Implemented enhancements:
- Procedure table has useless no_qualifier synonyms #83
Fixed bugs:
- RX_FREQUENCY valueset has changed #84
- Procedure table has useless no\_qualifier synonyms #83
- DIMCODEs in PCORnet_vital are wrong #82
- Wrong c_tooltip for Principal Procedure and Spelling Mistake in c_name and c_tooltip #81
- Procedure PPX:S #79
- Medication RX Quantity Unit #78
- Medication RX PRN Flag #77
v4.1a (2018-08-08)
v4.1 (2018-06-11)
Implemented enhancements:
- PCORnet labs requirements have changed; ontology expansion needed #74
Fixed bugs:
- PCORnet labs requirements have changed; ontology expansion needed #74
- QT_BREAKDOWN_PATH value for Age is inconsistent with PCORNET_DEMO c_fullname values #70
Closed issues:
Merged pull requests:
v3.1b (2017-11-20)
Implemented enhancements:
- Resync FixConceptDim with Oracle #65
Fixed bugs:
- FixConceptDim fails for ICD-10 codes that look like ICD-9 #67
- Orphaned HCPCS codes #66
- Gender identity dimcodes are incorrect #63
- Update the create_metadata_tables scripts with new OMOP columns #62
- create_metadata_tables in MSSQL does not include lab table #55
Closed issues:
- DX_ORIGIN has incorrect value in c_facttablecolumn #68
- V3.1 upgrade script error in insert row for ENR_BASIS:D #64
Merged pull requests:
v3.1a (2017-06-07)
Implemented enhancements:
- Add OMOP codes to ontology #61
v3.1 (2017-05-24)
Implemented enhancements:
- Add new CDMv3.1 elements #60
- Move C4 and HC to CH #59
- add basic support for loading ontology into Postgres #56
- SCHEMES is out of date #53
- Diagnosis: remove ICD-9 from ICD-10 tree? #49
- Encounter: Add Age at Visit tree #33
- Diagnosis ontology: ICD-10 tree upgrade #32
- Update ICD-10 diagnoses to be a crosswalk ontology. #28
- Update RxNorm ontology to newest version. #27
- Labs: consider all LOINC codes listed by PCORI #24
- Minor cleanup #23
- Release new pcornet_med ontology with pcori_ndc and pcori_rxnorm #14
- Release new QT_Breakdowns table #7
- Enrollment-based encounters should reference visit_dimension #4
- Enviromental exposure might need to be smoking & non-smoking both #2
- Age >85 should not be queryable individually! #1
Fixed bugs:
- VITALS breakdown is wrong #54
- Medications 2.2: missing 78k NDC codes! #43
- About 1200 codes don't have pcori_ndc or pcori_rxnorm #42
- Diagnosis 2.1.2: wacky dimcodes #36
- Concept dimension: inactives in the diagnoses/ICD-10 tree should be included #35
- Demographics: large ages still queryable #34
- dbo.stringpart function doesn't use @delimiter arg #31
- Medications: several duplicates #30
- Diagnosis ontology: ENCTYPE #29
- concept_dim updater skips hiddens but not inactives #25
- Diagnosis ontology: PDX #21
- meds and labs in scope now? README out of date? #20
- ICD-10 needs PCS and c_name fixes #18
- Labs ontology: creatinine appears twice #16
- Labs ontology: duplicate codes with same fullname #15
- Ontology file import - literal "NULL" converted to actual null #13
- PCORI_BASECODE incorrect for some principal discharge diagnosis flags #11
- Loading medication ontology with Oracle sqlldr results in error "column C_TOOLTIP. second enclosure string not present" #10
- Update schemes table #6
- HIV RNA tests in labs should be hidden #5
- Hispanic R refuse to answer missing from ontology #3
- Age \>85 should not be queryable individually! #1
Closed issues:
- Medication ontology: SHRINE interop below ingredient level? #52
- Age at visit does work in oracle #51
- need to correct metadata for non-hisppanic in demographics #50
- SCILHS ontology meta data tables do not include indexes for labs #48
- c_fullname in pcornet_lab fix. Connies issue #3. #46
- 'Hispanic' demographic fix. Connies issue #2. #45
- c_tooltip in pcornet_lab update. Connies Issue #1. #44
- c_dimcode needs a fix for several more pcornet_agetree.txt rows #39
- How are the "D~s1uh" parts of Diagnosis paths computed? #38
- pcornet_agetree weird c_dimcode for Age 24 #37
- Same Dx and PX c_basecodes #26
v2.0.2 (2015-12-16)
[Full Changelog](https://github.com/ARCH-commons/arch-ontology/compare/*CDM ontology, first major update*...v2.0.2)
6/13/14 - initial release
6/24/14 -
-
Changed export format (brackets no longer surround dates, null values are empty rather than “(null)”, file type is ASCII)
-
Set all update_date fields to be non-null
-
Corrected foreign characters, long hyphens, and backquotes that were invalid (content changes were mostly in the ICD-10 tree, a few in ICD-9 and HCPCS, the rest were in tooltips)
-
Fixed invalid c_path and c_symbol entries (not required for querying, SHRINE, or SMART - used by some tools like Lori’s mapping validator).
6/25/14 - Released TABLE_ACCESS in same export format as main table.
6/26/14 - Minor changes to ontology
-
BMI no longer greyed out
-
Only top-level folders are cases
-
Modifiers have been excluded from top-level folders (they are unqueryable anyway)
7/10/14 -
-
7/1/14
-
Age buckets had some errors in basecode, trailing slashes, c_path, and c_symbol
-
Some metadata XML was missing the XML header (but only for hidden elements)
-
Line breaks removed from metadata XML (to ease importing)
-
7/7/14
-
Biobank flag = No is hidden now; this should not have been queryable
-
7/10/14
-
Made all terms editable
-
Added version of tooltip column without linebreaks
7/22/14 - 399,921 rows
-
Added 129 ICD-9 codes that were retired by 2014AA but are still used.
-
Fixed an error in the dimcodes - they matched c_path instead of c_fullname
-
Added pcori_basecode column.
-
Removed pipes (|) from C_BASECODE.
7/29/14 - LCP
- Fixed the leaf to folder modification resulting from retired terms.
8/4/14 -
-
Fixed three HCPCS synonyms
-
Remove linefeeds from tooltips
8/7/14:
-
Removed start date from Enollment/Encounter-based so it will work on all db platforms.
-
Split ontology release into six tables.
-
Made uncommon/unused terminologies inactive (SNOMED, LOINC, ICD-10).
8/12:
- Removed duplicate ICD9:645 and ICD9:386.00 and renamed Sporting Injury from ICD9:E899 to ICD9:E889
8/13:
- Inserted CPT_2014AA from Bioportal into the procedures table
8/15:
- Updated sourcesystem_cd from ‘Integration_tool’ to ‘Integration’
8/18:
-
Added schemes table
-
Version concepts added
-
Inactive visual attributes propagate to children
-
CPT procedure modifiers folders is now actually a modifier folder
-
Deleted basecodes from internal CMS-DRG groupings - it never appears in data
-
Fixed top-level DRG basecodes
-
Added schemes to scheme-less basecodes
-
Made dates non-null in ontology (if a date was null, it was set to the update date)
8/19/14:
-
Fixed errors in dimcodes on Diagnosis\PDX and the version concepts.
-
Removed modifiers from the schemes table.
9/30/14:
-
Modifiers had C_FACTTABLECOLUMN=’concept_cd’ instead of ‘modifier_cd’.
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chart:n is now a computed value that returns 0, and chart:y returns all patients
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Enrollment table is fixed and reorganized - only encounter-based enrollment is now active and it is a computed value so no data needs to be entered
-
Vitals -> Height had a bug and was partially set up as a modifier
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Added vitals metadata_xml for normal ranges and unit conversions.
-
Made NI inactive in vitals
11/16/14:
-
Modifiers had C_FACTTABLECOLUMN=’concept_cd’ instead of ‘modifier_cd’.
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Made NI inactive - it is not computable
-
Merged in around 700 retired CPT codes
11/24/14:
-
Made NI inactive - it is not computable
-
Added MS-DRG tree and modified the DRG tree to reflect the two coding systems
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Changed all non-DRG queries to query the visit_dimension
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Changed top-level items to cases (containers)
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Bugfixes on some encounter items, especially the null flavors
-
Diagnosis modifiers had C_FACTTABLECOLUMN=’concept_cd’ instead of ‘modifier_cd’.
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pcori_basecode issues fixed (as defined by ontology_fix_script_v5, released with the transform)
-
Made version concept appear at end of list
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Changed C_COLUMNDATATYPE=’T’ for BIOBANK_FLAG:Y (queries do not run correctly if not) - this was part of a patch on 8/27/14.
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Made NI inactive on all remaining tables.
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Set HISPANIC yes and unknown to use dimcodes in the patient dimension by default.
-
Made changes to the pediatric age ontology per suggestions by Nate Apathy at Cerner Research:
-
2 months: changed label from "2 months old" to "02 months old" for sorting order
-
Changed "1 months" to "1 month" & "1 days" to "1 day"
-
0/1/2 months: changed type to folder so days display under in hierarchy
-
modified month ranges to be inclusive toward greater number vs. lesser number, to match format for years (e.g., “1 month old” means 0-1 months). This also fixed a bug in the Oracle version that caused months to not query properly.
-
Note that days still follow the non-standard format (“1 day old” means 0-1 days), for backward compatibility.
-
-
More fixes to the pediatric age ontology. Now using all of Cerner Research’s modifications. Of note, “days old” now follows consistent format with other ages.
-
HCPCS tooltips (including modifiers) now follow the i2b2 standard tooltip format
-
HCPCS modifiers are now correctly placed under one modifiers tree (rather than several separate trees for different classes of modifiers)
-
The encounters .txt file mistakenly contained an unnecessary column with linefeeds in v1.5.1. This column has been removed.
-
In Encounters and Procedures, cleaned up the Data Source modifier - Unknown and Other are now hidden, and No Information is active and by default returns all records
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In Demographics, cleaned up No Information - now always active and by default returns the count of patients with null in the specified column
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Fixed Ethnicity: greyed-out Non-Hispanic, which is a negated term and thus doesn’t make sense in an i2b2 ontology; fixed an issue on Hispanic with c_columnname in Oracle
-
Updated the schemes table
-
Labs 2.0: Developed initial labs tree based on CDM v2.0 specification and labs selected by SCILHS to meet PCORnet and other research requirements.
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Meds 2.0.1: Developed initial meds tree based on CDM v3.0 specification.
-
Developed refresh script for concept and modifier dimensions
-
Developed update script to add new CDM v3.0 fields to encounter, diagnosis, and vitals tables.
-
Added additional NDC codes to medications ontology.
-
Added meds release 2.0.2a. There were some errors in the meds modifiers (incorrect type N, DI entry entirely wrong).
-
Added meds release 2.0.2b. Prevnar pediatric suspension had a null hlevel.
-
Lab modifiers had concept_cd for facttable column (parallels meds fix in 202a).
-
Duplicates in labs table - removed
-
Modified tooltip of DX_SOURCE:FI to explain that Final can mean ambulatory.
* This Change Log was automatically generated by github_changelog_generator