docs(update): update docs

LeibnizDSMZ · Nov 21, 2024 · c844dbe · c844dbe
1 parent c0538b5
commit c844dbe
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Showing 7 changed files with 56 additions and 40 deletions.
diff --git a/docs/graph.md b/docs/graph.md
@@ -16,11 +16,6 @@ yeast
 filamentous
 }
 
-class `TypeStrain`{
-typeStrain: boolean
-source: string
-}
-
 class `Taxon`{
 name: string
 taxonRank: TaxonRank
@@ -64,6 +59,11 @@ name: string
 author: string
 }
 
+class `TypeStrain`{
+typeStrain: boolean
+source: string
+}
+
 class `TaxonWithSource`{
 name: string
 taxonRank: TaxonRank
@@ -588,9 +588,9 @@ source: string
 class `Microbe`{
 organismType: OrganismType
 morphType: Morph | null
-unifiedTypeStrain: boolean
+unifiedTypeStrain: boolean | null
+unifiedTaxon: Taxon | null
 typeStrain: array[TypeStrain]
-unifiedTaxon: Taxon
 taxon: array[TaxonWithSource]
 sample: array[Sample]
 isolation: array[Isolation]
@@ -628,13 +628,13 @@ sources:
 
 `Microbe` ..> `OrganismType`
 `Microbe` ..> `Morph`
-`Microbe` ..> `TypeStrain`
 `Microbe` ..> `Taxon`
 `Taxon` ..> `TaxonRank`
 `Taxon` ..> `TaxonStatus`
 `Taxon` ..> `Identifier`
 `Taxon` ..> `ScientificName`
 `Taxon` ..> `Taxon`
+`Microbe` ..> `TypeStrain`
 `Microbe` ..> `TaxonWithSource`
 `TaxonWithSource` ..> `TaxonRank`
 `TaxonWithSource` ..> `TaxonStatus`

diff --git a/docs/schema/02. morphType.md b/docs/schema/02. morphType.md
@@ -3,7 +3,7 @@
 Morph Type  
 
 Description:
-> Applicable to fungi only  
+> Applicable and required for fungi only  
 
 **string, null**
 

diff --git a/docs/schema/03. unifiedTypeStrain.md b/docs/schema/03. unifiedTypeStrain.md
@@ -1,8 +1,8 @@
 ---
 ## 03. unifiedTypeStrain
-Unified Type Strain  `Required`
+Unified Type Strain  
 
 Description:
 > Is this strain type for unified species  
 
-**boolean**
+**boolean, null**
diff --git a/docs/schema/05. unifiedTaxon.md → docs/schema/04. unifiedTaxon.md b/docs/schema/05. unifiedTaxon.md → docs/schema/04. unifiedTaxon.md
@@ -1,20 +1,20 @@
 ---
-## 05. unifiedTaxon
-Taxon  `Required`
+## 04. unifiedTaxon
+Unified Taxon  
 
 Description:
-> A class to take all information about a taxon for the new microbial data standard.  
+> Evaluated and updated taxonomy  
 
-**object**
+**object, null**
 
 ---
-## 05.1. unifiedTaxon.name
+## 04.1. unifiedTaxon.name
 Name  `Required`
 
 **string**
 
 ---
-## 05.2. unifiedTaxon.taxonRank
+## 04.2. unifiedTaxon.taxonRank
 TaxonRank  `Required`
 
 Description:
@@ -46,7 +46,7 @@ Enum:
 	domain
 
 ---
-## 05.3. unifiedTaxon.taxonStatus
+## 04.3. unifiedTaxon.taxonStatus
 TaxonStatus  `Required`
 
 Description:
@@ -66,7 +66,7 @@ Enum:
 	validly published synonym
 
 ---
-## 05.4. unifiedTaxon.identifier
+## 04.4. unifiedTaxon.identifier
 Identifier  
 
 Description:
@@ -75,61 +75,61 @@ Description:
 **array[object]**
 
 ---
-## 05.4.1. unifiedTaxon.identifier.name
+## 04.4.1. unifiedTaxon.identifier.name
 Name  `Required`
 
 **string**
 
 ---
-## 05.4.2. unifiedTaxon.identifier.value
+## 04.4.2. unifiedTaxon.identifier.value
 Value  `Required`
 
 **string**
 
 ---
-## 05.4.3. unifiedTaxon.identifier.propertyID
+## 04.4.3. unifiedTaxon.identifier.propertyID
 Property ID  
 
 **string, null**
 
 ---
-## 05.4.4. unifiedTaxon.identifier.url
+## 04.4.4. unifiedTaxon.identifier.url
 URL  
 
 **string, null**
 
 ---
-## 05.5. unifiedTaxon.scientificName
+## 04.5. unifiedTaxon.scientificName
 Scientific Name  
 
 **object, null**
 
 ---
-## 05.5.1. unifiedTaxon.scientificName.name
+## 04.5.1. unifiedTaxon.scientificName.name
 Name  `Required`
 
 **string**
 
 ---
-## 05.5.2. unifiedTaxon.scientificName.author
+## 04.5.2. unifiedTaxon.scientificName.author
 Author  `Required`
 
 **string**
 
 ---
-## 05.6. unifiedTaxon.alternateName
+## 04.6. unifiedTaxon.alternateName
 Alternate Name  
 
 **array[string]**
 
 ---
-## 05.7. unifiedTaxon.parentTaxon
+## 04.7. unifiedTaxon.parentTaxon
 Parent Taxon  
 
 **object, null**
 
 ---
-## 05.8. unifiedTaxon.sameAs
+## 04.8. unifiedTaxon.sameAs
 Same As  
 
 **array[string]**
diff --git a/docs/schema/04. typeStrain.md → docs/schema/05. typeStrain.md b/docs/schema/04. typeStrain.md → docs/schema/05. typeStrain.md
@@ -1,17 +1,17 @@
 ---
-## 04. typeStrain
-Type Strain  
+## 05. typeStrain
+Type Strain  `Required`
 
 **array[object]**
 
 ---
-## 04.1. typeStrain.typeStrain
+## 05.1. typeStrain.typeStrain
 Type Strain  `Required`
 
 **boolean**
 
 ---
-## 04.2. typeStrain.source
+## 05.2. typeStrain.source
 Source  `Required`
 
 Description:

diff --git a/docs/schema/06. taxon.md b/docs/schema/06. taxon.md
@@ -1,6 +1,6 @@
 ---
 ## 06. taxon
-Taxon  
+Taxon  `Required`
 
 **array[object]**
 

diff --git a/schema/microbe_schema.json b/schema/microbe_schema.json
@@ -3084,7 +3084,7 @@
         }
       ],
       "default": null,
-      "description": "Applicable to fungi only",
+      "description": "Applicable and required for fungi only",
       "title": "Morph Type"
     },
     "motility": {
@@ -3223,14 +3223,30 @@
       "type": "array"
     },
     "unifiedTaxon": {
-      "$ref": "#/$defs/Taxon",
+      "anyOf": [
+        {
+          "$ref": "#/$defs/Taxon"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "default": null,
       "description": "Evaluated and updated taxonomy",
       "title": "Unified Taxon"
     },
     "unifiedTypeStrain": {
+      "anyOf": [
+        {
+          "type": "boolean"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "default": null,
       "description": "Is this strain type for unified species",
-      "title": "Unified Type Strain",
-      "type": "boolean"
+      "title": "Unified Type Strain"
     },
     "wallConstituents": {
       "description": "",
@@ -3243,8 +3259,8 @@
   },
   "required": [
     "organismType",
-    "unifiedTypeStrain",
-    "unifiedTaxon",
+    "typeStrain",
+    "taxon",
     "sources"
   ],
   "title": "Microbe",