#316 improving HL7 to actually work and adding in HPO

RTXteam · Aug 19, 2023 · ae432ac · ae432ac
1 parent 2cfa148
commit ae432ac
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Showing 2 changed files with 23 additions and 2 deletions.
diff --git a/kg2_util.py b/kg2_util.py
@@ -73,6 +73,7 @@
 CURIE_PREFIX_HCPCS = 'HCPCS'
 CURIE_PREFIX_HGNC = 'HGNC'
 CURIE_PREFIX_HMDB = 'HMDB'
+CURIE_PREFIX_HP = 'HP'
 CURIE_PREFIX_IAO = 'IAO'
 CURIE_PREFIX_IDENTIFIERS_ORG_REGISTRY = 'identifiers_org_registry'
 CURIE_PREFIX_ISBN = 'ISBN'

diff --git a/umls_list_jsonl_to_kg_jsonl.py b/umls_list_jsonl_to_kg_jsonl.py
@@ -39,6 +39,7 @@
 HCPCS_PREFIX = kg2_util.CURIE_PREFIX_HCPCS
 HGNC_PREFIX = kg2_util.CURIE_PREFIX_HGNC
 HL7_PREFIX = kg2_util.CURIE_PREFIX_UMLS
+HPO_PREFIX = kg2_util.CURIE_PREFIX_HP
 
 UMLS_SOURCE_PREFIX = kg2_util.CURIE_PREFIX_UMLS_SOURCE
 
@@ -107,12 +108,12 @@ def get_basic_info(curie_prefix, node_id, info, accession_heirarchy):
     provided_by = make_node_id(UMLS_SOURCE_PREFIX, curie_prefix)
     cuis = info.get(CUIS_KEY, list())
     tuis = info.get(TUIS_KEY, list())
-    iri = IRI_MAPPINGS[curie_prefix] + node_id
-    if curie_prefix == kg2_util.UMLS_SOURCE_PREFIX:
+    if curie_prefix == kg2_util.CURIE_PREFIX_UMLS:
         if len(cuis) != 1:
             return None, None, None, None, None, None, None, None
         node_id = cuis[0]
     node_curie = make_node_id(curie_prefix, node_id)
+    iri = IRI_MAPPINGS[curie_prefix] + node_id
     category = TUI_MAPPINGS[str(tuple(tuis))]
 
     names = info.get(NAMES_KEY, dict())
@@ -267,6 +268,7 @@ def process_hl7_item(node_id, info, nodes_output, edges_output):
     provided_by = make_node_id(UMLS_SOURCE_PREFIX, 'HL7')
 
     # Currently not used, but extracting them in case we want them in the future - descriptions from https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/attribute_names.html
+    attributes = info.get(INFO_KEY, dict())
     hl7at = attributes.get('HL7AT', list())
     hl7ii = attributes.get('HL7II', list())
     hl7im = attributes.get('HL7IM', list())
@@ -306,6 +308,21 @@ def process_hl7_item(node_id, info, nodes_output, edges_output):
     make_umls_node(node_curie, iri, name, category, "2023", provided_by, synonyms, create_description("", tuis), nodes_output)
 
 
+def process_hpo_item(node_id, info, nodes_output, edges_output):
+    accession_heirarchy = ['PT', 'SY', 'ET', 'OP', 'IS', 'OET'] # https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/precedence_suppressibility.html
+    node_curie, iri, name, provided_by, category, synonyms, cuis, tuis = get_basic_info(HPO_PREFIX, node_id, info, accession_heirarchy)
+
+    # Currently not used, but extracting them in case we want them in the future
+    attributes = info.get(INFO_KEY, dict())
+    sid = attributes.get('SID', list())
+    hpo_comment = attributes.get('HPO_COMMENT', list())
+    date_created = attributes.get('DATE_CREATED', list())
+    syn_qualifier = attributes.get('SYN_QUALIFIER', list())
+    ref = attributes.get('REF', list())
+
+    make_umls_node(node_curie, iri, name, category, "2023", provided_by, synonyms, create_description("", tuis), nodes_output)
+
+
 if __name__ == '__main__':
     print("Starting umls_list_jsonl_to_kg_jsonl.py at", kg2_util.date())
     args = get_args()
@@ -368,6 +385,9 @@ def process_hl7_item(node_id, info, nodes_output, edges_output):
                 process_hl7_item(node_id, value, nodes_output, edges_output)
 
             if source == 'HPO':
+                process_hpo_item(node_id, value, nodes_output, edges_output)
+
+            if source == 'ICD10PCS':
                 name_keys.add(get_name_keys(value.get(NAMES_KEY, dict())))
                 attribute_keys.update(get_attribute_keys(value.get(INFO_KEY, dict())))