Page Comparison

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nci_merge: Merged SCUI current version NCI atoms

Code Block

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

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

Code Block

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

Code Block

-- 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--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 c1ca1.terminologyatoms_id = :terminologya1.id
        AND a.terminology = 'SNOMEDCT_USNCI'
        AND a1.terminology = 'SNOMEDCT_US'IN (SELECT 
       AND c.id = ca.concepts_id  terminology
      AND ca.atoms_id =FROM
a.id         AND c1.id = ca1.conceptsroot_idterminologies
        ANDWHERE
ca1.atoms_id = a1.id         AND a.termTypefamily = 'FNNCI'         AND a1.termTypeterminology != 'PTNCI')
        AND a.conceptId = a1.conceptId
        AND c.id != c1.id;

cdstysct_coc: Find concepts with Clinical Drug STY and any other STYsepfnpt: SNOMED concept clusters where the FN and PT terms are separated

Code Block

SELECT DISTINCT
    c.id conceptIdconceptId1, c1.id conceptId2
FROM
    concepts c,
    concepts_semantic_type_components cs
WHEREatoms ca,
     c.terminology = :terminologyatoms a,
    concepts c1,
   AND c.id = cs.concepts_idatoms ca1,
    atoms a1
WHERE
AND cs.concepts_id IN (SELECT c.terminology = :terminology
        AND  cs.concepts_id
 c1.terminology = :terminology
      FROM  AND a.terminology = 'SNOMEDCT_US'
       concepts c,AND a1.terminology = 'SNOMEDCT_US'
        AND c.id = ca.concepts_semantic_type_components cs,id
        AND ca.atoms_id = a.id
 semantic_type_components s      AND c1.id = WHEREca1.concepts_id
        AND ca1.atoms_id =  c.terminology = :terminologya1.id
        AND a.termType = 'FN'
        AND ca1.idtermType = cs.concepts_id'PT'
        AND a.conceptId = a1.conceptId
        AND csc.semanticTypes_id != sc1.id

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

Code Block

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

multsty:concepts with more than 3 STYs|

Code Block

SELECT DISTINCTIN (SELECT 
            cs.concepts_id
conceptId        FROM
	            concepts c,
            concepts_semantic_type_components cs,
            semantic_type_components s
WHERE  	c.terminology = :terminology
	    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
SemanticType relationships?

sfo_lfo: Short form in one concept, long form in another
Code Block
ShortForm/LongForm of what object?
deleted_cui: CUIs that are going away - will need bequeathal rel
Code Block
unpublishable NCIMTH concepts?

NON-required bins

rxnorm_merge

: RXCUI Merges

Same as nci_merge but with RXNORM

Code Block

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

Code Block

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

Code Block
SELECT c.id clusterId, c.id conceptId FROM concepts c, 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 c.id conceptId
FROM
  concepts c,
  concepts_atoms ca,
  atoms a
WHERE
  c.terminology = 'NCIMTH'
  AND c.id != c.terminologyId
  AND c.id = ca.concepts_id
  AND ca.atoms_id = a.id
  AND a.publishable = FALSE
  AND NOT c.id IN (
    SELECT
      DISTINCT c.id conceptId
    FROM
      concepts c,
      concepts_atoms ca,
      atoms a
    WHERE
      c.terminology = 'NCIMTH'
      AND c.id = ca.concepts_id
      AND ca.atoms_id = a.id
      AND a.publishable = TRUE
  )
  AND NOT c.id IN (
    SELECT
      DISTINCT c.id conceptId
    FROM
      concepts c,
      concept_relationships cr
    WHERE
      c.terminology = 'NCIMTH'
      AND c.id = cr.from_id
      AND cr.relationshipType like 'B%'
  )
  AND NOT c.id IN (
    SELECT
      c.id conceptId
    FROM
      concepts c,
      concepts_atoms ca
    WHERE
      c.terminology = 'NCIMTH'
      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'
      )
    GROUP BY
      ca.concepts_id
    HAVING
      COUNT(DISTINCT ca.atoms_id) = 1
  )
  AND NOT c.id IN (
    SELECT
      ca.concepts_id conceptId
    FROM
      mrcui mr,
      atomjpa_conceptterminologyids ac,
      concepts_atoms ca,
      concepts cpt
    WHERE
      mr.cui1 = ac.conceptTerminologyIds
      AND ca.atoms_id = ac.AtomJpa_id
      AND cpt.id = ca.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     c.terminology =atoms :terminologya
        ANDWHERE
c.id = ca.concepts_id         AND ca.atoms_id = a.id
                AND a.terminology =IN ('MDRNCIMTH' GROUP BY c.id
HAVING COUNT(DISTINCT a.descriptorId) > 1

pdq_merge: Merged SDUI current version PDQ atoms

Code Block
SELECT, 'MTH') c.id clusterId, c.id conceptId FROM AND a.termType = 'PN')

ambig_no_rel: Ambiguous concepts

c, concepts_atoms ca,
that lack an approved REL
Code Block
--Use Pre-programmed View ambig_concepts SELECT conceptId1, atomsconceptId2 aFROM WHERE c.terminology = :terminologyambig_concepts WHERE NOT (conceptId1 , conceptId2) IN (SELECT AND c.id = ca.concepts_id AND cacr.atomsfrom_id, = acr.to_id FROM 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

Code Block
SELECT DISTINCT_Relationships cr WHERE c.id conceptId FROMcr.publishable = TRUE atoms a, AND cr.workflowStatus in ('READY_FOR_PUBLICATION','PUBLISHED'))

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

Code Block

SELECT 
 atoms a1,  c1.id conceptId1, c2.id conceptsconceptId2
c,FROM
    concepts c1,
    concepts_atoms cac2,
    concepts_atoms ca1,
    terminologiesconcepts_atoms tca2,
    terminologies t1
WHERE
    c.terminology = :terminology
        AND c1.terminology = :terminology
        AND c.id = ca.concepts_id(SELECT 
       AND caa1.atoms_id =atomId1, aa2.id atomId2
    FROM
  AND c1.id = ca1.concepts_id   atoms a1, atoms a2
  AND ca1.atoms_id = a1.id WHERE
        AND aa1.terminologytermType = 'NCIPN'
        AND a.terminology = t.terminology AND a2.termType = 'PN'
    AND a.version = t.version     AND a1.stringClassId = a2.stringClassId
AND t.current = TRUE         AND a1.terminologyid != 'PDQ'
 a2.id) identicalPNAtoms
WHERE
      AND a1c1.terminology = t1.:terminology
        AND a1c2.versionterminology = t1.version:terminology
        AND t1c1.currentid = TRUEca1.concepts_id
        AND cc2.id = c1ca2.id

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

Code Block

SELECT DISTINCT
    c.id conceptId
FROMconcepts_id
    atoms a,    AND ca1.atoms a1,_id = identicalPNAtoms.atomId1
    concepts c,   AND  concepts c1,ca2.atoms_id = identicalPNAtoms.atomId2
     concepts_atoms ca,  AND c1.id  concepts_atoms ca1,!= c2.id

multiple_pn: Concepts with multiple MTH/PN atoms

Code Block

SELECT DISTINCT
    c.id terminologiesconceptId
t,FROM
    terminologiesconcepts t1c,
WHERE    atoms c.terminologya,
= :terminology   concepts_atoms ca
WHERE
   AND c1c.terminology = :terminology
        AND c.id = ca.concepts_id
        AND ca.atoms_id = a.id
        AND c1a.id = ca1.concepts_idterminology in ('MTH', 'NCIMTH')
        AND ca1a.atoms_idtermType = a1.id
        AND a.terminology = 'NCI'
        AND a'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 = t.:terminology
  and c.id = ca.concepts_id and  AND a.versionca.atoms_id = ta.versionid         AND t.currentand a.publishable = TRUEtrue
        AND a1and a.terminology =in 'SNOMEDCT_US'('NCIMTH','MTH')
        AND a1.terminologyand a.termType = t1.terminology'PN'
  and not c.id in (select conceptId1 AND a1.version = t1.version
        AND t1.current = TRUE
   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 ANDconcepts 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_atoms thatca
shareWHERE
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 DISTINCTc.terminology = :terminology
        AND c.id = ca.concepts_id
        AND ca.concepts_id IN (SELECT 
          c1.id conceptId1, c2ca.concepts_id conceptId2
    FROM      FROM
  concepts c1,         concepts_atoms ca1ca,
        atoms  a1,  atoms a
     concepts  c2, WHERE
       concepts_atoms ca2,    ca.atoms_id = a.id
  atoms a2     WHERE        AND c1a.terminology =IN ('MTH' , 'NCIMTH')
                AND c2a.terminologytermType = 'NCIMTHPN'
                AND c1a.idpublishable = ca1.concepts_id
     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
AND ca1.atoms_id = a1.id     LEFT JOIN
    concepts_semantic_type_components cs ANDON c2(c.id = ca2cs.concepts_id)
WHERE
	c.terminology= :terminology
         AND ca2c.atoms_idpublishable = a2.idTRUE
    AND cs.semanticTypes_id IS       AND c1.id != c2.id
 NULL

missing_sty: Reviewed concepts without releasable Semantic Types

Code Block

SELECT DISTINCT
    c.id conceptId
FROM
    concepts c
WHERE
   AND a1c.lowerNameHashterminology = a2.lowerNameHash:terminology
        AND c.publishable = TRUE
AND a1.id != a2.id     AND c.workflowStatus IN ('READY_FOR_PUBLICATION' , 'PUBLISHED')
  AND  a1.publishable = TRUE  AND NOT c.id IN (SELECT 
     AND a2.publishable = TRUE

Code Block

--Use Pre-programmed View ambig_concepts
 
SELECT c.id
      conceptId1, conceptId2 FROM
    ambig_concepts  WHERE     NOT ambig_concepts.conceptId1 IN (SELECT 
c,
            ca.concepts_id
semantic_type_components cs,
       FROM     semantic_type_components s
      concepts_atoms ca, WHERE
           atoms ac.terminology = :terminology
      WHERE          AND   cac.atoms_id = acs.concepts_id
                AND acs.terminology IN ('NCIMTH' , 'MTH')semanticTypes_id = s.id
                AND as.termTypepublishable = 'PN')
        AND NOT ambig_concepts.conceptId2 IN (SELECT 
            ca.concepts_id
        FROM
            concepts_atoms ca,
            atoms a
        WHERE
            ca.atoms_id = a.id
    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 = AND at.terminology
IN ('NCIMTH' , 'MTH')     AND c.version = t.version
        AND at.termType = 'PN')

ambig_no_rel: Ambiguous concepts that lack an approved REL

Code Block

--Use Pre-programmed View ambig_concepts

SELECTcurrent = TRUE
        AND  conceptId1, conceptId2
FROMc.id = cs.concepts_id
        AND ambig_concepts
WHEREcs.semanticTypes_id = s.id
      NOT (conceptId1 , conceptId2)AND s.semanticType IN ((SELECT DISTINCT
            cr.from_id, cr.to_idsemanticTypeCategoryMap_KEY sty
        FROM
            concept_Relationships crprojects a,
            WHEREProjectJpa_semanticTypeCategoryMap b
        WHERE
  cr.publishable = TRUE        a.id = b.ProjectJpa_id
  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
Code Block
SELECT DISTINCT c.id conceptId FROM AND semanticTypeCategoryMap concepts c,= 'chem' atoms a, concepts_atoms ca WHERE AND ca.terminology = :terminology))

go_chem: Current version GO concepts with CHEM STYs

Code Block

SELECT DISTINCT
    c.id conceptId
FROM
 AND c.id = ca.concepts_id c,
    concepts_semantic_type_components cs,
  AND ca.atoms_id = a.id  semantic_type_components s,
    terminologies t
WHERE
   AND ac.terminology in ('MTH', = 'NCIMTHGO')
        AND ac.termTypeterminology = '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

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

nosty: No STY

Code Block

SELECT DISTINCT
    c.id conceptId
FROM
    concepts c
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
       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

Code Block

SELECT DISTINCTsemanticTypeCategoryMap_KEY sty
        FROM
           c.id conceptIdprojects FROMa,
    concepts c WHERE     c.terminology = :terminology ProjectJpa_semanticTypeCategoryMap b
        ANDWHERE
c.publishable = TRUE         AND ca.workflowStatusid IN ('READY_FOR_PUBLICATION' , 'PUBLISHED')= b.ProjectJpa_id
          AND NOT c.id IN (SELECT  AND semanticTypeCategoryMap = 'chem'
         c.id       AND  FROM
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,
    concepts_semantic_type_components css,
    terminologies t
WHERE
     semantic_type_components sc.terminology = 'MDR'
        WHEREAND c.terminology = t.terminology
        AND c.terminologyversion = :terminologyt.version
        AND t.current = TRUE
        AND c.id = cs.concepts_id
        AND cs.semanticTypes_id = s.id
        AND cs.semanticTypes_id = s.ids.semanticType IN ((SELECT DISTINCT
            semanticTypeCategoryMap_KEY sty
      AND  s.publishableFROM
= 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 ProjectJpa_semanticTypeCategoryMap_KEY =b
'chemical'   and a.terminology = :terminology);   -- RickWHERE
update 3/2/2017 (select distinct semanticTypeCategoryMap_KEY sty from projects a, ProjectJpa_semanticTypeCategoryMap b where a.id = b.ProjectJpa_id
   and             AND semanticTypeCategoryMap = 'chem'
  and              AND a.terminology = :terminology)

go_chem: Current version GO concepts with CHEM STYs
)

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 DISTINCT
    c.id conceptId
FROM concepts c
WHERE  concepts c,
    concepts_semantic_type_components cs,
    semantic_type_components s,c.terminology = :terminolgy
AND c.publishable=TRUE
AND NOT EXISTS
    (SELECT * FROM deep_concept_relationships dcr
    terminologies t
WHERE     c.terminology = 'GO'
   role='FROM' AND
    AND c.terminologyid = t.terminology
 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
      AND c.versionid =conceptId
t.versionFROM
    concepts c,
  AND t.current =atoms TRUEa,
    concepts_atoms ca
WHERE
   AND c.idterminology = cs.concepts_id:terminology
        AND csc.semanticTypes_id = sca.concepts_id
        AND s.semanticType IN ((SELECT DISTINCT
            semanticTypeCategoryMap_KEY sty
        FROM
 ca.atoms_id = a.id
        AND a.terminology projects a,in ('NCI')
        AND a.termType =  ProjectJpa_semanticTypeCategoryMap b
        WHERE
   '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,
  a.id = b.ProjectJpaconcepts_idatoms ca1,
     concepts_atoms ca2,
    (SELECT 
  AND semanticTypeCategoryMap = 'chem'   a1.id atomId1, a2.id atomId2
    FROM
     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
Code Block
SELECT c.id conceptId FROM atoms a1, atoms a2 WHERE concepts c WHERE a1.lexicalClassId = c.terminology = :terminologya2.lexicalClassId AND NOT ca1.id IN (SELECT!= a2.id AND ca1.idpublishable = TRUE FROM AND a2.publishable = TRUE concepts c, AND a1.suppressible != concept_relationships cra2.suppressible) mixedSuppresLuiAtoms WHERE c.terminology = :terminology WHEREAND c.id = ca1.concepts_id AND crca1.fromatoms_id = c.idmixedSuppresLuiAtoms.atomId1 AND ca2.atoms_id = mixedSuppresLuiAtoms.atomId2 AND crca1.publishableconcepts_id = 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

...

ca2.concepts_id

~ 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

Version	Old Version 17	New Version Current
Changes made by	Rick Wood	Deborah Shapiro
Saved on	Mar 03, 2017	Mar 18, 2019

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