Page Comparison

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nci_merge: Merged SCUI current version NCI atoms

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select a.id clusterId, adistinct c.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 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 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

-- What put as clusterId/conceptId?
 
SELECT DISTINCT
    c.id conceptId,
    a.id,
    a.termType,
    a.conceptId,
    c1.id conceptId1,
    a1.id,
    a1.termType,
    a1.conceptId
FROM
    concepts c,
    concepts_atoms ca,
    atoms a,
    concepts c1,
    concepts_atoms ca1,
    atoms a1
WHERE
    c.terminology = 'SNOMEDCT_US--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 c1a1.terminology IN = 'SNOMEDCT_US'(SELECT 
        AND c.id = ca.concepts_id terminology
       AND ca.atoms_idFROM
= a.id         AND c1.id = ca1.concepts_id root_terminologies
        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

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SELECT DISTINCT
    c.id conceptId1, c1.id conceptIdconceptId2
FROM
    concepts c,
    concepts_semantic_type_components cs
WHEREatoms ca,
    atoms c.terminologya,
= :terminology   concepts c1,
    AND c.id = cs.concepts_idconcepts_atoms ca1,
    atoms a1
WHERE
   AND cs.concepts_id IN (SELECTc.terminology = :terminology
        AND c1.terminology = :terminology
  cs.concepts_id      AND a.terminology = FROM'SNOMEDCT_US'
        AND a1.terminology = 'SNOMEDCT_US'
concepts c,       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    c.terminologyca1.atoms_id = :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 cs.concepts_id
HAVING COUNT( concepts_semantic_type_components cs
WHERE
    c.terminology = :terminology
        AND c.id = cs.concepts_id)
 > 1

multsty:concepts with more than 3 STYs|

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SELECT DISTINCT     AND cs.concepts_id conceptIdIN (SELECT FROM
	concepts c,     concepts_semantic_type_components cs,     semantic_type_components s
WHERE
	c.terminology = :terminology
	AND c.id = cs.concepts_idcs.concepts_id
        FROM
       AND cs.semanticTypes_id = s.id GROUP BYconcepts 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,
    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

Code Block

SELECT 
    c.id clusterId, c.id ,
            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

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--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
            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,
    concepts_atoms
ca,
    atoms a
WHERE
    c.terminology = :terminology
        AND c.idpublishable = ca.concepts_idTRUE
        AND cac.atoms_idworkflowStatus = 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

Code Block

SELECT DISTINCT
   IN ('READY_FOR_PUBLICATION' , 'PUBLISHED')
        AND NOT c.id conceptId
FROM
    atoms a,IN (SELECT 
     atoms a1,     concepts c,.id
    concepts c1,   FROM
 concepts_atoms ca,     concepts_atoms ca1,     terminologiesconcepts tc,
    terminologies t1 WHERE     c.terminology = :terminology concepts_semantic_type_components cs,
        AND c1.terminology = :terminology semantic_type_components s
      AND c.id =WHERE
ca.concepts_id         AND ca.atoms_id = ac.id
terminology = :terminology
     AND c1.id = ca1.concepts_id         AND ca1c.atoms_id = a1cs.concepts_id
        AND a.terminology = 'NCI'         AND acs.terminologysemanticTypes_id = ts.terminologyid
        AND a.version = t.version         AND ts.currentpublishable = 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)

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_atomstype_components ca1cs,
    terminologies tsemantic_type_components s,
    terminologies t1t
WHERE
    c.terminology = :terminology'CBO'
        AND c1c.terminology = :t.terminology
        AND c.idversion = cat.concepts_idversion
        AND cat.atoms_idcurrent = a.idTRUE
        AND c1c.id = ca1cs.concepts_id
        AND ca1cs.atomssemanticTypes_id = a1s.id
        AND s.semanticType IN ((SELECT ANDDISTINCT
a.terminology = 'NCI'         AND a.terminology = t.terminology semanticTypeCategoryMap_KEY sty
        FROM
AND a.version = t.version         AND t.current = TRUEprojects a,
          AND a1.terminology = 'SNOMEDCT_US' ProjectJpa_semanticTypeCategoryMap b
        ANDWHERE
a1.terminology = t1.terminology         AND a1a.versionid = t1.version
   b.ProjectJpa_id
    AND t1.current = TRUE         AND c.idsemanticTypeCategoryMap = 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 --Create view ambig_concepts (conceptId1, conceptId2)

ambig_no_rel: Ambiguous concepts where at least one pair lacks an approved REL
pn_pn_ambig: Identical (same SUI) PN's in multiple concepts
multiple_pn: Concepts with multiple MTH/PN atoms
'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
   atoms a,c.terminology = 'GO'
  concepts_atoms ca WHERE    AND c.terminology = :t.terminology
        AND c.idversion = cat.concepts_idversion
        AND cat.atoms_idcurrent = a.idTRUE
        AND ac.terminologyid in ('MTH', 'NCIMTH')= cs.concepts_id
        AND acs.termTypesemanticTypes_id = '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 s.id
        AND s.semanticType IN ((SELECT DISTINCT
            semanticTypeCategoryMap_KEY sty
     concepts c  FROM
      LEFT JOIN     concepts_semantic_type_components cs ON (c.id = cs.concepts_id)
WHERE
	c.terminology= :terminologyprojects a,
           AND cs.semanticTypes_id IS NULL

missing_sty: Reviewed concepts without releasable Semantic Types

Code Block

-- Is 'Reviewed' =  workflowStatus.READY_FOR_PUBLICATION?  How about PUBLISHED?
 SELECT DISTINCT
    c.id conceptId
FROMProjectJpa_semanticTypeCategoryMap b
        WHERE
            a.id = b.ProjectJpa_id
       concepts c WHERE 	c.terminology= :terminology     AND c.workflowStatussemanticTypeCategoryMap = 'READY_FOR_PUBLICATIONchem'
                AND NOT c.id IN (SELECT a.terminology = :terminology))

mdr_chem: Current version MDR concepts with CHEM STYs

Code Block

SELECT DISTINCT
    c.id conceptId
FROM
    concepts c.id,
    concepts_semantic_type_components cs,
   FROM semantic_type_components s,
    terminologies t
WHERE
   concepts c,.terminology = 'MDR'
        AND  concepts_semantic_type_components cs,c.terminology = t.terminology
        AND c.version   semantic_type_components s= t.version
        AND WHEREt.current  = TRUE
        AND c.terminologyid = :terminologycs.concepts_id
        AND cs.semanticTypes_id = s.id
    AND c.id = cs.concepts_id AND s.semanticType IN ((SELECT DISTINCT
           AND cs.semanticTypessemanticTypeCategoryMap_idKEY =sty
s.id        FROM
        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,projects a,
            ProjectJpa_semanticTypeCategoryMap b
where
        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'
  andAND 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 )

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 = 'GO':terminolgy
AND        AND c.terminology = t.terminologyc.publishable=TRUE
AND NOT EXISTS
    (SELECT * FROM deep_concept_relationships dcr
AND c.version = t.version  WHERE role='FROM' AND
    AND tc.currentid = TRUE
 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.id = cs.concepts_idconceptId
FROM
    concepts c,
  AND cs.semanticTypes_id = s.idatoms a,
    concepts_atoms ca
WHERE
 AND s.semanticType IN ((SELECT DISTINCT
 c.terminology = :terminology
        AND c.id = semanticTypeCategoryMapca.concepts_KEYid
sty        AND FROMca.atoms_id = a.id
          projects a,
   AND a.terminology in ('NCI')
        ProjectJpa_semanticTypeCategoryMap b
        WHERE
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
    a.id = b.ProjectJpa_idconcepts c,
    concepts_atoms 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 atoms a1, atoms c.ida2 conceptId FROM WHERE concepts c WHERE ca1.terminologylexicalClassId = :terminology a2.lexicalClassId AND NOT ca1.id IN (SELECT!= a2.id AND ca1.idpublishable = TRUE FROM AND a2.publishable = TRUE concepts c, AND a1.suppressible != a2.suppressible) mixedSuppresLuiAtoms concept_relationshipsWHERE cr c.terminology = :terminology WHERE AND c.id = ca1.concepts_id cr.from AND ca1.atoms_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 15	New Version Current
Changes made by	Rick Wood	Deborah Shapiro
Saved on	Mar 02, 2017	Mar 18, 2019

Versions Compared

Key

NON-required bins

NON-required bins