Update nfdi4chem_michi.yaml

NFDI4Chem · May 28, 2024 · d7b6b47 · d7b6b47
1 parent c66fab5
commit d7b6b47
Showing 1 changed file with 32 additions and 6 deletions.
diff --git a/src/nfdi4chem_michi/schema/nfdi4chem_michi.yaml b/src/nfdi4chem_michi/schema/nfdi4chem_michi.yaml
@@ -87,16 +87,42 @@ classes:
   # chemical entities
   MaterialEntity:
     class_uri: BFO:0000040
-    description: Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time)
+    description: "Material entities are three-dimensional entities (entities extended in three spatial dimensions), 
+    as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended 
+    also along the dimension of time)"
 
   ChemicalEntity:
-    class_uri: CHEBI:24431
-
-  Molecule:
-    description: A molecular entity
+    is_a: MaterialEntity
+    class_uri: CHEBI:23367
+    description: "Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, 
+    complex, conformer etc., identifiable as a separately distinguishable entity."
+    comments:
+      - "We do not use (ignore) the chemical entity class from CHEBI as this is only a grouping class, and chemical 
+      entity is rather that which constitutes a chemical substance"
 
   ChemicalSubstance:
-    description:
+    is_a: ChemicalEntity
+    class_uri: CHEBI:59999
+    description: A chemical entity that is composed of parts
+    slots:
+      - has provenance # range: information about the chemical substance that determines where it came from
+      - has chemical substance part
+      - has space group
+    examples:
+      - a polymer
+      - a mixture of ethanol and methanol
+    comments:
+      - "CHEBI definition: A chemical substance is a portion of matter of constant composition, composed of molecular
+      entities of the same type or of different types."
+
+  ChemicalSubstancePart:
+    is_a: ChemicalEntity
+    description: A part of a chemical substance with a distinct identity
+    slots:
+      - is part of chemical substance
+      -
+
+
 
   # devices
   Device: