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

--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 a1.terminology IN (SELECT 
            terminology
        FROM
            root_terminologies
        WHERE
            family = 'NCI' AND terminology != 'NCI')
        AND a.conceptId = a1.conceptId
        AND c.id != c1.id

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

Code Block

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

Code Block

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|

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
-- Skip for now unpublishable NCIMTH concepts?

...

rxnorm_merge: RXCUI Merges
Same as nci_merge but with RXNORM
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='RXNORM' group by a.id conceptId having count(distinct c.conceptIdid)>1

cbo_merge: Merged SCUI current version CBO atoms
Same as nci_merge but with CBO
Code Block
select distinct ac.id clusterId, a.id conceptId conceptId from concepts ac, concepts_atoms bca, atoms c a where ac.terminology = :terminology and ac.id = bca.concepts_id and bca.atoms_id = ca.id and a.publishable = true and ca.terminology='CBO' group by ac.id having count(distinct ca.conceptId)>1

mdr_merge: Merged SDUI current version MDR atoms

Code Block

SELECT 
    c.id clusterId,select distinct c.id conceptId FROM
from    concepts c,
    concepts_atoms ca,
    atoms a
WHERE
   where c.terminology = :terminology
        AND and c.id = ca.concepts_id         AND caand ca.atoms_id = a.id and a.publishable = true
  and  AND a.terminology = 'MDR'
GROUPgroup BYby c.id HAVINGhaving COUNTcount(DISTINCTdistinct a.descriptorId) > 1>1

pdq_merge: Merged SDUI current version PDQ atoms

Code Block

SELECT 
    c.id clusterId, select distinct c.id conceptId FROM
   from concepts c,
    concepts_atoms ca,     atoms a
WHERE
   where c.terminology = :terminology
        ANDand c.id = ca.concepts_id         AND and ca.atoms_id = a.id and a.publishable = true
  and  AND a.terminology = 'PDQ'
GROUPgroup BYby c.id HAVINGhaving COUNTcount(DISTINCTdistinct a.descriptorId) > 1>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

SELECTselect DISTINCTdistinct     c.id conceptId FROM
from concepts c,  concepts_atoms aca, atoms a
where c.terminology atoms= a1,:terminology
    conceptsand c,.id = ca.concepts_id and ca.atoms_id = a.id and concepts c1,
a.publishable = true
   concepts_atoms ca,
    concepts_atoms ca1,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
    terminologies t,
c.id conceptId
FROM
   terminologies t1atoms WHEREa,
    catoms 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 stringambig_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 SELECT

Code Block

select distinct c.id conceptId FROM
 from   concepts c,     concepts_atoms ca, WHEREatoms a
where   c.terminology = :terminology
        ANDand c.id = ca.concepts_id and ca.atoms_id = a.id and a.publishable = true
 AND ca.concepts_id IN (SELECTand a.terminology in ('NCIMTH','MTH')
  and a.termType = 'PN'
  and not    ca.concepts_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  FROMpublishable atoms are MTH/PN or NCIMTH/PN
 
SELECT 
    c.id conceptId
FROM
    concepts_atoms cac,
    concepts_atoms ca
WHERE
    c.terminology atoms= a:terminology
        WHEREAND c.id = ca.concepts_id
        AND ca.atomsconcepts_id = a.idIN (SELECT 
            ca.concepts_id
  AND a.terminology IN ('MTH' , 'NCIMTH') FROM
            concepts_atoms ca,
 AND a.termType = 'PN'           atoms a
        WHERE
   AND a.publishable = true) GROUP BY ca.concepts_id HAVING COUNT(DISTINCT ca.atoms_id) = 1

nosty: No STY

Code Block

SELECT DISTINCT a.id
       c.id conceptId FROM     concepts c AND a.terminology IN ('MTH' , 'NCIMTH')
  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
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
WHERE     c.terminology = :terminology LEFT JOIN
    concepts_semantic_type_components cs ANDON (c.publishableid = TRUE
  cs.concepts_id)
WHERE
	c.terminology= :terminology
     AND ccs.workflowStatussemanticTypes_id IN ('READY_FOR_PUBLICATION' , 'PUBLISHED')
    IS NULL

missing_sty: Reviewed concepts without releasable Semantic Types

Code Block

SELECT DISTINCT
   AND NOT c.id INconceptId
(SELECTFROM
    concepts c
WHERE
      c.idterminology = :terminology
      FROM  AND c.publishable = TRUE
       concepts AND c,.workflowStatus IN ('READY_FOR_PUBLICATION' , 'PUBLISHED')
        concepts_semantic_type_components cs,
  AND NOT c.id IN (SELECT 
        semantic_type_components s   c.id
     WHERE   FROM
         c.terminology = :terminology concepts    c,
           AND c.id = cs.concepts_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.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)

go_chem: Current version GO concepts with CHEM STYs

SELECT

Code Block

SELECT DISTINCT
    c.id conceptId
FROM
    concepts c,
    concepts_semantic_type_components cs,
    semantic_type_components s,
    terminologies t
WHERE
    c.terminology = 'GOCBO'
        AND c.terminology = t.terminology
        AND c.version = t.version
        AND t.current = TRUE
        AND c.id = cs.concepts_id
        AND cs.semanticTypes_id = s.id
        AND s.semanticType IN ((SELECT DISTINCT
            semanticTypeCategoryMap_KEY sty
        FROM
            projects a,
            ProjectJpa_semanticTypeCategoryMap b
        WHERE
            a.id = b.ProjectJpa_id
                AND semanticTypeCategoryMap = 'chem'
                AND a.terminology = :terminology))

go_chem: Current version GO concepts with CHEM STYs

Code Block

SELECT DISTINCT
    c.id conceptId
FROM
    concepts c,
    concepts_semantic_type_components cs,
    semantic_type_components s,
    terminologies t
WHERE
    c.terminology = 'GO'
        AND c.terminology = t.terminology
        AND c.version = t.version
        AND t.current = TRUE
        AND c.id = cs.concepts_id
        AND cs.semanticTypes_id = s.id
        AND s.semanticType IN ((SELECT DISTINCT
            semanticTypeCategoryMap_KEY sty
        FROM
            projects a,
            ProjectJpa_semanticTypeCategoryMap b
        WHERE
            a.id = b.ProjectJpa_id
                AND semanticTypeCategoryMap = 'chem'
                AND a.terminology = :terminology))

mdr_chem: Current version MDR concepts with CHEM STYs

Code Block

SELECT DISTINCT
    c.id conceptId
FROM
    concepts c,
    concepts_semantic_type_components cs,
    semantic_type_components s,
    terminologies t
WHERE
    c.terminology = 'MDR'
        AND c.terminology = t.terminology
        AND c.version = t.version
        AND t.current = TRUE
        AND c.id = cs.concepts_id
        AND cs.semanticTypes_id = s.id
        AND s.semanticType IN ((SELECT DISTINCT
            semanticTypeCategoryMap_KEY sty
        FROM
            projects a,
            ProjectJpa_semanticTypeCategoryMap b
        WHERE
            a.id = b.ProjectJpa_id
                AND semanticTypeCategoryMap = 'chem'
                AND a.terminology = :terminology))

true_orphan: Concepts with no releasable relationships to any other concept

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

deleted_cui_split: Complex split/merge case CUIs that are going away - will need bequeathal
Code Block
--Skip for now
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 ANDconceptId
c.versionFROM
= t.version   concepts c,
    AND t.current = TRUEatoms a,
    concepts_atoms ca
WHERE
   AND c.idterminology = cs.concepts_id:terminology
        AND csc.semanticTypes_id = sca.id
        AND s.semanticType IN ((SELECT DISTINCT
            semanticTypeCategoryMap_KEY styconcepts_id
        AND FROMca.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 atoms a1, atoms a2 c.id conceptIdWHERE FROM concepts c WHERE a1.lexicalClassId = a2.lexicalClassId c.terminology = :terminology AND NOT ca1.id != a2.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.from_id = c.idatoms_id = mixedSuppresLuiAtoms.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 19	New Version 20
Changes made by	Rick Wood	Rick Wood
Saved on	Mar 03, 2017	Mar 06, 2017

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