ICD-10 Concept search | emtelligent Documentation

Synopsis

This page contains queries that uses the Snomed ICD-10 ontology to return ICD-10 coded entities extracted from the FINDINGS and IMPRESSIONS sections of Radiology reports.

This page contains two queries:

The first query finds ICD-10 mapped entities and returns the ICD-10 code and corresponding Snomed description.
The second query extends the first by also retrieving the Snomed concept ID and fully-qualified concept description. This is possible because the NLP API performs post-coordination of entities after data extraction. Moreover, the NLP API uses the ICD-10 mapping from Snomed CT ensuring that every ICD-10 mapped entity is also mapped to a Snomed concept ID.

Processing Requirements

This query assumes that at least the following processing options were enabled:

--feature snomed-ontology, snomedicd10-ontology
--store-sections-and-sentences

For this query, Radiology imaging studies were processed with the following document type:

--category Radiology
--subcategory CT

Clinical Context

The World Health Organization’s (WHO) International Statistical Classification of Diseases and Related Health Problems (ICD) 10th revision (ICD-10) is a widely used medical coding system, used for billing and data structuring purposes world-wide. Unfortunately, while its textual description of concepts is highly specific (e.g. Injury, poisoning and certain other consequences of external causes), many clinicians would not use such long and highly specific descriptions in their clinical notes.

The NLP API uses the SNOMED-to-ICD-10 mappings provided in the SNOMED ontology to map commonly-used clinical terms to ICD-10 concepts. The query below is an example of how these highly useful ICD-10 concepts can be extracted from medical text that uses common, colloquial medical language. In addition, the NLP API provides the SNOMED-to-ICD-10 mapping guidance that can be used to further refine the coding via manual methods.

SQL query

Query 1: Find ICD-10 coded entities

SQL

SELECT c.concept_id, d.category, fe.section_name, fe.text, fe.polarity, fe.uncertainty, c.description, sen_l.text
FROM foundentity fe
        JOIN foundentityconcept fec ON fe.id = fec.found_entity_id
        JOIN concept c ON fec.concept_id = c.concept_id AND fec.concept_ontology = c.ontology
        JOIN foundentitylocation fel ON fe.id = fel.found_entity_id
        JOIN location l ON fel.location_id = l.id AND l.type_ = 'sentence'
        JOIN sentencelocation sen_l ON sen_l.id = l.location_id
        JOIN document d ON l.document_id = d.id
WHERE c.ontology = 'snomed_icd10' --!! Replace with ontology of choice e.g. snomed, umls, radlex, loinc
AND d.category = 'Radiology'
AND fe.section_name IN ('FINDINGS', 'IMPRESSION');

concept_id	category	section_name	text	polarity	uncertainty	description
A09.9	Radiology	FINDINGS	enteritis	asserted	certain	Infectious gastroenteritis and colitis, unspecified (Disease or Syndrome)
A09.9	Radiology	IMPRESSION	enteritis	asserted	certain	Infectious gastroenteritis and colitis, unspecified (Disease or Syndrome)
C43.9	Radiology	IMPRESSION	metastatic malignant melanoma	asserted	certain	Malignant melanoma of skin, unspecified (Neoplastic Process)
C50.9	Radiology	IMPRESSION	breast cancer	asserted	certain	Malignant neoplasm of breast of unspecified site (Neoplastic Process)
C79.9	Radiology	IMPRESSION	metastatic malignant melanoma	asserted	certain	Secondary malignant neoplasm of unspecified site (Neoplastic Process)
C79.9	Radiology	IMPRESSION	metastases	negated	uncertain	Secondary malignant neoplasm of unspecified site (Neoplastic Process)
C79.9	Radiology	IMPRESSION	metastases	negated	certain	Secondary malignant neoplasm of unspecified site (Neoplastic Process)
C80.9	Radiology	IMPRESSION	malignancy	negated	uncertain	Malignant neoplasm without specification of site (Neoplastic Process)
D16.9	Radiology	FINDINGS	enchondroma	asserted	uncertain	Benign neoplasm of bone and articular cartilage, unspecified (Neoplastic Process)
D16.9	Radiology	IMPRESSION	enchondroma	asserted	uncertain	Benign neoplasm of bone and articular cartilage, unspecified (Neoplastic Process)

Query 2: ICD-10 coded entities and corresponding Snomed concepts

SQL

-- Find ICD10 Code and corresponding SNOMED CT fully-specified concept name
WITH icd10_mapped_entities AS (
    SELECT fe.id, c.concept_id, c.description, fe.polarity, fe.uncertainty, fe.text
    FROM foundentity fe
            JOIN foundentityconcept fec on fe.id = fec.found_entity_id
            JOIN concept c on c.concept_id = fec.concept_id and c.ontology = fec.concept_ontology AND
                                c.ontology = 'snomed_icd10'),
    snomed_mapped_entities AS (
        SELECT fe.id, c.concept_id, c.description, fe.polarity, fe.uncertainty, fe.text
        FROM foundentity fe
                JOIN foundentityconcept fec on fe.id = fec.found_entity_id
                JOIN concept c on c.concept_id = fec.concept_id and c.ontology = fec.concept_ontology AND
                                    c.ontology = 'snomed')
SELECT icd10_mapped_entities.id as entityId,
    icd10_mapped_entities.concept_id as icd10_id,
    icd10_mapped_entities.description as icd10,
    snomed_mapped_entities.concept_id as sct_id,
    snomed_mapped_entities.description as snomed,
    fe.polarity,
    fe.uncertainty,
    fe.section_name,
    fe.text as term,
    sl.text  as sentence
FROM icd10_mapped_entities
        JOIN snomed_mapped_entities ON icd10_mapped_entities.id = snomed_mapped_entities.id
        JOIN foundentity fe ON fe.id = icd10_mapped_entities.id
        JOIN foundentitylocation fel on fe.id = fel.found_entity_id
        JOIN location l on fel.location_id = l.id AND l.type_ = 'sentence'
        JOIN document d ON l.document_id = d.id
        JOIN sentencelocation sl on sl.id = l.location_id AND l.type_ = 'sentence'
WHERE fe.polarity = 'asserted'
AND fe.uncertainty = 'certain'
AND d.category = 'Radiology'
AND fe.section_name IN ('FINDINGS', 'IMPRESSION');

entityid	icd10_id	icd10	sct_id	snomed	polarity	uncertainty	section_name	term
611	K42.9	Umbilical hernia without obstruction or gangrene (Acquired Abnormality)	396347007	Umbilical hernia (disorder)	asserted	certain	FINDINGS	umbilical hernia
614	A09.9	Infectious gastroenteritis and colitis, unspecified (Disease or Syndrome)	64613007	Inflammation of small intestine (disorder)	asserted	certain	FINDINGS	enteritis
634	A09.9	Infectious gastroenteritis and colitis, unspecified (Disease or Syndrome)	64613007	Inflammation of small intestine (disorder)	asserted	certain	IMPRESSION	enteritis
636	K42.9	Umbilical hernia without obstruction or gangrene (Acquired Abnormality)	396347007	Umbilical hernia (disorder)	asserted	certain	IMPRESSION	umbilical hernia
643	K62.9	Disease of anus and rectum, unspecified (Disease or Syndrome)	300312006	Lesion of rectum (disorder)	asserted	certain	FINDINGS	rectal wall thickening
646	L90.5	Scar conditions and fibrosis of skin (Acquired Abnormality)	275322007	Scar (disorder)	asserted	certain	FINDINGS	Scarring
650	M47.99	Spondylosis, unspecified (Disease or Syndrome)	8847002	Spondylosis (disorder)	asserted	certain	FINDINGS	Multilevel degenerative changes
651	K76.0	Fatty (change of) liver, not elsewhere classified (Disease or Syndrome)	197321007	Steatosis of liver (disorder)	asserted	certain	IMPRESSION	Fatty liver
746	K76.0	Fatty (change of) liver, not elsewhere classified (Disease or Syndrome)	197321007	Steatosis of liver (disorder)	asserted	certain	FINDINGS	hepatic fatty infiltration
749	I70.0	Atherosclerosis of aorta (Disease or Syndrome)	81817003	Atherosclerosis of aorta (disorder)	asserted	certain	FINDINGS	aorta atherosclerosis

Next steps

This query pattern is applicable to other report types and sections. You may also want to filter the dataset returned limiting it to just those terms which were experienced by the patient by using the experiencer relation. An example of this query pattern is provided here.