Content Comparison

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nci_merge: Merged SCUI current version NCI atoms

Code Block

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--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.id conceptId,terminology = :terminology
    a.id,    AND ac1.termType,terminology = :terminology
  a.conceptId,      c1AND c.id conceptId1,
    a1.id,= ca.concepts_id
    a1.termType,    AND a1ca.conceptIdatoms_id FROM= a.id
   concepts c,    AND c1.id = ca1.concepts_atomsid
ca,     atoms a,  AND ca1.atoms_id = conceptsa1.id
c1,     concepts_atoms ca1,  AND a.terminology  atoms a1
WHERE
    c.terminology = 'SNOMEDCT_US'= 'NCI'
        AND c1a1.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 = 'FN'
       NCI' 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 conceptId1, csc1.concepts_id conceptIdconceptId2
FROM
    concepts_semantic_type_components cs
WHERE c,
    cs.concepts_idatoms INca,
(SELECT    atoms a,
    concepts c1,
  cs.  concepts_idatoms ca1,
    atoms a1
WHERE
 FROM   c.terminology = :terminology
       concepts_semantic_type_components cs,
   AND c1.terminology = :terminology
         semantic_type_components sAND a.terminology = 'SNOMEDCT_US'
        AND WHEREa1.terminology = 'SNOMEDCT_US'
        AND  csc.semanticTypes_id = sca.concepts_id
             AND ca.atoms_id = a.id
  AND s.semanticType = 'Clinical Drug') GROUP BYAND csc1.concepts_id HAVING= COUNT(csca1.concepts_id)
  > 1;

multsty:concepts with more than 3 STYs|

Code Block

SELECT DISTINCT    AND csca1.conceptsatoms_id conceptId= a1.id
FROM     concepts_semantic_type_components cs,  AND a.termType  semantic_type_components s
WHERE= 'FN'
        AND a1.termType = 'PT'
        AND csa.semanticTypes_idconceptId = s.id
GROUP BY cs.concepts_id
HAVING COUNT(cs.concepts_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 Blockselect a.id clusterId, a.id conceptId from concepts a, concepts_atoms b, atoms c where a
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 a
AND c.id =
b
cs.concepts_id
and
b.atoms_id
=
c.id
AND cs.concepts_id IN (SELECT
and
c.terminology='RXNORM'
group
by
a.id
having
count(distinct
c.conceptId)>1cbo_merge: Merged SCUI current version CBO atoms
Same as nci_merge but with CBO
Code Blockselect
a.id
clusterId,
a
cs.concepts_id
conceptId
from
concepts
a,
concepts_atoms
b,
atoms
c
FROM
where
a.terminology
=
:terminology
and
a.id
=
b.
concepts
_id
c,
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
If SDUI, return descriptor ID instead of conceptId?
pdq_merge: Merged SDUI current version PDQ atoms
sct_sepfnpt: SNOMED concept clusters where the FN and PT terms are separated
- DUPLICATE of above
rxnorm_split: RXCUI splits
Code Block
see split query above

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

Code Block

SELECT DISTINCTconcepts_semantic_type_components cs,
            semantic_type_components s
        WHERE
ca.concepts_id conceptId FROM     atoms a,    c.terminology atoms= a1,:terminology
    concepts_atoms ca,     concepts_atoms ca1,     terminologies t,
    terminologies t1
WHEREAND c.id = cs.concepts_id
      ca.atoms_id = a.id         AND ca1cs.atomssemanticTypes_id = a1s.id
        AND a.terminology = 'NCI'         AND as.terminologysemanticType = t.terminology
        AND a.version = t.version
'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
AND t.current = true	concepts c,
    concepts_semantic_type_components cs,
    AND a1.terminology = 'PDQ'
        AND a1semantic_type_components s
WHERE
	c.terminology = t1.:terminology
        	AND a1c.versionid = t1.version
 cs.concepts_id
      AND t1cs.currentsemanticTypes_id = trues.id
GROUP BY c.id
HAVING COUNT(c.id)   
        AND ca.concepts_id = ca1.concepts_id

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

Code Block

SELECT DISTINCT 
    ca.concepts_id conceptId
FROM
    atoms a,
    atoms a1,
    concepts_atoms ca,
    concepts_atoms ca1,
    terminologies t,
    terminologies t1
WHERE
    ca.atoms_id = a.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 ca.concepts_id = ca1.concepts_id

ambig_no_ncimth_pn: Ambiguous concepts where at least one has no PN (sepstring)
Code Block
Ambiguous?
ambig_no_mth_pn: Ambiguous concepts where at least one has no PN (sepstring)
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
Code Block
SELECT DISTINCT ca.concepts_id conceptId FROM atoms a, concepts_atoms ca WHERE ca.atoms_id = a.> 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
            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 acs.terminologysemanticTypes_id = 'MTH's.id
        AND a.termType = 'PN'
GROUP BY ca.concepts_id
HAVING COUNT(ca.concepts_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
nosty: No STY
Code Block
SELECT DISTINCTs.semanticType IN ((SELECT DISTINCT semanticTypeCategoryMap_KEY sty c.id conceptId FROM concepts c projects a, LEFT JOIN concepts_semantic_type_components cs ON (c.id = cs.concepts_id) WHEREProjectJpa_semanticTypeCategoryMap b cs.semanticTypes_id IS NULL
missing_sty: Reviewed concepts without releasable Semantic Types
Code Block
-- Is 'Reviewed'WHERE = workflowStatus.READY_FOR_PUBLICATION? How about PUBLISHED? SELECT DISTINCT a.id = cb.ProjectJpa_id conceptId FROM concepts c WHERE AND c.workflowStatussemanticTypeCategoryMap = 'READY_FOR_PUBLICATIONchem' AND NOT c.id IN (SELECT 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 =        concepts c,
  :terminolgy
AND c.publishable=TRUE
AND NOT EXISTS
    (SELECT * FROM   conceptsdeep_semanticconcept_type_components cs,relationships dcr
            semantic_type_components s
 WHERE role='FROM' AND
     c.id WHERE
     = 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 = cs.concepts_idconceptId FROM concepts c, atoms a, 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 aconcepts_atoms ca
WHERE
    c.terminology = :terminology
        AND c.id = bca.ProjectJpaconcepts_id
  and semanticTypeCategoryMap_KEY = 'chemical'   andAND a.terminology = :terminology);

go_chem: Current version GO concepts with CHEM STYs

Code Block

--Not sure about final line.
 
SELECT DISTINCTca.atoms_id = a.id
       c.id conceptIdAND FROMa.terminology in ('NCI')
  concepts c,     concepts_semantic_type_components cs,
    semantic_type_components s,
    terminologies t
WHEREAND 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.terminologyid =conceptId
'GO'FROM
    concepts c,
  AND c.terminology = t.terminology concepts_atoms ca1,
    concepts_atoms ca2,
  AND c.version = t.version(SELECT 
       AND ta1.currentid = true
atomId1, a2.id atomId2
    FROM
  AND c.id = cs.concepts_id     atoms a1, atoms a2
AND cs.semanticTypes_id = s.id WHERE
       AND sa1.semanticTypelexicalClassId LIKE 'Chem%'

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= a2.lexicalClassId c.id conceptId FROM conceptsAND c WHERE a1.id != a2.id NOT c.id IN (SELECT AND a1.publishable = TRUE c.id FROMAND a2.publishable = TRUE concepts c, AND a1.suppressible != a2.suppressible) mixedSuppresLuiAtoms WHERE concept_relationships crc.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 13	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