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Add sat and rel data in rxnorm concepts
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@NikitaSinc
NikitaSinc committed Jan 10, 2024
1 parent 531b35b commit 95d5e24
Showing 1 changed file with 151 additions and 22 deletions.
173 changes: 151 additions & 22 deletions src/ftr/extraction/rxnorm.clj
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Original file line number Diff line number Diff line change
Expand Up @@ -84,23 +84,56 @@
["suppress" {:type "text"}]
["cvf" {:type "text"}]
["empt" {:type "text"}]
["idx" {:type "serial"}]]
:rxnrel-columns
[["rxcui1" {:type "text"}]
["rxaui1" {:type "text"}]
["stype1" {:type "text"}]
["rel" {:type "text"}]
["rxcui2" {:type "text"}]
["rxaui2" {:type "text"}]
["stype2" {:type "text"}]
["rela" {:type "text"}]
["rui" {:type "text"}]
["srui" {:type "text"}]
["sab" {:type "text"}]
["sl" {:type "text"}]
["rg" {:type "text"}]
["dir" {:type "text"}]
["suppress" {:type "text"}]
["cvf" {:type "text"}]
["empt" {:type "text"}]
["idx" {:type "serial"}]]
:rxnsat-columns
[["rxcui" {:type "text"}]
["lui" {:type "text"}]
["sui" {:type "text"}]
["rxaui" {:type "text"}]
["stype" {:type "text"}]
["code" {:type "text"}]
["atui" {:type "text"}]
["satui" {:type "text"}]
["atn" {:type "text"}]
["sab" {:type "text"}]
["atv" {:type "text"}]
["suppress" {:type "text"}]
["cvf" {:type "text"}]
["empt" {:type "text"}]
["idx" {:type "serial"}]]})


(defn prepare-rxnconso-table!
"Prepares the RXNCONSO table by dropping it if it exists and then creating it afresh.
RXNCONSO talbe represent info about RxNorm concepts.
(defn prepare-table!
"Prepares the table by dropping it if it exists and then creating it afresh.
Arguments:
Arguments:
db - the database connection to be used for executing the SQL commands."
[db]
(drop-table-if-exists db "RXNCONSO")
[db table-name table-columns]
(drop-table-if-exists db table-name)
(q! db
{:ql/type :pg/create-table
:table-name "RXNCONSO"
:table-name table-name
:if-not-exists true
:columns (:rxnconso-columns tables-columns)}))
:columns table-columns}))


(defn filter-out-known-files
Expand All @@ -109,7 +142,7 @@
Arguments
rxnorm-files - collection of files constucted by `get&wrap-rxnorm-files` fn"
[rxnorm-files]
(let [known-files #{"RXNCONSO.RRF"}]
(let [known-files #{"RXNCONSO.RRF" "RXNREL.RRF" "RXNSAT.RRF"}]
(into #{} (filter #(contains? known-files (:file-name %))) rxnorm-files)))


Expand Down Expand Up @@ -149,7 +182,9 @@
- `db`: A database connection string.
- `path`: The file path to the directory containing RxNorm RRF files."
[db path]
(prepare-rxnconso-table! db)
(prepare-table! db "RXNCONSO" (:rxnconso-columns tables-columns))
(prepare-table! db "RXNREL" (:rxnrel-columns tables-columns))
(prepare-table! db "RXNSAT" (:rxnsat-columns tables-columns))
(let [rxnorm-files (get&wrap-rxnorm-files path)
known-rxnorm-files (filter-out-known-files rxnorm-files)]
(doseq [{:keys [file table-name]} known-rxnorm-files]
Expand All @@ -167,8 +202,21 @@
:from :rxnconso
:where ^:pg/op[:<> :sab "RXNORM"]}) ;; Codes with sab != RXNORM - requires tricky licensing process, so we omit them.

(q! db {:ql/type :pg/delete
:from :rxnrel
:where ^:pg/op[:<> :sab "RXNORM"]})

(q! db {:ql/type :pg/delete
:from :rxnsat
:where ^:pg/op[:<> :sab "RXNORM"]})

(create-idx db :rxnconso "code")
(create-idx db :rxnconso "tty")))
(create-idx db :rxnconso "tty")
(create-idx db :rxnrel "rxcui1")
(create-idx db :rxnrel "rxcui2")
(create-idx db :rxnrel "rela")
(create-idx db :rxnsat "atv")
(create-idx db :rxnsat "atn")))


(defmethod u/*fn ::create-value-set [cfg]
Expand All @@ -192,7 +240,52 @@
(load-rxnorm-data db (or source-urls source-url))
{})


(def rxnsat-atn-collections
{:all ["AMBIGUITY_FLAG"
"NDC"
"ORIG_CODE"
"ORIG_SOURCE"
"RXN_ACTIVATED"
"RXN_AI"
"RXN_AM"
"RXN_AVAILABLE_STRENGTH"
"RXN_BN_CARDINALITY"
"RXN_BOSS_FROM"
"RXN_BOSS_STRENGTH_DENOM_UNIT"
"RXN_BOSS_STRENGTH_DENOM_VALUE"
"RXN_BOSS_STRENGTH_NUM_UNIT"
"RXN_BOSS_STRENGTH_NUM_VALUE"
"RXN_HUMAN_DRUG"
"RXN_IN_EXPRESSED_FLAG"
"RXN_OBSOLETED"
"RXN_QUALITATIVE_DISTINCTION"
"RXN_QUANTITY"
"RXN_STRENGTH"
"RXN_VET_DRUG"
"RXTERM_FORM"]

:multi ["ORIG_SOURCE"
"RXN_AM"
"RXN_BOSS_FROM"
"AMBIGUITY_FLAG"
"RXN_AVAILABLE_STRENGTH"
"RXN_OBSOLETED"
"RXN_ACTIVATED"
"ORIG_CODE"
"RXN_AI"]

:single ["RXN_IN_EXPRESSED_FLAG"
"RXN_HUMAN_DRUG"
"RXN_BOSS_STRENGTH_DENOM_VALUE"
"RXN_BOSS_STRENGTH_NUM_VALUE"
"RXN_QUANTITY"
"RXN_BOSS_STRENGTH_NUM_UNIT"
"RXN_BOSS_STRENGTH_DENOM_UNIT"
"RXN_BN_CARDINALITY"
"RXN_STRENGTH"
"RXN_VET_DRUG"
"RXTERM_FORM"
"RXN_QUALITATIVE_DISTINCTION"]})


(defmethod u/*fn ::create-concepts-copy-out-obj [{:as _cfg,
Expand All @@ -205,11 +298,11 @@
:select {:suppress :suppress
:rxcui :rxcui
:displays [:pg/sql "jsonb_agg(str order by CASE WHEN tty='SCD' THEN 110 WHEN tty='SCDG' THEN 120 WHEN tty='SCDF' THEN 130 WHEN tty='SCDC' THEN 140 WHEN tty='SBD' THEN 210 WHEN tty='SBDG' THEN 220 WHEN tty='SBDF' THEN 230 WHEN tty='SBDC' THEN 240 WHEN tty='MIN' THEN 310 WHEN tty='PIN' THEN 320 WHEN tty='IN' THEN 330 WHEN tty='GPCK' THEN 410 WHEN tty='BPCK' THEN 420 WHEN tty='PSN' THEN 510 WHEN tty='SY' THEN 520 WHEN tty='TMSY' THEN 530 WHEN tty='BN' THEN 610 WHEN tty='DF' THEN 710 WHEN tty='ET' THEN 720 WHEN tty='DFG' THEN 730 ELSE NULL END)"]}
;; ^--- RXCONSO might contain multiple entries for a single RXCUI value. These entries
;; represent various additional variations of the same atom. We empirically determine
;; the 'priorities' of such variations to select the primary variant for the 'display'
;; value, while preserving the additional variants in the 'other-display' property.
;; https://www.nlm.nih.gov/research/umls/rxnorm/docs/appendix5.html
;; ^--- RXCONSO might contain multiple entries for a single RXCUI value. These entries
;; represent various additional variations of the same atom. We empirically determine
;; the 'priorities' of such variations to select the primary variant for the 'display'
;; value, while preserving the additional variants in the 'other-display' property.
;; https://www.nlm.nih.gov/research/umls/rxnorm/docs/appendix5.html
:from :rxnconso
:group-by {:rxcui :rxcui :suppress :suppress}}}
:select {:ql/type :pg/select
Expand All @@ -222,10 +315,46 @@
:valueset
^:pg/fn[:jsonb_build_array (:url value-set)]
:property ^:pg/fn [:jsonb_strip_nulls
^:pg/obj {:other-display [:cond
[:= ^:pg/fn[:jsonb_array_length [:- :preparations.displays 0]] 0] nil
[:- :preparations.displays 0]]
:suppressible-flag :preparations.suppress}]}}
[:||
^:pg/obj {:other-display [:cond
[:= ^:pg/fn[:jsonb_array_length [:- :preparations.displays 0]] 0] nil
[:- :preparations.displays 0]]
:suppressible-flag :preparations.suppress}

{:ql/type :pg/cte
:with {:attrs
{:ql/type :pg/select
:select {:name :atn
:value ^:pg/fn[:jsonb_agg :atv]}
:from :rxnsat
:where [:and
[:= :rxcui :preparations.rxcui]
[:in :atn [:pg/params-list (:multi rxnsat-atn-collections)]]]
:group-by :atn
:union-all {:wha {:ql/type :pg/sub-select
:select {:name :atn
:value ^:pg/fn[:to_jsonb :atv]}
:from :rxnsat
:where [:and
[:= :rxcui :preparations.rxcui]
[:in :atn [:pg/params-list (:single rxnsat-atn-collections)]]]}}}}
:select {:ql/type :pg/select
:select ^:pg/fn[:jsonb_object_agg :name :value]
:from :attrs}}

{:ql/type :pg/cte
:with {:rels
{:ql/type :pg/select
:select {:relation :rela
:object ^:pg/fn[:jsonb_agg :rxcui1]}
:from :rxnrel
:where [:= :rxcui2 :preparations.rxcui]
:group-by :relation}}
:select {:ql/type :pg/select
:select ^:pg/fn[:jsonb_object_agg :relation :object]
:from :rels}

}]]}}
:from :preparations
:order-by :rxcui}}
pstmnt ^PreparedStatement (jdbc/prepare connection (dsql/format query) {:fetch-size 1000})]
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