Makefile

@@ -17,6 +17,7 @@ build/linkml-docs: \
 	build/linkml-docs/s/base/unreleased \
 	build/linkml-docs/s/flat-base/unreleased \
 	build/linkml-docs/s/flat-users/unreleased \
+	build/linkml-docs/s/flat-data/unreleased \
 	build/linkml-docs/s/simpleinput/unreleased
 build/linkml-docs/s/%: src/%.yaml src/%/extra-docs
 	$(MAKE) imports-remote
@@ -63,6 +64,7 @@ check-models: \
 	checkmodel/base/unreleased \
 	checkmodel/flat-base/unreleased \
 	checkmodel/flat-users/unreleased \
+	checkmodel/flat-data/unreleased \
 	checkmodel/simpleinput/unreleased
 checkmodel/%: src/%.yaml
 	@echo [Check $<]
@@ -97,6 +99,8 @@ check-validation: \
 	checkvalidation/flat-base/unreleased \
 	convertexamples/flat-users/unreleased \
 	checkvalidation/flat-users/unreleased \
+	convertexamples/flat-data/unreleased \
+	checkvalidation/flat-data/unreleased \
 	convertexamples/simpleinput/unreleased \
 	checkvalidation/simpleinput/unreleased
 checkvalidation/%:
@@ -116,6 +120,7 @@ convert-examples: \
 	convertexamples/base/unreleased \
 	convertexamples/flat-base/unreleased \
 	convertexamples/flat-users/unreleased \
+	convertexamples/flat-data/unreleased \
 	convertexamples/simpleinput/unreleased
 convertexamples/%: src/%.yaml src/%/examples
 	# loop over all examples, skip the schema file itself

extra-docs/index.md

@@ -7,13 +7,14 @@ ALL CONTENT HERE IS UNRELEASED AND MAY CHANGE ANY TIME
 
 ## Schemas
 
-The schemas below are used in different components of the metadata system.
+The schemas below represent aspect models that are used in different components
-They jointly build on the [DataLad concepts](https://concepts.datalad.org)
+of the metadata system.  They jointly build on the [DataLad
-schema toolbox.
+concepts](https://concepts.datalad.org) schema toolbox.
 
 - [Base schema](s/base/unreleased/index.md)
 - [Flat base schema](s/flat-base/unreleased/index.md)
 - [Flat users schema](s/flat-users/unreleased/index.md)
+- [Flat data schema](s/flat-data/unreleased/index.md)
 - [Simple input (deprecated)](s/simpleinput/unreleased/index.md)
 
 

mkdocs.yml

@@ -7,6 +7,7 @@ nav:
     - Base (unreleased): s/base/unreleased/index.md
     - Flat base (unreleased): s/flat-base/unreleased/index.md
     - Flat users (unreleased): s/flat-users/unreleased/index.md
+    - Flat study (unreleased): s/flat-data/unreleased/index.md
     - Simple input (deprecated): s/simpleinput/unreleased/index.md
 plugins:
   - mermaid2
@@ -18,6 +19,7 @@ plugins:
           's/base/index.md': 's/base/unreleased/index.md'
           's/flat-base/index.md': 's/flat-base/unreleased/index.md'
           's/flat-users/index.md': 's/flat-users/unreleased/index.md'
+          's/flat-data/index.md': 's/flat-data/unreleased/index.md'
           's/simpleinput/index.md': 's/simpleinput/unreleased/index.md'
   - search
 site_author: PsyInf group at INM-7

src/flat-data/unreleased.yaml

@@ -0,0 +1,286 @@
+id: https://concepts.inm7.de/s/flat-data/unreleased
+name: inm7-flat-data-schema
+version: UNRELEASED
+status: eunal:concept-status/DRAFT
+title: Data models for INM7 study-related concepts for data discovery
+description: |
+  The classes and slots in this schema support modeling ...
+
+  More information may be available on the schema's [about page](about).
+
+  The schema definition is available as
+
+  - [JSON-LD context](../unreleased.jsonld)
+  - [LinkML YAML](../unreleased.yaml)
+  - [OWL TTL](../unreleased.owl.ttl)
+  - [SHACL TTL](../unreleased.shacl.ttl)
+
+comments:
+  - ALL CONTENT HERE IS UNRELEASED AND MAY CHANGE ANY TIME
+
+license: CC-BY-4.0
+
+prefixes:
+  ADMS: http://www.w3.org/ns/adms#
+  dash: http://datashapes.org/dash#
+  dcterms: http://purl.org/dc/terms/
+  dlidentifiers: https://concepts.datalad.org/s/identifiers/unreleased/
+  dlschemas: https://concepts.datalad.org/s/
+  dlthings: https://concepts.datalad.org/s/things/v1/
+  dltypes: https://concepts.datalad.org/s/types/unreleased/
+  eunal: http://publications.europa.eu/resource/authority/
+  inm7schemas: https://concepts.inm7.de/s/
+  inm7fb: https://concepts.inm7.de/s/flat-base/unreleased/
+  inm7fs: https://concepts.inm7.de/s/flat-data/unreleased/
+  inm7: https://inm7.de/ns/
+  inm7usrmgt: https://inm7.de/ns/usrmgt/
+  linkml: https://w3id.org/linkml/
+  orcid: https://orcid.org/
+  owl: http://www.w3.org/2002/07/owl#
+  rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
+  rdfs: http://www.w3.org/2000/01/rdf-schema#
+  sh: http://www.w3.org/ns/shacl#
+  skos: http://www.w3.org/2004/02/skos/core#
+  spdx: http://spdx.org/rdf/terms#
+  w3ctr: https://www.w3.org/TR/
+  xsd: http://www.w3.org/2001/XMLSchema#
+
+default_prefix: inm7fs
+
+emit_prefixes:
+  - dlidentifiers
+  - dlthings
+  - dltypes
+  - inm7
+  - inm7fb
+  - inm7fs
+  - rdf
+  - rdfs
+  - skos
+  - xsd
+
+imports:
+  - inm7schemas:flat-base/unreleased
+
+slots:
+  conforms_to:
+    description: >-
+      An established standard to which the subject conforms.
+    range: Thing
+    comments:
+      - This property SHOULD be used to indicate a model, schema, ontology, view or profile that the subject conforms to.
+    exact_mappings:
+      - dcterms:conformsTo
+
+  dimensions:
+    description: >-
+      Associated outcome variables.
+    range: Dimension
+    multivalued: true
+
+  distributions:
+    description: >-
+      Available distributions of the dataset or data item.
+    multivalued: true
+    range: Distribution
+    exact_mappings:
+      - dcat:distribution
+    broad_mappings:
+      - sio:SIO_000341
+
+  factors:
+    description: >-
+      Influencing factors.
+    range: Factor
+    multivalued: true
+
+  factor_level_of:
+    description: >-
+      A factor the subject is a (sub)level of.
+    range: Factor
+
+  instruments:
+    description: >-
+      Employed instruments.
+    range: Instrument
+    multivalued: true
+
+  subject_type:
+    description: >-
+      A classifier that identifies the nature/type of a subject.
+      For specimen (a subject derived/taken from another subject),
+      this classifier should be more precise than the classifier
+      of the source subject.
+    range: SubjectType
+
+  protocols:
+    description: >-
+      Implemented protocols.
+    range: Protocol
+    multivalued: true
+
+  specimen_of:
+    description: >-
+      Source subject.
+    range: Subject
+
+  study:
+    description: >-
+      Study context.
+    range: Study
+
+  subjects:
+    description: >-
+      Studied subjects.
+    range: Subject
+    multivalued: true
+
+
+classes:
+  Dataset:
+    is_a: Thing
+    mixins:
+      - CurationAid
+    description: >-
+      A collection of data, published or curated by a single agent. This is a
+      conceptual entity. A single dataset might be available in more than
+      one representation, with differing schematic layouts, formats, and
+      serializations.
+    slots:
+      - conforms_to
+      - name
+      - short_name
+
+  DataItem:
+    is_a: Thing
+    mixins:
+      - CurationAid
+    description: >-
+      A single data item, the building block of Datasets. This is a
+      conceptual entity. A DataItem might be available in more than
+      one representation, with differing formats, and serializations.
+    slots:
+      - distributions
+      - dimensions
+
+
+  Distribution:
+    is_a: Thing
+    description: >-
+      A specific representation of a resource, which may come in the form of
+      a physical object, or an electronic file, or an archive or directory
+      of many files, may be standalone or part of a larger collection.
+
+  Dimension:
+    is_a: Thing
+    mixins:
+      - CurationAid
+    description: >-
+      A dependent or outcome variable.
+    slots:
+      - name
+      - short_name
+
+  Factor:
+    is_a: Thing
+    mixins:
+      - CurationAid
+    description: >-
+      A tag associated with a categorical, independent variable in a study
+      design. Factors can have an investigative role (e.g., treatments), or
+      have an organizational nature (e.g., site labels).
+    slots:
+      - name
+      - factor_level_of
+      - short_name
+    comments:
+      - The relationship of a factor "level" with the broader factor can be
+        described via `broader_mappings`.
+
+  Instrument:
+    is_a: Thing
+    mixins:
+      - CurationAid
+    description: >-
+      A material entity that is designed to perform a function in a scientific
+      investigation, but is not a reagent.
+    slots:
+      - name
+      - short_name
+    exact_mappings:
+      - obo:OBI_0000968
+
+  Protocol:
+    is_a: Thing
+    mixins:
+      - CurationAid
+    description: >-
+      A plan specification which has sufficient level of detail and
+      quantitative information to communicate it between investigation
+      agents, so that different investigation agents will reliably be
+      able to independently reproduce the process.
+    slots:
+      - name
+      - short_name
+    exact_mappings:
+      - obo:OBI_0000272
+
+  Study:
+    is_a: Thing
+    mixins:
+      - CurationAid
+    description: >-
+      TODO
+    slots:
+      # focus on "design" aspects.
+      # leave out incremental items, such as a growing list of
+      # subjects or procedures. These are move efficiently
+      # reported by submitting new records that reference
+      # a study, vs updating a study record multiple times.
+      - dimensions
+      - factors
+      - instruments
+      - protocols
+      - name
+      - short_name
+
+  StudyActivity:
+    is_a: Thing
+    mixins:
+      - CurationAid
+    description: >-
+      An activity in the context of a study, where one or more subjects
+      are studied under the influence of certain factors, with one or
+      more instruments, following a set of protocols 
+    slots:
+      - factors
+      - instruments
+      - protocols
+      - study
+      - subjects
+
+  Subject:
+    is_a: Thing
+    mixins:
+      - CurationAid
+    description: >-
+      A subject is an entity being investigated in a study. This is a
+      contextual entity. One and the same entity can be different
+      subjects in two different studies.
+    slots:
+      - name
+      - specimen_of
+      - study
+      - subject_type
+    slot_usage:
+      specimen_of:
+        range: Subject
+
+  SubjectType:
+    is_a: Thing
+    mixins:
+      - CurationAid
+    description: >-
+      Classifier for the nature of a subject.
+    slots:
+      - name

src/flat-data/unreleased/examples/Study-1.json

@@ -0,0 +1,75 @@
+{
+  "pid": "inm7:study/demo",
+  "relations": {
+    "inm7:dim/age": {
+      "pid": "inm7:dim/age",
+      "description": "How long something has existed; elapsed time since birth.",
+      "exact_mappings": [
+        "obo:NCIT_C25150"
+      ],
+      "schema_type": "inm7fs:Dimension",
+      "name": "Age"
+    },
+    "inm7:fac/site": {
+      "pid": "inm7:fac/site",
+      "schema_type": "inm7fs:Factor",
+      "name": "Site"
+    },
+    "inm7:fac/site/fzj": {
+      "pid": "inm7:fac/site/fzj",
+      "schema_type": "inm7fs:Factor",
+      "name": "FZJ Campus",
+      "factor_level_of": "inm7:fac/site"
+    },
+    "inm7:inst/q1": {
+      "pid": "inm7:inst/q1",
+      "schema_type": "inm7fs:Instrument",
+      "name": "Custom questionnaire for subject demographics"
+    },
+    "inm7:prot/demographics-v1": {
+      "pid": "inm7:prot/demographics-v1",
+      "schema_type": "inm7fs:Protocol",
+      "name": "INM7 SOP for gathering demographic information"
+    },
+    "inm7:sub/hgd54732": {
+      "pid": "inm7:sub/hgd54732",
+      "schema_type": "inm7fs:Subject",
+      "name": "HGD54732"
+    },
+    "inm7:studyact/demo/sub1-sess1-demographics": {
+      "pid": "inm7:studyact/demo/sub1-sess1-demographics",
+      "schema_type": "inm7fs:StudyActivity",
+      "factors": [
+        "inm7:fac/site/fzj"
+      ],
+      "instruments": [
+        "inm7:inst/q1"
+      ],
+      "protocols": [
+        "inm7:prot/demographics-v1"
+      ],
+      "study": "inm7:study/demo",
+      "subjects": [
+        "inm7:sub/hgd54732"
+      ]
+    }
+  },
+  "description": "",
+  "schema_type": "inm7fs:Study",
+  "dimensions": [
+    "inm7:dim/age"
+  ],
+  "factors": [
+    "inm7:fac/site",
+    "inm7:fac/site/fzj"
+  ],
+  "instruments": [
+    "inm7:inst/q1"
+  ],
+  "protocols": [
+    "inm7:prot/demographics-v1"
+  ],
+  "name": "Demo study",
+  "short_name": "demo",
+  "@type": "Study"
+}

src/flat-data/unreleased/examples/Study-1.yaml

@@ -0,0 +1,49 @@
+pid: inm7:study/demo
+name: Demo study
+short_name: demo
+description: >-
+  
+relations:
+  inm7:dim/age:
+    schema_type: inm7fs:Dimension
+    name: Age
+    description: >-
+      How long something has existed; elapsed time since birth.
+    exact_mappings:
+      - obo:NCIT_C25150
+  inm7:fac/site:
+    schema_type: inm7fs:Factor
+    name: Site
+  inm7:fac/site/fzj:
+    schema_type: inm7fs:Factor
+    name: FZJ Campus
+    factor_level_of: inm7:fac/site
+  inm7:inst/q1:
+    schema_type: inm7fs:Instrument
+    name: Custom questionnaire for subject demographics
+  inm7:prot/demographics-v1:
+    schema_type: inm7fs:Protocol
+    name: INM7 SOP for gathering demographic information
+  inm7:sub/hgd54732:
+    schema_type: inm7fs:Subject
+    name: HGD54732
+  inm7:studyact/demo/sub1-sess1-demographics:
+    schema_type: inm7fs:StudyActivity
+    study: inm7:study/demo
+    factors:
+      - inm7:fac/site/fzj
+    instruments:
+      - inm7:inst/q1
+    protocols:
+      - inm7:prot/demographics-v1
+    subjects:
+      - inm7:sub/hgd54732
+dimensions:
+  - inm7:dim/age
+factors:
+  - inm7:fac/site
+  - inm7:fac/site/fzj
+instruments:
+  - inm7:inst/q1
+protocols:
+  - inm7:prot/demographics-v1

src/flat-data/unreleased/validation/Study.valid.cfg.yaml

@@ -0,0 +1,9 @@
+schema: src/flat-data/unreleased.yaml
+target_class: Study
+data_sources:
+  - src/flat-data/unreleased/examples/Study-1.yaml
+plugins:
+  JsonschemaValidationPlugin:
+    closed: true
+    include_range_class_descendants: false
+  RecommendedSlotsPlugin: