data and model. If true covariance is known, it is the Best Linear Unbiased Estimation (BLUE) method under these assumptions, Uniformly Minimum-Variance Unbiased Estimator (UMVUE) with addition of a Gaussian assumption.
Philippe Rocca-Serra
Tom Nichols
http://en.wikipedia.org/wiki/Generalized_least_squares and Tom Nichols
GLS estimation
http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/gls.html
generalized least squares estimation
STATO:0000373
the iteratively reweighted least squares estimation is a model parameter estimation which is a practical implementation of Weighted Least Squares, where the heterogeneous variances of the errors are estimated from the residuals of the regression model, providing an estimate for the weights. Each successive estimate of the weights improves the estimation of the regression parameters, which in turn are used to compute residuals and update the weights
Alejandra Gonzalez-Beltran
Camille Maumet
Orlaith Burke
Philippe Rocca-Serra
Tom Nichols
Tom Nichols
iteratively reweighted least squares estimation
STATO:0000374
the feasible generalized least squares estimation is a model parameter estimation which is a practical implementation of Generalised Least Squares, where the covariance of the errors is estimated from the residuals of the regression model, providing the information needed to whiten the data and model. Each successive estimate of the whitening matrix improves the estimation of the regression parameters, which in turn are used to compute residuals and update the whitening matrix.
Alejandra Gonzalez-Beltran
Camille Maumet
Orlaith Burke
Philippe Rocca-Serra
Tom Nichols
Tom Nichols
feasible generalized least squares estimation
STATO:0000376
Z-statistic is a statistic computed from observations and used to produce a p-value when compared to a Standard Normal Distribution in a statistical test called the Z-test.
Alejandra Gonzalez-Beltran
Camille Maument
Philippe Rocca-Serra
Thomas Nichols
http://en.wikipedia.org/wiki/Z-test
Z-statistic
STATO:0000405
A covariance structure where no restrictions are made on the covariance between any pair of measurements.
Alejandra Gonzalez-Beltran
Camille Maumet
Philippe Rocca-Serra
Thomas Nichols
http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm#statug.mixed.mixedcovstruct
unstructured covariance structure
0
0
dctype:Image
A visual representation other than text.
Examples include images and photographs of physical objects, paintings, prints, drawings, other images and graphics, animations and moving pictures, film, diagrams, maps, musical notation. Note that Image may include both electronic and physical representations.
fsl:FSL_0000002
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/FSL_DriftModel.txt
A 'Drift Model' in which the drifts are modeled with a Gaussian-weighted running line smoother, fit to and subtracted from the data and each column of the 'Design Matrix'.
Discussed at https://github.com/incf-nidash/nidm/issues/298
Gaussian Running Line Drift Model
nidm:NIDM_0000001
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ContrastEstimation.txt
The process of performing a [obo:contrast estimation](http://purl.obolibrary.org/obo/STATO_0000383) at each element (e.g., pixel, voxel, vertex, or face) of a map
Discussed at https://github.com/incf-nidash/nidm/issues/276 and https://github.com/ISA-tools/stato/issues/23
Contrast Estimation
nidm:NIDM_0000002
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ContrastMap.txt
A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a [contrast estimate](http://purl.obolibrary.org/obo/STATO_0000384).
Discussed in https://github.com/incf-nidash/nidm/issues/255
Contrast Map
nidm:NIDM_0000003
Under discussion at https://github.com/ISA-tools/stato/issues/28
TN
Arbitrarily Correlated Error
true
nidm:NIDM_0000004
A map in which all values are 0, 1 or NaN. Usually, selected elements (e.g., pixels, voxels, vertices, or faces) have a value of 1 and excluded elements (i.e. the background) have a value of 0 or NaN
Discussed at https://github.com/incf-nidash/nidm/pull/258
Binary Map
nidm:NIDM_0000005
The 'Binomial Distribution' is a discrete probability distribution which describes the probability of k successes in n draws with replacement from a finite population of size N. The 'Binomial Distribution' is frequently used to model the number of successes in a sample of size n drawn with replacement from a population of size N. The 'Binomial Distribution' gives the discrete probability distribution of obtaining exactly n successes out of N Bernoulli trials (where the result of each Bernoulli trial is true with probability p and false with probability q=1-p ) notation: B(n,p) The mean is N*p The variance is N*p*q. (Definition from STATO).
Binomial Distribution
true
http://purl.obolibrary.org/obo/STATO_0000276
nidm:NIDM_0000006
A collection of elements related by one or more criteria.
Cluster
true
Discussed in https://github.com/incf-nidash/nidm/issues/71.
nidm:NIDM_0000007
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ClusterDefinitionCriteria-06.txt
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ClusterDefinitionCriteria-18.txt
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ClusterDefinitionCriteria-26.txt
Set of criterion specified a priori to define the clusters reported after 'Inference' (e.g. pixel or voxel 'Connectivity Criterion').
Cluster Definition Criteria
nidm:NIDM_0000008
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ClusterLabelsMap.txt
A map whose value at each element (e.g., pixel, voxel, vertex, or face) denotes cluster membership within the excursion set. Each cluster is denoted by a different integer and all members of the same cluster have the same value.
Discussed at https://github.com/incf-nidash/nidm/issues/282
Cluster Labels Map
nidm:NIDM_0000011
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ConjunctionInference.txt
Statistically testing for the joint significance of multiple effects, with emphasis on rejecting all (instead of one or more) of the respective null hypotheses.
Term discussed in https://github.com/incf-nidash/nidm/pull/134
Conjunction Inference
nidm:NIDM_0000012
The criterion used to characterize two voxels, pixels or vertices as 'connected'.
Discussed in https://github.com/incf-nidash/nidm/pull/201
TN, KH, CM
Connectivity Criterion
nidm:NIDM_0000013
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ContrastStandardErrorMap.txt
A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a [standard error of a contrast estimate](http://purl.obolibrary.org/obo/STATO_0000385).
Discussed in https://github.com/incf-nidash/nidm/issues/255.
Contrast Standard Error Map
nidm:NIDM_0000015
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/Coordinate.txt
Discussed in https://github.com/incf-nidash/nidm/pull/144 and https://github.com/incf-nidash/nidm/pull/172
Coordinate
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C44465
nidm:NIDM_0000016
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/CoordinateSpace.txt
An entity with spatial attributes (e.g., dimensions, units, and voxel-to-world mapping) that provides context to a 'Map' (e.g., a 'Statistic Map', a 'Contrast Map'...).
Under discussion at https://github.com/incf-nidash/nidm/issues/290
Coordinate Space
nidm:NIDM_0000017
Custom (unknown) reference space selected by the user
Discussed at https://github.com/incf-nidash/nidm/issues/284
Custom Coordinate System
nidm:NIDM_0000018
Scaling applied to the data before parameter estimation, including specification of the 'target Intensity'.
Discussed at https://github.com/incf-nidash/nidm/issues/285
Data Scaling
true
0
0
0
nidm:NIDM_0000019
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/DesignMatrix.txt
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/DesignMatrix_1stLevel.txt
A [stato:design matrix](http://purl.obolibrary.org/obo/STATO_0000289), with additional neuroimaging attributes, including HRF and drift for first-level fMRI models
Discussed at https://github.com/incf-nidash/nidm/issues/274
Design Matrix
stato:design matrix
nidm:NIDM_0000020
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/DisplayMaskMap.txt
A 'Binary Map' used by an activity that changed the voxels displayed, but did not alter the space in which the activity was performed (e.g. at the level of 'Inference', this mask is called "contrast masking" in both FSL & SPM and does not alter voxel-wise corrected p-values)
Discussed at: https://github.com/incf-nidash/nidm/pull/258 and https://github.com/incf-nidash/nidm/pull/157
Display Mask Map
nidm:NIDM_0000022
Probability distribution used to model the error.
Error Distribution
true
nidm:NIDM_0000023
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ErrorModel-OLS.txt
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ErrorModel-SPMnonSphericity.txt
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ErrorModel-WLS.txt
Model used to describe the random variation of the error term as part of parameter estimation, including specification of the error probability distribution, its variance and dependence both spatially and across observations.
Error Model
nidm:NIDM_0000024
Under discussion at https://github.com/ISA-tools/stato/issues/28
TN
Under gaussianity assumption this is equivalent to compound symmetry but not in general.
Exchangeable Error
0
nidm:NIDM_0000025
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ExcursionSetMap.txt
A map in which the set of elements (e.g., pixels, voxels, vertices, or faces) not selected by the 'Inference' activity is set to zero or NaN
Discussed in the Neuroimaging terms spreadsheet and in https://github.com/incf-nidash/nidm/issues/256.
Excursion Set Map
nidm:NIDM_0000026
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ExtentThreshold-FDR.txt
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ExtentThreshold-Unc.txt
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ExtentThresholdStat_clusterSizeResels.txt
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ExtentThreshold_equivThresh-FWER.txt
A numerical value that establishes a lower bound on cluster-sizes and can be specified by the user in terms of FWER-corrected p-value, uncorrected p-value or minimum cluster size in voxels
Discussed at https://github.com/incf-nidash/nidm/pull/273
Extent Threshold
nidm:NIDM_0000027
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/NIDMBundle.txt
'NIDM Object Model' representing the results of a mass univariate neuroimaging study and targeting the application of meta-analysis. The specification is available at: http://nidm.nidash.org/specs/nidm-results.html
Discussed at https://github.com/incf-nidash/nidm/pull/137
NIDM-Results
nidm:NIDM_0000028
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/DesignMatrix_1stLevel-FIR.txt
Set of Finite impulse response (FIR) filters, with FIR the convolution kernel is represented as a set of discrete fixed-width "impulses" (definition adapted from [FSL wiki](http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/feat5/detail.html))
Discussed at https://github.com/incf-nidash/nidm/issues/281
Finite Impulse Response Basis Set
nidm:NIDM_0000029
'Hemodynamic Response Function' which is a difference of two gamma probability density functions.
Discussed at https://github.com/incf-nidash/nidm/issues/281
Gamma Difference HRF
nidm:NIDM_0000030
Set of gamma probability density functions.
Discussed at https://github.com/incf-nidash/nidm/issues/281
Gamma Basis Set
nidm:NIDM_0000031
'Hemodynamic Response Function' which is a gamma probability density function.
Discussed at https://github.com/incf-nidash/nidm/issues/281
Gamma HRF
nidm:NIDM_0000032
A normal distribution is a continuous probability distribution described by a probability distribution function described here: http://mathworld.wolfram.com/NormalDistribution.html (Definition from STATO).
Gaussian Distribution
true
http://purl.obolibrary.org/obo/STATO_0000227
nidm:NIDM_0000033
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/GrandMeanMap.txt
A map whose value at each element (e.g., pixel, voxel, vertex, or face) is the mean over all observations of that element in the input maps (after any scaling of those input maps)
Discussed at https://github.com/incf-nidash/nidm/issues/288
Grand Mean Map
nidm:NIDM_0000034
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/HeightThreshold-FDR.txt
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/HeightThreshold-Stat.txt
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/HeightThreshold-Unc.txt
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/HeightThreshold_equivThresh-FWER.txt
A numerical value that establishes a lower bound on statistic values and can be specified by the user in terms of FWER-corrected p-value, uncorrected p-value or minimum statistic value.
Discussed at https://github.com/incf-nidash/nidm/issues/280
Height Threshold
nidm:NIDM_0000035
'Hemodynamic Response Function' basis that can on its own be used to represent the idealised 'Hemodynamic Response Function'.
Discussed at https://github.com/incf-nidash/nidm/issues/281
Hemodynamic Response Function
nidm:NIDM_0000036
Discussed at https://github.com/incf-nidash/nidm/issues/281
A set of functions that, when convolved with the anticipated neural responses, yield a set of regressors to model the anticipated hemodynamic responses.
Convolution Basis Set
nidm:NIDM_0000037
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/DesignMatrix_1stLevel_HRFBasis2_HRFBasis3-InformedBasisSet.txt
'Hemodynamic Response Function' basis which is the derivative of an 'Hemodynamic Response Function'.
Discussed at https://github.com/incf-nidash/nidm/issues/281
Hemodynamic Response Function Derivative
nidm:NIDM_0000048
Under discussion at https://github.com/ISA-tools/stato/issues/28
TN
Independent Error
nidm:NIDM_0000049
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/Inference-OneTailed.txt
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/Inference-TwoTailed.txt
Statistical 'Inference' is a process of drawing conclusions following data analysis using statistical methods (statistical tests) and evaluating whether to reject or accept null hypothesis. (definition from STATO).
Inference
http://purl.obolibrary.org/obo/STATO_0000299
nidm:NIDM_0000051
MNI 305 coordinate system or any coordinate system derived from MNI 305.
Discussed at https://github.com/incf-nidash/nidm/issues/284
MNI Coordinate System
birnlex_2125
0
0
0
0
nidm:NIDM_0000052
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/Map_atLocation-nii.txt
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/Map_atLocation_hasMapHeader-img.txt
Ordered set of values corresponding to the discrete sampling of some process (e.g. brain MRI data measured on a regular 3D lattice; or brain cortical surface data measured irregularly over the cortex).
Discussed in https://github.com/incf-nidash/nidm/pull/149
Map
0
0
0
0
nidm:NIDM_0000053
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/MapHeader.txt
A file associated with a Map to provide header information (e.g. NIfTI header file)
Discussed at https://github.com/incf-nidash/nidm/issues/289
Map Header
nidm:NIDM_0000054
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/MaskMap.txt
A 'Binary Map' representing the exact set of elements (e.g., pixels, voxels, vertices, and faces) in which an activity was performed (e.g. the mask map generated by the model parameter estimation activity represents the exact set of voxels in which the mass univariate model was estimated) and/or restraining the space in which an activity was performed (e.g. the mask map used by 'Inference')
Discussed at: https://github.com/incf-nidash/nidm/pull/258 and https://github.com/incf-nidash/nidm/issues/155
Mask Map
nidm:NIDM_0000056
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ModelParametersEstimation.txt
the process of performing a [obo:model parameter estimation](http://purl.obolibrary.org/obo/STATO_0000119) at each element (e.g., pixel, voxel, vertex, or face) of a map
Discussed at: https://github.com/incf-nidash/nidm/issues/141
Model Parameter Estimation
nidm:NIDM_0000057
Abstraction on the data model, developed for a specific application/use-case/task at hand, that specifies the components and relations necessary for use by these applications. The same object model can be reused by multiple applications (e.g., meta-analysis, Neurovault).
Discussed at https://github.com/incf-nidash/nidm/pull/137
NIDM Object Model
nidm:NIDM_0000058
Probability distribution estimated empirically on the data without assumptions on the shape of the probability distribution.
Non Parametric Distribution
true
nidm:NIDM_0000059
Probability distribution estimated empirically on the data assuming only symmetry of the probability distribution.
Non Parametric Symmetric Distribution
nidm:NIDM_0000060
Re-use "one tailed test" from STATO.
One Tailed Test
http://purl.obolibrary.org/obo/STATO_0000286
nidm:NIDM_0000061
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ParameterEstimateMap.txt
A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a [model parameter estimate](http://purl.obolibrary.org/obo/STATO_0000144).
Discussed in https://github.com/incf-nidash/nidm/issues/255 and https://github.com/incf-nidash/nidm/issues/141 (see also https://github.com/ISA-tools/stato/issues/18)
Parameter Estimate Map
nidm:NIDM_0000062
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/Peak_ValueP.txt
A map element (e.g., pixel, voxel, vertex, or face) which is a local maximum in the supra-threshold cluster and complies with the 'Peak definition criteria'.
Discussed at https://github.com/incf-nidash/nidm/issues/283
Peak
nidm:NIDM_0000063
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/PeakDefinitionCriteria_MaxPeaks.txt
Set of criterion specified a priori to define the 'Peak's reported after 'Inference' (e.g. maximum number of 'Peak's within a cluster, minimum distance between 'Peak's).
Discussed in https://github.com/incf-nidash/nidm/pull/200
Peak Definition Criteria
nidm:NIDM_0000064
The criterion used to characterize two pixels as 'connected'. In two dimensions voxels that are connected can share an edge (4-connected) or, edge or corner (8-connected).
Discussed in https://github.com/incf-nidash/nidm/pull/201
Pixel Connectivity Criterion
nidm:NIDM_0000065
Poisson distribution is a probability distribution used to model the number of events occurring within a given time interval. It is defined by a real number (Î») and an integer k representing the number of events and a function. The expected value of a Poisson-distributed random variable is equal to Î» and so is its variance. (Definition from STATO).
Poisson Distribution
true
http://purl.obolibrary.org/obo/STATO_0000051
nidm:NIDM_0000066
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ResidualMeanSquaresMap.txt
A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a [residual mean square](http://purl.obolibrary.org/obo/STATO_0000375).
Discussed at https://github.com/incf-nidash/nidm/issues/255.
Residual Mean Squares Map
nidm:NIDM_0000067
Customised set of basis functions.
Discussed at https://github.com/incf-nidash/nidm/issues/281
Custom Basis Set
nidm:NIDM_0000068
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/SearchSpaceMaskMap.txt
A 'Mask Map' representing the set of elements (e.g., pixels, voxels, vertices, or faces) in which the 'Inference' was performed
Discussed at: https://github.com/incf-nidash/nidm/pull/258
Search Space Mask Map
nidm:NIDM_0000069
Set of Fourier basis.
Discussed at https://github.com/incf-nidash/nidm/issues/281
Fourier Basis Set
nidm:NIDM_0000070
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/SupraThresholdCluster.txt
A cluster of map elements (e.g., pixels, voxels, vertices, and faces) that were selected by the 'Inference' activity and are contiguous according to the cluster 'Connectivity Criterion'.
Supra-Threshold Cluster
Discussed in https://github.com/incf-nidash/nidm/issues/71.
nidm:NIDM_0000071
Map-wise dependence structure of a parameter in the 'Error Model' (i.e. variance or dependence parameter). For example, whether a temporal autocorrelation parameter is estimated at each element separately, estimated using data in a local neighbourhood, or estimated using all elements in the map.
Discussed at https://github.com/incf-nidash/nidm/issues/194
Error Parameter Map-Wise Dependence
nidm:NIDM_0000072
Parameter estimated as constant over a entire set of elements considered (e.g. those in the analysis mask).
Discussed at https://github.com/incf-nidash/nidm/issues/194
Constant Parameter
nidm:NIDM_0000073
Parameter whose estimation at a given element does not depend on any other element.
Discussed at https://github.com/incf-nidash/nidm/issues/194
Independent Parameter
nidm:NIDM_0000074
Parameter whose estimation at a given element depends on a local neighborhood of elements
Discussed at https://github.com/incf-nidash/nidm/issues/194
Regularized Parameter
nidm:NIDM_0000075
Parent of all reference spaces except "Subject".
Discussed at https://github.com/incf-nidash/nidm/issues/284
This is meant to be used for retrospective export when exact template is unknown.
Standardized Coordinate System
nidm:NIDM_0000076
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/StatisticMap-T.txt
A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a [statistic](http://purl.obolibrary.org/obo/STATO_0000039).
Discussed at https://github.com/incf-nidash/nidm/issues/255
Statistic Map
nidm:NIDM_0000077
Reference space corresponding to the subject brain (no spatial normalization applied).
Discussed at https://github.com/incf-nidash/nidm/issues/284
Used in FSL and SPM un-registered data.
Subject Coordinate System
nidm:NIDM_0000078
Reference space defined by the dissected brain used for the Talairach and Tournoux atlas (cf. http://www.talairach.org/about.html)
Discussed at https://github.com/incf-nidash/nidm/issues/284
Talairach Coordinate System
http://www.talairach.org/
nidm:NIDM_0000079
Re-use "two tailed test" from STATO
Two Tailed Test
http://purl.obolibrary.org/obo/STATO_0000287
nidm:NIDM_0000080
The criterion used to characterize two voxels as 'connected'. In three dimensions voxels that are connected can share a voxel face (6-connected), face or edge (18-connectec), or face, edge, or corner (26-connected).
Discussed in https://github.com/incf-nidash/nidm/pull/201
Voxel Connectivity Criterion
nidm:NIDM_0000081
Reference space on which real-world positions are expressed (cf. [Nifti-1 FAQ question 14](http://nifti.nimh.nih.gov/nifti-1/documentation/faq#Q14) and [Understanding affines on nipy](http://nipy.org/nipy/stable/devel/code_discussions/understanding_affines.html)
). A world coordinate system can be represented by an image obtained by registering an initial set of images, using a given normalization algorithm to match a target template.
Discussed at https://github.com/incf-nidash/nidm/issues/284
World Coordinate System
nidm:NIDM_0000087
A model used to compensate for low frequency baseline drifts when analyzing functional MRI data at the subject level.
Discussed at https://github.com/incf-nidash/nidm/issues/298
Drift Model
nidm:NIDM_0000110
'Hemodynamic Response Function' which is a gaussian kernel.
Discussed at https://github.com/incf-nidash/nidm/issues/281
Gaussian HRF
nidm:NIDM_0000135
A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a contrast variance (i.e. the square of a [standard error of a contrast estimate](http://purl.obolibrary.org/obo/STATO_0000385))
Discussed at https://github.com/incf-nidash/nidm/issues/287
Contrast Variance Map
nidm:NIDM_0000140
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/FSL_ClusterCenterOfGravity.txt
A centre of gravity of the cluster, equivalent to the concept of Centre Of Gravity for a object with distributed mass, where intensity substitutes for mass in this case. The 'Coordinate' of the centre of gravity is the weighted average of the cluster element (e.g., pixels, voxels, vertices, or faces) 'Coordinate's, where the weighting factors are the cluster element intensities. (definition adapted from http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Cluster)
Discussed at https://github.com/incf-nidash/nidm/pull/257
Cluster Center Of Gravity
http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Cluster
nidm:NIDM_0000144
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/SPM_ReselsPerVoxelMap.txt
A map whose value at each element (e.g., pixel, voxel, vertex, or face) location is the number of resels per voxel.
Resels Per Voxel Map
nidm:NIDM_0000150
A Linear (order 1) spline, providing an estimate that is continuous over time (in contrast to a FIR basis, which is discontinuous between each time bin). This is called TENT in AFNI's 3dDeconvolve program.
Discussed at https://github.com/incf-nidash/nidm/issues/281
Linear Spline Basis Set
nidm:NIDM_0000151
A set of Sine waves of differing frequencies (definition adapted from [FSL wiki](http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/feat5/detail.html)).
Discussed at https://github.com/incf-nidash/nidm/issues/281
Sine Basis Set
nidm:NIDM_0000160
A p-value reported without correction for multiple testing.
Discussed in [Neuroimaging terms spreadsheet](https://docs.google.com/spreadsheets/d/16pC2cDsdxlzv2CzlNMtStqt5-xHwDEsU6MjZVxWhrE4/edit?usp=sharing)
P-Value Uncorrected
nidm:NIDM_0000162
A numerical value that establishes a bound on a set of statistic values and can be specified by the user in terms of FWER-corrected p-value, uncorrected p-value, FDR-corrected q-value or statistic value
Threshold
nidm:NIDM_0000163
A map whose value at each element (e.g., pixel, voxel, vertex, or face) is the extra sum of squares divided by the 'effect Degrees of Freedom' (i.e. the numerator of an F-statistic).
Discussed in https://github.com/incf-nidash/nidm/issues/235
Contrast Explained Mean Square Map
nidm:NIDM_0000164
Tool used to process neuroimaging data.
Neuroimaging Analysis Software
nidm:NIDM_0000165
Tool used to export results produced by a neuroimaging software (SPM, FSL, AFNI...) into a NIDM-Results archive.
NIDM-Results Exporter
nidm:NIDM_0000166
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/Export.txt
The process of exporting results created by a neuroimaging software (SPM, FSL, AFNI...) into a NIDM-Results archive.
NIDM-Results Export
nidm:NIDM_0000167
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ExporterSoftware-FSL.txt
Python library for the export of feat folders (generated by FSL) to NIDM-Results. Source available at: https://github.com/incf-nidash/nidm-results_fsl/.
nidmfsl
nidm:NIDM_0000168
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ExporterSoftware-SPM.txt
Matlab m file for the export of SPM results to NIDM-Results. Source available at: http://www.fil.ion.ucl.ac.uk/spm/download/toolbox/NIDM/spm_nidm.zip/.
spm_results_nidm
nidm:NIDM_0000169
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/Data_wasAttributedTo.txt
Information about the input Data, including scaling applied to the data before parameter estimation..
Discussed at ...
Data
spm:SPM_0000002
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/SPM_DriftModel.txt
A 'Drift Model' in which the drifts are modeled by a Discrete Cosine Transform basis added to regression model
Discussed at https://github.com/incf-nidash/nidm/issues/298
Discrete Cosine Transform basis Drift Model
spm:SPM_0000005
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/SPM_KConjunctionInference.txt
The process of testing the joint significance of multiple effects to infer that some (not necessarily all) of the respective effects are real (i.e. their null hypotheses are false). If there are K effects considered, the 'partial Conjunction Degree' u is the number non-null effects allowed as part of partial conjunction null hypothesis; if the partial conjunction null is rejected, it may be inferred that u+1 or more effects are real. The case of u=K-1 corresponds to proper "'Conjunction Inference'", while the case of u=0 corresponds to "global null" conjunction test. See [Friston et al. (2005). Conjunction revisited. NeuroImage, 25(3), 661-7.](http://dx.doi.org/10.1016/j.neuroimage.2005.01.013).
Discussed at https://github.com/incf-nidash/nidm/issues/294
Partial Conjunction Inference
prv:PropertyReification
The class, which describes the relations of a property reification. That means, its "shortcut relation", its
reification class, and the properties that are relating to the subject and object of the "shortcut relation".
Property Reification
testing
src:SCR_002823
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/FSL_Software.txt
A comprehensive library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. The tools include registration, atlases, Diffusion MRI tools for parameter reconstruction and probabilistic taractography, and a viewer. FSL runs on Apple and PCs (Linux and Windows), and is very easy to install. Most of the tools can be run both from the command line and as GUIs ('point-and-click' graphical user interfaces). Several complementary brain atlases, integrated into FSLView and Featquery, allowing viewing of structural and cytoarchitectonic standard space labels and probability maps for cortical and subcortical structures and white matter tracts. Atlases included with FSL: * Harvard-Oxford cortical and subcortical structural atlases * Julich histological atlas * JHU DTI-based white-matter atlases * Oxford thalamic connectivity atlas * Talairach atlas * MNI structural atlas * Cerebellum atlas FSL is written mainly by members of the Analysis Group, FMRIB, Oxford, UK.
FSL
src:SCR_007037
https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/SPM_Software.txt
Software package for the analysis of brain imaging data sequences. The sequences can be a series of images from different cohorts, or time-series from the same subject. The current release is designed for the analysis of fMRI, PET, SPECT, EEG and MEG.
SPM
nlx:birnlex_2094
http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF
http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated
2006-05-15
2006-10-11
Imaging instrument
Imaging instrument
nlx:birnlex_2100
http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF
http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated
2006-05-15
2006-10-11
MRI scanner
Magnetic resonance imaging scanner
Magnetic resonance imaging scanner
nlx:birnlex_2177
http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner
http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated
C0024485
2007-03-07
http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS_defSource
2008-05-01
_7_2.2
MRI
An imaging protocol where images are acquired using a Magnetic Resonance Imaging device.
MRI protocol
* MRI uses radiofrequency waves and a strong magnetic field rather than x-rays to provide amazingly clear and detailed pictures of internal organs and tissues. The technique is valuable for the diagnosis of many pathologic conditions, including cancer, heart and vascular disease, stroke, and joint and musculoskeletal disorders. (NCI)
* Non-invasive method of demonstrating internal anatomy based on the principle that atomic nuclei in a strong magnetic field absorb pulses of radiofrequency energy and emit them as radiowaves which can be reconstructed into computerized images. The concept includes proton spin tomographic techniques. (MSH)
* non-invasive method of demonstrating internal anatomy based on the principle that atomic nuclei in a strong magnetic field absorb pulses of radiofrequency energy and emit them as radiowaves which can be reconstructed into computerized images; concept includes proton spin tomographic techniques. (CSP)
MRI protocol
nlx:birnlex_2250
http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated
2007-10-09
2007-10-09
_7_2.2.2
fMRI
Functional MRI protocol
Functional MRI protocol
nlx:birnlex_2251
http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated
2007-10-09
http://fmri.ucsd.edu/Research/whatisfmri.html
2007-10-09
_7_2.2.1
MRI
Structural MRI protocol
A structural MRI protocol is an MRI protocol that provides information to qualitatively and quantitatively describe the shape, size, and integrity of gray and white matter structures in the brain.
Structural MRI protocol
nlx:ixl_0050000
2016-02-12
https://en.wikipedia.org/wiki/Positron_emission_tomography
PET scanner
Positron emission tomography scanner
A Positron emission tomography scanner is a device used in a nuclear medicine to observe metabolic processes in the body.
Positron emission tomography scanner
nlx:ixl_0050001
2016-02-12
https://en.wikipedia.org/wiki/Single-photon_emission_computed_tomography
SPECT scanner
Single-photon emission computed tomography scanner
A Single-photon emission computed tomography scanner is a device used in nuclear medicine tomographic imaging to measure perfusion in the body using gamma rays.
Single-photon emission computed tomography scanner
nlx:ixl_0050002
2016-02-12
https://en.wikipedia.org/wiki/Magnetoencephalography
MEG machine
Magnetoencephalography machine
A Magnetoencephalography machine is a device used in functional neuroimaging for mapping brain activity by recording magnetic fields produced by electrical currents occurring naturally in the brain, using very sensitive magnetometers..
Magnetoencephalography machine
nlx:ixl_0050003
2016-02-12
https://en.wikipedia.org/wiki/Electroencephalography
EEG machine
Electroencephalography machine
A Electroencephalography machine is a device used in electrophysiology to record electrical activity of the brain..
Electroencephalography machine
nlx:ixl_0050004
2016-02-15
http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS_defSource
Anatomical MRI protocol
An anatomical MRI protocol is a structural MRI protocol that can be used to delineate the anatomy, for example by the way of a segmentation or parcellation.
nlx:nlx_inv_20090249
February 9, 2009
UMLS, C1136216
Diffusion-weighted imaging protocol
A magnetic resonance imaging protocol that is sensitive to the diffusion of water molecules.
Diffusion-weighted imaging protocol
Activity
Association
Delegation
rdf:Property
owl:Class
owl:Thing
prov:Activity
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
prov:ActivityInfluence
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.
prov:Agent
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
prov:AgentInfluence
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.
prov:Association
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, prov:baking prov:wasAssociatedWith prov:baker; prov:qualifiedAssociation [ a prov:Association; prov:agent prov:baker; prov:foo prov: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
prov:Attribution
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, prov:cake prov:wasAttributedTo prov:baker; prov:qualifiedAttribution [ a prov:Attribution; prov:entity prov:baker; prov:foo prov: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
prov:Bundle
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
prov:Collection
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
prov:Communication
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, prov:you_jumping_off_bridge prov:wasInformedBy prov:everyone_else_jumping_off_bridge; prov:qualifiedCommunication [ a prov:Communication; prov:activity prov:everyone_else_jumping_off_bridge; prov:foo prov: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
prov:Delegation
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, prov:mixing prov:wasAssociatedWith prov:toddler . prov:toddler prov:actedOnBehalfOf prov:mother; prov:qualifiedDelegation [ a prov:Delegation; prov:entity prov:mother; prov:foo prov: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
prov:Derivation
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, prov:chewed_bubble_gum prov:wasDerivedFrom prov:unwrapped_bubble_gum; prov:qualifiedDerivation [ a prov:Derivation; prov:entity prov:unwrapped_bubble_gum; prov:foo prov: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
prov:End
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, prov:ball_game prov:wasEndedBy prov:buzzer; prov:qualifiedEnd [ a prov:End; prov:entity prov:buzzer; prov:foo prov: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
prov:Entity
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
prov:EntityInfluence
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.
prov:Generation
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, prov:cake prov:wasGeneratedBy prov:baking; prov:qualifiedGeneration [ a prov:Generation; prov:activity prov:baking; prov:foo prov: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
prov:Influence
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, prov:stomach_ache prov:wasInfluencedBy prov:spoon; prov:qualifiedInfluence [ a prov:Influence; prov:entity prov:spoon; prov:foo prov: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
prov:InstantaneousEvent
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.
prov:Invalidation
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, prov:uncracked_egg prov:wasInvalidatedBy prov:baking; prov:qualifiedInvalidation [ a prov:Invalidation; prov:activity prov:baking; prov:foo prov: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
prov:Location
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
prov:Organization
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
prov:Person
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
prov:Plan
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
prov:PrimarySource
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, prov:blog prov:hadPrimarySource prov:newsArticle; prov:qualifiedPrimarySource [ a prov:PrimarySource; prov:entity prov:newsArticle; prov:foo prov: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
prov:Quotation
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, prov:here_is_looking_at_you_kid prov:wasQuotedFrom prov:casablanca_script; prov:qualifiedQuotation [ a prov:Quotation; prov:entity prov:casablanca_script; prov:foo prov: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
prov:Revision
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, prov:draft_2 prov:wasRevisionOf prov:draft_1; prov:qualifiedRevision [ a prov:Revision; prov:entity prov:draft_1; prov:foo prov: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
prov:Role
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
prov:SoftwareAgent
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
prov:Start
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, prov:foot_race prov:wasStartedBy prov:bang; prov:qualifiedStart [ a prov:Start; prov:entity prov:bang; prov:foo prov: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
prov:Usage
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, prov:keynote prov:used prov:podium; prov:qualifiedUsage [ a prov:Usage; prov:entity prov:podium; prov:foo prov: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
example to be eventually removed
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
metadata complete
term created to ease viewing/sort terms for development purpose, and will not be included in a release
organizational term
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
ready for release
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
metadata incomplete
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
uncurated
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
pending final vetting
Terms with this status should eventually replaced with a term from another ontology.
Alan Ruttenberg
group:OBI
to be replaced with external ontology term
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
Alan Ruttenberg
group:OBI
requires discussion
SVN $Revision: 717 $
IAO Release 2015-02-23
'Hemodynamic Response Function' which is a fixed difference of two gamma probability density functions - a standard positive function at normal lag, and a small, delayed, negated gamma probability density function, which attempts to model the late undershoot (definition adapted [FSL wiki](http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/feat5/detail.html))
Discussed at https://github.com/incf-nidash/nidm/issues/281
FSL's Gamma Difference HRF
'Hemodynamic Response Function' basis that is the derivative with respect to time of the FSL's Gamma Difference heamodynamic response function.
Discussed at https://github.com/incf-nidash/nidm/issues/281
FSL's Temporal Derivative
'Hemodynamic Response Function' which is a fixed gamma probability density function. This is the default in FSL.
FSL's Gamma HRF
Reference space defined as the stereotaxic average of 27 T1-weighted MRI scans of the same individual transformed into the Talairach stereotaxic space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres and http://neuro.debian.net/pkgs/mni-colin27-nifti.html). This is the default in SPM96 (cf. [MRC CBSU Wiki](http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach)).
Discussed at https://github.com/incf-nidash/nidm/issues/284
used in SPM96 (cf. http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach)
Colin27 Coordinate System
http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres
Reference space defined as the average of 452 T1-weighted MRIs of normal young adult brains after 12 parameter AIR linear transform to the MNI 305 space (cf. http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml and http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach)
Discussed at https://github.com/incf-nidash/nidm/issues/284
Icbm452 Air Coordinate System
http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml
Reference space defined as the average of 452 T1-weighted MRIs of normal young adult brains after affine and 5 order polynomial non-linear warping to the MNI 305 space (cf. http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml and http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach)
Discussed at https://github.com/incf-nidash/nidm/issues/284
Icbm452 Warp5 Coordinate System
http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml
Reference space which is the average of 152 T1-weighted MRI scans, linearly transformed onto the MNI 305 reference space (definition adapted from: http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin). This is the default in SPM99 to SPM8 (cf. [MRC CBSU Wiki](http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach) and spm8/spm_templates.man.
Discussed at https://github.com/incf-nidash/nidm/issues/284
used in SPM99 to SPM8 (cf. http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach and spm8/spm_templates.man)
Icbm Mni152 Linear Coordinate System
http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin
Reference space defined as the average of 152 T1-weighted MRI scans, non-linearly transformed to MNI152 linear space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details).
Discussed at https://github.com/incf-nidash/nidm/issues/284
Icbm Mni152 Non Linear2009a Asymmetric Coordinate System
http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009
Reference space defined as the average of 152 T1-weighted MRI scans, non-linearly transformed to to form a symmetric model in MNI152 linear space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details).
Discussed at https://github.com/incf-nidash/nidm/issues/284
Icbm Mni152 Non Linear2009a Symmetric Coordinate System
http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009
Reference space defined as the average of 152 T1-weighted MRI scans in high-resolution, non-linearly transformed to MNI152 linear space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details).
Discussed at https://github.com/incf-nidash/nidm/issues/284
Icbm Mni152 Non Linear2009b Asymmetric Coordinate System
http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009
Reference space defined as the average of 152 T1-weighted MRI scans in high-resolution, non-linearly transformed to form a symmetric model in MNI152 linear space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details).
Discussed at https://github.com/incf-nidash/nidm/issues/284
Icbm Mni152 Non Linear2009b Symmetric Coordinate System
http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009
Reference space defined as the average of 152 T1-weighted MRI scans, non-linearly transformed to MNI152 linear space using the N3 algorithm (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details).
Discussed at https://github.com/incf-nidash/nidm/issues/284
Used in DARTEL toolbox in SPM12b (cf. spm12b/spm_templates.man)
Icbm Mni152 Non Linear2009c Asymmetric Coordinate System
http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009
Reference space defined as the average of 152 T1-weighted MRI scans, non-linearly transformed to form a symmetric model in MNI152 linear space using the N3 algorithm (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details). This is the default for DARTEL toolbox in SPM12b (cf. spm12/spm_templates.man).
Discussed at https://github.com/incf-nidash/nidm/issues/284
Icbm Mni152 Non Linear2009c Symmetric Coordinate System
http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009
Reference space defined as the average of 152 T1-weighted MRI scans, linearly and non-linearly (6 iterations) transformed to form a symmetric model in Talairach space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6)
Discussed at https://github.com/incf-nidash/nidm/issues/284
Used in FSL (cf. http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlases)
Icbm Mni152 Non Linear6th Generation Coordinate System
http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6
Reference space defined by the average of the 549 subjects from the IXI dataset linearly transformed to the ICBM MNI 452 (cf. spm12/spm\_templates.man and http://biomedic.doc.ic.ac.uk/brain-development/index.php?n=Main.Datasets). This is the default in SPM12 (cf. spm12/spm_templates.man).
Discussed at https://github.com/incf-nidash/nidm/issues/284
Used in SPM12b (cf. spm12b/spm_templates.man)
Ixi549 Coordinate System
http://biomedic.doc.ic.ac.uk/brain-development/index.php?n=Main.Datasets
Reference space defined as the average of 305 T1-weighted MRI scans, linearly transformed to Talairach space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/MNI305 for more details)
Discussed at https://github.com/incf-nidash/nidm/issues/284
Mni305 Coordinate System
http://www.bic.mni.mcgill.ca/ServicesAtlases/MNI305
A pair of pixels are 4-Connected if they share an edge.
Discussed in https://github.com/incf-nidash/nidm/pull/201
pixel4connected
A pair of pixels are 8-Connected if they share an edge or corner.
Discussed in https://github.com/incf-nidash/nidm/pull/201
pixel8connected
A pair of voxels are 18-Connected if they share a face or edge.
Discussed in https://github.com/incf-nidash/nidm/pull/201
voxel18connected
A pair of voxels are 26-Connected if they share a face, edge or corner.
Discussed in https://github.com/incf-nidash/nidm/pull/201
voxel26connected
A pair of voxels are 6-Connected if they share a face.
Discussed in https://github.com/incf-nidash/nidm/pull/201
voxel6connected
'Hemodynamic Response Function' basis that is the derivative with respect to spatial dispersion of the SPM's Canonical heamodynamic response function.
Discussed at https://github.com/incf-nidash/nidm/issues/281
SPM's Dispersion Derivative
'Hemodynamic Response Function' which is a fixed difference of two gamma probability density functions and is denoted by "canonical HRF" in SPM. This is the default in SPM
Discussed at https://github.com/incf-nidash/nidm/issues/281
SPM's Canonical HRF
'Hemodynamic Response Function' basis that is the derivative with respect to time of the SPM's Canonical heamodynamic response function.
Discussed at https://github.com/incf-nidash/nidm/issues/281
SPM's Temporal Derivative
Recommendation version 2013-04-30
2008-01-14
Creator
An entity primarily responsible for making the resource.
Examples of a Creator include a person, an organization, or a service. Typically, the name of a Creator should be used to indicate the entity.
A second property with the same name as this property has been declared in the dcterms: namespace (http://purl.org/dc/terms/). See the Introduction to the document "DCMI Metadata Terms" (http://dublincore.org/documents/dcmi-terms/) for an explanation.
1999-07-02
Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource.
1999-07-02
A second property with the same name as this property has been declared in the dcterms: namespace (http://purl.org/dc/terms/). See the Introduction to the document "DCMI Metadata Terms" (http://dublincore.org/documents/dcmi-terms/) for an explanation.
Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource.
An account of the resource.
An account of the resource.
2008-01-14
Description
2008-01-14
A name given to the resource.
A second property with the same name as this property has been declared in the dcterms: namespace (http://purl.org/dc/terms/). See the Introduction to the document "DCMI Metadata Terms" (http://dublincore.org/documents/dcmi-terms/) for an explanation.
Title
1999-07-02
Property that associates a 'World Coordinate System' to the 'Coordinate Space'.
Discussed at https://github.com/incf-nidash/nidm/issues/284
in World Coordinate System
This document is published by the Provenance Working Group (http://www.w3.org/2011/prov/wiki/Main_Page).
If you wish to make comments regarding this document, please send them to public-prov-comments@w3.org (subscribe public-prov-comments-request@w3.org, archives http://lists.w3.org/Archives/Public/public-prov-comments/). All feedback is welcome.
W3C PROVenance Interchange Ontology (PROV-O)
Recommendation version 2013-04-30
An empty collection is a collection without members.
EmptyCollection
expanded
prov:EmptyCollection
collections
http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig
specializationOf
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-specialization
expanded
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.
alternate
generalizationOf
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-specialization
wasRevisionOf
derivations
expanded
hadRevision
A revision is a derivation that revises an entity into a revised version.