bluebrain / nexus-bbp-domains

BBP domains specification (schemas, vocabularies)

nexus-bbp-domains

License

The license for all codes in this repository is [Apache 2] (http://www.apache.org/licenses/LICENSE-2.0) while the license for all schemas and data is CC-BY-4.0

Funding & Acknowledgements

The development of this project was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology.

COPYRIGHT (c) 2017–2021 Blue Brain Project/EPFL

nexus-bbp-domains's Issues

Set Creative Commons Corporation Attribution 4.0 International as LICENSE

Since the workbench is now externalised (see #53 ) then there is no Scala code in this repository. The Apache 2 license can be removed and replaced by the Creative Commons Corporation Attribution 4.0 International LICENSE.

Replace "NeuronTracing" with "Reconstruction" activity in prov template

Reconstruction from imageStack and reconstruction from slice should be aligned by using the same activity naming.

Add patchedCellCollection schema to experiment module

Add neurontracing from imagestack provenance template

Add PatchedCell schema to experiment module

Missing protocol entity in Reconstruction activity

A protocol entity is missing for the Reconstruction activity in the file nexus-bbp-domains/docs/src/main/paradox/assets/provtemplates/morphology-reconstruction-prov-template.svg

Describe download information for data attached to an instance

How data download information can be described:

• a download link
• metadata about the content: size, digest, mediaType
• where the data is stored ?

Add slice schema to experiment module

Add morphology reconstruction provenance template

Initialize electrophysiology module

• Create a sbt module named bbp-electrophysiology
• Update the build.sbt file to take into account the created module
• Initialize the module with license information

Create bbp domain core schemas

Core schemas are schemas to be reused by other bbp domains like atlas, ephors and morphology.

Here are some examples:

• activity (extends the prov activity schema defined in nexus-prov)
• entity
• collection
• vector3d
• ...

Initialized bbp atlas domain schemas

• Schema creation
• tests

Initialize BBP core, atlas and experiment domains

Include a workbench to initialise the tests

Initialized bbp experiment domain schemas

The bbp experiment domain needs to be initialised with schemas reused by the atlas, ephys and morphology domains:

• protocol
• subject collection

Add stimulusExperiment schema to electrophysiology module

new relation QualifiedGeneration

There is a QualifiedAssociation, a QualifiedUsage but no QualifiedGeneration.
For instance a software execution returns multiple artefacts of the same kind. I want to be able to distinguish them. (That is a simular concept to the name of an output parameter in a function).

Add the fixedStainedSlice schema to the morphology module

new QualifiedIsPartOf relationship

We need a relation between activities describing that an activity is a subactivity of another activity.
There is a IsPartOf Relationship:
We want a qualified relationship so that we can distinguish the multiple subactivity. The qualification applies to the relationship not on the activity itself.

example: project "nexus 2017" is an activity that has a "specification" activity, "development" activity, "test" activity and finally "maintenance" activity.

Initialise bbp core vocabulary

Create a model for storing a provenance template

We need a way to represent a provenance template so that it can be stored in nexus-kg and accessible through search. The chosen model should enable:

• the retrieval of a template that can be used to describe the provenance of an entity of a given type
• the comparison between a provenance template and the actual provenance description of a given entity.

Create a folder to store the provenance templates for the different bbp domains

Add wholeCellPatchClamp schema to experiment module

Add patchedslice schema to experiment module

Add the acquisitionAnnotation schema to the morphology module

Add the reconstruction and reconstructedCell schemas to the morphology module

Initialized nexus-kg schemas

The BBP domain schemas depends on nexus-kg schemas through schema imports (for person, organization and software agent). So those schemas need to be available in the class path in order to be resolved by the workbench when they are imported.

Add wholecellpatchclamp-recording-prov-template figure

Add figure showing entities, activites, agents and relations of the whole-cell patch clamp recording provenance template.

Fix file location of wrong-type instance of patchedSlice

file location at same level as version folder, should be inside version folder

Initialize domains documentation

Create a minimal documentation structure for the different domains in blue brain using "com.lightbend.paradox" sbt plugin

Reuse the sbt-nexus-workbench plugin

Currently a local workbench scala module is being used to run schemas' tests. As the new sbt-nexus-workbench is published, we need to reuse it and remove the local module.

Update workbench to 0.2.0

Add 'wasGeneratedBy' shape to trace schema

'wasGeneratedBy' property shape with class StimulusExperiment is missing from trace schema

Add subject schema to experiment module

Fix type prefix in brainSlicing schema

• targetClass should be nsg:BrainSlicing

Add brainSlicing schema to experiment module

Use rdfs:label to add a human readable description for bbp/core/activity schema

Currently bbp/core/activity schema uses "sh:description" to add label on the local this:ActivityShape.
rdfs:label should be used.

Initialize vocabs, mappings and docs

Add the annotatedSlice schema to the morphology module

Initialise BBP simulation domain

Create a scala module for the BBP simulation domain.

Create a brain location shacl schema

A shape for describing location of cell in a brain atlas or in a given slice.
The location can be qualitative like brain region, layer and/or spatial like coordinates.
In case of coordinates a spatialReferenceSystem should be present.

Update bbp/core/activity schema to normalize role value across bbp domains

Currently the nexus/prov/activity schema requires any hadRole value to be a valid IRI. In addition, we need to enforce that all hadRole values across bbp domains need to conform to bbp/core/typedlabeledontologyterm/RoleOntologyTermShape (with a mandatory label).

The following node shape needs to be added in bbp/core/activity:

{
"@id": "this:HadRoleValueShape",
"@type": "sh:NodeShape",
"targetObjectsOf": "prov:hadRole",
"label": "The value of prov:hadRole should conform to bbp/core/typedlabeledontologyterm/RoleOntologyTermShape",
"node": "{{base}}/data/bbp/core/typedlabeledontologyterm/RoleOntologyTermShape"
}

Add the fixedStainMount schema to the morphology module

Add terminology for the the morphology module in neurosciencegraph and typedlabeledontologyterm files

Create bounding box schema for atlas

Add traceGeneration schema to electrophysiology module

Add atlas registration provenance template

Use sbt-nexus for driving the build / publish tasks

Add transform morphology to atlas space prov template

Add morphology module to root aggregate in build file

Initialize morphology module

• Create a sbt module named bbp-morphology
• Update the build.sbt file to take into account the created module
• Initialize the module with license information