Merge pull request #3 from anak-velazquez/develop

Develop
anak-velazquez · Aug 5, 2024 · ecd3a85 · ecd3a85
2 parents 05c0f6a + 5f22976
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diff --git a/README.md b/README.md
@@ -28,6 +28,44 @@ See also uris-and-mappings: https://linkml.io/linkml/schemas/models.html
 * Chemical Entities Mixtures and Reactions Ontological Framework
 * NeXus definitions?? -
 
+# Conventions
+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 
+
 ## Website
 
 [https://anak-velazquez.github.io/hzb-metadata-schema](https://anak-velazquez.github.io/hzb-metadata-schema)

diff --git a/project/excel/hzb_metadata_schema.xlsx b/project/excel/hzb_metadata_schema.xlsx
diff --git a/project/graphql/hzb_metadata_schema.graphql b/project/graphql/hzb_metadata_schema.graphql
@@ -1,16 +1,35 @@
 # metamodel_version: 1.7.0
+type CatalysisSample
+  {
+    category: String!
+    primaryEmail: String
+    birthDate: Date
+    ageInYears: Integer
+    vitalStatus: PersonStatus
+    sampleEnvironment: String
+  }
+
+interface ChemicalOrDrugOrTreatment
+  {
+  }
+
+type Device
+  {
+    category: String!
+  }
+
+interface Entity
+  {
+  }
+
 type NamedThing
   {
-    id: Uriorcurie!
-    name: String
-    description: String
+    category: String!
   }
 
 type Sample
   {
-    id: Uriorcurie!
-    name: String
-    description: String
+    category: String!
     primaryEmail: String
     birthDate: Date
     ageInYears: Integer

diff --git a/project/jsonld/hzb_metadata_schema.context.jsonld b/project/jsonld/hzb_metadata_schema.context.jsonld
@@ -1,15 +1,24 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2024-07-23T13:57:41",
+      "generation_date": "2024-08-05T15:01:14",
       "source": "hzb_metadata_schema.yaml"
    },
    "@context": {
+      "BFO": "http://example.org/UNKNOWN/BFO/",
+      "CHEBI": "http://example.org/UNKNOWN/CHEBI/",
+      "CHEMBL.COMPOUND": "http://example.org/UNKNOWN/CHEMBL.COMPOUND/",
+      "MAXO": "http://example.org/UNKNOWN/MAXO/",
       "PATO": {
          "@id": "http://purl.obolibrary.org/obo/PATO_",
          "@prefix": true
       },
+      "PUBCHEM.COMPOUND": "http://example.org/UNKNOWN/PUBCHEM.COMPOUND/",
+      "STY": "http://example.org/UNKNOWN/STY/",
+      "UMLSSG": "http://example.org/UNKNOWN/UMLSSG/",
+      "WIKIDATA": "http://example.org/UNKNOWN/WIKIDATA/",
       "biolink": "https://w3id.org/biolink/",
+      "dcid": "http://example.org/UNKNOWN/dcid/",
       "example": "https://example.org/",
       "hzb_metadata_schema": "https://w3id.org/anak-velazquez/hzb-metadata-schema/",
       "linkml": "https://w3id.org/linkml/",
@@ -24,6 +33,12 @@
          "@type": "xsd:date",
          "@id": "schema:birthDate"
       },
+      "sample_environment": {
+         "@id": "sample_environment"
+      },
+      "category": {
+         "@id": "category"
+      },
       "description": {
          "@id": "schema:description"
       },
@@ -47,8 +62,20 @@
          },
          "@id": "vital_status"
       },
+      "CatalysisSample": {
+         "@id": "CatalysisSample"
+      },
+      "ChemicalOrDrugOrTreatment": {
+         "@id": "ChemicalOrDrugOrTreatment"
+      },
+      "Device": {
+         "@id": "Device"
+      },
+      "Entity": {
+         "@id": "Entity"
+      },
       "NamedThing": {
-         "@id": "schema:Thing"
+         "@id": "NamedThing"
       },
       "Sample": {
          "@id": "Sample"

diff --git a/project/jsonld/hzb_metadata_schema.jsonld b/project/jsonld/hzb_metadata_schema.jsonld
@@ -39,6 +39,18 @@
   "default_prefix": "hzb_metadata_schema",
   "default_range": "string",
   "types": [
+    {
+      "name": "chemical_formula_value",
+      "definition_uri": "https://w3id.org/anak-velazquez/hzb-metadata-schema/ChemicalFormulaValue",
+      "description": "A chemical formula",
+      "notes": [
+        "Should be implemented as a stronger type"
+      ],
+      "from_schema": "https://w3id.org/anak-velazquez/hzb-metadata-schema",
+      "base": "str",
+      "uri": "http://www.w3.org/2001/XMLSchema#string",
+      "@type": "TypeDefinition"
+    },
     {
       "name": "string",
       "definition_uri": "https://w3id.org/linkml/String",
@@ -385,10 +397,6 @@
       ],
       "slot_uri": "http://schema.org/identifier",
       "identifier": true,
-      "owner": "NamedThing",
-      "domain_of": [
-        "NamedThing"
-      ],
       "range": "uriorcurie",
       "required": true,
       "@type": "SlotDefinition"
@@ -402,10 +410,6 @@
         "http://schema.org/name"
       ],
       "slot_uri": "http://schema.org/name",
-      "owner": "NamedThing",
-      "domain_of": [
-        "NamedThing"
-      ],
       "range": "string",
       "@type": "SlotDefinition"
     },
@@ -418,10 +422,6 @@
         "http://schema.org/description"
       ],
       "slot_uri": "http://schema.org/description",
-      "owner": "NamedThing",
-      "domain_of": [
-        "NamedThing"
-      ],
       "range": "string",
       "@type": "SlotDefinition"
     },
@@ -483,6 +483,18 @@
       "range": "PersonStatus",
       "@type": "SlotDefinition"
     },
+    {
+      "name": "catalysisSample__sample_environment",
+      "from_schema": "https://w3id.org/anak-velazquez/hzb-metadata-schema",
+      "slot_uri": "https://w3id.org/anak-velazquez/hzb-metadata-schema/sample_environment",
+      "alias": "sample_environment",
+      "owner": "CatalysisSample",
+      "domain_of": [
+        "CatalysisSample"
+      ],
+      "range": "string",
+      "@type": "SlotDefinition"
+    },
     {
       "name": "sampleCollection__entries",
       "from_schema": "https://w3id.org/anak-velazquez/hzb-metadata-schema",
@@ -498,7 +510,15 @@
       "@type": "SlotDefinition"
     },
     {
-      "name": "Sample_primary_email",
+      "name": "category",
+      "from_schema": "https://w3id.org/anak-velazquez/hzb-metadata-schema",
+      "slot_uri": "https://w3id.org/anak-velazquez/hzb-metadata-schema/category",
+      "range": "string",
+      "required": true,
+      "@type": "SlotDefinition"
+    },
+    {
+      "name": "sample_primary_email",
       "definition_uri": "https://w3id.org/anak-velazquez/hzb-metadata-schema/primary_email",
       "description": "The main email address of a person",
       "from_schema": "https://w3id.org/anak-velazquez/hzb-metadata-schema",
@@ -518,24 +538,83 @@
       "range": "string",
       "pattern": "^\\S+@[\\S+\\.]+\\S+",
       "@type": "SlotDefinition"
+    },
+    {
+      "name": "namedThing_category",
+      "from_schema": "https://w3id.org/anak-velazquez/hzb-metadata-schema",
+      "is_a": "category",
+      "domain": "NamedThing",
+      "slot_uri": "https://w3id.org/anak-velazquez/hzb-metadata-schema/category",
+      "alias": "category",
+      "owner": "NamedThing",
+      "domain_of": [
+        "NamedThing"
+      ],
+      "is_usage_slot": true,
+      "usage_slot_name": "category",
+      "range": "string",
+      "required": true,
+      "@type": "SlotDefinition"
     }
   ],
   "classes": [
     {
-      "name": "NamedThing",
-      "definition_uri": "https://w3id.org/anak-velazquez/hzb-metadata-schema/NamedThing",
-      "description": "A generic grouping for any identifiable entity",
+      "name": "ChemicalOrDrugOrTreatment",
+      "id_prefixes": [
+        "PUBCHEM.COMPOUND",
+        "CHEMBL.COMPOUND",
+        "CHEBI",
+        "MAXO"
+      ],
+      "definition_uri": "https://w3id.org/anak-velazquez/hzb-metadata-schema/ChemicalOrDrugOrTreatment",
       "from_schema": "https://w3id.org/anak-velazquez/hzb-metadata-schema",
-      "mappings": [
-        "schema:Thing"
+      "mixin": true,
+      "slot_usage": {},
+      "class_uri": "https://w3id.org/anak-velazquez/hzb-metadata-schema/ChemicalOrDrugOrTreatment",
+      "@type": "ClassDefinition"
+    },
+    {
+      "name": "Device",
+      "definition_uri": "https://w3id.org/anak-velazquez/hzb-metadata-schema/Device",
+      "description": "A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment",
+      "from_schema": "https://w3id.org/anak-velazquez/hzb-metadata-schema",
+      "narrow_mappings": [
+        "UMLSSG:DEVI",
+        "STY:T074",
+        "STY:T075",
+        "STY:T203",
+        "STY:T122"
       ],
+      "is_a": "NamedThing",
+      "slots": [
+        "namedThing_category"
+      ],
+      "slot_usage": {},
+      "class_uri": "https://w3id.org/anak-velazquez/hzb-metadata-schema/Device",
+      "@type": "ClassDefinition"
+    },
+    {
+      "name": "CatalysisSample",
+      "definition_uri": "https://w3id.org/anak-velazquez/hzb-metadata-schema/CatalysisSample",
+      "description": "core parameters of a catalysis sample #metadata terms (parameters) are mapped to nfdi voc4cat",
+      "from_schema": "https://w3id.org/anak-velazquez/hzb-metadata-schema",
+      "is_a": "Sample",
       "slots": [
-        "id",
-        "name",
-        "description"
+        "namedThing_category",
+        "sample_primary_email",
+        "birth_date",
+        "age_in_years",
+        "vital_status",
+        "catalysisSample__sample_environment"
       ],
       "slot_usage": {},
-      "class_uri": "http://schema.org/Thing",
+      "attributes": [
+        {
+          "name": "sample_environment",
+          "@type": "SlotDefinition"
+        }
+      ],
+      "class_uri": "https://w3id.org/anak-velazquez/hzb-metadata-schema/CatalysisSample",
       "@type": "ClassDefinition"
     },
     {
@@ -545,10 +624,8 @@
       "from_schema": "https://w3id.org/anak-velazquez/hzb-metadata-schema",
       "is_a": "NamedThing",
       "slots": [
-        "id",
-        "name",
-        "description",
-        "Sample_primary_email",
+        "namedThing_category",
+        "sample_primary_email",
         "birth_date",
         "age_in_years",
         "vital_status"
@@ -578,13 +655,43 @@
       "class_uri": "https://w3id.org/anak-velazquez/hzb-metadata-schema/SampleCollection",
       "tree_root": true,
       "@type": "ClassDefinition"
+    },
+    {
+      "name": "Entity",
+      "definition_uri": "https://w3id.org/anak-velazquez/hzb-metadata-schema/Entity",
+      "description": "Root Biolink Model class for all things and informational relationships, real or imagined.",
+      "from_schema": "https://w3id.org/anak-velazquez/hzb-metadata-schema",
+      "abstract": true,
+      "slot_usage": {},
+      "class_uri": "https://w3id.org/anak-velazquez/hzb-metadata-schema/Entity",
+      "@type": "ClassDefinition"
+    },
+    {
+      "name": "NamedThing",
+      "definition_uri": "https://w3id.org/anak-velazquez/hzb-metadata-schema/NamedThing",
+      "description": "a databased entity or concept/class",
+      "from_schema": "https://w3id.org/anak-velazquez/hzb-metadata-schema",
+      "exact_mappings": [
+        "BFO:0000001",
+        "WIKIDATA:Q35120",
+        "UMLSSG:OBJC",
+        "STY:T071",
+        "dcid:Thing"
+      ],
+      "is_a": "Entity",
+      "slots": [
+        "namedThing_category"
+      ],
+      "slot_usage": {},
+      "class_uri": "https://w3id.org/anak-velazquez/hzb-metadata-schema/NamedThing",
+      "@type": "ClassDefinition"
     }
   ],
   "metamodel_version": "1.7.0",
   "source_file": "hzb_metadata_schema.yaml",
-  "source_file_date": "2024-07-23T13:56:55",
-  "source_file_size": 2243,
-  "generation_date": "2024-07-23T13:57:41",
+  "source_file_date": "2024-08-05T15:01:08",
+  "source_file_size": 4633,
+  "generation_date": "2024-08-05T15:01:15",
   "@type": "SchemaDefinition",
   "@context": [
     "project/jsonld/hzb_metadata_schema.context.jsonld",