WIP #50

doc/api/schemas/_index.yaml

@@ -2,6 +2,8 @@ item:
   $ref: "./item.yaml"
 limit:
   $ref: "./limit.yaml"
+referenceId:
+  $ref: "./referenceId.yaml"
 referenceItem:
   $ref: "./referenceItem.yaml"
 referenceObject:
@@ -10,6 +12,8 @@ referenceObject:
 #   $ref: "./referenceOption.yaml"
 referenceResult:
   $ref: "./referenceResult.yaml"
+structureId:
+  $ref: "./structureId.yaml"
 structureItem:
   $ref: "./structureItem.yaml"
 structureObject:

doc/api/schemas/referenceId.yaml

@@ -0,0 +1,8 @@
+title: ReferenceId
+type: object
+properties:
+  doi:
+    description: |
+      DOI
+    example: "10.1080/1057563021000040466"
+    type: string

doc/api/schemas/referenceItem.yaml

@@ -13,6 +13,8 @@ properties:
     default: ~
     example: "10.1080/1057563021000040466"
     type: string
+  # external_id:
+  #   $ref: "./referenceId.yaml"
   # option:
   #   $ref: "./referenceOption.yaml"
   # filter:

doc/api/schemas/referenceObject.yaml

@@ -4,8 +4,10 @@ properties:
   doi:
     description: |
       DOI
-    type: string
     example: "10.1080/1057563021000040466"
+    type: string
+  # external_ids:
+  #   $ref: "./referenceId.yaml"
   # title:
   #   description: |
   #     Title

doc/api/schemas/referenceResult.yaml

@@ -7,8 +7,8 @@ properties:
       IDs
     type: array
     items:
+      example: [ 44488598 ]
       type: integer
-    example: [ 44488598 ]
   objects:
     $ref: "./referenceObject.yaml"
   count:

doc/api/schemas/structureId.yaml

@@ -0,0 +1,28 @@
+title: StructureId
+type: object
+properties:
+  chebi:
+    description: |
+      ChEBI identifier
+    example: 80907
+    type: integer
+  chembl:
+    description: |
+      ChEMBL identifier
+    example: "CHEMBL456137"
+    type: string
+  chemspider:
+    description: |
+      ChemSpider identifier
+    example: 141471
+    type: integer
+  kegg:
+    description: |
+      KEGG identifier
+    example: "C17071"
+    type: string
+  pubchem:
+    description: |
+      PubChem (CID) identifier
+    example: 161036
+    type: integer

doc/api/schemas/structureItem.yaml

@@ -13,6 +13,8 @@ properties:
     default: ~
     example: "C=C[C@@H]1[C@@H]2CCOC(=O)C2=CO[C@H]1O[C@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)OC(=O)C4=C(C=C(C=C4C5=CC(=CC=C5)O)O)O"
     type: string
+  # external_id:
+  #   $ref: "./structureId.yaml"
   option:
     $ref: "./structureOption.yaml"
   # filter:

doc/api/schemas/structureObject.yaml

@@ -1,8 +1,10 @@
 title: StructureObject
 type: object
 properties:
-  structure_smiles:
+  smiles:
     description: |
       Structure SMILES
-    type: string
     example: "C=C[C@@H]1[C@@H]2CCOC(=O)C2=CO[C@H]1O[C@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O"
+    type: string
+  # external_id:
+  #   $ref: "./structureId.yaml"

doc/api/schemas/structureResult.yaml

@@ -5,10 +5,10 @@ properties:
   ids:
     description: |
       IDs
-    type: array
+    example: [ 27151406 ]
     items:
       type: integer
-    example: [ 27151406 ]
+    type: array
   objects:
     $ref: "./structureObject.yaml"
   count:

doc/api/schemas/taxonId.yaml

@@ -0,0 +1,68 @@
+title: TaxonObject
+type: object
+properties:
+  col:
+    description: |
+      Catalogue Of Life ID
+    example: "6KB7S"
+    type: string
+  eol:
+    description: |
+      Encyclopedia Of Life ID
+    example: 483956
+    type: integer
+  gbif:
+    description: |
+      Global Biodiversity Information Facility Taxon ID
+    example: 3170040
+    type: integer
+  inat:
+    description: |
+      iNaturalist taxon ID
+    example: 142299
+    type: integer
+  ipni:
+    description: |
+      International Plant Names Index ID
+    example: "368453-1"
+    type: string
+  irmng:
+    description: |
+      Interim Register of Marine and Nonmarine Genera ID
+    example: 10921368
+    type: integer
+  itis:
+    description: |
+      Integrated Taxonomic Information System ID
+    example: 505985
+    type: integer
+  ncbi:
+    description: |
+      NCBI taxon ID
+    example: 172557
+    type: integer
+  otl:
+    description: |
+      Open Tree of Life ID
+    example: 346679
+    type: integer
+  powo:
+    description: |
+      Plants of the World Online ID
+    example: "urn:lsid:ipni.org:names:368453-1"
+    type: string
+  tropicos:
+    description: |
+      Tropicos ID
+    example: 13800021
+    type: integer
+  wfo:
+    description: |
+      World Flora Online ID
+    example: "wfo-0000697915"
+    type: string
+  worms:
+    description: |
+      Encyclopedia Of Life ID
+    example: 1
+    type: integer

doc/api/schemas/taxonItem.yaml

@@ -14,6 +14,8 @@ properties:
     # The mistake is on purpose
     example: "Gentiana luteha"
     type: string
+  # external_id:
+  #   $ref: "./taxonId.yaml"
   option:
     $ref: "./taxonOption.yaml"
   # filter:

doc/api/schemas/taxonObject.yaml

@@ -4,5 +4,7 @@ properties:
   name:
     description: |
       Name
-    type: string
     example: "Gentiana lutea"
+    type: string
+  # external_id:
+  #   $ref: "./taxonId.yaml"

doc/api/schemas/taxonResult.yaml

@@ -5,10 +5,10 @@ properties:
   ids:
     description: |
       IDs
-    type: array
+    example: [ 158572 ]
     items:
       type: integer
-    example: [ 158572 ]
+    type: array
   objects:
     $ref: "./taxonObject.yaml"
   count:

doc/api/schemas/tripletResult.yaml

@@ -6,12 +6,12 @@ properties:
     title: Triplets
     description: |
       Triplets of reference, structure and taxon IDs
-    type: array
+    example : [ [44488598, 27151406, 158572] ]
     items:
       type: array
       items:
         type: integer
-    example : [ [44488598, 27151406, 158572] ]
+    type: array
   references:
     $ref: "./referenceObject.yaml"
   structures: