Page Comparison

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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
TODO: add UNIONs to check other relationship tables other than concept_relationships

Code Block
SELECT c.id conceptId FROM concepts c WHERE c.terminology = :terminology AND NOT c.id IN (SELECT c.id FROM concepts c, concept_relationships cr WHERE cr.from_id = c.id AND cr.publishable = TRUE)

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

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Version	Old Version 24	New Version 25
Changes made by	jo	jo
Saved on	Jul 27, 2017	Aug 11, 2017

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