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Overview

QA Bin Definitions

Parameters :terminology (e.g. NCIMTH) and :version (e.g. latest) are allowed in the queries.\

TODO:

  1. Look up definitions of bins (e.g. logically what do they do, we'll need descriptions too
  2. Write up description
  3. Write and test query (with :terminology/:version interpolations)

REQUIRED bins

  • nci_merge: Merged SCUI current version NCI atoms

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

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

    TBD: 
select distinct a.id conceptId 
from concepts a, concepts_atoms b, atoms c
where a.terminology = :terminology
  and a.id = b.concepts_id and b.atoms_id = c.id 
  and c.terminology in (select terminology from root_terminologies where family = 'NCI' and terminology != 'NCI')
group by a.id having count(distinct c.conceptId)>1

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

    -- ATOM Terminology = SNOMEDCT_US?  Because only project-terminology concepts are visible through UI...
 
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

    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|

    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

    SemanticType relationships?

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

    ShortForm/LongForm of what object?

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

     
unpublishable NCIMTH concepts?

NON-required bins

  • rxnorm_merge: RXCUI Merges

    • Same as nci_merge but with RXNORM

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

  • cbo_merge: Merged SCUI current version CBO atoms

    • Same as nci_merge but with CBO

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

  • mdr_merge: Merged SDUI current version MDR atoms

    SELECT 
    c.id clusterId, 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.terminology = 'MDR'
GROUP BY c.id
HAVING COUNT(DISTINCT a.descriptorId) > 1

  • pdq_merge: Merged SDUI current version PDQ atoms

    SELECT 
    c.id clusterId, 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.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

     

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

    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

    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)

    --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
    --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

    --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

  • multiple_pn: Concepts with multiple MTH/PN atoms

    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

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

  • pn_orphan: MTH/PNs on their own

    --Concepts whose only publishable atoms are MTH/PN or NCIMTH/PN

  • nosty: No STY

    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 cs.semanticTypes_id IS NULL

  • missing_sty: Reviewed concepts without releasable Semantic Types

    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

  • -- 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)
 
 



  • go_chem: Current version GO concepts with CHEM STYs

    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

    • See above

  • true_orphan: Concepts with no releaseable relationships to any other concept

    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

  • split_demotions: Demotions overlapping with a bad merge that was split
  • nci_pt_mrg: Merged current version NCI/PT atoms
  • mxsuppr: Concepts with identical LUI atoms that have mixed suppressibility

.~ Mixed status concepts 196 Sat Jan 7 09:19:47 2017
~ Suppressible preferred name (level 0,9) 0 Sat Jan 7 09:19:58 2017

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