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Overview

QA Bin Definitions

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

TODO:

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

REQUIRED bins

  • nci_merge: Merged SCUI current version NCI atoms

    select 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='NCI'
group by a.id having count(distinct c.conceptId)>1

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

    TBD: 
select 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

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

  • multsty: concepts with more than 3 STYs|
     

  • styisa: One STY is an ancestor of another in the STY isa hierarchy
     

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

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

NON-required bins

  • rxnorm_merge: RXCUI Merges
    • Same as nci_merge but with RXNORM

  •  cbo_merge: Merged SCUI current version CBO atoms
    • Same as nci_merge but with CBO
  • sct_sepfnpt: SNOMED concept clusters where the FN and PT terms are separated

  • rxnorm_split: RXCUI splits

    see split query above



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

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

  • ambig_no_ncimth_pn: Ambiguous concepts where at least one has no PN (sepstring)

  • 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

  • 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

  • cbo_chem: Current version CBO concepts with CHEM STYs

  • go_chem: Current version GO concepts with CHEM STYs

  • mdr_chem: Current version MDR concepts with CHEM STYs

  • true_orphan

  • sfo_lfo

  • deleted_cui_split

 

 

# Source merge rules

Merged SCUI current version NCI atoms

Merged SDUI current version MDR atoms

Merged SDUI current version PDQ atoms

Merged SCUI current version CBO atoms

RXCUI Merges

 

# Source split rules

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

SNOMED concept clusters where the FN and PT terms are separated

RXCUI Splits

 

# Cross source merge rules

Concepts containing current version NCI and current version PDQ atoms

Concepts containing current version NCI and current version SNOMEDCT atoms

 

# NCIMTH/PN rules

Ambiguous concepts where at least one has no PN (sepstring)

Ambiguous concepts where at least one has no PN (sepstring)

Ambiguous concepts where at least one pair lacks an approved REL

Identical (same SUI) PN's in multiple concepts

Concepts with multiple MTH/PN atoms

Concept has MTH/PN atom but no ambiguous string

MTH/PN atom is ambiguous but has no matching ambiguous string

 

 

# General PN rules

MTH/PNs on their own

 

# STY rules

Find concepts with Clinical Drug STY and any other STY

No STY

concepts with more than 3 STYs

Reviewed concepts without releasable Semantic Types

One STY is an ancestor of another in the STY isa hierarchy

Current version CBO concepts with CHEM STYs

Current version GO concepts with CHEM STYs

Current version MDR concepts with CHEM STYs

 

 

# Relationship rules

Concepts with no releaseable relationships to any other concept

Short form in one concept, long form in another

 

# CUI rules

Potential missed synonmym between CL* and CO*

CUIs that are going away - will need bequeathal rel

Complex split/merge case CUIs that are going away - will need bequeathal rel

CUIS that are going away (without MTH-only) - will need bequeathal rel

 

# Other rules

Concepts with identical LUI atoms that have mixed suppressibility

 

# Awaiting Questions

Merged current version NCI/PT atoms

Demotions overlapping with a bad merge that was split

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