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README.md

@@ -1,29 +1,14 @@
-# operando catalysis (meta)data schema
+# HZB (meta)data schema: operando catalysis
 
 (Meta)data schema for operando catalysis: A datamodel for describing entities and their semantic associations (vocabularies/ontologies) for scientific (particularly catalytic) data at HZB, particularly for operando and in situ characterization of catalytic materials.
 
 At the moment, this schema is organized into 2 separate modules:
-* energy definitions (lab-based)
-* matter definitions (synchrotron-based)
+* catlabs definitions (catalysis lab-based)
+* BESSY definitions (synchrotron-based)
+* operandoCatalysis definitions (catalysis + synchrotron-based)
+* core (common)
 
-# Basic content for our yml schema definitions:
-* names, identifiers, and metadata
-  * id – the unique identifier for the schema, as a IRI
-  * name – the schema name. Use only alphanumeric characters, underscores, and dashes
-  * description – a summary of the schema. Can include markdown formatting
-  * license – CC0 recommended (I put MIT just to have something now, has to be changed)
-* modules
-  * imports – allows for modular development. See imports
-* prefix management
-  * prefixes – A map of prefixes. See prefixes
-  * default_prefixes – The prefix used for all elements in this schema
-  * default_curi_maps – prefix maps from prefixcommons
-* other
-  * default_range – The default range for all slots
-
-See also uris-and-mappings: https://linkml.io/linkml/schemas/models.html 
-
-# Mappings to: 
+### Mappings to: 
 * voc4cat
 * Chemical Entities Mixtures and Reactions Ontological Framework
 * NeXus definitions?? -
@@ -57,45 +42,3 @@ Use the `make` command to generate project artefacts:
 
 This project was made with
 [linkml-project-cookiecutter](https://github.com/linkml/linkml-project-cookiecutter).
-
-
-
-
-# Conventions and notes
-ATM following the same conventions a Biolink. In Biolink Model YAML any class, slot, or type is defined in `sentence case`  form. When this model is compiled to various forms (like JSON-Schema, OWL, Markdown) the representation is based on the following convention:
-
-- classes are named in `CamelCase`  form
-- slots are named in `snake_case` form
-- types are named in `snake_case` form
-
-At a glance the structure is as follows,
-- Classes
-
-  - Entities
-  - Associations
-  - Mixins
-- Slots
-  - Predicates
-  - Node Properties
-  - Edge Properties
-- Types
-
-A `class` represents an entity or an association. A class can have one more `slots` (properties). Within the Biolink Model there are two hierarchies of classes: `Named Things` and `Associations`; Named Things are disjoint from Associations. They do share a common ancestor class: `entity`.
-
-`Named Things`: classes that represent real world entities such as genes, diseases, chemical substances, etc. In a graph serialization, 'Named Things' are represented by nodes in a graph. Each class in the named thing has one or more slots (properties). The root of the "Named Things" hierarchy is the biolink:NamedThing class.
-
-`Associations`: classes that represent an assertion or statement. In RDF sense, an association is an `rdf:Statement`. In a graph formalism, associations are represented using edges in a graph. In general, Associations have three main properties (or slots): subject: the subject of the association; predicate: the predicate or relationship between the subject and the object of the association; object: the object of the association These three properties (or slots) define what Biolink calls a "core triple".
-
-A `slot` is similar to `rdf:Property` where it can link: i) an instance of a class to another instance of a class; ii) an instance of a class to a literal/data type. slot_usage slot can be used to specify how a particular slot ought to be used in a class.
-
-The `mixin:true` setting is used to extend the properties (or slots) of a class, without changing its position in the class hierarchy. Mixins can be extremely helpful in a number of ways: 1) to generalize a set of attributes that can apply to classes in different parts of the class hierarchy, 2) reduce duplication of shared attributes between classes that do not inherit from one another.
-
-The `aliases` slot can be used to define a list of aliases for a Model class (or slot). This is useful for adding synonymous names to your class (or slot).
-
-
-The `slot_uri` slot can be used to define a canonical URI that is the true representation for that particular slot. That is, the value of slot_uri can be used interchangeably with the slot being defined.
-
-`id_prefixes` slot can be used to define a list of valid ID prefixes that instances of this class ought to have as part of their CURIE. The order of the list matters since its a prioritized list with the ID prefix with the highest priority appearing at the top of the list.
-
-Please check more details here: https://github.com/biolink/biolink-model/blob/master/src/docs/understanding-the-model.md 
-

project/graphql/hzb_metadata_schema.graphql

@@ -1,43 +1,274 @@
 # metamodel_version: 1.7.0
-type CatalysisSample
+type Beamline
+  {
+    id: Uriorcurie!
+    iri: String
+    name: String
+    category: String!
+  }
+
+type BeamlineExperiment
   {
+    id: Uriorcurie!
+    iri: String
+    name: String
+    category: String!
+  }
+
+type BeamlineScientist
+  {
+    id: Uriorcurie!
+    iri: String
+    name: String
     category: String!
     primaryEmail: String
     birthDate: Date
     ageInYears: Integer
-    vitalStatus: PersonStatus
-    sampleEnvironment: String
+    gender: GenderEnum
+    hasEmploymentHistory: [String]
+  }
+
+type CatalysisSample
+  {
+    id: Uriorcurie!
+    iri: String
+    name: String
+    category: String!
+  }
+
+type CatalysisSampleCollection
+  {
+    entries: [CatalysisSample]
+  }
+
+type Catalyst
+  {
+    id: Uriorcurie!
+    iri: String
+    name: String
+    category: String!
   }
 
 interface ChemicalOrDrugOrTreatment
   {
   }
 
+type DataCite
+  {
+    id: Uriorcurie!
+    iri: String
+    name: String
+    category: String!
+  }
+
 type Device
   {
+    id: Uriorcurie!
+    iri: String
+    name: String
+    category: String!
+  }
+
+type EMILOAESE
+  {
+    id: Uriorcurie!
+    iri: String
+    name: String
+    category: String!
+  }
+
+type EMILPink
+  {
+    id: Uriorcurie!
+    iri: String
+    name: String
     category: String!
   }
 
 interface Entity
   {
+    id: Uriorcurie!
+    iri: String
+    name: String
   }
 
-type NamedThing
+type Experiment
   {
+    id: Uriorcurie!
+    iri: String
+    name: String
     category: String!
   }
 
-type Sample
+type Measurement
+  {
+    id: Uriorcurie!
+    iri: String
+    name: String
+    category: String!
+  }
+
+type Mixture
+  {
+    id: Uriorcurie!
+    iri: String
+    name: String
+    category: String!
+  }
+
+type MySpot
+  {
+    id: Uriorcurie!
+    iri: String
+    name: String
+    category: String!
+  }
+
+type NamedEntity
+  {
+    id: Uriorcurie!
+    iri: String
+    name: String
+    category: String!
+  }
+
+type Parameter
   {
+    id: Uriorcurie!
+    iri: String
+    name: String
+    category: String!
+  }
+
+type Person
+  {
+    id: Uriorcurie!
+    iri: String
+    name: String
     category: String!
     primaryEmail: String
     birthDate: Date
     ageInYears: Integer
-    vitalStatus: PersonStatus
+    gender: GenderEnum
+    hasEmploymentHistory: [String]
+  }
+
+type PowderCatalyst
+  {
+    id: Uriorcurie!
+    iri: String
+    name: String
+    category: String!
+  }
+
+type Process
+  {
+    id: Uriorcurie!
+    iri: String
+    name: String
+    category: String!
+  }
+
+type Project
+  {
+    id: Uriorcurie!
+    iri: String
+    name: String
+    category: String!
+  }
+
+type Reaction
+  {
+    id: Uriorcurie!
+    iri: String
+    name: String
+    category: String!
+  }
+
+type ReactionProduct
+  {
+    id: Uriorcurie!
+    iri: String
+    name: String
+    category: String!
+  }
+
+type ReactionProductCollection
+  {
+    entries: [ReactionProduct]
+  }
+
+type Reactor
+  {
+    id: Uriorcurie!
+    iri: String
+    name: String
+    category: String!
+  }
+
+type Recipe
+  {
+    id: Uriorcurie!
+    iri: String
+    name: String
+    category: String!
+  }
+
+type Sample
+  {
+    id: Uriorcurie!
+    iri: String
+    name: String
+    category: String!
   }
 
 type SampleCollection
   {
     entries: [Sample]
   }
 
+type SampleEnvironment
+  {
+    id: Uriorcurie!
+    iri: String
+    name: String
+    category: String!
+  }
+
+type SamplePositioning
+  {
+    id: Uriorcurie!
+    iri: String
+    name: String
+    category: String!
+  }
+
+type Scientist
+  {
+    id: Uriorcurie!
+    iri: String
+    name: String
+    category: String!
+    primaryEmail: String
+    birthDate: Date
+    ageInYears: Integer
+    gender: GenderEnum
+    hasEmploymentHistory: [String]
+  }
+
+type ThinFilmCatalyst
+  {
+    id: Uriorcurie!
+    iri: String
+    name: String
+    category: String!
+  }
+
+type Workflow
+  {
+    id: Uriorcurie!
+    iri: String
+    name: String
+    category: String!
+  }
+