Added ICD10 description tiers

.sqlfluff

@@ -0,0 +1,7 @@
+[sqlfluff]
+templater = jinja
+dialect = athena
+sql_file_exts = .sql,.sql.jinja
+exclude_rules=
+    # UMLS uses reserved keywords as column names, tsk tsk
+    references.keywords

README.md

@@ -33,6 +33,13 @@ that concept A is a member of concept B (i.e. is a child, or is explicitly marke
 being a tradename/member belonging to the parent concept).
 - **mrconso_drugs** a subset of the entity list in mrconso, limited to vocabularies
 specifically dealing with drug identifiers (i.e. SNOMED, RxNorm, etc.)
+- **mrconso_icd10cm**/**mrrel__icd10cm** are slices of the respective main tables,
+only containing records from the ICD10 coding system
+- **icd10_(type)** are slices of a given coding system at the relevant level of the
+ICD10 hierarchy (category,block,chapter,code)
+- **icd10_tree** provides a relation-navigable code hierarchy of the individual levels
+in the ICD10 hierarchy
+
 
 ## Licensing details
 

cumulus_library_umls/__init__.py

@@ -1 +1 @@
-__version__ = "1.1.0"
+__version__ = "2.0.0"

cumulus_library_umls/ancilary_tables.sql

@@ -0,0 +1,349 @@
+-- A collection of convenience views for UMLS data
+
+-- Selecting only child relationships FROM mrrel
+CREATE TABLE IF NOT EXISTS umls__mrrel_is_a AS
+SELECT
+    cui1,
+    aui1,
+    stype1,
+    rel,
+    cui2,
+    aui2,
+    stype2,
+    rela,
+    rui,
+    srui,
+    sab,
+    sl,
+    rg,
+    dir,
+    suppress,
+    cvf
+FROM umls__mrrel
+WHERE (
+    rel = 'CHD'
+    OR rela IN (
+        'isa',
+        'tradename_of',
+        'has_tradename',
+        'has_basis_of_strength_substance'
+    )
+)
+AND rel NOT IN ('RB', 'PAR');
+
+-- Selecting only drug-related concepts FROM mrconso
+CREATE TABLE IF NOT EXISTS umls__mrconso_drugs AS
+SELECT
+    cui,
+    lat,
+    ts,
+    lui,
+    stt,
+    sui,
+    ispref,
+    aui,
+    saui,
+    scui,
+    sdui,
+    sab,
+    tty,
+    code,
+    str
+FROM umls__mrconso
+WHERE sab IN (
+    'ATC',
+    'CVX',
+    'DRUGBANK',
+    'GS',
+    'MED-RT',
+    'MMSL',
+    'MMX',
+    'MTHCMSFRF',
+    'MTHSPL',
+    'NDDF', 'RXNORM', 'SNOMEDCT_US', 'USP', 'VANDF'
+);
+
+-- ICD-10CM convenience views
+
+CREATE TABLE IF NOT EXISTS umls__mrconso_icd10cm AS
+SELECT
+    cui,
+    lat,
+    ts,
+    lui,
+    stt,
+    sui,
+    ispref,
+    aui,
+    saui,
+    scui,
+    sdui,
+    sab,
+    tty,
+    code,
+    str,
+    length(code) AS code_len
+FROM umls__mrconso
+WHERE sab = 'ICD10CM';
+
+CREATE TABLE IF NOT EXISTS umls__mrrel_icd10cm AS
+SELECT
+    cui1,
+    aui1,
+    stype1,
+    rel,
+    cui2,
+    aui2,
+    stype2,
+    rela,
+    rui,
+    srui,
+    sab,
+    sl,
+    rg,
+    dir,
+    suppress,
+    cvf
+FROM umls__mrrel
+WHERE sab = 'ICD10CM';
+
+-- The following views slice out individual ICD layers.
+-- This lines up with how a human might traverse the nomenclature to find
+-- a set of codes related to a specific condition.
+
+CREATE TABLE IF NOT EXISTS umls__icd10_chapter AS
+SELECT DISTINCT
+    r.rui,
+    r.cui1,
+    r.cui2,
+    c.tty,
+    c.code_len,
+    c.code,
+    c.str
+FROM umls__mrrel_icd10cm AS r,
+    umls__mrconso_icd10cm AS c
+WHERE
+    c.tty IN ('HT')
+    AND c.code LIKE '%-%'
+    AND r.cui1 = 'C2880081'
+    AND r.cui2 = c.cui
+ORDER BY c.code ASC;
+
+CREATE TABLE IF NOT EXISTS umls__icd10_block AS
+SELECT DISTINCT
+    r.rui,
+    r.cui1,
+    r.cui2,
+    c.tty,
+    c.code_len,
+    c.code,
+    c.str
+FROM umls__mrrel_icd10cm AS r,
+    umls__mrconso_icd10cm AS c,
+    umls__icd10_chapter AS par
+WHERE
+    c.tty IN ('HT')
+    AND r.rel = 'CHD'
+    AND c.code LIKE '%-%'
+    AND r.cui1 = par.cui2
+    AND r.cui2 = c.cui
+ORDER BY c.code ASC;
+
+CREATE TABLE IF NOT EXISTS umls__icd10_category AS
+SELECT DISTINCT
+    r.rui,
+    r.cui1,
+    r.cui2,
+    c.tty,
+    c.code_len,
+    c.code,
+    c.str
+FROM umls__mrrel_icd10cm AS r,
+    umls__mrconso_icd10cm AS c,
+    umls__icd10_block AS par
+WHERE
+    c.tty IN ('HT', 'PT')
+    AND c.code_len = 3
+    AND r.rel = 'CHD'
+    AND r.cui1 = par.cui2
+    AND r.cui2 = c.cui
+ORDER BY c.code ASC;
+
+CREATE TABLE IF NOT EXISTS umls__icd10_code AS
+
+WITH code_5 AS (
+    SELECT DISTINCT
+        r.rui,
+        r.cui1,
+        r.cui2,
+        c.tty,
+        c.code_len,
+        c.code,
+        c.str
+    FROM umls__mrrel_icd10cm AS r,
+        umls__mrconso_icd10cm AS c,
+        umls__icd10_category AS par
+    WHERE
+        c.tty IN ('HT', 'PT')
+        AND c.code LIKE '%.%'
+        AND (c.code_len = 5 OR c.code LIKE '%.%X%')
+        AND r.rel = 'CHD'
+        AND r.cui1 = par.cui2
+        AND r.cui2 = c.cui
+),
+
+code_6 AS (
+    SELECT DISTINCT
+        r.rui,
+        r.cui1,
+        r.cui2,
+        c.tty,
+        c.code_len,
+        c.code,
+        c.str
+    FROM umls__mrrel_icd10cm AS r,
+        umls__mrconso_icd10cm AS c,
+        code_5 AS par
+    WHERE
+        c.tty IN ('HT', 'PT')
+        AND c.code LIKE '%.%'
+        AND (c.code_len = 6 OR c.code LIKE '%.%X%')
+        AND r.rel = 'CHD'
+        AND r.cui1 = par.cui2
+        AND r.cui2 = c.cui
+),
+
+code_7 AS (
+    SELECT DISTINCT
+        r.rui,
+        r.cui1,
+        r.cui2,
+        c.tty,
+        c.code_len,
+        c.code,
+        c.str
+    FROM umls__mrrel_icd10cm AS r,
+        umls__mrconso_icd10cm AS c,
+        code_6 AS par
+    WHERE
+        c.tty IN ('HT', 'PT')
+        AND c.code LIKE '%.%'
+        AND (c.code_len = 7 OR c.code LIKE '%.%X%')
+        AND c.code LIKE '%.%'
+        AND r.rel = 'CHD'
+        AND r.cui1 = par.cui2
+        AND r.cui2 = c.cui
+    ORDER BY c.code ASC
+),
+
+code_8 AS (
+    SELECT DISTINCT
+        r.rui,
+        r.cui1,
+        r.cui2,
+        c.tty,
+        c.code_len,
+        c.code,
+        c.str
+    FROM umls__mrrel_icd10cm AS r,
+        umls__mrconso_icd10cm AS c,
+        code_7 AS par
+    WHERE
+        c.tty IN ('HT', 'PT')
+        AND c.code LIKE '%.%'
+        AND (c.code_len = 8 OR c.code LIKE '%.%X%')
+        AND c.code LIKE '%.%'
+        AND r.rel = 'CHD'
+        AND r.cui1 = par.cui2
+        AND r.cui2 = c.cui
+    ORDER BY c.code ASC
+)
+
+SELECT
+    rui,
+    cui1,
+    cui2,
+    tty,
+    code_len,
+    code,
+    str,
+    5 AS depth
+FROM code_5
+UNION
+SELECT
+    rui,
+    cui1,
+    cui2,
+    tty,
+    code_len,
+    code,
+    str,
+    6 AS depth
+FROM code_6
+UNION
+SELECT
+    rui,
+    cui1,
+    cui2,
+    tty,
+    code_len,
+    code,
+    str,
+    7 AS depth
+FROM code_7
+UNION
+SELECT
+    rui,
+    cui1,
+    cui2,
+    tty,
+    code_len,
+    code,
+    str,
+    8 AS depth
+FROM code_8;
+
+CREATE OR REPLACE VIEW umls__icd10_tree AS
+SELECT
+    rui,
+    cui1,
+    cui2,
+    tty,
+    code_len,
+    code,
+    str,
+    2 AS depth
+FROM umls__icd10_chapter
+UNION
+SELECT
+    rui,
+    cui1,
+    cui2,
+    tty,
+    code_len,
+    code,
+    str,
+    3 AS depth
+FROM umls__icd10_block
+UNION
+SELECT
+    rui,
+    cui1,
+    cui2,
+    tty,
+    code_len,
+    code,
+    str,
+    4 AS depth
+FROM umls__icd10_category
+UNION
+SELECT
+    rui,
+    cui1,
+    cui2,
+    tty,
+    code_len,
+    code,
+    str,
+    depth
+FROM umls__icd10_code

cumulus_library_umls/manifest.toml

@@ -3,7 +3,8 @@ study_prefix = "umls"
 [table_builder_config]
 file_names = [
     "umls_builder.py",
-    "static_builder.py"
+    "static_builder.py",
+    "ancilary_tables.sql"
 ]
 
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