Title: Issues with Version 2.71 of LNC-DE-DE

Problem: The 2021AB version of the UMLS Metathesaurus includes version 2.71 of LNC-DE-DE (LOINC Linguistic Variant - German, Germany). LOINC found issues with this version and reverted to version 2.70. For the most current versions of LOINC Linguistic Variants, see: https://loinc.org/downloads/accessory-files/#loinc-linguistic-variants.

Solution: This error will be corrected in the 2022AA Release.

Date Posted: November 1, 2021

Title: MRREL.RRF SCTSPA error

Problem: 22 rows in MRREL have the wrong relation label (RELA). The issue affects SAB=SCTSPA rows where RELA=has_count_of_active_ingredient and RELA=count_of_active_ingredient_of. For SAB=SCTSPA, these relation labels should be swapped. Rows with RELA=has_count_of_active_ingredient should have RELA=count_of_active_ingredient_of, and rows with RELA=count_of_active_ingredient_of should have RELA=has_count_of_active_ingredient.

Solution: This error will be corrected in the 2021AB Release.

Date Posted: May 3, 2021

Title: MRCONSO.RRF error

Problem: MRCONSO.RRF contains an incorrect row listing SAB=SRC and TTY=PT.  PT is not a valid term type for SAB=SRC.
The incorrect row is: C4318590|ENG|P|L14292498|PF|S17373750|Y|A28572588||||SRC|PT|NOCODE|PICRASMA EXCELSA (ingredient)|0|N||

Solution: This error will be corrected in the 2018AA Release.

Date Posted: November 6, 2017

Title: MetamorphoSys Validation Error

Problem: There is a known problem with MetamorphoSys that prevents it from validating files.

Solution: NLM is working to resolve this error.

Date Posted: May 8, 2013

Title: MRSAB includes incorrect version date for LNC_NEUROQOL

Problem: The MRSAB file lists LNC_NEUROQOL with a 2001 version date for its VSAB.

Solution: The correct version date is 2010. This error will be corrected in the 2012AB Release.

Date Posted: May 7, 2012

Title: 2011AB Database Load Script Error

Problem: Term type list (TTYL) field length is not sufficient.

Solution: Edit the corresponding table creation script (e.g. oracle_tables.sql or mysql_tables.sql) and change the length of the TTYL field to 400 instead of 300. For Oracle users, also edit the MRSAB.ctl file and set TTYL field to char(400) instead of char(300).

Date Posted: December 1, 2011

Title: MeSH Data Error

Problem: An invalid MeSH tree number, D12.776.157.057.000 , for MeSH ID D058927 appears in the MRSAT file (both ORF and RRF formats). Its CUI is C2936832.

Solution: The correct tree number is D12.776.157.057.001. This error will be corrected in the 2012AA Release.

Date Posted: November 16, 2011

Title: Encoding error causes display problems for MedlinePlus definitions

Problem: Characters in MedlinePlus definitions are not displayed correctly in MRDEF.RRF.

Solution: This error will be corrected in the 2011AB Release.

Date Posted: June 16, 2011

Title: SPECIALIST Lexicon & Lexical Tools installation progress bar reads beyond 100%

Problem: When installing the SPECIALIST Lexicon & Lexical Tools on various platforms, the progress bar reads beyond 100%. This is a display bug that does not affect output or subset completion.

Solution: This error will be corrected in the 2011AB Release.

Date Posted: May 5, 2011

Title: Precedence Filter Bug and Missing Rows in MRRANK.RRF

Problem: When copying an old configuration (.properties) file from a previous MetamorphoSys release to re-use in the current release, the Precedence Filter may not pick up new term types added between the current release and the last release.  This leads to missing rows in MRRANK.RRF.

Solution: This error will be corrected in the 2011AB Release. The workaround is to point ‘default_subset_config_uri’ in your configuration file to ‘%MMSYS_HOME%\config\2011AA\user.a.prop’.

Date Posted: May 5, 2011

Title: Subset creation progress bar reads beyond 100%

Problem: When creating a subset on various platforms, the progress bar reads beyond 100% (into the millions). This is a display bug that does not affect output or subset completion.

Solution: This error will be corrected in the 2011AA Release.

Date Posted: November 22, 2010

Title: OMIM Data Errors

Problem:

• Two HT terms were misspelled in the file received from the source. The terms GENITOURINIARY and NEPLASIA were placed under the RHT, adding two false axes to the hierarchy. Both of these terms are also present in their correctly spelled forms, GENITOURINARY and NEOPLASIA.
• The OMIM term “Behavioral/psychiatric manifestations” (UMLS CUI C1854373) has two erroneous variant terms, “Psychiatric/behavioral manifestations” and “Behavioral/psychiatric Manifestations”.

Solution:

The corrected terms will be present in the next version of OMIM in the Metathesaurus.

Date Posted: November 3, 2009

Title: LNC215 to CPT2005 Mappings Bug

This bug affects the following Metathesaurus files: MRCONSO.RRF, MRSAT.RRF, MRMAP.RRF, MRRANK.RRF

Problem: MRCONSO.RRF contains Mapset metadata CUIs that describe mappings in the UMLS. These CUIs are all assigned the term type (TTY) 'XM'. The CUI 'C1704201' contains the term 'LNC215 to CPT2005 Mappings' which is the only term in this CUI. In 2009AA, this term was erroneously assigned an NLM 'MTHU' code that was shared by an term with a higher ranking term type (MRRANK.RRF). Due to the error, all of the rows in MRMAP.RRF that contain the data for the 'LNC215 to CPT2005 Mappings' are attached to the wrong CUI ('C2599619' rather than 'C1704201'). All of the attributes associated with this map in MRSAT.RRF are also attached to AUI 'A16416485', which belongs to CUI 'C2599619'

Date Posted: May 22, 2009

Title: SQL Load Script produces errors related to ' \|' character sequence

The following applies to users attempting to load the 2008AB RRF data into a MySQL database using the MetamorphoSys-generated MySQL load scripts.

Problem:

Due a '\|' character sequence in the 2008AB data, the following MySQL error message is displayed while loading RRF data into a database: Warning (Code 1264): Out of range value adjusted for column 'SRL.'

1. Open up the mysql_tables.sql file in your MetamorphoSys output directory.
2. Change the following line from:
   • load data local infile 'MRCONSO.RRF' into table MRCONSO fields terminated by '|' lines terminated by '\n'   to the following:
   • load data local infile 'MRCONSO.RRF' into table MRCONSO fields terminated by '|' ESCAPED BY '' lines terminated by '\n'
3. Save and close the file, then re-run the script.

Date Posted: December 16, 2008

Title: MetaMap NLP View label missing from Content View Restrictor Window

Problem: On the Restrict Searches and Views Option, Content View Restrictor screen, the name of the third content view (MetaMap NLP View) is missing.

Solution: This error will be corrected in the 2009AA release.

Date Posted: November 17, 2008

Title: Advanced Suppressibility Options Error

Problem: When using Advanced Suppressibility Options to remove suppressible term types from a customized Metathesaurus subset, MetamorphoSys may not have removed all of the appropriate rows/data from the customized Metathesaurus MRHIER.RRF file.

Solution: Log in to the UMLSKS and download the updated 2008AB UMLS Release files. Note: The Build Date of the correct version of MetamorphoSys is 2008_11_20_06_34_04 (located in Help --> About MetamorphoSys, in the Welcome to MetamorphoSys window).

Date Posted: November 24, 2008

Title: Validation Error when running off DVD

Problem: Users who have a DVD read/write drive will receive this error when attempting to validate the UMLS 2007AB DVD.

Solution: Until the user clicks "OK" the installation process can not go forward. Clicking "OK" will allow the validation to complete by writing the file to another location.

Date Posted: July 2, 2007

Title: Non-ASCII UTF-8 dash characters in 5 RxNorm, MTHSPL CODES not removed by MetamorphoSys Output Option

Problem: Who is affected? Users who
 (1) include RxNorm or MTHSPL data in their customized Metathesaurus subsets, and who also
 (2) use the Output Option in MetamorphoSys to exclude non-UTF-8 characters from their subset

MetamorphoSys fails to remove the following non-ASCII UTF-8 dash characters in the CODE field in the following 5 rows in MRSAT (2007AB):
 
C0716197|L6401119|S7339522|A11769224|AUI|0025–1961|AT69824745||NDC|MTHSPL|0025-1961-30|N||
C0716197|L6401119|S7339522|A11769224|AUI|0025–1961|AT69829041||SPL_SET_ID|MTHSPL|0B0BA593-FE54-456C-A3D7-651C 50036E3E|N||
C0716197|L6401119|S7339522|A11769224|AUI|0025–1961|AT69831407||RXCUI|RXNORM|687204|N||
C0716197|L6401119|S7339522|A11769224|AUI|0025–1961|AT69851217||DM_SPL_ID|MTHSPL|2746|N||
C0716197|L6401119|S7339522|A11769224|AUI|0025–1961|AT69853512||RXAUI|RXNORM|2621866|N||

It fails to remove the non-ASCII UTF-8 dash in in the CODE field of one MRCONSO row:

C0716197|ENG|S|L6401119|PF|S7339522|Y|A11769224||||MTHSPL|DP|0025–1961|Metronidazole 750 MILLIGRAM In 1 TABLET ORAL TABLET, FILM COATED, EXTENDED RELEASE [Flagyl ER]|0|N||

The dash character in these rows is not an ASCII dash, but rather the UTF-8 dash: 
0x2013|U+2013|EN DASH|General Punctuation|1

Solution: The Unicode character U+2013 is represented in UTF-8 as a sequence of the following 3 bytes (in octal):
\342, \200 and \223.

Use the following perl script to make the change in the appropriate file:
perl -ne '{s/\342\200\223/-/g;print}' MRCONSO.RRF
or
perl -ne '{s/\342\200\223/-/g;print}' MRSAT.RRF

These errors will be corrected in the 2007AC release.

Date Posted: July 2, 2007

Title: Bad LOINC Relationship data in early release

Problem: Relationship data was incorrect in an early edition of the 2007AA release. Users who downloaded the release prior to the official announcement will find incorrect LOINC mapped-to relationships in the file MRREL.

Solution: The information has been corrected in the official 2007AA release. Users should download these files which were made available on 1/29/07.

Date Posted: January 30, 2007

Title: MetamorphoSys Content View Filter Tab

Problem:

1. Enabling the Content View Filter creates a blank tab. The Natural Language Processing Content View Filter is not displayed and cannot be selected.
2. Users are unable to navigate away from the blank tab.  (Temporary and immediate Solution:   Disable the Content View Filter.)

Solution: The error exists in the files MMSYS/config/mmsys.a.prop and MMSYS/config/mmsys.b.prop.

Add the lines below to the both of both files:  

gov.nih.nlm.mms.filters.ContentViewFilter.name_2=MetaMap NLP View
gov.nih.nlm.mms.filters.ContentViewFilter.description_2=It represents the strict model of data used by MetaMap.
gov.nih.nlm.mms.filters.ContentViewFilter.code_2=256

Adding these lines will correct the error and allow users to enable a Content View Filter that correctly displays the Natural Language Processing filter. 

Date Posted: November 3, 2006

Title: Advanced Suppressibility Options -->Remove Suppressible Term Types Option does not remove Term Types

Problem: Users who create an ORF subset and select one or all of the following options: Remove Source Term Type Suppressible Data, Remove Editor Assigned Suppressible Data, or Remove Obsolete Data, will find the line "Suppressible terms were included in the subset." at the bottom of their MMSYS.log file.

Solution: The error exists in the production of the log file, not in the data files. Examination of the data files will show that suppressible terms were not included in the subset, in relation to the options the user checked. (For example, if Remove Obsolete Data was checked only obsolete terms will be removed.) The error in the log file will be corrected for the 2006AD release.

Date Posted: July 14, 2006

Title: In the RRF Browser, Find command does not highlight terms

Problem: On Mac, Solaris, and Linux platforms: when using the find command, found terms are not highlighted until the user moves (scrolls up or down) within the window.

Solution: The error will be corrected for the 2006AD release.

Date Posted: July 14, 2006

Title: Java Issues After Installing J2SE 5.0 Release 4 Update

Problem: The software update for Java 2 Platform Standard Edition (J2SE) 5.0 Release 4 for Mac OS X v10.4.5 will change the default version of Java virtual machine from Java 1.4.2 to Java 5.0. This may cause problems with MetamorphoSys.

Solution: Reset the default Java virtual machine. Instructions are available from Apple at http://docs.info.apple.com/article.html?artnum=303526. The 2006AC release of the UMLS will call the correct JRE, regardless of the default settings.

Date Posted: 5/08/06

Title: Incorrect MeSH ^® Relationships

Problem:

In the UMLS 2006AA release available for download from 2/13/06 to 2/24/06, erroneous relationships were present in the MRREL file and duplicated in the files MRHIER, MRFILES, and MRCOLS.

Solution: A corrected release was made available for download from the UMLSKS on 3/2/2006.

Date Posted: 2/24/2006

C0000039|A7439429|1|A7455821|MSHFRE||A7474418.A7456206.A7456207.A7461322.A7452688.A7440176.A7452689.A7455821|||

 C0000139|A7480712|1|A7504811|MSHGER||A7533768.A7484783.A7525302.A7504817.A7504811|||

#!/usr/local/bin/perl

open (MRCONSO,"MRCONSO.RRF") || die "Could not open MRCONSO.RRF : $! $?\n"; while (‹MRCONSO›) {
chop;
split /\|/;
$auis{$_[7]} = 1;
}
close (MRCONSO);
open (MRHIER,"MRHIER.RRF") || die "Could not open MRHIER.RRF : $! $?\n"; while (‹MRHIER›) {
chop;
split /\|/;
$ptr = $_[6];
@ptr_auis = split /./, $ptr;
$missing = 0;
foreach $aui (@ptr_auis) {
unless ($auis{$aui}) {
$missing = 1;
last;
}
}
print "$_\n" unless $missing;
}
close (MRHIER);

Date Posted: 2/13/2006

Title: ATN Field Too Short in the ORF File MRCOLS

Problem: When generating an ORF subset with the database load script option, the ATN field is set to 20 chars instead of 50.  Any sources that have ATN values greater than 20 that are loaded into a database using one of our scripts produces an error (data is longer than the field length).

Solution: After generating subset and the load script, edit the load script to make ATN field 50 chars. This issue will be resolved in the 2006AA release.

Date Posted: 11/30/2005

Title: TS Fields in MRCON Not Properly Computed for Editor Suppressed Atoms

Problem: When generating an ORF subset from ORF input, the TS fields in MRCON are not properly computed for editor suppressed atoms.

Solution: This issue will be resolved in the 2006AA release.

Date Posted: 11/30/2005

Title: MeSH Attribute Information Incorrectly Represented

Problem: The data problem reported on 7/19/2005 has been fixed. In the original 2005AB release (release date 20050615), some data in the following MeSH attributes were incorrectly represented in the Metathesaurus files MRSAT and MRREL: 

• AN
• EC
• OL
• AQL
• FX
• PA
• CX
• HN
• PM
• DC
• MDA
• RN
• DS
• MMR
• RR
• DX
• MN

Attributes from other sources, and MeSH data in other Metathesaurus files, including MRCONSO, MRDEF, MRSTY, and MRHIER, were unaffected.

Solution: Licensees who use MeSH attribute data in their research or applications should use the corrected 2005AB UMLS release. The corrected 2005AB UMLS release carries the release date of 20050718. Release date is included in the release.dat and mmsys.log files.

Date Posted: 7/26/2005

Title: MetamorphoSys Errors Associated with Mac OS Tiger

Problem: We have found issues in the most recent Tiger update (10.4.2) that may cause new problems for users, including application crashes. We are investigating and expect Apple to remedy these issues. One specific Problem: Mac OS Tiger users receive an error message stating "Resources temporarily unavailable" when running MetamorphoSys.

Solution: This error has been corrected in the 2005AC release of the UMLS. If you must use an older version, close all unnecessary applications. Macintosh Tiger users (OS X 10.4) are reminded to quit all other applications (including dashboard widgets) to avoid the Mac "resource temporarily unavailable" error.

Date Posted: 7/27/2005

Title: Differing MD5 Files for AMBIGLUI.RRF, AMBIGSUI.RRF, MRAUI.RRF, MRCUI.RRF, MRSMAP.RRF, and MRSMAP.RRF

Problem: MD5 files created using Windows are not the same as MD5 files created on other operating systems.

Solution: There is no solution at this time. This problem will be corrected in the 2005AC release.

Date Posted: 6/15/2005

Title: Disk Full Errors Are Not Detected and Reported in MetamorphoSys

Problem: In some circumstances disk full errors are not properly detected. MetamorphoSys may appear to complete correctly but files are corrupted. Files may include truncated lines or null characters inserted into the data.

Solution: Users must be certain that they have adequate disk space before using MetamorphoSys.

Date Posted: 6/15/2005

Title: Invalid Data in NDDF Update; Also Affects RxNorm Subsets

Problem: There are serious errors in the NDDF update in 2005AA that affect not only NDDF in the Metathesaurus, but also RxNorm. Drug data that was added to the Metathesaurus from the November NDDF update are correct, but over 100,000 NDDF drug names already in the Metathesaurus were incorrectly marked as obsolete. NDDF data, as a separate source, and within the RxNorm subset, should not be used, or should be used with extreme caution.

Solution: A new RxNorm Cumulative Release File, including corrected NDDF data, will be available in late February or early March.
NDDF will be corrected in the UMLS 2005AB release, scheduled to be available in April 2005.
See also: RxNorm Cumulative Update.

Date Posted: 2/8/2005

Title: RxNorm Cumulative Update: Non-Matching Codes for RxNorm Atoms

Problem: The RxNorm Cumulative Update of 11/17/2004 contains non-matching codes for RxNorm atoms. This update is based on the 2004AC release of the UMLS, but contains all new codes for RxNorm atoms. These codes do not correspond to previously assigned codes and the update cannot be applied to existing RxNorm data.

Solution: RxNorm data will be resynchronized with the 2005AA release, updated with SNOMED CT drug data, and the full and corrected Cumulative RxNorm will be released in late February or early March.

Date Posted: 2/8/2005

Title: Missing Codes in Spanish and Portuguese Translations of MeSH 2005 (MSHSPA and MSHPOR)

Problem: For 2005AA, the Spanish and Portuguese translations of MeSH 2005 (MSHSPA and MSHPOR) do not include the MeSH Descriptor Number in the CODE field in MRCONSO.RRF (MRCON in ORF).

Solution: Problem will be corrected in 2005AB.

Date Posted: 1/18/2005

Title: ORF Database Load Scripts for Those Who Downloaded 2004AB Before Friday, July 23rd

Problem: The Original Release Format (ORF) MySql and Oracle load scripts for indexes are missing column names.

Solution:

1. Manually insert column names into script for indexes
   or
2. Download and unzip the mmsys.zip file (64364251 bytes or 61 MB), then re-run MetamorphoSys to recreate your data

Date Posted: 7/27/2004

Condition: User selects RxNorm subset from the initial Default Subsets list, then disables the filter by unchecking the box on the RxNorm Output Options tab.

Bug: Unchecking the box does not disable the filter. The RxNorm filter is applied regardless of the state of the checkbox.

Temporary Fix for 2004AB: Do not pick RxNorm filter on the Install menu and then attempt to deselect this option on the RxNorm Output Option tab.

To be corrected in the 2004AC release.

Date Posted: 7/20/2004