Merge pull request #159 from x-atlas-consortia/jas_celltypes_stellar_dct

Enhancements to support new cell type annotations

hs-ontology-api-spec.yaml

@@ -1395,7 +1395,7 @@ components:
                     example: multimerin-1
         organs:
           type: array
-          description: Organs associated with the cell type, based on relationships in the Human Resource Atlas and Azimuth
+          description: Organs associated with the cell type, based on relationships in the Human Resource Atlas and various annotations (including Azimuth and STELLAR)
           items:
             type: object
             properties:
@@ -1411,6 +1411,10 @@ components:
                 type: string
                 description: Name (preferred term) for organ in source
                 example: heart
+              annotation:
+                type: string
+                description: SAB of the cell type annotation
+                example: AZ
     FieldDescriptionsResponse:
       type: object
       description: Descriptions for ingest metadata fields

src/hs_ontology_api/cypher/celltypedetail.cypher

@@ -1,4 +1,4 @@
-// Return detailed inforomation on cell types, based on a input list of AZ terms.
+// Return detailed information on cell types, based on a input list of CL codes.
 
 CALL
 // Get CUIs of concepts for cell types that match the criteria.
@@ -13,9 +13,12 @@ CALL
 WITH [$ids] AS ids
 
 // APRIL 2024 Bug fix to use CodeID instead of CODE for cases of leading zeroes in strings.
-OPTIONAL MATCH (pCL:Concept)-[:CODE]->(cCL:Code)
-WHERE CASE WHEN ids[0]<>'' THEN ANY(id in ids WHERE cCL.CodeID='CL:'+id) ELSE 1=1 END RETURN DISTINCT pCL.CUI AS CLCUI}
-
+// JANUARY 2025 Because PATO and UBERON are ingested prior to CL, some CL codes will associate with multiple concepts.
+// Use the concept that is associated with the code during the CL ingestion, which can be identified by the use of a
+// preferred term (term of relationship type PT).
+OPTIONAL MATCH (pCL:Concept)-[:CODE]->(cCL:Code)-[r:PT]->(tCL:Term)
+WHERE r.CUI = pCL.CUI
+AND CASE WHEN ids[0]<>'' THEN ANY(id in ids WHERE cCL.CodeID='CL:'+id) ELSE 1=1 END RETURN DISTINCT pCL.CUI AS CLCUI}
 CALL
 {
 
@@ -68,6 +71,9 @@ ORDER BY CLID, ret_value
 
 UNION
 
+// January 2025 - expand to include mappings from STELLAR and DeepCellType annotations. All references to 'AZ' and 'Azimuth' should
+// be considered references to an annotation.
+
 // Cell types - Azimuth/UBERON organ list
 // The Azimuth ontology:
 // 1. Assigns AZ cell codes to AZ organ codes.
@@ -86,16 +92,17 @@ CALL
 	WITH CLCUI
 	OPTIONAL MATCH (pCL:Concept)-[:CODE]->(cCL:Code)-[rCL]->(tCL:Term),
 	(pCL:Concept)-[:CODE]->(cAZ:Code)-[rAZ]->(tAZ:Term)
-	WHERE pCL.CUI=CLCUI AND rCL.CUI=pCL.CUI AND cCL.SAB='CL' AND cAZ.SAB='AZ'
+	WHERE pCL.CUI=CLCUI AND rCL.CUI=pCL.CUI AND cCL.SAB='CL'
+	AND cAZ.SAB IN['AZ','STELLAR','DCT']
 	RETURN DISTINCT cCL.CodeID as CLID,cAZ.CodeID AS AZID
 }
 //Use the AZ codes to map to concepts that have located_in relationships with AZ organ codes.
 //The AZ organ codes are cross-referenced to UBERON codes. Limit the located_in relationships to those from AZ.
 CALL
 {   WITH AZID
-    OPTIONAL MATCH (cAZ:Code)<-[:CODE]-(pAZ:Concept)-[rAZUB:located_in]->(pUB:Concept)-[:CODE]->(cUB:Code)-[rUB:PT]->(tUB:Term)
-    WHERE rAZUB.SAB='AZ' AND rUB.CUI=pUB.CUI AND cAZ.CodeID=AZID AND cUB.SAB='UBERON'
-    RETURN cUB.CodeID+'|'+ tUB.name + '' as UBERONID
+    MATCH (cAZ:Code)<-[:CODE]-(pAZ:Concept)-[rAZUB:located_in]->(pUB:Concept)-[:CODE]->(cUB:Code)-[rUB:PT]->(tUB:Term)
+    WHERE rAZUB.SAB IN ['AZ','STELLAR','DCT'] AND rUB.CUI=pUB.CUI AND cAZ.CodeID=AZID AND cUB.SAB='UBERON'
+    RETURN cUB.CodeID+'|'+ tUB.name + '|' + rAZUB.SAB as UBERONID
 }
 WITH CLID,UBERONID
 RETURN DISTINCT CLID, 'cell_types_organ' as ret_key, apoc.text.join(COLLECT(DISTINCT UBERONID),",")  AS ret_value

src/hs_ontology_api/models/celltypedetail_organ.py

@@ -5,6 +5,10 @@
 # Used by the celltypes endpoint.
 # Contains information on an organ associated with a cell type identified in Cell Ontology.
 
+# JAS January 2025
+# Added annotation key to the organs object, which describes the annotation used assign organs to cell types.
+# Annotations include Azimuth (the original annotation), STELLAR, and DeepCellType
+
 from __future__ import absolute_import
 from typing import List
 from ubkg_api.models.base_model_ import Model
@@ -17,48 +21,55 @@ def __init__(self, organ=None):
 
         :param organ: delimited string describing the organ.
         The format of the string is
-        <SAB>:<id>|<code>|preferred term
+        <SAB>:<id>|<code>|preferred term|annotation
 
         """
         # Types for JSON objects
         self.openapi_types = {
             'id': str,
             'source': str,
-            'name': str
+            'name': str,
+            'annotation': str
         }
         # Attribute mappings used by the base Model class to assert key/value pairs.
         self.attribute_map = {
             'id': 'id',
             'source': 'source',
-            'name': 'name'
+            'name': 'name',
+            'annotation': 'annotation'
         }
 
         # Property assignments
         if organ is None:
             id = 'unknown'
             source = 'unknown'
             name = 'unknown'
+            annotation = 'unknown'
         else:
             organ_info = organ.split('|')
             if len(organ_info) == 1:
                 id = organ_info
                 source = ''
                 name = ''
+                annotation = ''
             else:
                 source = organ_info[0].split(':')[0]
                 id = organ_info[0].split(':')[1]
                 name = organ_info[1]
+                annotation = organ_info[2]
 
         self._id = id
         self._source = source
         self._name = name
+        self._annotation = annotation
 
     def serialize(self):
         # Key/value format of response.
         return {
             "id": self._id,
             "source": self._source,
-            "name": self._name
+            "name": self._name,
+            "annotation": self._annotation
         }
 
     @classmethod
@@ -131,3 +142,22 @@ def name(self, name):
         """
         self._name = name
 
+    @property
+    def annotation(self):
+        """
+        Gets the annotation of this CelltypeDetailOrgan.
+
+        :return: The annotation of the organ
+        :rtype: str
+        """
+        return self._annotation
+
+    @annotation.setter
+    def annotation(self, annotation):
+        """
+        Sets the annotation of this CelltypeDetailOrgan
+        :param annotation: The name of the organ.
+        :type annotation: str
+        """
+        self._annotation = annotation
+