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| URI | http://schema.org/givenName |
| Label | given Name |
@prefix : <https://neuroshapes.org/> .
@prefix commonshapes: <https://neuroshapes.org/commons/> .
@prefix context: <https://incf.github.io/neuroshapes/contexts/> .
@prefix datashapes: <https://neuroshapes.org/dash/> .
@prefix dc: <http://purl.org/dc/elements/1.1/> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix ns1: <https://bluebrain.github.io/nexus/vocabulary/> .
@prefix ns2: <https://neuroshapes.org/> .
@prefix nsg: <https://neuroshapes.org/> .
@prefix nsg1: <https://bbp-nexus.epfl.ch/vocabs/bbp/neurosciencegraph/core/v0.1.0/> .
@prefix nxv: <https://bbp-nexus.epfl.ch/vocabs/nexus/core/terms/v0.1.0/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix provcommonshapes: <https://provshapes.org/commons/> .
@prefix provdatashapes: <https://provshapes.org/datashapes/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix schema: <http://schema.org/> .
@prefix sh: <http://www.w3.org/ns/shacl#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix vann: <http://purl.org/vocab/vann/> .
@prefix void: <http://rdfs.org/ns/void#> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
schema:givenName a owl:ObjectProperty ;
rdfs:label "given Name"@en .
{
"@context": {
"": "https://neuroshapes.org/",
"commonshapes": "https://neuroshapes.org/commons/",
"context": "https://incf.github.io/neuroshapes/contexts/",
"datashapes": "https://neuroshapes.org/dash/",
"dc": "http://purl.org/dc/elements/1.1/",
"dcterms": "http://purl.org/dc/terms/",
"ns1": "https://bluebrain.github.io/nexus/vocabulary/",
"ns2": "https://neuroshapes.org/",
"nsg": "https://neuroshapes.org/",
"nsg1": "https://bbp-nexus.epfl.ch/vocabs/bbp/neurosciencegraph/core/v0.1.0/",
"nxv": "https://bbp-nexus.epfl.ch/vocabs/nexus/core/terms/v0.1.0/",
"owl": "http://www.w3.org/2002/07/owl#",
"prov": "http://www.w3.org/ns/prov#",
"provcommonshapes": "https://provshapes.org/commons/",
"provdatashapes": "https://provshapes.org/datashapes/",
"rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdfs": "http://www.w3.org/2000/01/rdf-schema#",
"schema": "http://schema.org/",
"sh": "http://www.w3.org/ns/shacl#",
"skos": "http://www.w3.org/2004/02/skos/core#",
"vann": "http://purl.org/vocab/vann/",
"void": "http://rdfs.org/ns/void#",
"xml": "http://www.w3.org/XML/1998/namespace",
"xsd": "http://www.w3.org/2001/XMLSchema#"
},
"@id": "schema:givenName",
"@type": "owl:ObjectProperty",
"rdfs:label": {
"@language": "en",
"@value": "given Name"
}
}
| URI | https://neuroshapes.org/AcquisitionAnnotation |
| rdfs:label | Acquisition Annotation |
| Description | The Acquisition Annotation is an activity in which an image of a labeled (e.g. by DAB staining) brain slice is acquired and annotated. This can follow e.g. a whole-cell patch clamp recording in which individual neurons are filled with biocytin and then stained. In the LNMC laboratory at EPFL, the acquisition and annotation procedure follows the protocol described here: dx.doi.org/10.17504/protocols.io.ujweupe and dx.doi.org/10.17504/protocols.io.ujveun6. |
| rdfs:subClassOf (2) | :ExperimentalActivityprov:Activity |
| URI | https://neuroshapes.org/AffineLinearTransform |
| rdfs:label | Affine Linear Transform |
| Description | The Affine Linear Transform is a function between affine spaces which preserves points, straight lines and planes. |
| rdfs:subClassOf (2) | :Transformprov:Entity |
| URI | https://neuroshapes.org/Analysis |
| rdfs:label | Analysis |
| Description | The Analysis is an activity in which a model (e.g. a circuit) is examined with respect to a certain property / characteristic (e.g. total pathway strength). An analysis typically generates an analysis result which contains the outcome of the analysis. |
| rdfs:subClassOf (1) | prov:Activity |
| URI | https://neuroshapes.org/AnalysisResult |
| rdfs:label | Analysis Result |
| Description | The Analysis Result is an entity generated by an analysis activity. This can e.g. be a numerical value such as the total pathway strength of a circuit or an artefact generated by the analysis. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/AnnotatedSlice |
| rdfs:label | Annotated Slice |
| Description | The Annotated Slice is an entity which is a revision of a brain slice entity. In the annotated slice, some aspects of the brain slice are annotated, e.g. the location and name of stained cells contained within the slice or anatomical demarcations visible on the slice. In the LNMC laboratory at EPFL, a custom annotation Macro was created using Fiji to create a pipeline for the annotation of slices. This is described here: dx.doi.org/10.17504/protocols.io.ujveun6. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/Annotation |
| rdfs:label | Annotation |
| Description | An Annotation is an entity. Typically, an Annotation has a single Body, which is a comment or other descriptive resource, and a single Target that the Body is somehow "about". The Annotation likely also has additional descriptive properties (see: https://www.w3.org/TR/annotation-model/#annotations). |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/AnnotationBody |
| rdfs:label | Annotation Body |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/AnnotationTarget |
| rdfs:label | Annotation Target |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/ApicalAnnotation |
| rdfs:label | Apical Annotation |
| Description | The Apical Annotation is an annotation activity in which the apical dendrite of a neuron morphology reconstruction is annotated. |
| rdfs:subClassOf (1) | prov:Activity |
| URI | https://neuroshapes.org/AtlasConstruction |
| rdfs:label | Atlas Construction |
| Description | The Atlas Construction is an activity in which the components of a brain atlas (as used by Blue Brain) are generated from a collection of subjects (e.g. rat subjects). The components of a constructed atlas comprise the parcellation image data, the parcellation labels and the template image data. |
| rdfs:subClassOf (1) | prov:Activity |
| URI | https://neuroshapes.org/AtlasRelease |
| rdfs:label | Atlas Release |
| Description | The Atlas Release is an entity which describes the release of a brain atlas. An atlas release can be described by the release date and the template volume, parcellation volume, parcellation ontology and spatial reference system used. |
| rdfs:subClassOf (2) | :BrainAtlasprov:Entity |
| URI | https://neuroshapes.org/AtlasSpatialReferenceSystem |
| rdfs:label | Atlas Spatial Reference System |
| Description | The Atlas Spatial Reference System is an entity which is the spatial reference system used as reference for a brain atlas. It can be described by information about the point of origin of the reference system, the orientation of the refernece system, the bounding box usde and the dimension unit of the brain atlas space. |
| rdfs:subClassOf (4) | :SpatialReferenceSystem:CoordinateSystemprov:Entityprov:Location |
| URI | https://neuroshapes.org/BiologicalSex |
| rdfs:label | Biological Sex |
| Description | Biological Sex refers to ... |
| URI | https://neuroshapes.org/BluePyEfeFeatures |
| rdfs:label | Blue Py Efe Features |
| Description | The Blue Py Efe Features is an entity generated by the extraction of electrophysiological features from electrophysiology traces with the help of the "Electrophys Feature Extraction Library (eFEL)" (https://github.com/BlueBrain/eFEL). Example features are action potential width or action potential amplitude. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/BoundingBox |
| rdfs:label | Bounding Box |
| Description | The Bounding Box is an entity used in the context of a brain atlas and represents the imaginary box around the image data. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/BrainAtlas |
| rdfs:label | BrainAtlas |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/BrainAtlasRelease |
| rdfs:label | Brain Atlas Release |
| Description | The Atlas Release is an entity which describes the release of a brain atlas. An atlas release can be described by the release date and the template volume, parcellation volume, parcellation ontology and spatial reference system used. |
| rdfs:subClassOf (3) | :AtlasRelease:BrainAtlasprov:Entity |
| URI | https://neuroshapes.org/BrainAtlasSpatialReferenceSystem |
| rdfs:label | Brain Atlas Spatial Reference System |
| Description | The Atlas Spatial Reference System is an entity which is the spatial reference system used as reference for a brain atlas. It can be described by information about the point of origin of the reference system, the orientation of the refernece system, the bounding box usde and the dimension unit of the brain atlas space. |
| rdfs:subClassOf (5) | :AtlasSpatialReferenceSystem:SpatialReferenceSystem:CoordinateSystemprov:Entityprov:Location |
| URI | https://neuroshapes.org/BrainImaging |
| rdfs:label | Brain Imaging |
| Description | The Brain Imaging is an activty in which images of brain tissue are acquired, typically as image stacks. Brain imaging can be conducted using a range of different techniques, such as functional magnetic resonance imaging (fMRI). |
| rdfs:subClassOf (2) | :ExperimentalActivityprov:Activity |
| URI | https://neuroshapes.org/BrainLocation |
| rdfs:label | Brain Location |
| rdfs:subClassOf (2) | prov:Entityprov:Location |
| URI | https://neuroshapes.org/BrainParcellationDataLayer |
| rdfs:label | Brain Parcellation Data Layer |
| Description | The Brain Parcellation Data Layer is an entity relevant in the context of the representation of volumetric data. It describes the data layer containing information about the brain parcellation, i.e. the demarcations of individual brain regions in the context of a specific brain atlas. It belongs to the voxel brain data shape definition. Voxel Brain is an in-house service of the Blue Brain Project which helps to access data already positioned in a volumetric atlas space. |
| rdfs:subClassOf (4) | :VolumetricDataLayer:Volume:NdRasterprov:Entity |
| URI | https://neuroshapes.org/BrainParcellationMesh |
| rdfs:label | Brain Parcellation Mesh |
| Description | The Brain Parcellation Mesh is an entity containing the meshing information for brain parcels. A mesh in the context of brain parcels describes the 'surface' of the individual brain parcels. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/BrainSlicing |
| rdfs:label | Brain Slicing |
| Description | The Brain Slicing describes an activity in which brain tissue is sliced using e.g. a vibratome for further experimentation such as whole-cell patch clamp recordings. In the LNMC laboratory at EPFL, the brain slicing procedure follows the protocol described here: dx.doi.org/10.17504/protocols.io.uqbevsn. |
| rdfs:subClassOf (2) | :ExperimentalActivityprov:Activity |
| URI | https://neuroshapes.org/BrainTemplateDataLayer |
| rdfs:label | Brain Template Data Layer |
| Description | A brain template is a volumetric dataset that represent a brain, usually being the result of averaging data from multiple individuals, but not always. It is usually used as a layout or background to provide context for other data to be displayed with. |
| rdfs:subClassOf (4) | :VolumetricDataLayer:Volume:NdRasterprov:Entity |
| URI | https://neuroshapes.org/Cell |
| rdfs:label | Cell |
| Description | The Cell is an entity describing any kind of biological cell. Biological cells consist of biomolecules and cytoplasm enclosed within a membrane. Examples of more speciliased biological cells in the brain include e.g. neurons and astrocytes. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/CellDensityDataLayer |
| rdfs:label | Cell Density Data Layer |
| Description | The Cell Density Data Layer is an entity relevant in the context of the representation of volumetric data. It describes the data layer containing information about the density of cell types. It belongs to the voxel brain data shape definition. Voxel Brain is an in-house service of the Blue Brain Project which helps to access data already positioned in a volumetric atlas space. |
| rdfs:subClassOf (4) | :VolumetricDataLayer:Volume:NdRasterprov:Entity |
| URI | https://neuroshapes.org/CellPlacement |
| rdfs:label | Cell Placement |
| Description | The Cell Placement is an entity describing how the cells of a circuit are placed in 3D space, e.g. the placement of neurons with a specific morphology. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/CellType |
| rdfs:label | Cell Type Ontology. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/CircuitCellProperties |
| rdfs:label | Circuit Cell Properties |
| Description | The Circuit Cell Properties is an entity about the cell properties of cells in a digitally reconstructed circuit of brain cells. These can include e.g. the cell placement or cell orientation. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/ComponentDimension |
| rdfs:label | Component Dimension |
| URI | https://neuroshapes.org/Configuration |
| rdfs:label | Configuration |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/Contribution |
| rdfs:label | Contribution |
| rdfs:subClassOf (2) | prov:Associationprov:AgentInfluence |
| URI | https://neuroshapes.org/CoordinateSystem |
| rdfs:label | CoordinateSystem |
| rdfs:subClassOf (2) | prov:Entityprov:Location |
| URI | https://neuroshapes.org/DeformableTransform |
| rdfs:label | Deformable Transform |
| Description | The Deformable Transform includes parametric and non-parametric functions and is typically described by a displacement vector field. |
| rdfs:subClassOf (2) | :Transformprov:Entity |
| URI | https://neuroshapes.org/DetailedCircuit |
| rdfs:label | Detailed Circuit |
| Description | The Detailed Circuit is a model instance describing a digital representation of a neural circuit comprising a collection of edges (representing the connections between neurons) and nodes (representing the neurons). |
| rdfs:subClassOf (2) | :ModelInstanceprov:Entity |
| URI | https://neuroshapes.org/DocumentIndexSelector |
| rdfs:label | Document Index Selector |
| rdfs:subClassOf (2) | :Selectorprov:Location |
| URI | https://neuroshapes.org/EModel |
| rdfs:label | EModel |
| Description | The E-Model is a model instance describing the characteristic electrical behaviour of an electrical type of a neuron. At the Blue Brain Project, electrical types of neurons were classified based on an extended version of the Petilla convention (https://doi.org/10.1038/nrn2402). |
| rdfs:subClassOf (2) | :ModelInstanceprov:Entity |
| URI | https://neuroshapes.org/EModelBuilding |
| rdfs:label | EModel Building |
| Description | The E-Model Building is an activity of generating an e-model by using a neuron morphology to fit model parameters. |
| rdfs:subClassOf (1) | prov:Activity |
| URI | https://neuroshapes.org/EModelRelease |
| rdfs:label | EModel Release |
| Description | An E-Model Release is a model release which describes the release of a set of e-models (i.e. the output of the software package BluePyOpt (https://github.com/BlueBrain/BluePyOpt)) for further use in the reconstruction and simulation pipeline. |
| rdfs:subClassOf (2) | :ModelReleaseprov:Entity |
| URI | https://neuroshapes.org/EModelScript |
| rdfs:label | EModel Script |
| Description | The E-Model Script is an entity describing the script (typically a .mod file) used for a particular electrical model of a single cell. |
| rdfs:subClassOf (2) | :ModelScriptprov:Entity |
| URI | https://neuroshapes.org/ETypeFeatureProtocol |
| rdfs:label | EType Feature Protocol |
| Description | The E-Type Feature Protocol is a model instance describing the extracted electrical features for an electrical type and the corresponding protocols. |
| rdfs:subClassOf (2) | :ModelInstanceprov:Entity |
| URI | https://neuroshapes.org/EdgeCollection |
| rdfs:label | Edge Collection |
| Description | The Edge Collection is an entity representing a collection of connections between neurons in a network of neurons represented as a graph. In this graph representation, nodes represent neurons and edges the connections between neurons. More detailed information can be found on the SONATA data format guide: https://github.com/AllenInstitute/sonata/blob/master/docs/SONATA_DEVELOPER_GUIDE.md#representing-edges. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/ElectricalSeries |
| rdfs:label | ElectricalSeries |
| rdfs:subClassOf (2) | :TimeSeriesprov:Entity |
| URI | https://neuroshapes.org/EmodelFeatureGeneration |
| rdfs:label | Emodel Feature Generation |
| rdfs:subClassOf (3) | prov:Generationprov:ActivityInfluenceprov:InstantaneousEvent |
| URI | https://neuroshapes.org/EquationSelector |
| rdfs:label | Equation Selector |
| rdfs:subClassOf (2) | :Selectorprov:Location |
| URI | https://neuroshapes.org/ExperimentalActivity |
| rdfs:label | Experimental Activity |
| Description | An Experimental Activity is an activity in a scientific experiment. Examples for experimental activities include e.g. brain slicing, whole cell patch clamp or reconstruction of a neuron morphology. |
| rdfs:subClassOf (1) | prov:Activity |
| URI | https://neuroshapes.org/ExperimentalProtocol |
| rdfs:label | Experimental Protocol |
| Description | The Experimental Protocol is an entity describing a protocol used in a scientific experiment. Examples for experimental protocols include e.g. the protocol used to perform the reconstruction of a neuron morphology. |
| rdfs:subClassOf (2) | :Protocolprov:Entity |
| URI | https://neuroshapes.org/FigureSelector |
| rdfs:label | Figure Selector |
| rdfs:subClassOf (2) | :Selectorprov:Location |
| URI | https://neuroshapes.org/FixationStainingMounting |
| rdfs:label | Fixation Staining Mounting |
| Description | The Fixation Staining Mounting describes an activity in which brain tissue such as a brain slice is fixed (e.g. with formaldehyde), stained (e.g. using DAB staining) and mounted (onto an object slide for viewing with a microscope). The activity can follow e.g. a whole-cell patch clamp recording in which individual neurons are filled with biocytin. In the LNMC laboratory at EPFL, the fixation, staining and mounting procedure follows the protocol described here: dx.doi.org/10.17504/protocols.io.ujxeupn and dx.doi.org/10.17504/protocols.io.ujteunn. |
| rdfs:subClassOf (2) | :ExperimentalActivityprov:Activity |
| URI | https://neuroshapes.org/FixedStainedSlice |
| rdfs:label | Fixed Stained Slice |
| Description | The Fixed Stained Slice is an entity which describes a brain slice which was fixed (using e.g. paraformaldehyde fixative) and stained (using e.g. the DAB-reaction to highlight biocytin-filled neurons in the brain slice). The fixed stained slice is a revision of a brain slice. |
| rdfs:subClassOf (2) | :Sliceprov:Entity |
| URI | https://neuroshapes.org/GeneExpressionVolumetricDataLayer |
| rdfs:label | Gene Expression Volumetric Data Layer |
| Description | Used to label volumetric dataset that are showing gene expression, in general being the result of a marker expression. This specialisation of Volumetric Data Layer adds a property "gene" (string). |
| rdfs:subClassOf (4) | :VolumetricDataLayer:Volume:NdRasterprov:Entity |
| URI | https://neuroshapes.org/GeometricShape |
| rdfs:label | Geometric Shape |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/HostCell |
| rdfs:label | Host Cell |
| Description | The Host Cell is an entity describing a biological cell which serves as a host for the expression of a specific gene of interest. This is e.g. used to study individual ion channels. A common example for a host cell line is the Chinese Hamster Ovary cell line. |
| rdfs:subClassOf (2) | :Cellprov:Entity |
| URI | https://neuroshapes.org/ImageStack |
| rdfs:label | Image Stack |
| Description | The Image Stack is an entity describing an acquired stack of images of e.g. brain tissue. The stack of images is a series of 2D images which are stacked together to form volumetric data. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/ImageVolume |
| rdfs:label | Image Volume |
| Description | The Image Volume is an entity describing volumetric image data of e.g. brain tissue. An image volume is composed of voxels, the 3D equivalent to pixels in a 2D image. |
| rdfs:subClassOf (3) | :Volume:NdRasterprov:Entity |
| URI | https://neuroshapes.org/InVitroSliceReconstructedPatchedNeuron |
| rdfs:label | In Vitro Slice Reconstructed Patched Neuron |
| rdfs:subClassOf (6) | :ReconstructedPatchedCell:ReconstructedNeuronMorphology:NeuronMorphology:Morphologyprov:Entity:ReconstructedCell |
| URI | https://neuroshapes.org/InVitroSliceWholeCellPatchClampElectrophysiologyTrace |
| rdfs:label | In Vitro Slice Whole Cell Patch Clamp Electrophysiology Trace |
| rdfs:subClassOf (4) | :Trace:ElectricalSeries:TimeSeriesprov:Entity |
| URI | https://neuroshapes.org/InVitroWholeBrainReconstructedNeuronMorphology |
| rdfs:label | In Vitro Whole Brain Reconstructed Neuron Morphology |
| rdfs:subClassOf (6) | :ReconstructedWholeBrainCell:ReconstructedNeuronMorphology:NeuronMorphology:Morphologyprov:Entity:ReconstructedCell |
| URI | https://neuroshapes.org/IntraCellularSharpElectrode |
| rdfs:label | Intra Cellular Sharp Electrode |
| Description | The Intracellular Sharp Electrode is an activity in which single cells in a brain slice are recorded intracellularly using sharp electrodes. The micropipette (i.e. electrode) used for intracellular sharp electrode recordings are similar to the ones used for patch clamp recordings but have a much smaller opening at the tip. |
| rdfs:subClassOf (2) | :ExperimentalActivityprov:Activity |
| URI | https://neuroshapes.org/IntraCellularSharpElectrodeRecordedCell |
| rdfs:label | Intra Cellular Sharp Electrode Recorded Cell |
| Description | The Intracellular Sharp Electrode Recorded Cell is an entity describing a cell which was recorded using the intracellular sharp electrode technique. Typically, the recorded cell is a neuron. |
| rdfs:subClassOf (2) | :Cellprov:Entity |
| URI | https://neuroshapes.org/IntraCellularSharpElectrodeRecordedCellCollection |
| rdfs:label | Intra Cellular Sharp Electrode Recorded Cell Collection |
| rdfs:subClassOf (2) | prov:Collectionprov:Entity |
| URI | https://neuroshapes.org/IntraCellularSharpElectrodeRecordedSlice |
| rdfs:label | Intra Cellular Sharp Electrode Recorded Slice |
| Description | The Intracellular Sharp Electrode Recorded Slice is a brain slice entity which was used in an intracellular sharp electrode recording. The intracellular sharp electrode recorded slice contains cells which were recorded using sharp electrodes. |
| rdfs:subClassOf (2) | :Sliceprov:Entity |
| URI | https://neuroshapes.org/IonChannelGene |
| rdfs:label | Ion Channel Gene |
| Description | The Ion Channel Gene is an entity describing the gene encoding a particular ion channel. Ion channels are proteins which allow ions to pass through the membrane of cells by forming a pore-like structure. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/IonChannelMechanismRelease |
| rdfs:label | Ion Channel Mechanism Release |
| Description | An Ion Channel Mechanism Release is a model release which describes the release of a set of subcellular models (such as ion channel mechanisms) for further use in the reconstruction and simulation pipeline. |
| rdfs:subClassOf (2) | :ModelReleaseprov:Entity |
| URI | https://neuroshapes.org/LabeledCell |
| rdfs:label | Labeled Cell |
| Description | The Labeled Cell is an entity describing a biological cell which was labeled using a particular dye (e.g. lucifer yellow) or chemical reaction (e.g. DAB-reaction) to make this particular cell 'visible'. In patch-clamp recordings, individual cells are typically filled with biocytin which is then visualised through the DAB-reaction or binding to a streptavidin-fluorophore conjugate. |
| rdfs:subClassOf (2) | :Cellprov:Entity |
| URI | https://neuroshapes.org/LabeledCellCollection |
| rdfs:label | Labeled Cell Collection |
| rdfs:subClassOf (2) | prov:Collectionprov:Entity |
| URI | https://neuroshapes.org/License |
| rdfs:label | License |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/LinearTransform |
| rdfs:label | Linear Transform |
| Description | The Linear Transform is a function, including rigid and affine functions, described by a 3x4 matrix. |
| rdfs:subClassOf (2) | :Transformprov:Entity |
| URI | https://neuroshapes.org/MEModel |
| rdfs:label | MEModel |
| Description | The ME-Model is a model instance describing the morpho-electrical type of a neuron. At the Blue Brain Project, electrical types of neurons were classified based on an extended version of the Petilla convention (https://doi.org/10.1038/nrn2402). Naming of morphological types was based on most commonly used names (https://doi.org/10.1016/j.cell.2015.09.029). |
| rdfs:subClassOf (2) | :ModelInstanceprov:Entity |
| URI | https://neuroshapes.org/MEModelRelease |
| rdfs:label | MEModel Release |
| Description | An ME-Model Release is a model release which combines a specific e-model release and a specific morphology release for further use in the reconstruction and simulation pipeline. |
| rdfs:subClassOf (2) | :ModelReleaseprov:Entity |
| URI | https://neuroshapes.org/ModelInstance |
| rdfs:label | Model Instance |
| Description | The Model Instance is an entity describing details about a digital representation of e.g. neural circuits. In the context of simulation neuroscience, it describes what is being modelled, and to which brain region and species this model applies. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/ModelRelease |
| rdfs:label | Model Release |
| Description | The Model Release is an entity describing a particular model instance or a collection thereof which has been agreed on (e.g. based on criteria regarding quality or completeness) to be available for further use in the reconstruction and simulation pipeline. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/ModelReleaseIndex |
| rdfs:label | Model Release Index |
| Description | The Model Release Index is en entity describing the indices relevant to a given model release. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/ModelScript |
| rdfs:label | ModelScript |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/ModelValidation |
| rdfs:label | Model Validation |
| Description | The Model Validation is an activity in which a specific model instance is validated against a specific set of data used as reference for the validation. The model validation activity generates a validation result. |
| rdfs:subClassOf (1) | prov:Activity |
| URI | https://neuroshapes.org/Morphology |
| rdfs:label | Morphology |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/MorphologyDiversification |
| rdfs:label | Morphology Diversification |
| Description | The Morphology Diversification is an activity in which a morphology release is generated from a set of neuron morphologies by applying various diversification protocols such as neuron morphology repair, scaling, grafting, cloning or mix-and-matching. |
| rdfs:subClassOf (1) | prov:Activity |
| URI | https://neuroshapes.org/MorphologyMesh |
| rdfs:label | Morphology Mesh |
| Description | The Morphology Mesh is an entity which describes a mesh representation of neuron morphologies. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/MorphologyMeshGeneration |
| rdfs:label | Morphology Mesh Generation |
| Description | The Morphology Mesh Generation is an activity which describes the generation of a mesh representation of a neuron morphology from an experimental reconstructed cell. |
| rdfs:subClassOf (1) | prov:Activity |
| URI | https://neuroshapes.org/MorphologyOrientationDataLayer |
| rdfs:label | Morphology Orientation Data Layer |
| Description | The Morphology Orientation Data Layer is a volumetric data layer entity which belongs to the voxel brain data shape definition and descirbes the orientation of morphologies. Voxel Brain is an in-house service of the Blue Brain Project which helps to access data already positioned in a volumetric atlas space. |
| rdfs:subClassOf (4) | :VolumetricDataLayer:Volume:NdRasterprov:Entity |
| URI | https://neuroshapes.org/MorphologyRelease |
| rdfs:label | Morphology Release |
| Description | A Morphology Release is a model release which describes a set of neuron morphologies for further use in the reconstruction and simulation pipeline. |
| rdfs:subClassOf (2) | :ModelReleaseprov:Entity |
| URI | https://neuroshapes.org/NISSLImageDataLayer |
| rdfs:label | NISSLImage Data Layer |
| Description | The Nissl Image Data Layer is a volumetric data layer entity which belongs to the voxel brain data shape definition and describes the Nissl-stained image data. Voxel Brain is an in-house service of the Blue Brain Project which helps to access data already positioned in a volumetric atlas space. |
| rdfs:subClassOf (4) | :VolumetricDataLayer:Volume:NdRasterprov:Entity |
| URI | https://neuroshapes.org/NdRaster |
| rdfs:label | Nd Raster |
| Description | NdRaster stands for n-dimensional raster dataset. It can represent an 2D image (png, tiff, jpeg, etc.), a 3D volume (NRRD, NIfTI, Minc, etc.), an image over time (animated sequence, video, etc.), a volume over time (fMRI), a 1D record (sound, EEG). It can handle multiple channel (color image, multiple-probe EEG, differential volumes, etc.) as well as a transformation in another space. The schema also enforce the presence of low level encoding information such as the data type, the endianness and the type of compression. This schema covers most raster types bur will generally be extended for convenience with schema that specialises into a certain type of data (see: VolumetricDataLayer, for 3D dataset) |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/NeuronDensity |
| rdfs:label | Neuron Density |
| Description | the number of neurons per unit volume |
| URI | https://neuroshapes.org/NeuronMorphology |
| rdfs:label | Neuron Morphology |
| rdfs:subClassOf (2) | :Morphologyprov:Entity |
| URI | https://neuroshapes.org/NeuronMorphologyModel |
| rdfs:label | Neuron Morphology Model |
| Description | A Morphology is a model instance of a neuron morphology, typically described by its m-type and distribution. |
| rdfs:subClassOf (4) | :ModelInstanceprov:Entity:NeuronMorphology:Morphology |
| URI | https://neuroshapes.org/NeuronMorphologyReconstruction |
| rdfs:label | Neuron Morphology Reconstruction |
| rdfs:subClassOf (3) | :Reconstruction:ExperimentalActivityprov:Activity |
| URI | https://neuroshapes.org/NodeCollection |
| rdfs:label | Node Collection |
| Description | The Node Collection is an entity representing a collection of neurons represented as a graph. In this graph representation, nodes represent neurons and edges the connections between neurons. More detailed information can be found on the SONATA data format guide: https://github.com/AllenInstitute/sonata/blob/master/docs/SONATA_DEVELOPER_GUIDE.md#representing-edges. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/OntologyConversion |
| rdfs:label | Ontology Conversion |
| Description | The Ontology Conversion is an activty which converts a brain parcellation label into a brain parcellation ontology. |
| rdfs:subClassOf (1) | prov:Activity |
| URI | https://neuroshapes.org/PDFAreaSelector |
| rdfs:label | PDFArea Selector |
| rdfs:subClassOf (2) | :Selectorprov:Location |
| URI | https://neuroshapes.org/PHDataLayer |
| rdfs:label | PHData Layer |
| Description | The PH Data Layer is a volumetric data layer entity which belongs to the voxel brain data shape definition and describes the PH data. Voxel Brain is an in-house service of the Blue Brain Project which helps to access data already positioned in a volumetric atlas space. |
| rdfs:subClassOf (4) | :VolumetricDataLayer:Volume:NdRasterprov:Entity |
| URI | https://neuroshapes.org/ParcellationImageData |
| rdfs:label | Parcellation Image Data |
| Description | The Parcellation Image Data is an entity either describing an image stack, an image volume or a document atlas. |
| rdfs:subClassOf (3) | :Volume:NdRasterprov:Entity |
| URI | https://neuroshapes.org/ParcellationLabel |
| rdfs:label | Parcellation Label |
| Description | The Parcellation Label is an entity describing a set of human-readable brain parcellation labels and the respective atlas version for which the brain parcellation labels were used. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/ParcellationMeshGeneration |
| rdfs:label | Parcellation Mesh Generation |
| Description | The Parcellation Mesh Generation is an activity which uses a brain parcellation volume to generate a brain parcellation mesh. |
| rdfs:subClassOf (1) | prov:Activity |
| URI | https://neuroshapes.org/ParcellationOntology |
| rdfs:label | Parcellation Ontology |
| Description | The Parcellation Ontology is an entity which describes the brain parcellation ontology in the context of a specific brain atlas version. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/ParcellationReconstruction |
| rdfs:label | Parcellation Reconstruction |
| Description | The Parcellation Reconstruction is an activity which describes the brain parcellation volume reconstruction whereby a brain parcellation volume is generated from brain parcellation data. |
| rdfs:subClassOf (1) | prov:Activity |
| URI | https://neuroshapes.org/ParcellationVolume |
| rdfs:label | Parcellation Volume |
| Description | The Parcellation Volume is a brain image volume which is registered in an atlas spatial reference system. |
| rdfs:subClassOf (4) | :VolumetricDataLayer:Volume:NdRasterprov:Entity |
| URI | https://neuroshapes.org/PatchClamp |
| rdfs:label | Patch Clamp |
| Description | The Patch Clamp is an activty describing an experimental method used in electrophysiology to study ionic currents across biological membranes. It is primarily used to study excitable cells such as neurons. |
| rdfs:subClassOf (2) | :ExperimentalActivityprov:Activity |
| URI | https://neuroshapes.org/PatchedCell |
| rdfs:label | Patched Cell |
| Description | The Patched Cell is an entity which describes a biological cell that was patched using a patch-clamp technique. |
| rdfs:subClassOf (2) | :Cellprov:Entity |
| URI | https://neuroshapes.org/PatchedCellCollection |
| rdfs:label | Patched Cell Collection |
| rdfs:subClassOf (2) | prov:Collectionprov:Entity |
| URI | https://neuroshapes.org/PatchedSlice |
| rdfs:label | Patched Slice |
| Description | The Patched Slice is an entity which is a revision of a brain slice entity which was used in a patch-clamp experiment and typically contains a number of patched cells. |
| rdfs:subClassOf (2) | :Sliceprov:Entity |
| URI | https://neuroshapes.org/Protocol |
| rdfs:label | Protocol |
| Description | The Protocol is an entity which describes a procedural method used in a science context to provide details about design and implementation of e.g. experiments. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/ReconstructedCell |
| rdfs:label | Reconstructed Cell |
| Description | The Reconstructed Cell is an entity which describes a morphology reconstruction of a biological cell. Neuron morphology reconstructions are typically performed manually or semi-automatically by using neuron tracing software such as Neurolucida (https://www.mbfbioscience.com/neurolucida). |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/ReconstructedCellFormatConversion |
| rdfs:label | Reconstructed Cell Format Conversion |
| Description | The Reconstructed Cell Format Conversion is an activity whereby the file format of a given reconstructed cell entity is converted into another. Typically, this concerns conversions from ASC to SWC format or vice versa. |
| rdfs:subClassOf (1) | prov:Activity |
| URI | https://neuroshapes.org/ReconstructedCellRelease |
| rdfs:label | Reconstructed Cell Release |
| Description | The Reconstructed Cell Release is an entity which describes a set of reconstructed cell entities for further use. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/ReconstructedCellReleaseGeneration |
| rdfs:label | Reconstructed Cell Release Generation |
| Description | The Reconstructed Cell Release Generation describes the context of the generation of a reconstructed cell release. |
| rdfs:subClassOf (3) | prov:Generationprov:ActivityInfluenceprov:InstantaneousEvent |
| URI | https://neuroshapes.org/ReconstructedCellReleaseProcess |
| rdfs:label | Reconstructed Cell Release Process |
| Description | The Reconstructed Cell Release Process is an activity which uses a set of reconstructed cell entites to generate a reconstructed cell release. |
| rdfs:subClassOf (1) | prov:Activity |
| URI | https://neuroshapes.org/ReconstructedNeuronMorphology |
| rdfs:label | Reconstructed Neuron Morphology |
| Description | The Reconstructed Neuron Morphology is an entity which describes a morphology reconstruction of a biological Neuron. Neuron morphology reconstructions are typically performed manually or semi-automatically by using neuron tracing software such as Neurolucida (https://www.mbfbioscience.com/neurolucida). |
| rdfs:subClassOf (4) | :NeuronMorphology:Morphologyprov:Entity:ReconstructedCell |
| URI | https://neuroshapes.org/ReconstructedPatchedCell |
| rdfs:label | Reconstructed Patched Cell |
| Description | The Reconstructed Patched Cell is a reconstructed cell entity which was reconstructed from a biological cell used in a patch-clamp experiment. |
| rdfs:subClassOf (5) | :ReconstructedNeuronMorphology:NeuronMorphology:Morphologyprov:Entity:ReconstructedCell |
| URI | https://neuroshapes.org/ReconstructedPatchedNeuronMorphology |
| rdfs:label | ReconstructedPatchedNeuronMorphology |
| rdfs:subClassOf (6) | :ReconstructedPatchedCell:ReconstructedNeuronMorphology:NeuronMorphology:Morphologyprov:Entity:ReconstructedCell |
| URI | https://neuroshapes.org/ReconstructedWholeBrainCell |
| rdfs:label | Reconstructed Whole Brain Cell |
| Description | The Reconstructed Whole Brain Cell is a reconstructed cell entity which was reconstructed from a whole brain image stack or volume. |
| rdfs:subClassOf (5) | :ReconstructedNeuronMorphology:NeuronMorphology:Morphologyprov:Entity:ReconstructedCell |
| URI | https://neuroshapes.org/ReconstructedWholeBrainNeuronMorphology |
| rdfs:label | ReconstructedWholeBrainNeuronMorphology |
| rdfs:subClassOf (6) | :ReconstructedWholeBrainCell:ReconstructedNeuronMorphology:NeuronMorphology:Morphologyprov:Entity:ReconstructedCell |
| URI | https://neuroshapes.org/Reconstruction |
| rdfs:label | Reconstruction |
| Description | The Reconstruction is an activity that describes the reconstruction of e.g. a neuron morphology. Typically, the reconstruction is performed manually or semi-automatically using reconstruction software such as Neurolucida (https://www.mbfbioscience.com/neurolucida). |
| rdfs:subClassOf (2) | :ExperimentalActivityprov:Activity |
| URI | https://neuroshapes.org/ReconstructionCorrection |
| rdfs:label | Reconstruction Correction |
| Description | The Reconstruction Correction is an activity in which errors such as deviations in the Z values of a contour ('z-jumps') of a reconstructed cell entity are corrected and a corrected revision of the reconstructed cell entity is generated. |
| rdfs:subClassOf (1) | prov:Activity |
| URI | https://neuroshapes.org/ReconstructionFromImage |
| rdfs:label | Reconstruction From Image |
| Description | The Reconstruction From Image is a reconstruction activity that describes the reconstruction of e.g. a neuron morphology from an image stack (rather than a 'live' reconstruction directly from the tissue). Typically, the reconstruction is performed manually or semi-automatically using reconstruction software such as Neurolucida (https://www.mbfbioscience.com/neurolucida). |
| rdfs:subClassOf (3) | :Reconstruction:ExperimentalActivityprov:Activity |
| URI | https://neuroshapes.org/RegionOfInterest |
| rdfs:label | Region Of Interest |
| Description | The Region Of Interest is an entity which allows to select an area of interest within a dataset . In the context of brain image volumes, this can e.g. be a sub-volume outlined by contours within the bigger brain image volume. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/RigidLinearTransform |
| rdfs:label | Rigid Linear Transform |
| Description | The Rigid Linear Transform is a linear function described by a 3x4 matrix. |
| rdfs:subClassOf (2) | :Transformprov:Entity |
| URI | https://neuroshapes.org/RotationalMatrix |
| rdfs:label | Rotational Matrix |
| Description | The Rotational Matrix is a matrix which describes a matrix used to e.g. perform a rotation in Euclidean space. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/Selector |
| rdfs:label | Selector |
| rdfs:subClassOf (1) | prov:Location |
| URI | https://neuroshapes.org/SimplifiedCircuit |
| rdfs:label | Simplified Circuit |
| Description | The Simplified Circuit is a model instance describing a neural circuit composed of a collection of nodes and edges. The simplified circuit applies to a given brain region and species. |
| rdfs:subClassOf (2) | :ModelInstanceprov:Entity |
| URI | https://neuroshapes.org/Simulation |
| rdfs:label | Simulation |
| Description | The Simulation is an activity which uses a model instance and a provided configuration to generate a variable report indicating the values of the variables which were simulated in the activity. In the context of simulation neuroscience, this can e.g. be the simulation of the eletrical behaviour in simplified neural circuit. |
| rdfs:subClassOf (1) | prov:Activity |
| URI | https://neuroshapes.org/SingleCellSimulationTrace |
| rdfs:label | Single Cell Simulation Trace |
| Description | The Single Cell Simulation Trace is a trace entity describing one simulated electrical trace / recording of a single cell. Typically, a trace describes the voltage or current changes across the cell membrane as a function of time. |
| rdfs:subClassOf (4) | :Trace:ElectricalSeries:TimeSeriesprov:Entity |
| URI | https://neuroshapes.org/SingleCellTraceGeneration |
| rdfs:label | Single Cell Trace Generation |
| Description | The Single Cell Trace Generation is an activity describing the generation of a trace of a simulated single cell. |
| rdfs:subClassOf (1) | prov:Activity |
| URI | https://neuroshapes.org/Slice |
| rdfs:label | Slice |
| Description | The Slice is an entity describing a brain slice, i.e. a slice of tissue cut from a brain. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/SliceCollection |
| rdfs:label | Slice Collection |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/SpatialIndex |
| rdfs:label | Spatial Index |
| Description | The Spatial Index is an entity used to locate elements in a spatial dataset, such as brain image volumes. Spatial indices can be used for spatial queries. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/SpatialIndexDerivation |
| rdfs:label | Spatial Index Derivation |
| Description | The Spatial Index Derivation is the derivation of a spatial index from an entity, such as a detailed circuit. |
| rdfs:subClassOf (2) | prov:Derivationprov:EntityInfluence |
| URI | https://neuroshapes.org/SpatialReferenceSystem |
| rdfs:label | Spatial Reference System |
| rdfs:subClassOf (3) | :CoordinateSystemprov:Entityprov:Location |
| URI | https://neuroshapes.org/Species |
| rdfs:label | NCBI species taxonomy ontology |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/Sphere |
| rdfs:label | Sphere |
| rdfs:subClassOf (2) | :GeometricShapeprov:Entity |
| URI | https://neuroshapes.org/StimulusExperiment |
| rdfs:label | Stimulus Experiment |
| Description | The Stimulus Experiment is an activity describing the experiment in which a particular stimulus, such as a current step, is applied to e.g. a patched cell entity to evoke and record the cell's current or voltage response. |
| rdfs:subClassOf (2) | :ExperimentalActivityprov:Activity |
| URI | https://neuroshapes.org/SubCellularModel |
| rdfs:label | Sub Cellular Model |
| Description | The Subcellualr Model is a model instance describing the subcellular mechanisms of a model neuron, such as ion channel mechanisms. |
| rdfs:subClassOf (2) | :ModelInstanceprov:Entity |
| URI | https://neuroshapes.org/SubCellularModelScript |
| rdfs:label | Sub Cellular Model Script |
| Description | The Sub-Cellular Model Script is an entity describing scripts used to model sub-cellular mechanisms such as ionic currents across a membrane. |
| rdfs:subClassOf (2) | :ModelScriptprov:Entity |
| URI | https://neuroshapes.org/Subject |
| rdfs:label | Subject |
| Description | The Subject is a biological entity which was used for an experiment or which participated in a scientific study. A subject is typically a person or an animal. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/SubjectCollection |
| rdfs:label | Subject Collection |
| rdfs:subClassOf (2) | prov:Collectionprov:Entity |
| URI | https://neuroshapes.org/SynapseRelease |
| rdfs:label | Synapse Release |
| Description | A Synapse Release is a model release which describes a set of synapse models for further use in the reconstruction and simulation pipeline (in the context of the Blue Brain Project, they are currently identified by a git hash). |
| rdfs:subClassOf (2) | :ModelReleaseprov:Entity |
| URI | https://neuroshapes.org/TableSelector |
| rdfs:label | Table Selector |
| rdfs:subClassOf (2) | :Selectorprov:Location |
| URI | https://neuroshapes.org/Target |
| rdfs:label | Target |
| Description | The Target is an entity which describes an entity which is aimed at by another entity. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/TemplateImageData |
| rdfs:label | Template Image Data |
| Description | The Template Image Data is an image stack or image volume which is used as template in the context of e.g. a brain atlas. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/TemplateReconstruction |
| rdfs:label | Template Reconstruction |
| Description | The Template Reconstruction is an activity which describes the reconstruction of a brain parcellation template volume from template image data. |
| rdfs:subClassOf (1) | prov:Activity |
| URI | https://neuroshapes.org/TemplateVolume |
| rdfs:label | Template Volume |
| Description | The Template Volume is a brain image volume which is used as template in the context of a brain atlas. |
| rdfs:subClassOf (4) | :VolumetricDataLayer:Volume:NdRasterprov:Entity |
| URI | https://neuroshapes.org/TextPositionTarget |
| rdfs:label | Text Position Target |
| rdfs:subClassOf (2) | :AnnotationTargetprov:Entity |
| URI | https://neuroshapes.org/Threshold |
| rdfs:label | Threshold |
| Description | The Threshold is an entity which describes the amount, level or limit on a defined scale. It is used to indicate that something changes when this amount, level or limit is reached. In the context of neuroscience, this can e.g. be the voltage level above which action potentials are evoked in a cell. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/TimeSeries |
| rdfs:label | TimeSeries |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/Trace |
| rdfs:label | Trace |
| Description | The Trace is an entity which describes a variable as a function of time. In the context of neuroscience, this can e.g. be the recorded voltage or current changes across the cell membrane of a patched cell. |
| rdfs:subClassOf (3) | :ElectricalSeries:TimeSeriesprov:Entity |
| URI | https://neuroshapes.org/TraceCollection |
| rdfs:label | Trace Collection |
| Description | The Trace Collection is a collection of traces which may need to be grouped togetherh for further use based on specific selection criteria. |
| rdfs:subClassOf (2) | prov:Collectionprov:Entity |
| URI | https://neuroshapes.org/TraceFeature |
| rdfs:label | Trace Feature |
| Description | The Trace Feature is an entity which describes a particular characteristic of a trace. In the context of neuroscience, this can e.g. be a particular electrical feature extracted from a recorded trace such as the width of a spike at threshold. The eFEL software can be used to extract such electrical trace features: https://github.com/BlueBrain/eFEL. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/TraceFeatureExtraction |
| rdfs:label | Trace Feature Extraction |
| Description | The Trace Feature Extraction is an activity which describes the extraction of a trace feature from a defined collection of traces. The feature extraction can be performed using software tools like eFEL: https://github.com/BlueBrain/eFEL. |
| rdfs:subClassOf (1) | prov:Activity |
| URI | https://neuroshapes.org/TraceGeneration |
| rdfs:label | Trace Generation |
| Description | The Trace Generation is an activity describing the generation of a trace. |
| rdfs:subClassOf (3) | prov:Generationprov:ActivityInfluenceprov:InstantaneousEvent |
| URI | https://neuroshapes.org/Transfection |
| rdfs:label | Transfection |
| Description | The Transfection is an activity which describes the process of deliberately introducing naked or purified nucleic acids into eukaryotic cells. |
| rdfs:subClassOf (2) | :ExperimentalActivityprov:Activity |
| URI | https://neuroshapes.org/Transform |
| rdfs:label | Transform |
| Description | The Transform is an entity which describes a mathematical function. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/TransformableObject |
| rdfs:label | Transformable Object |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/Transformation |
| rdfs:label | Transformation |
| Description | The Transformation is an activity describing the transformation of one transformable object into another. Output and input object of the transformation should have the same type. Examples for transformable objects are images or in the context of neuroscience, neuron morphology reconstructions. |
| rdfs:subClassOf (1) | prov:Activity |
| URI | https://neuroshapes.org/TwoPhotonImageDataLayer |
| rdfs:label | Two Photon Image Data Layer |
| Description | The Two Photon Image Data Layer is an entity relevant in the context of the representation of volumetric data. It describes the data layer containing images acquired using the two-photon imaging method. It belongs to the voxel brain data shape definition. Voxel Brain is an in-house service of the Blue Brain Project which helps to access data already positioned in a volumetric atlas space. |
| rdfs:subClassOf (4) | :VolumetricDataLayer:Volume:NdRasterprov:Entity |
| URI | https://neuroshapes.org/ValidationResult |
| rdfs:label | Validation Result |
| Description | The Validation Result is an entity which describes the result of the validation of e.g. a model instance or a simulation. The validation result can comprise validation data such as scores or figures. |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/VariableReport |
| rdfs:label | Variable Report |
| rdfs:subClassOf (1) | prov:Entity |
| URI | https://neuroshapes.org/Volume |
| rdfs:label | Volume |
| rdfs:subClassOf (2) | :NdRasterprov:Entity |
| URI | https://neuroshapes.org/VolumeImageStack |
| rdfs:label | VolumeImageStack |
| rdfs:subClassOf (3) | :Volume:NdRasterprov:Entity |
| URI | https://neuroshapes.org/VolumeParcellation |
| rdfs:label | VolumeParcellation |
| rdfs:subClassOf (3) | :Volume:NdRasterprov:Entity |
| URI | https://neuroshapes.org/VolumetricDataLayer |
| rdfs:label | Volumetric Data Layer |
| Description | The Volumetric Data Layer is an entity relevant in the context of the representation of volumetric data. It belongs to the voxel brain data shape definition. Voxel Brain is an in-house service of the Blue Brain Project which helps to access data already positioned in a volumetric atlas space. |
| rdfs:subClassOf (3) | :Volume:NdRasterprov:Entity |
| URI | https://neuroshapes.org/WholeBrainImageStack |
| rdfs:label | WholeBrainImageStack |
| rdfs:subClassOf (2) | :ImageStackprov:Entity |
| URI | https://neuroshapes.org/WholeCellPatchClamp |
| rdfs:label | Whole Cell Patch Clamp |
| Description | The Whole Cell Patch Clamp is a patch clamp activty describing an experimental method used in electrophysiology to study ionic currents over the membrane of the entire cell. It is primarily used to study excitable cells such as neurons. |
| rdfs:subClassOf (3) | :PatchClamp:ExperimentalActivityprov:Activity |
| URI | http://webprotege.stanford.edu/RDwMWiQQPVCynF3uQT1yeiR |
| rdfs:label | Neuron |
| rdfs:subClassOf (2) | :Cellprov:Entity |
| URI | oa:FragmentSelector |
| rdfs:label | Fragment Selector |
| rdfs:subClassOf (2) | :Selectorprov:Location |
| URI | oa:TextPositionSelector |
| rdfs:label | Text Position Selector |
| rdfs:subClassOf (2) | :Selectorprov:Location |
| URI | http://www.w3.org/ns/prov#Activity |
| rdfs:label | Activity type ontology |
| Description | 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 (https://www.w3.org/TR/prov-o/#Activity) |
| URI | http://www.w3.org/ns/prov#ActivityInfluence |
| rdfs:label | Activity influence |
| Description | It is not recommended that the type ActivityInfluence be asserted without also asserting one of its more specific subclasses. 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. |
| URI | http://www.w3.org/ns/prov#Agent |
| rdfs:label | Agent |
| Description | 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 (https://www.w3.org/TR/prov-o/#Agent). |
| URI | http://www.w3.org/ns/prov#AgentInfluence |
| rdfs:label | Agent influence |
| Description | 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. |
| URI | http://www.w3.org/ns/prov#Association |
| rdfs:label | Association |
| Description | An instance of prov:Association provides additional descriptions about the binary prov:wasAssociatedWith relation from an prov:Activity to some prov:Agent that had some responsiblity for it. For example, :baking prov:wasAssociatedWith :baker; prov:qualifiedAssociation [ a prov:Association; prov:agent :baker; :foo :bar ]. |
| rdfs:subClassOf (1) | prov:AgentInfluence |
| URI | http://www.w3.org/ns/prov#Collection |
| rdfs:label | Collection |
| Description | 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 (https://www.w3.org/TR/prov-o/#Collection). |
| rdfs:subClassOf (1) | prov:Entity |
| URI | http://www.w3.org/ns/prov#Derivation |
| rdfs:label | Derivation |
| Description | 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. |
| rdfs:subClassOf (1) | prov:EntityInfluence |
| URI | http://www.w3.org/ns/prov#EmptyCollection |
| rdfs:label | Empty Collection |
| Description | An empty collection is a collection without members (https://www.w3.org/TR/prov-o/#EmptyCollection). |
| rdfs:subClassOf (1) | prov:Entity |
| URI | http://www.w3.org/ns/prov#Entity |
| rdfs:label | Entity |
| Description | An entity is a physical, digital, conceptual, or other kind of thing with some fixed aspects; entities may be real or imaginary (https://www.w3.org/TR/prov-o/#Entity). |
| URI | http://www.w3.org/ns/prov#EntityInfluence |
| rdfs:label | Entity influence |
| Description | 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. |
| URI | http://www.w3.org/ns/prov#Generation |
| rdfs:label | Generation |
| Description | 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 (https://www.w3.org/TR/prov-o/#Generation). |
| rdfs:subClassOf (2) | prov:ActivityInfluenceprov:InstantaneousEvent |
| URI | http://www.w3.org/ns/prov#InstantaneousEvent |
| rdfs:label | Instantaneous event |
| Description | 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. |
| URI | http://www.w3.org/ns/prov#Invalidation |
| rdfs:label | Invalidation |
| Description | 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. |
| rdfs:subClassOf (2) | prov:ActivityInfluenceprov:InstantaneousEvent |
| URI | http://www.w3.org/ns/prov#Location |
| rdfs:label | Location |
| Description | 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. |
| URI | http://www.w3.org/ns/prov#Revision |
| rdfs:label | Entity revision |
| Description | An instance of prov:Revision provides additional descriptions about the binary prov:wasRevisionOf relation from some newer prov:Entity to an earlier prov:Entity. For example, :draft_2 prov:wasRevisionOf :draft_1; prov:qualifiedRevision [ a prov:Revision; prov:entity :draft_1; :foo :bar ]. |
| rdfs:subClassOf (2) | prov:Derivationprov:EntityInfluence |
| URI | http://www.w3.org/ns/prov#SoftwareAgent |
| rdfs:label | Software Agent |
| Description | A software agent is running software (https://www.w3.org/TR/prov-o/#SoftwareAgent). |
| rdfs:subClassOf (1) | prov:Agent |
| URI | http://www.w3.org/ns/prov#Usage |
| rdfs:label | Usage |
| Description | An instance of prov:Usage provides additional descriptions about the binary prov:used relation from some prov:Activity to an prov:Entity that it used. For example, :keynote prov:used :podium; prov:qualifiedUsage [ a prov:Usage; prov:entity :podium; :foo :bar ]. |
| rdfs:subClassOf (2) | prov:EntityInfluenceprov:InstantaneousEvent |
| URI | http://schema.org/DataDownload |
| rdfs:label | Data Download |
| Description | A dataset in downloadable form. |
| URI | http://schema.org/Dataset |
| rdfs:label | Dataset |
| rdfs:subClassOf (1) | prov:Entity |
| URI | http://schema.org/Organization |
| rdfs:label | Organization |
| Description | An organization such as a school, NGO, corporation, club, etc (https://schema.org/Organization). |
| rdfs:subClassOf (1) | prov:Agent |
| URI | http://schema.org/Person |
| rdfs:label | Person |
| Description | A person (alive, dead, undead, or fictional) (https://schema.org/Person). |
| rdfs:subClassOf (1) | prov:Agent |
| URI | http://schema.org/QuantitativeValue |
| rdfs:label | Quantitative Value |
| Description | A point value or interval for product characteristics and other purposes. |
| URI | http://www.w3.org/2004/02/skos/core#ConceptScheme |
| rdfs:label | Concept Scheme |