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Rick Wood

Deborah Shapiro

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  • nci_merge: Merged SCUI current version NCI atoms

    Code Block
    select distinct c.id conceptId 
from concepts c, concepts_atoms ca, atoms a
where c.terminology = :terminology
  and c.id = ca.concepts_id and ca.atoms_id = a.id and a.publishable = true
  and a.terminology='NCI'
group by c.id having count(distinct a.conceptId)>1


  • nci_sub_split: Split SCUI current version NCI (or sub-source) atoms

    Code Block
    --Identify Sub-source atoms that aren't in the same concept as the NCI atom with the same conceptId
 
SELECT DISTINCT
    c.id conceptId1, c1.id conceptId2
FROM
    concepts c,
    concepts_atoms ca,
    atoms a,
    concepts c1,
    concepts_atoms ca1,
    atoms a1
WHERE
    c.terminology = :terminology
        AND c1.terminology = :terminology
        AND c.id = ca.concepts_id
        AND ca.atoms_id = a.id
        AND c1.id = ca1.concepts_id
        AND ca1.atoms_id = a1.id
        AND a.terminology = 'NCI'
        AND a1.terminology IN (SELECT 
            terminology
        FROM
            root_terminologies
        WHERE
            family = 'NCI' AND terminology != 'NCI')
        AND a.conceptId = a1.conceptId
        AND c.id != c1.id


  • sct_sepfnpt: SNOMED concept clusters where the FN and PT terms are separated

    Code Block
    SELECT DISTINCT
    c.id conceptId1, c1.id conceptId2
FROM
    concepts c,
    concepts_atoms ca,
    atoms a,
    concepts c1,
    concepts_atoms ca1,
    atoms a1
WHERE
    c.terminology = :terminology
        AND c1.terminology = :terminology
        AND a.terminology = 'SNOMEDCT_US'
        AND a1.terminology = 'SNOMEDCT_US'
        AND c.id = ca.concepts_id
        AND ca.atoms_id = a.id
        AND c1.id = ca1.concepts_id
        AND ca1.atoms_id = a1.id
        AND a.termType = 'FN'
        AND a1.termType = 'PT'
        AND a.conceptId = a1.conceptId
        AND c.id != c1.id


  • cdsty_coc: Find concepts with Clinical Drug STY and any other STY

    Code Block
    SELECT DISTINCT
    c.id conceptId
FROM
    concepts c,
    concepts_semantic_type_components cs
WHERE
    c.terminology = :terminology
        AND c.id = cs.concepts_id
        AND cs.concepts_id IN (SELECT 
            cs.concepts_id
        FROM
            concepts c,
            concepts_semantic_type_components cs,
            semantic_type_components s
        WHERE
            c.terminology = :terminology
                AND c.id = cs.concepts_id
                AND cs.semanticTypes_id = s.id
                AND s.semanticType = 'Clinical Drug')
GROUP BY cs.concepts_id
HAVING COUNT(cs.concepts_id) > 1


  • multsty:concepts with more than 3 STYs|

    Code Block
    SELECT DISTINCT
    cs.concepts_id conceptId
FROM
	concepts c,
    concepts_semantic_type_components cs,
    semantic_type_components s
WHERE
	c.terminology = :terminology
	AND c.id = cs.concepts_id
    AND cs.semanticTypes_id = s.id
GROUP BY c.id
HAVING COUNT(c.id) > 3


  • styisa:One STY is an ancestor of another in the STY isa hierarchy

    Code Block
    select t1.conceptId from 
(select c.id conceptId, st.id styId, st.treeNumber from concepts c, concepts_semantic_type_components cstc, (select stc.id, st.treeNumber from semantic_type_components stc join semantic_types st on (stc.semanticType = st.expandedForm)) st
WHERE c.terminology = :terminology
AND c.id = cstc.concepts_id
AND cstc.semanticTypes_id = st.id) t1
JOIN 
(select c.id conceptId, st.id styId, st.treeNumber from concepts c, concepts_semantic_type_components cstc, (select stc.id, st.treeNumber from semantic_type_components stc join semantic_types st on (stc.semanticType = st.expandedForm)) st
WHERE c.terminology = :terminology
AND c.id = cstc.concepts_id
AND cstc.semanticTypes_id = st.id) t2
on  (t1.conceptId = t2.conceptId and t1.styId != t2.styId and t1.treeNumber != t2.treeNumber)
WHERE t2.treeNumber like concat(t1.treeNumber, '.%')


  • sfo_lfo: Short form in one concept, long form in another

    Code Block
    --ShortForm/LongForm are related atoms
  -- These live in the DB as "SY" atom relationships with RELA value either equal to "expanded_form_of" or starting with "mth_" and ending with "_form_of"
 
SELECT 
    c1.id conceptId1, c2.id conceptId2
FROM
    concepts c1,
    concepts_atoms ca1,
    atoms a1,
    concepts c2,
    concepts_atoms ca2,
    atoms a2,
    (SELECT 
        ar.from_id, ar.to_id
    FROM
        atom_relationships ar
    WHERE
        publishable = TRUE
            AND relationshipType = 'SY'
            AND (additionalRelationshipType = 'expanded_form_of'
            OR additionalRelationshipType LIKE 'mth_%_form_of')) sfoLfoRels
WHERE
    c1.terminology = 'NCIMTH'
        AND c2.terminology = 'NCIMTH'
        AND c1.id = ca1.concepts_id
        AND ca1.atoms_id = a1.id
        AND c2.id = ca2.concepts_id
        AND ca2.atoms_id = a2.id
        AND a1.id = sfoLfoRels.from_id
        AND a2.id = sfoLfoRels.to_id
        AND c1.id != c2.id


  • deleted_cui: CUIs that are going away - will need bequeathal rel

    Code Block
    SELECT
DISTINCT   DISTINCT  c.id conceptId
FROM
    concepts c,
    concepts_atoms ca,
 
  atoms a
WHERE

   c.terminology = :terminology'NCIMTH'
  AND c.id != c.terminologyId
  AND c.id = ca.concepts_id
     
  AND ca.atoms_id = a.id
     
  AND a.publishable = TRUE
     FALSE
  AND NOT c.id IN (SELECT
DISTINCT    SELECT
      DISTINCT  c.id conceptId
   
    FROM
     
      concepts c,
     
      concepts_atoms ca,
     
      atoms a
    WHERE
   WHERE   c.terminology = 'NCIMTH'
      AND c.terminologyid = :terminologyca.concepts_id
                AND c.id = ca.concepts_id
                AND ca.AND ca.atoms_id = a.id
     
          AND a.publishable = FALSE)

     

     

    deleted_cui_nomth - requested by Lori, not tested yet

    Code Block
    SELECT DISTINCT
 TRUE
  )
  c.id conceptId
FROM
    concepts c,
    concepts_atoms ca,
    atoms a
WHERE
    c.terminology = :terminology
        AND c.id = ca.concepts_id
        AND ca.atoms_id = a.id
        AND a.suppressible = TRUE
        AND NOT c.id IN (SELECT DISTINCT
            c.id conceptId
        FROM
            concepts c,
            concepts_atoms ca,
            atoms a
        WHERE
            c.terminology = :terminology
                AND c.id = ca.concepts_id
    AND NOT c.id IN (
    SELECT
      ANDDISTINCT cac.atoms_id conceptId
= a.id   FROM
      concepts c,
     AND a.suppressible = FALSE) concept_relationships cr
    WHERE
    AND NOT c.idterminology IN= ('NCIMTH'
        SELECTAND c.id conceptId= cr.from_id
      AND FROMcr.relationshipType like 'B%'
  )
  AND     conceptsNOT c,.id IN (
    SELECT
     concepts_atoms ca,
 c.id conceptId
    FROM
      atomsconcepts ac,
        WHERE
concepts_atoms ca
    WHERE
      c.terminology =:terminology 'NCIMTH'
      AND c.id = ca.concepts_id
      AND a.terminology='MTH'ca.concepts_id IN (
        SELECT
       AND c.id = ca.concepts_id
        FROM
          ANDconcepts_atoms ca.atoms_id = a.id,
          atoms a
        WHERE
  AND a.publishable = TRUE     ca.atoms_id = a.id
 MINUS         SELECTAND c.id conceptIda.terminology IN ('MTH', 'NCIMTH')
        FROM  AND a.termType = 'PN'
      )
concepts c,   GROUP BY
        ca.concepts_atomsid
ca,    HAVING
      COUNT(DISTINCT  atoms aca.atoms_id) = 1
  )
  AND NOT c.id WHEREIN (
    SELECT
      c.terminology=:terminology
ca.concepts_id conceptId
    FROM
      mrcui mr,
  AND a.terminology!='MTH'   atomjpa_conceptterminologyids ac,
            AND c.id = ca.concepts_idconcepts_atoms ca,
      concepts cpt
    WHERE
    AND  camr.atoms_idcui1 = aac.idconceptTerminologyIds
      AND ca.atoms_id = ac.AtomJpa_id
      AND acpt.publishableid = TRUEca.concepts_id
      AND cpt.terminology = 'NCIMTH'
      )AND ac.conceptTerminologyIds_KEY = 'NCIMTH'
      AND mr.rel = 'DEL'
   )

     

     

NON-required bins

  • rxnorm_merge: RXCUI Merges

    • Same as nci_merge but with RXNORM

      Code Block
      select distinct c.id conceptId 
from concepts c, concepts_atoms ca, atoms a
where c.terminology = :terminology
  and c.id = ca.concepts_id and ca.atoms_id = a.id and a.publishable = true
  and a.terminology='RXNORM'
group by a.conceptId having count(distinct c.id)>1



  • cbo_merge: Merged SCUI current version CBO atoms

    • Same as nci_merge but with CBO

      Code Block
      select distinct c.id conceptId 
from concepts c, concepts_atoms ca, atoms a
where c.terminology = :terminology
  and c.id = ca.concepts_id and ca.atoms_id = a.id and a.publishable = true
  and a.terminology='CBO'
group by c.id having count(distinct a.conceptId)>1


  • mdr_merge: Merged SDUI current version MDR atoms

    Code Block
    select distinct c.id conceptId 
from concepts c, concepts_atoms ca, atoms a
where c.terminology = :terminology
  and c.id = ca.concepts_id and ca.atoms_id = a.id and a.publishable = true
  and a.terminology='MDR'
group by c.id having count(distinct a.descriptorId)>1


  • pdq_merge: Merged SDUI current version PDQ atoms

    Code Block
    select distinct c.id conceptId 
from concepts c, concepts_atoms ca, atoms a
where c.terminology = :terminology
  and c.id = ca.concepts_id and ca.atoms_id = a.id and a.publishable = true
  and a.terminology='PDQ'
group by c.id having count(distinct a.descriptorId)>1


  • sct_sepfnpt: SNOMED concept clusters where the FN and PT terms are separated
    • DUPLICATE of above

  • rxnorm_split: RXCUI splits

    Code Block
    select distinct c.id conceptId 
from concepts c, concepts_atoms ca, atoms a
where c.terminology = :terminology
  and c.id = ca.concepts_id and ca.atoms_id = a.id and a.publishable = true
  and a.terminology='RXNORM'
group by a.conceptId having count(distinct c.id)>1


  • nci_pdq_merge: Concepts containing current version NCI and current version PDQ atoms

    Code Block
    SELECT DISTINCT
    c.id conceptId
FROM
    atoms a,
    atoms a1,
    concepts c,
    concepts c1,
    concepts_atoms ca,
    concepts_atoms ca1,
    terminologies t,
    terminologies t1
WHERE
    c.terminology = :terminology
        AND c1.terminology = :terminology
        AND c.id = ca.concepts_id
        AND ca.atoms_id = a.id
        AND c1.id = ca1.concepts_id
        AND ca1.atoms_id = a1.id
        AND a.terminology = 'NCI'
        AND a.terminology = t.terminology
        AND a.version = t.version
        AND t.current = TRUE
        AND a1.terminology = 'PDQ'
        AND a1.terminology = t1.terminology
        AND a1.version = t1.version
        AND t1.current = TRUE
        AND c.id = c1.id


  • nci_sct_merge: Concepts containing current version NCI and current version SNOMEDCT atoms

    Code Block
    SELECT DISTINCT
    c.id conceptId
FROM
    atoms a,
    atoms a1,
    concepts c,
    concepts c1,
    concepts_atoms ca,
    concepts_atoms ca1,
    terminologies t,
    terminologies t1
WHERE
    c.terminology = :terminology
        AND c1.terminology = :terminology
        AND c.id = ca.concepts_id
        AND ca.atoms_id = a.id
        AND c1.id = ca1.concepts_id
        AND ca1.atoms_id = a1.id
        AND a.terminology = 'NCI'
        AND a.terminology = t.terminology
        AND a.version = t.version
        AND t.current = TRUE
        AND a1.terminology = 'SNOMEDCT_US'
        AND a1.terminology = t1.terminology
        AND a1.version = t1.version
        AND t1.current = TRUE
        AND c.id = c1.id


  • ambig_no_pn: Ambiguous concepts where at least one has no MTH/PN nor NCIMTH/PN (sepstring)

    Code Block
    --Ambiguous concept = concepts that share atoms that have the same case-insensitive name
-- This is used by several of the below queries, so it should be created as a VIEW
 
CREATE VIEW ambig_concepts AS
    SELECT DISTINCT
        c1.id conceptId1, c2.id conceptId2
    FROM
        concepts c1,
        concepts_atoms ca1,
        atoms a1,
        concepts c2,
        concepts_atoms ca2,
        atoms a2
    WHERE
        c1.terminology = 'NCIMTH'
            AND c2.terminology = 'NCIMTH'
            AND c1.id = ca1.concepts_id
            AND ca1.atoms_id = a1.id
            AND c2.id = ca2.concepts_id
            AND ca2.atoms_id = a2.id
            AND c1.id < c2.id
            AND a1.lowerNameHash = a2.lowerNameHash
            AND a1.id != a2.id
            AND a1.publishable = TRUE
            AND a2.publishable = TRUE


    Code Block
    --Use Pre-programmed View ambig_concepts
 
SELECT 
    conceptId1, conceptId2
FROM
    ambig_concepts
WHERE
    NOT ambig_concepts.conceptId1 IN (SELECT 
            ca.concepts_id
        FROM
            concepts_atoms ca,
            atoms a
        WHERE
            ca.atoms_id = a.id
                AND a.terminology IN ('NCIMTH' , 'MTH')
                AND a.termType = 'PN')
        AND NOT ambig_concepts.conceptId2 IN (SELECT 
            ca.concepts_id
        FROM
            concepts_atoms ca,
            atoms a
        WHERE
            ca.atoms_id = a.id
                AND a.terminology IN ('NCIMTH' , 'MTH')
                AND a.termType = 'PN')


  • ambig_no_rel: Ambiguous concepts that lack an approved REL

    Code Block
    --Use Pre-programmed View ambig_concepts

SELECT 
    conceptId1, conceptId2
FROM
    ambig_concepts
WHERE
    NOT (conceptId1 , conceptId2) IN (SELECT 
            cr.from_id, cr.to_id
        FROM
            concept_Relationships cr
        WHERE
            cr.publishable = TRUE
            AND cr.workflowStatus in ('READY_FOR_PUBLICATION','PUBLISHED'))


  • pn_pn_ambig: Identical (same SUI) PN's in multiple concepts

    Code Block
    SELECT 
    c1.id conceptId1, c2.id conceptId2
FROM
    concepts c1,
    concepts c2,
    concepts_atoms ca1,
    concepts_atoms ca2,
    (SELECT 
        a1.id atomId1, a2.id atomId2
    FROM
        atoms a1, atoms a2
    WHERE
        a1.termType = 'PN'
            AND a2.termType = 'PN'
            AND a1.stringClassId = a2.stringClassId
            AND a1.id != a2.id) identicalPNAtoms
WHERE
    c1.terminology = :terminology
        AND c2.terminology = :terminology
        AND c1.id = ca1.concepts_id
        AND c2.id = ca2.concepts_id
        AND ca1.atoms_id = identicalPNAtoms.atomId1
        AND ca2.atoms_id = identicalPNAtoms.atomId2
        AND c1.id != c2.id


  • multiple_pn: Concepts with multiple MTH/PN atoms

    Code Block
    SELECT DISTINCT
    c.id conceptId
FROM
    concepts c,
    atoms a,
    concepts_atoms ca
WHERE
    c.terminology = :terminology
        AND c.id = ca.concepts_id
        AND ca.atoms_id = a.id
        AND a.terminology in ('MTH', 'NCIMTH')
        AND a.termType = 'PN'
GROUP BY c.id
HAVING COUNT(c.id) > 1


  • pn_no_ambig: Concept has MTH/PN atom but no ambiguous string

    Code Block
    select distinct c.id conceptId 
from concepts c, concepts_atoms ca, atoms a
where c.terminology = :terminology
  and c.id = ca.concepts_id and ca.atoms_id = a.id and a.publishable = true
  and a.terminology in ('NCIMTH','MTH')
  and a.termType = 'PN'
  and not c.id in (select conceptId1 from ambig_concepts)


  • ambig_pn: MTH/PN atom is ambiguous but has no matching ambiguous string

    Drop. No longer useful. 

  • pn_orphan: MTH/PNs on their own

    Code Block
    --Concepts whose only publishable atoms are MTH/PN or NCIMTH/PN
 
SELECT 
    c.id conceptId
FROM
    concepts c,
    concepts_atoms ca
WHERE
    c.terminology = :terminology
        AND c.id = ca.concepts_id
        AND ca.concepts_id IN (SELECT 
            ca.concepts_id
        FROM
            concepts_atoms ca,
            atoms a
        WHERE
            ca.atoms_id = a.id
                AND a.terminology IN ('MTH' , 'NCIMTH')
                AND a.termType = 'PN'
                AND a.publishable = true)
GROUP BY ca.concepts_id
HAVING COUNT(DISTINCT ca.atoms_id) = 1


  • nosty: No STY

    Code Block
    SELECT DISTINCT
    c.id conceptId
FROM
    concepts c
        LEFT JOIN
    concepts_semantic_type_components cs ON (c.id = cs.concepts_id)
WHERE
	c.terminology= :terminology
    AND c.publishable = TRUE
    AND cs.semanticTypes_id IS NULL


  • missing_sty: Reviewed concepts without releasable Semantic Types

    Code Block
    SELECT DISTINCT
    c.id conceptId
FROM
    concepts c
WHERE
    c.terminology = :terminology
        AND c.publishable = TRUE
        AND c.workflowStatus IN ('READY_FOR_PUBLICATION' , 'PUBLISHED')
        AND NOT c.id IN (SELECT 
            c.id
        FROM
            concepts c,
            concepts_semantic_type_components cs,
            semantic_type_components s
        WHERE
            c.terminology = :terminology
                AND c.id = cs.concepts_id
                AND cs.semanticTypes_id = s.id
                AND s.publishable = TRUE)


  • cbo_chem: Current version CBO concepts with CHEM STYs

    Code Block
    -- to find chemical semantic types
(select distinct semanticTypeCategoryMap sty
from projects a, ProjectJpa_semanticTypeCategoryMap b
where a.id = b.ProjectJpa_id
  and semanticTypeCategoryMap_KEY = 'chemical'
  and a.terminology = :terminology);
 
-- Rick update 3/2/2017
(select distinct semanticTypeCategoryMap_KEY sty
from projects a, ProjectJpa_semanticTypeCategoryMap b
where a.id = b.ProjectJpa_id
  and semanticTypeCategoryMap = 'chem'
  and a.terminology = :terminology)
 
 


    Code Block
    SELECT DISTINCT
    c.id conceptId
FROM
    concepts c,
    concepts_semantic_type_components cs,
    semantic_type_components s,
    terminologies t
WHERE
    c.terminology = 'CBO'
        AND c.terminology = t.terminology
        AND c.version = t.version
        AND t.current = TRUE
        AND c.id = cs.concepts_id
        AND cs.semanticTypes_id = s.id
        AND s.semanticType IN ((SELECT DISTINCT
            semanticTypeCategoryMap_KEY sty
        FROM
            projects a,
            ProjectJpa_semanticTypeCategoryMap b
        WHERE
            a.id = b.ProjectJpa_id
                AND semanticTypeCategoryMap = 'chem'
                AND a.terminology = :terminology))



  • go_chem: Current version GO concepts with CHEM STYs

    Code Block
    SELECT DISTINCT
    c.id conceptId
FROM
    concepts c,
    concepts_semantic_type_components cs,
    semantic_type_components s,
    terminologies t
WHERE
    c.terminology = 'GO'
        AND c.terminology = t.terminology
        AND c.version = t.version
        AND t.current = TRUE
        AND c.id = cs.concepts_id
        AND cs.semanticTypes_id = s.id
        AND s.semanticType IN ((SELECT DISTINCT
            semanticTypeCategoryMap_KEY sty
        FROM
            projects a,
            ProjectJpa_semanticTypeCategoryMap b
        WHERE
            a.id = b.ProjectJpa_id
                AND semanticTypeCategoryMap = 'chem'
                AND a.terminology = :terminology))


  • mdr_chem: Current version MDR concepts with CHEM STYs

    Code Block
    SELECT DISTINCT
    c.id conceptId
FROM
    concepts c,
    concepts_semantic_type_components cs,
    semantic_type_components s,
    terminologies t
WHERE
    c.terminology = 'MDR'
        AND c.terminology = t.terminology
        AND c.version = t.version
        AND t.current = TRUE
        AND c.id = cs.concepts_id
        AND cs.semanticTypes_id = s.id
        AND s.semanticType IN ((SELECT DISTINCT
            semanticTypeCategoryMap_KEY sty
        FROM
            projects a,
            ProjectJpa_semanticTypeCategoryMap b
        WHERE
            a.id = b.ProjectJpa_id
                AND semanticTypeCategoryMap = 'chem'
                AND a.terminology = :terminology))


  • true_orphan: Concepts with no releasable relationships to any other concept
    Uses the "deep relationships" query; only needs to search FROM role since rels are bidirectional

    Code Block
    SELECT c.id conceptId
FROM concepts c
WHERE c.terminology = :terminologyterminolgy
AND c.publishable=TRUE
AND NOT EXISTS
    (SELECT * FROM deep_concept_relationships dcr
     WHERE role='FROM' AND
     c.id = dcr.concepts_id)


  • deleted_cui_split: Complex split/merge case CUIs that are going away - will need bequeathal

    Drop

  • split_demotions: Demotions overlapping with a bad merge that was split
    Drop. No longer useful. 

     

  • nci_pt_mrg: Merged current version NCI/PT atoms

    Code Block
    SELECT DISTINCT
    c.id conceptId
FROM
    concepts c,
    atoms a,
    concepts_atoms ca
WHERE
    c.terminology = :terminology
        AND c.id = ca.concepts_id
        AND ca.atoms_id = a.id
        AND a.terminology in ('NCI')
        AND a.termType = 'PT'
GROUP BY c.id
HAVING COUNT(c.id) > 1


  • mxsuppr: Concepts with identical LUI atoms that have mixed suppressibility

    Code Block
     SELECT DISTINCT
    c.id conceptId
FROM
    concepts c,
    concepts_atoms ca1,
    concepts_atoms ca2,
    (SELECT 
        a1.id atomId1, a2.id atomId2
    FROM
        atoms a1, atoms a2
    WHERE
        a1.lexicalClassId = a2.lexicalClassId
            AND a1.id != a2.id
            AND a1.publishable = TRUE
            AND a2.publishable = TRUE
            AND a1.suppressible != a2.suppressible) mixedSuppresLuiAtoms
WHERE
    c.terminology = :terminology
        AND c.id = ca1.concepts_id
        AND ca1.atoms_id = mixedSuppresLuiAtoms.atomId1
        AND ca2.atoms_id = mixedSuppresLuiAtoms.atomId2
        AND ca1.concepts_id = ca2.concepts_id


...