model_utils.icd
- class pytrial.model_utils.icd.ICD9Graph(input_dir=None)[source]
Bases:
pytrial.model_utils.icd.ICDGraphBase
Get an ICD-9 knowledge graph to query parental and children nodes for each code.
- Returns
self.graph (nx.DiGraph) – The hierarchy of ICD codes stored as graph in networkx.
self.codes (list[str]) – All the unique codes.
- class pytrial.model_utils.icd.ICD10Graph(input_dir=None, version='2021')[source]
Bases:
pytrial.model_utils.icd.ICDGraphBase
Get an ICD-10 knowledge graph to query parental and children nodes for each code.
- Parameters
input_dir (str) – The dir that stores the hierarchy files.
version ({'2022', '2021','2020','2019'}) – The version of ICD-10 codes.
- Returns
self.graph (nx.DiGraph) – The hierarchy of ICD codes stored as graph in networkx.
self.codes (list[str]) – All the unique codes.
- class pytrial.model_utils.icd.ICD9_DX_VOC(input_dir='./resources')[source]
Bases:
object
Get a vocabulary containing the mapping of ICD9 Diagnosis code and its names.
- Parameters
input_dir (str) – The dir that stores ICD9-dx file.
- class pytrial.model_utils.icd.ICD9_SG_VOC(input_dir='./resources')[source]
Bases:
object
Get a vocabulary containing the mapping of ICD9 procedure code and its names.
- Parameters
input_dir (str) – The dir that stores ICD9-sg file.
- pytrial.model_utils.icd.get_icd10_from_nih(term)[source]
Query related ICD-10 codes for input terms.
- Parameters
term (str or list[str]) – Disease names or a list of disease names.
- Returns
Outputs ICD codes
- Return type
list[str] or list[list[str]]
- pytrial.model_utils.icd.get_icd9dx_from_nih(term)[source]
Query related ICD-9-CM diagnosis codes for input terms.
- Parameters
term (str or list[str]) – Disease names or a list of disease names.
- Returns
Outputs ICD codes
- Return type
list[str] or list[list[str]]
- pytrial.model_utils.icd.get_icd9sg_from_nih(term)[source]
Query related ICD-9-CM procedure codes for input terms.
- Parameters
term (str or list[str]) – Disease names or a list of disease names.
- Returns
Outputs ICD codes
- Return type
list[str] or list[list[str]]
- pytrial.model_utils.icd.get_condition_synonym_from_nih(term)[source]
Query relevant medical conditions taking input symptoms/diseases using API: https://clinicaltables.nlm.nih.gov/apidoc/conditions/v3/doc.html
- Parameters
term (str or list[str]) – Disease names or a list of disease names.
- Returns
Outputs ICD codes
- Return type
list[str] or list[list[str]]