MedDRA --> Standard Condition Map

[ericaVoss]

There are two main issues when going from MedDRA --> SNOMED:

1. Directionality in Vocabularies The original mapping used in the OMOP Vocab is SNOMED -> MedDRA. Sometimes a specific SNOMED term gets mapped to a broad MedDRA term, in that direction it is correct. However if you flip the direction, it may not still hold true.

Take the example of MedDRA term Malaria in the OMOP Vocab. It has direct mappings to these SNOMEDs: 432690 Maternal malaria during pregnancy - baby delivered 434424 Malaria in mother complicating pregnancy, childbirth AND/OR puerperium 438067 Malaria 4058268 H/O: malaria

It is correct to say that “Malaria in mother complicating pregnancy, childbirth AND/OR puerperium” in SNOMED is a “Malaria” in MedDRA. But it is not correct to say “Malaria” (MedDRA) is a “Malaria in mother complicating pregnancy, childbirth AND/OR puerperium” (SNOMED). What we really want to say is “Malaria” (MedDRA) is a “Malaria” (SNOMED)

This isn’t a problem with the Vocab, just a new use case – we want to be able to go MedDRA --> SNOMED without casting to large of net.

2. Concept Ancestor I was trying to use CONCEPT_ANCESTOR before in my mapping but it casts just too wide of a net. Using CONCEPT_RELATIONSHIP is best.

After speaking with Patrick we really need to generate an appropriate mapping for MedDRA --> SNOMED for CEM. I’m going to do the following:

1. Pull MedDRAs of interest from FAERS/AEOLUS and get frequency of usage from it.
2. “[01] Only 1 Vocab Map” - Using the 'SNOMED - MedDRA eq' relationship, any time there is only one SNOMED mapped to a MedDRA automatically assume it is what we want.
3. “[02] Exact String Match” - Look for exact match string between MedDRA CONCEPT_NAME to SNOMED CONCEPT_NAME
4. “[03] Select a Parent” - If there are multiple SNOMEDs mapped to a MedDRA look at their ancestors and pick the one they all share and that is closest in relationship distance. Exclude broad concepts like “Disease” or “Clinical Finding”
5. Else no map

Using this process, I was able to map about 40% of the codes (doesn’t mean the map is perfect – especially with the “[03] Select a Parent” option).

The next step would be to put this through USAGI. I would auto accept my mapping using “[01] Only 1 Vocab Map” and “[02] Exact String Match”. I would review “[03] Select a Parent” to make sure it didn’t go to high or to a bad spot. Then use USAGI to map things that didn’t get a map.

I am interested if you have any thoughts about our need for a MedDRA  SNOMED mapping for CEM and how to go about it.

---

For AEOLUS we shouldn't just use a Meddra to SNOMED mapping, we have learned this isn't very good.

I should look for some type of combination of: 1) Leverage frequency to know which codes are most important 2) Do exact string matching 3) See if the meddra mapping helps at all 4) USAGI

WITH CTE_FAERS_MEDDRA_USAGE AS (
    SELECT SOURCE_CODE_2 AS MEDDRA_CONCEPT_ID, c.CONCEPT_NAME AS MEDDRA_CONCEPT_NAME, c.VOCABULARY_ID AS MEDDRA_VOCABULARY_ID,
        COUNT(DISTINCT UNIQUE_IDENTIFIER) AS FAERS_DISTINCT_REPORT_TYPES, SUM(CASE_COUNT) AS FAERS_SUM_REPORT
    FROM CLEAN.AEOLUS a
        JOIN vocabulary.CONCEPT c
            ON CAST(c.CONCEPT_ID AS VARCHAR(100)) = a.SOURCE_CODE_2
            --AND c.CONCEPT_ID = 36718566
    GROUP BY SOURCE_CODE_2, c.CONCEPT_NAME, c.VOCABULARY_ID
), 
CTE_MEDDRA_TO_SNOMED AS (
    SELECT CAST(c.CONCEPT_ID AS VARCHAR(100)) AS MEDDRA_CONCEPT_ID, c.CONCEPT_NAME AS MEDDRA_CONCEPT_NAME, c.VOCABULARY_ID AS MEDDRA_VOCABUALRY_ID, 
        cr.RELATIONSHIP_ID,
        c2.CONCEPT_ID AS SNOMED_CONCEPT_ID, c2.CONCEPT_NAME AS SNOMED_CONCEPT_NAME, c2.VOCABULARY_ID AS SNOMED_VOCABULARY_ID, c2.DOMAIN_ID AS SNOMED_DOMAIN_ID
    FROM vocabulary.CONCEPT c
        JOIN vocabulary.CONCEPT_RELATIONSHIP cr
            ON cr.CONCEPT_ID_2 = c.CONCEPT_ID
            AND UPPER(cr.RELATIONSHIP_ID) = 'SNOMED - MEDDRA EQ'
        JOIN vocabulary.CONCEPT c2
            ON c2.CONCEPT_ID = cr.CONCEPT_ID_1
            AND UPPER(c2.DOMAIN_ID) = 'CONDITION'
), 
CTE_COUNT_SNOMED AS (
    SELECT MEDDRA_CONCEPT_ID, COUNT(DISTINCT SNOMED_CONCEPT_ID) AS SNOMED_COUNT
    FROM CTE_MEDDRA_TO_SNOMED
    GROUP BY MEDDRA_CONCEPT_ID
), 
CTE_SELECT_A_PARENT AS (
    SELECT *
    FROM (
        SELECT ms.MEDDRA_CONCEPT_ID, ms.MEDDRA_CONCEPT_NAME,
            c1.CONCEPT_ID AS SNOMED_CONCEPT_ID, c1.CONCEPT_NAME, SUM(MAX_LEVELS_OF_SEPARATION) AS SUM_DISTANCES, COUNT(DISTINCT ms.SNOMED_CONCEPT_ID) AS SNOMED_COUNT, 
            ROW_NUMBER() OVER (PARTITION BY ms.MEDDRA_CONCEPT_ID ORDER BY SUM(MAX_LEVELS_OF_SEPARATION)) AS ROW_NUM
        FROM CTE_MEDDRA_TO_SNOMED ms
            JOIN CTE_COUNT_SNOMED cs
                ON cs.MEDDRA_CONCEPT_ID = ms.MEDDRA_CONCEPT_ID
                AND SNOMED_COUNT > 1
            JOIN vocabulary.CONCEPT_ANCESTOR ca
                ON ca.DESCENDANT_CONCEPT_ID = ms.SNOMED_CONCEPT_ID
            JOIN vocabulary.CONCEPT c1
                ON c1.CONCEPT_ID = ca.ANCESTOR_CONCEPT_ID
                AND UPPER(c1.DOMAIN_ID) = 'CONDITION' 
                AND UPPER(c1.STANDARD_CONCEPT) = 'S'
        GROUP BY ms.MEDDRA_CONCEPT_ID, ms.MEDDRA_CONCEPT_NAME, c1.CONCEPT_ID, c1.CONCEPT_NAME, cs.SNOMED_COUNT
        HAVING COUNT(DISTINCT ms.SNOMED_CONCEPT_ID) = cs.SNOMED_COUNT
    ) z
    WHERE z.ROW_NUM = 1
),
CTE_EXACT_MATCH AS (
    SELECT CAST(c.CONCEPT_ID As VARCHAR(100)) AS MEDDRA_CONCEPT_ID, c2.CONCEPT_ID AS SNOMED_CONCEPT_ID
    FROM vocabulary.CONCEPT c
        JOIN vocabulary.CONCEPT c2
            ON UPPER(c2.CONCEPT_NAME) = UPPER(c.CONCEPT_NAME)
            AND UPPER(c2.DOMAIN_ID) = 'CONDITION'
            AND UPPER(c2.STANDARD_CONCEPT) = 'S'
    WHERE UPPER(c.VOCABULARY_ID) = 'MEDDRA'
), 
CTE_MAPPING_MEDDRA AS (
    SELECT DISTINCT 
        mu.MEDDRA_CONCEPT_ID, mu.MEDDRA_CONCEPT_NAME, MEDDRA_VOCABULARY_ID,
        ms.RELATIONSHIP_ID, 
        CASE
            WHEN cs.SNOMED_COUNT = 1 THEN '[01] Only 1 Vocab Map'
            WHEN em.SNOMED_CONCEPT_ID IS NOT NULL THEN '[02] Exact String Match'
            WHEN p.SNOMED_CONCEPT_ID IS NOT NULL THEN '[03] Select a Parent'
            ELSE NULL
        END AS SNOMED_MAPPING_TYPE,
        CASE
            WHEN cs.SNOMED_COUNT = 1 THEN ms.SNOMED_CONCEPT_ID
            WHEN em.SNOMED_CONCEPT_ID IS NOT NULL THEN em.SNOMED_CONCEPT_ID
            WHEN p.SNOMED_CONCEPT_ID IS NOT NULL THEN p.SNOMED_CONCEPT_ID
            ELSE NULL
        END AS SNOMED_CONCEPT_ID,
        cs.SNOMED_COUNT, 
        mu.FAERS_DISTINCT_REPORT_TYPES, 
        mu.FAERS_SUM_REPORT
    FROM CTE_FAERS_MEDDRA_USAGE mu
        LEFT OUTER JOIN CTE_COUNT_SNOMED cs
            ON cs.MEDDRA_CONCEPT_ID = mu.MEDDRA_CONCEPT_ID
        LEFT OUTER JOIN CTE_MEDDRA_TO_SNOMED ms
            ON mu.MEDDRA_CONCEPT_ID = ms.MEDDRA_CONCEPT_ID
        LEFT OUTER JOIN CTE_EXACT_MATCH em
            ON em.MEDDRA_CONCEPT_ID = mu.MEDDRA_CONCEPT_ID
        LEFT OUTER JOIN CTE_SELECT_A_PARENT p
            ON p.MEDDRA_CONCEPT_ID = mu.MEDDRA_CONCEPT_ID
            AND p.SNOMED_CONCEPT_ID NOT IN (
                /*BROAD CONCEPTS*/
                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            )
), 
CTE_FINAL_MAP AS (
    SELECT DISTINCT m.MEDDRA_CONCEPT_ID, m.MEDDRA_CONCEPT_NAME, m.MEDDRA_VOCABULARY_ID, 
        m.SNOMED_MAPPING_TYPE,
        c1.CONCEPT_ID AS SNOMED_CONCEPT_ID, c1.CONCEPT_NAME AS SNOMED_CONCEPT_NAME, c1.VOCABULARY_ID AS SNOMED_VOCABULARY_ID, 
        m.FAERS_DISTINCT_REPORT_TYPES, m.FAERS_SUM_REPORT
    FROM CTE_MAPPING_MEDDRA m
        LEFT OUTER JOIN vocabulary.CONCEPT c1
            ON c1.CONCEPT_ID = m.SNOMED_CONCEPT_ID
)
SELECT c.CONCEPT_CODE AS SOURCE_CODE, fm.MEDDRA_CONCEPT_ID AS SOURCE_CONCEPT_ID, c.VOCABULARY_ID AS SOURCE_VOCABULARY_ID,
    c.CONCEPT_NAME AS SOURCE_CODE_DESCRIPTION, 
    SNOMED_CONCEPT_ID AS TARGET_CONCEPT_ID, SNOMED_CONCEPT_NAME AS TARGET_CONCEPT_NAME,
    SNOMED_VOCABULARY_ID AS TARGET_VOCABULARY_ID,
    '1/1/1970' AS VALID_START_DATE,
    '12/31/2099' AS VALID_END_DATE,
    NULL AS INVALID_REASON, 
    SNOMED_MAPPING_TYPE, FAERS_DISTINCT_REPORT_TYPES, FAERS_SUM_REPORT
FROM CTE_FINAL_MAP fm
    JOIN vocabulary.CONCEPT c
        ON CAST(c.CONCEPT_ID AS VARCHAR(100)) = fm.MEDDRA_CONCEPT_ID
ORDER BY FAERS_SUM_REPORT DESC, SOURCE_CODE_DESCRIPTION

[ericaVoss]

Implemented everything except the USAGI mapping

[schuemie]

Maybe helpful: I notice that a lot of times the order of the words in a term is the only difference between MEDDRA and SNOMED. For example 'Jaundice neonatal' vs 'Neonatal jaundice'. You could get way more string matches if you did some more string normalization beforehand, like putting words in alphabetic order before matching.

Another normalization step to think of adding is stop word removal. For example, removing 'of' from 'Tuberculosis of spleen' will make it match with 'Spleen tuberculosis' after word-order normalization. In the past, I've used this highly restrictive set of stop words: 'of', 'the', 'and', and 'in', but you could go wild and use something like the PubMed Stop Word List.

I don't know how easy that is to do inside SQL, but it is trivial in R, especially when using the stringr package.

I think I would only do this in the subset of matches identified using the 'MedDRA - SNOMED eq' relationship to prevent spurious mappings, but I'm not sure how complete that mapping is.

[rkboyce]

Also, check out the following:

• Our friends at NLM did an analysis of using UMLS concept mappings to do the job. The results summarize many of the issues but indicate some sub-set of mappings that are possibly usable: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2815504/

• This work was extended and a manually curated set of mappings created focusing on AE terms that occur most frequently in a 1 year sample of FAERS: https://bmcmedinformdecismak.biomedcentral.com/articles/10.1186/1472-6947-10-66

-- Most of the mappings might still be useful - data file with the mapping was a supplement to the paper and is still available here - https://static-content.springer.com/esm/art%3A10.1186%2F1472-6947-10-66/MediaObjects/12911_2009_367_MOESM1_ESM.XLS

• Sauvignet advanced to work by using AE physiologic location and other semantic relationships: https://www.ncbi.nlm.nih.gov/pubmed/?term=27348725

-- We might be able to access their OntoADR tool but the last time I sent an email I received no reply.