Initialize Literature Annotation domain model #192
Conversation
ghost
added
the
|
@apdavison
|
|
v0.2.0 adds the The goal was to have feedback first but it was needed to add this to make the data findable in Nexus. |
| "@id": "AnnotationShape", | ||
| "@type": "sh:NodeShape", | ||
| "nodeKind": "sh:BlankNodeOrIRI", | ||
| "class": "oa:Annotation", |
There was a problem hiding this comment.
should we replace this with a comment? Or add a comment to point out that we capture the oa:Annotation description in these shapes? Also, can "sh:class" be used outside property shapes? @MFSY
There was a problem hiding this comment.
I did it to so that oa:Annotation is in @typefor all instances using directly or indirectly AnnotationShape.
| { | ||
| "path": "oa:hasTarget", | ||
| "name": "Target", | ||
| "description": "The relationship between an Annotation and its Target.", |
There was a problem hiding this comment.
Maybe provide description in sentence case (i.e. annotation and target lower case) @MFSY
| { | ||
| "path": "oa:hasBody", | ||
| "name": "Body", | ||
| "description": "The relationship between an Annotation and its Body.", |
There was a problem hiding this comment.
annotation and body lower case?
| "@id": "TargetShape", | ||
| "@type": "sh:NodeShape", | ||
| "nodeKind": "sh:BlankNodeOrIRI" | ||
| }, |
There was a problem hiding this comment.
Is this shape necessary since there are no property shapes defined in it?
There was a problem hiding this comment.
I did it to make explicit the specialization by SelectorTargetShape as the latter is not the only kind of oa:hasTarget. Besides I did it because I wanted to have a shape for this property in the generic nsg:AnnotationShape.
| "@id": "BodyShape", | ||
| "@type": "sh:NodeShape", | ||
| "nodeKind": "sh:BlankNodeOrIRI" | ||
| }, |
There was a problem hiding this comment.
Is this shape necessary since there are no property shapes defined in it?
There was a problem hiding this comment.
Same as nsg:TargetShape.
| "minCount": 1 | ||
| } | ||
| ] | ||
| } |
There was a problem hiding this comment.
Instead of creating the ContributionShape here, the existing agent shape https://github.com/INCF/neuroshapes/blob/master/modules/core/src/main/resources/schemas/neurosciencegraph/core/agent/v0.1.0.json could be used as value of the node "nsg:contribution" in the property shapes of this schema
There was a problem hiding this comment.
I did it to enforce the fact that we want to have IRI of agents so that they come from a defined list, i.e. are not defined in this payload. Besides, the existing shapes for agents are not in a good 'shape':
https://github.com/BlueBrain/nexus-prov/blob/master/modules/prov/src/main/resources/schemas/nexus/provsh/agent/v1.0.0.json
https://github.com/BlueBrain/nexus-prov/blob/master/modules/prov/src/main/resources/schemas/nexus/prov/agent/v1.0.0.json
| "@context": [ | ||
| "{{base}}/contexts/neurosciencegraph/core/schema/v0.2.0", | ||
| { | ||
| "@base": "{{base}}/schemas/neurosciencegraph/commons/selectors/v0.2.0/shapes/" |
There was a problem hiding this comment.
We might want to rename it to commons/selector/v0.2.0 to have it consistent with other schemas (i.e. schema name singular)?
There was a problem hiding this comment.
If I remember correctly, @MFSY said to use the plural form for the ones where I did this. To be confirmed.
| "description": "The class of the Selector.", | ||
| "minCount": 1, | ||
| "maxCount": 1 | ||
| } |
There was a problem hiding this comment.
What is the purpose of this property shape "Selector type"? Aren't you enforcing the type anyways through the "class" key in the individual selector shapes?
There was a problem hiding this comment.
Yes, through the sh:class constraint in the specialised SelectorShapes, an rdf:type is already required. However, I also wanted to have a generic SelectorShape reusable by others and a oa:Selector requires a rdf:type.
| "name": "End offset", | ||
| "description": "The end position of the segment of text. The character is not included within the segment.", | ||
| "datatype": "xsd:integer", | ||
| "minInclusive": 0, |
There was a problem hiding this comment.
Maybe put minInclusive: 1 since the value can never be 0 (because the value is not included in the segment and the oa:start property needs to be less than the oa:end property)
There was a problem hiding this comment.
I agree. I have just done it because this is how it is described in https://www.w3.org/TR/annotation-vocab/#end.
| "maxCount": 1 | ||
| }, | ||
| { | ||
| "path": "dcterms:conformsTo", |
There was a problem hiding this comment.
Maybe add a description?
There was a problem hiding this comment.
I think I need to add it.
| "name": "Quantity type", | ||
| "description": "The type of the measured quantity represented by the variable.", | ||
| "minCount": 1, | ||
| "maxCount": 1 |
There was a problem hiding this comment.
Longer term, this shape should probably re-use the TypedLabeledOntologyTerm schema (https://github.com/INCF/neuroshapes/blob/master/modules/commons/src/main/resources/schemas/neurosciencegraph/commons/typedlabeledontologyterm/v0.1.4.json) with an included OntologyTermShape for the quantity types
There was a problem hiding this comment.
Looks good. To be seen with @MFSY for the specific XyzOntologyTermShape.
| "@context": [ | ||
| "{{base}}/contexts/neurosciencegraph/core/schema/v0.2.0", | ||
| { | ||
| "@base": "{{base}}/schemas/neurosciencegraph/core/selectors/v0.2.0/shapes/" |
There was a problem hiding this comment.
We might want to rename it to core/selector/v0.2.0 to have it consistent with other schemas (i.e. schema name singular)?
There was a problem hiding this comment.
See comment for selectors above.
| "@context": [ | ||
| "{{base}}/contexts/neurosciencegraph/core/schema/v0.2.0", | ||
| { | ||
| "@base": "{{base}}/schemas/neurosciencegraph/commons/variables/v0.2.0/shapes/" |
There was a problem hiding this comment.
We might want to rename it to commons/variable/v0.2.0 to have it consistent with other schemas (i.e. schema name singular)?
There was a problem hiding this comment.
See comment made for selectors.
| "@context": [ | ||
| "{{base}}/contexts/neurosciencegraph/core/schema/v0.2.0", | ||
| { | ||
| "@base": "{{base}}/schemas/neurosciencegraph/core/variables/v0.2.0/shapes/" |
There was a problem hiding this comment.
We might want to rename it to core/variable/v0.2.0 to have it consistent with other schemas (i.e. schema name singular)?
There was a problem hiding this comment.
See comment for selectors above.
| "class": "nsg:AreaTarget" | ||
| } | ||
| ], | ||
| "maxCount": 1 |
There was a problem hiding this comment.
As far as I understood, the Web Annotation Data Model (https://www.w3.org/TR/annotation-model/#bodies-and-targets) specifies, that the minCount for a target is 1 while there is no minCount on the body (see excerpts below). Should the property shape oa:hasTarget hence have a minCount of 1 and the minCount constraint on the oa:hasBody property shape below be removed?
The relationship between an Annotation and its Target.
There must be 1 or more target relationships associated with an Annotation.
The relationship between an Annotation and its Body.
There should be 1 or more body relationships associated with an Annotation but there may be 0.
There was a problem hiding this comment.
oa:hasTarget has already a sh:minCount of 1 because ParameterAnnotationShape is specializing AnnotationShape where there is this constraint.
oa:hasBody has sh:minCount of 1 because it is a ParameterAnnotationShape aso it needs parameters and I wanted to differentiate it from the annotations of facts which are not modeled yet and which have not parameters.
| "@type": "sh:NodeShape", | ||
| "nodeKind": "sh:BlankNodeOrIRI", | ||
| "targetClass": "nsg:PointValueParameter", | ||
| "comment": "Parameter shape for the value(s) of an unidimensional variable (i.e., not establishing a relationship between a dependant and an independent variable).", |
There was a problem hiding this comment.
a unidimensional
|
More general comments:
|
| ] | ||
| } | ||
| ] | ||
| }, |
There was a problem hiding this comment.
Alternatively, AlgebraicValueShape could be modelled like the AgeShape in the subject schema:
{
"@id": "this:AgeShape",
"@type": "sh:NodeShape",
"property": [
{
"path": "nsg:period",
"name": "Period",
"in": [
"Pre-natal",
"Post-natal"
],
"minCount": 1,
"maxCount": 1
},
{
"path": "schema:value",
"name": "Age value",
"node": "{{base}}/schemas/neurosciencegraph/commons/quantitativevalue/v0.1.0/shapes/QuantitativeValueShape",
"minCount": 1,
"maxCount": 1
}
]
}
by extending the QuantitativeValueShape with an nsg:statistic property shape (just like the AgeShape extends the QuantitativeValueShape with the nsg:period property shape).
There was a problem hiding this comment.
QuantitativeValueShape is broader. We might want to use it.
https://github.com/INCF/neuroshapes/blob/master/modules/commons/src/main/resources/schemas/neurosciencegraph/commons/quantitativevalue/v0.1.2.json
- Restricted the domain to annotating entities based on web annotation data model - Used nsg namespace instead of oa for hasTarget, hasBody, hasSource,hasSelector, Annotation - Removed targetClass assertion from all schemas in commons domain - Added a seeAlso links towards the web annotation recommendation - Used schema:value instead of nsg:text and rdf:value - Renamed IndexSelectorShape to DocumentIndexSelectorShape - Directly use DocumentIndexSelectorShape instead of FigureSelectorShape - Removed FigureSelectorShape because it does not add anything new on top of DocumentIndexSelectorShape - Removed EquationSelectorShape - Renamed AreaSelectorShape to DocumentAreaSelectorShape - Renamed selectors schema with annotationselector - Removed @base and use this instead - Removed the different *TargetShape in the core domain - Removed core/EquationTargetShape - Removed selector schema from core domain
Hello,
Here is the first iteration of the Literature Annotation domain model.
It's goal is to achieve #51. It is related to #43 and #49.
Created SHACL shapes are compliant with W3C Web Annotation recommendations.
Known current limitations:
1 - Annotation of facts are not modelled yet. These annotations do not have parameters.
2 - Literature references are not modelled yet. Reason: prioritization and some work has already been done on the subject in #43. TODO: Contribute to @apdavison proposition.
3 - Provenance is not modelled explicitly yet. Implicitly, it is:
hasBody),hasTarget) which describe precisely where the information come from in the literature reference (hasSelector) and which literature reference it is (hasSource).contribution.agent).4 - The NeuroCurator field 'relationship' which describes more precisely on what the measure of a parameter is has not been modelled yet.
5 -
rdf:valueanddcterms:conformsTohas not been added to/contexts/neurosciencegraph/core/data/vx.x.xyet.6 -
schema:unitCodehas been explicitly asked to be used instead ofschema:unitTexteven though values corresponds to the later definition for now.7 - Literature references without DOI or PMID are currently not modelled for the
hasSourceproperty.Known tricky cases:
8 - Should
TargetShapeexists?9 - Should
BodyShapeexists?10 - There is no check at the SHACL level to declare invalid instances with a required property with an empty string as value.