Snowmed OHDSI GIthub Vocabulary-v5.0 process question

[heschmidt04]

Question:
I want to confirm that this SnowMed process is still needed to load the SnowMed vocabulary files from Athena before I have to figure out how to get an environment that is outside of my M1 laptop to configure the dependencies.

This github information below is 2 years old I wonder if it is still relevant.
https://github.com/OHDSI/Vocabulary-v5.0/tree/880fc17ce4ec9c14b7c3e1d9f5fa199c1a997aec/SNOMED
Dependencies wise... it looks like it needs a UMed account, a specific file download, and R for my laptop. (My M1 laptop has issues with R because of a RJava dependency afaik)

I sent this along to Marty for discussion this Thursday 8/3/2023 in the OHDSI CHoRUS B2AI Standards Module Office Hours

I'm willing to help create a Docker image with help from a SME (subject matter export) and/or port the data for other folks to use if we don't break any licenses or rules in doing that.

Best regards,
Heidi

[clermontg]

I did not do this. Rather I downloaded all csv's files from the ATHENA download site. After creating the empty tables (and PK/FK) in an OMOP instance using the recommended DDL using for example:

---

CREATE TABLE mladi_OMOP54.CONCEPT (
concept_id integer NOT NULL,
concept_name varchar(255) NOT NULL,
domain_id varchar(20) NOT NULL,
vocabulary_id varchar(20) NOT NULL,
concept_class_id varchar(20) NOT NULL,
standard_concept varchar(1) NULL,
concept_code varchar(50) NOT NULL,
valid_start_date date NOT NULL,
valid_end_date date NOT NULL,
invalid_reason varchar(1) NULL );

ALTER TABLE mladi_OMOP54.CONCEPT ADD CONSTRAINT xpk_CONCEPT PRIMARY KEY (concept_id);CREATE INDEX idx_concept_concept_id ON mladi_OMOP54.CONCEPT (concept_id ASC);
#CLUSTER mladi_OMOP54.concept USING idx_concept_concept_id ;
CREATE INDEX idx_concept_code ON mladi_OMOP54.CONCEPT (concept_code ASC);
CREATE INDEX idx_concept_vocabluary_id ON mladi_OMOP54.CONCEPT (vocabulary_id ASC);
CREATE INDEX idx_concept_domain_id ON mladi_OMOP54.CONCEPT (domain_id ASC);
CREATE INDEX idx_concept_class_id ON mladi_OMOP54.CONCEPT (concept_class_id ASC);
ALTER TABLE mladi_OMOP54.CONCEPT ADD CONSTRAINT fpk_CONCEPT_domain_id FOREIGN KEY (domain_id) REFERENCES mladi_OMOP54.DOMAIN (DOMAIN_ID);
ALTER TABLE mladi_OMOP54.CONCEPT ADD CONSTRAINT fpk_CONCEPT_vocabulary_id FOREIGN KEY (vocabulary_id) REFERENCES mladi_OMOP54.VOCABULARY (VOCABULARY_ID);
ALTER TABLE mladi_OMOP54.CONCEPT ADD CONSTRAINT fpk_CONCEPT_concept_class_id FOREIGN KEY (concept_class_id) REFERENCES mladi_OMOP54.CONCEPT_CLASS (CONCEPT_CLASS_ID);

-------------------------------------- and so forth for all vocab tables

I simply imported the csv into the tables.

In our case at Pitt, had to create an ICD-10 to SNOMED lookup table as all of our local diagnostic codes are ICD-10 and not SNOMED