In this Update
We are delighted to present you with another feature-packed LOINC release. Here's the outline of what we'll cover:
- LOINC content highlights
- New content
- Content edits
- New and updated LOINC release artifacts
- LOINC Change Snapshot File
- LOINC Consumer Name File
- LOINC Answer File
- LOINC Display Name File
- LOINC Group File
- LOINC Multiaxial Hierarchy File
- LOINC Part File
- LOINC/RSNA Radiology Playbook
- LOINC License
- LOINC Linguistic Variant Updates
- Changes to the public LOINC data files in this release
- LOINC Table
- Notice of changes to the public LOINC data files for the December 2019 Release
- LOINC Linguistic Variant File
- RELMA release highlights
- Web-based Panels and Forms browser
- FHIR Terminology Services API
- Updated LOINC content available through the API
- LOINC content highlights
Read on for the full details.
This section describes the most important changes included in the current LOINC release.
As always, see the documentation included with each release artifact for more information.
LOINC version 2.66 contains 91,388 terms, an increase of 2,117 since version 2.65. Overall, this release includes 606 new laboratory, 325 new clinical, and 1,186 new survey terms.
Some of the new content highlights in this version:
- Over 300 new terms for microbiology and susceptibility testing, including 40 panels and over 100 terms with System of Respiratory.lower, or Genital to increase usability where more specific terms exist
- Approximately 90 new terms in the CLASS DRUG/TOX
- Two new panels for blood group antigens by genotyping:
- Forty molecular pathology terms, including APOL1 inferred genotype [Identifier] in Plasma from Donor 92636-0
- Approximately 50 new radiology procedure terms
- Over 100 new terms to complete the LOINC representation of the Minimum Data Set (MDS) for Public Health Emergency Operations Centers (EOC) [CDC Emergency Operations Centers] 89724-9
- Public health reporting terms related to:
- Carbon monoxide exposure
- Travel history
- Severe weather events
- Birth and Fetal death reporting
- Over 50 terms for complex disease and exposure data elements for work with Research Triangle Institute (RTI)'s PhenX Toolkit
- New clinical and survey panels, including:
- Minimum Data Set (MDS) - version 3.0 - Resident Assessment Instrument (RAI) version 1.17.1 (10 different item sets) 90472-2
- Sixty two new Patient-Reported Outcomes Measurement Information System (PROMIS) panels representing various adult, parent proxy, and pediatric item banks and short forms
- Protocol for Responding to and Assessing Patients' Assets, Risks and Experiences (PRAPARE) 93025-5
- STarT Back Screening Tool panel 91349-1
- General Well-Being Schedule - 18 item 91629-6
- Mood and Feelings Questionnaire
This release contains a total of 3,703 deprecated terms, of which 649 were deprecated since version 2.65. In addition, about 4,150 terms have been edited.
Changes based on internal review or as part of an ongoing project
- Added Fetal to the Component for terms representing prenatal testing performed using cell-free DNA to clarify that the result is about the fetus
- Terms used to report the "disposition" of the patient (i.e. location/status) at discharge were updated (where needed) to Discharge disposition for consistency. Based on these updates, several terms were deprecated because they were duplicates.
- The Component for terms representing sexual activity were updated to include the phrase sexual activity to help clarify the meaning and distinguish from terms representing the biological sex.
- Updated Gender to Sex in Component and Adjustment where it is meant to represent biological sex
- Updated Method for Troponin T.cardiac [Mass/volume] in Serum or Plasma by High sensitivity method 67151-1 from Detection limit <= 5 ng/L to High sensitivity
- Updated Scale for 54 terms from OrdQn to Ord because genotyping does not produce quantitative susceptibility results
- Introduced tall man lettering for drugs based on recommendations from the Institute for Safe Medication Practices
- Updated older molecular pathology terms with Property Prid and Scale Nar to have Find and Doc, respectively, to align with the current LOINC model for representing information collections such as molecular pathology test reports
- In general we do not update LOINC terms with Status of Deprecated. However, in this release we made an exception. We updated specific aspects of deprecated terms for consistency, to support LOINC term to LOINC Part linking, and in the Consumer names project. Changes to deprecated terms include:
- For consistency, added - to terms that had missing Property, Time, System, and/or Scale
- Updated ??? to - in the Property for two terms
- Removed period (.) characters in Long Common Name (LCN) that were appended for the sole purpose of making the names syntactically unique. With agreement from the LOINC Committee, truly duplicate concepts can now have duplicate LCNs.
- Corrected the UCUM units for several terms
- Removed the limited number of existing values from the CONSUMER_NAME field as part of the new Consumer Names project; the field itself was not removed. New Consumer Names are provided in pre-production status in the separate LOINC Consumer Name File to facilitate review and comments by the user community.
- Added the PhenX protocol ID to the Component for nearly 350 PhenX panels
- Updated Component for approximately 100 radiology terms based on the LOINC/RadLex Committee's decision to adopt the AMA/ACR definitions for "aspiration" and "drainage".
- For consistency across terms, updated the Component and/or Long Common Name for 15 radiology terms that represent arthrocentesis procedures, with percutaneous aspiration of fluid in the Component and arthrocentesis in the Long Common Name
Changes based on community input
- Removed the Method from a handful of terms that represent generic concepts without the need for distinguishing the technique or methodology. An example is Tobacco smoking status 72166-2.
- Over 600 terms in ATTACH* Class were deprecated because the use case for which these terms were created no longer exists. This decision was supported by the HL7 Attachments Workgroup.
- Updated the LL1859-9 Answer List that is linked to Specimen type 66746-9 to include more than coag-related specimens
- Updated Component for Parasite identified in Blood by Light microscopy 17784-0 from Parasites to Parasite identified and Property from Find to Prid to align this term with other parasite terms with Scale of Nom
- The System for Gabapentin [Mass/volume] in Serum, Plasma, or Blood 9738-6 was updated from Ser/Plas to Ser/Plas/Bld
- Addition of synonyms:
- tumor marker to all Parts of type Component that represent tumor markers
- Human respirovirus 1 and Human respirovirus 3 for Parainfluenza virus 1 and Parainfluenza virus 3, respectively
- Human rubulavirus 2 and Human rubulavirus 4 for Parainfluenza virus 2 and Parainfluenza virus 4, respectively
- Trospectomycin for Trospectinomycin
- Allergen code f447 for Peanut rAra h 6 LP263675-3
- Clostridium was updated to Clostridioides in Component Parts to align with current nomenclature
- Renin [Units/volume] in Plasma 30895-7 was un-discouraged based on reporting information from Italy
- Corrected Amino acids panel [Molar ratio] - Urine 74991-1 to include Anserine term instead of the Arsenic one
- Deprecated 22 limited use LABORDER terms. These terms were originally created for Canada Health Infoway, but are no longer in use and cause confusion for mappers
- Updated or removed the ObservationRequiredInPanel (R/O/C) from several terms in lab panels and/or added terms to a handful of panels to be more inclusive of different reporting styles
- Minor updates were made to multiple names and term descriptions to fix typos and for readability
New and updated LOINC release artifacts
NEW LOINC Change Snapshot File
The purpose of the LOINC Change Snapshot File is to provide a structured record of the key changes to LOINC content that occurred in this release. In this inaugural Alpha.1 release, we have focused only on changes in Status for LOINC Terms and LOINC Parts. There are separate .csv files for changes to LOINC terms and LOINC Parts.
The LoincChangeSnapshot contains records for all LOINC terms that had a change in Status between LOINC version 2.65 and version 2.66, such as from TRIAL to ACTIVE, or ACTIVE to DEPRECATED.
The PartChangeSnapshot contains records for several sets of LOINC Parts with change in Status between LOINC version 2.65 and version 2.66. The first set are those that were used in version 2.65 of the Multiaxial Hierarchy that are no longer used in the version 2.66 hierarchy. The second set are Parts that were associated with a LOINC term via relationships in the LoincPartLink file in version 2.65, but that are no longer associated with any term in the current version (2.66). Prior to this release and the advent of the PartChangeSnapshot file, such Parts were removed from LOINC release artifacts without further record of them. Now, both of these sets of Parts are recorded in PartChangeSnapshot file. The first set would typically be labeled with a Status of DEPRECATED and the second set would have a Status of INACTIVE. The third set of Parts contained in the PartChangeSnapshot file are those that had a Status of ACTIVE and were linked with a LOINC term in the LoincPartLink file in version 2.65, but that in the current release are DEPRECATED but still present in the Part.csv file and LoincPartLink.csv file. This occurs primarily when the Part is associated with a LOINC term that is DEPRECATED and we have determined that Part should not be used in the future.
Design notes and request for comment
In these files, we purposefully used the Property field to carry the identification of the attribute of the LOINC Term or Part that changed. This use of Property is the same meaning as in our FHIR CodeSystem representation, and not the same as the (Kind of) Property of the LOINC Fully Specified Name.
Within our internal LOINC management system, we are now tracking "change reasons" at the more detailed field level (rather only than at the level of the whole Term) and therefore in this artifact we can reflect these more precise, field-level descriptions.
We intentionally do not include terms first added to LOINC in this release, since that information is already available in the LOINC Table via the VersionFirstReleased field.
We intend to expand the set of changes represented in this artifact over time, both in terms of number of attributes and the set of release artifacts. This will be a work in progress and we are eager to hear user feedback about the approach.
NEW LOINC Consumer Name File
We are delighted to announce the inaugural release of the LOINC Consumer Name File. This file contains a revised and expanded set of names for LOINC terms designed to be more easily understood by consumers and suitable for display in consumer-facing applications. The present scope covers all Laboratory LOINC terms and a subset of Clinical LOINC terms. The ConsumerName is created algorithmically, based on manually crafted labels (names) for each Part. These names do not represent each of the defining Parts of a given term, are not unique, and do not include an indicator that a term is deprecated.
Please see the documentation for additional explanation. We are pleased with this initial Alpha.1 release of these Consumer Names, but welcome your feedback and expect to make iterative refinements to the approach over time.
The LOINC Consumer Names are intended for downstream display only and are not intended to be used at any point in the clinical workflow, nor for the purpose of mapping local terms to LOINC.
LOINC Answer File
The release has been incremented to version 2.66, a production version. After multiple pre-production VersionType releases, we have received no significant public comments about its structure and have not identified any major format changes needed at this time.
LOINC Display Name File
We have updated the LOINC Display Name File to Beta.2 VersionType because we received no significant public comments about its structure and have not identified any major format changes that are needed. Before promoting this artifact to production status, we are seeking user feedback on our approach for deprecated and duplicate terms as described below.
In this Beta.2 release, there are two primary changes:
- Angle brackets (<>) have been removed from the DisplayName for terms with a Status of DEPRECATED.
- We now allow truly duplicate terms to have the same DisplayName so that data can be appropriately aggregated for display downstream. Previously, an arbitrary character such as a dot (.) was used to make them unique.
If there are no significant public comments about these two changes, we anticipate promoting Display Names to production status with the next LOINC release. Production status would entail including the Display Names in a new field within the main LOINC Table, and most likely discontinuing publication of this separate artifact.
LOINC Group File
This release has been upgraded to Beta.3 VersionType because we received no significant public comments about its structure and have not identified any major format changes that are needed.
In this release, 26,524 unique LOINC terms are contained in one or more Groups.
LOINC Multiaxial Hierarchy File
In this release the Multiaxial Hierarchy received a major version update to 3.0-Alpha.1 because it contains significant updates to the hierarchy creation process, including:
- Using the Component Parts that include Suffixes (that are represented in the LoincPartLink File as LinkTypeName Primary) rather than the ones that only contain the core analyte (represented in the LoincPartLink File with LinkTypeName SyntaxEnhancement and Property analyte-core Parts)
- Including the Class in addition to the Component+System in the Multiaxial Parts that organize terms
- Using PartTypeName Class Parts for the upper level nodes
- Accounting for the Super System
These changes corrected several issues:
- Terms with a Challenge and/or a Method are now correctly placed under the Component+System+Class rather than Component alone
- Terms in Class CHEM and CHAL are now placed in their respective branches rather than being duplicated across both branches
- Terms with different meanings based on the Suffix, e.g., Hepatitis B virus surface Ab and Hepatitis B virus surface Ag are now separated into different branches
- Terms with Super Systems are now separated from those without, such as Ser/Plas and Ser/Plas^Donor
We also added more Component Parts for clinical terms to the hierarchy in the areas of Cardiology, Dental, Ophthalmology/Optometry, and Respiratory/Ventilator. Terms in these areas are thus no longer lumped under the ClinicalNotYetCategorized node. In addition, we moved panel Class nodes under their corresponding primary Class (e.g., PANEL.MICRO under MICRO) as a more logical home in the hierarchy.
The net result of these changes is that thousands of new Multiaxial Parts were created, and simultaneously, thousands of previously used Multiaxial Parts became obsolete. These obsolete Parts now have a Status of DEPRECATED and are included in the new ChangeSnapshot File so that users will still have a record of them.
We seek user feedback about each of these major changes, but most specifically about the approach to including the Class in the construction of the hierarchy nodes.
LOINC Part File
We have made significant changes to the contents and structure of this artifact since the last release; therefore, the version has been incremented to 3.0-Alpha 1. The three major changes are summarized below and are described in detail in the companion file LoincPartLinkEnrichmentReleaseNotes.html included in the archive.
The size of LoincPartLink.csv is big! In fact, it exceeds the row capacity of Excel and LibreOffice. Please be aware of this fact when using this file. The overall size of the zip archive is quite small, because of compression. We may consider splitting up the file (e.g. by LinkTypeName) and seek user feedback about this.
The major changes implemented for this release include:
- Specialized aspects of our names have been clearly labeled by defining relationships. Using the convention established in the HL7 FHIR standard, we added a new attribute called Property that identifies these relationships. LOINC users should note that this use of Property describes the relationship between a Part and a LOINC term, and is different from the term's Kind of Property axis used in the Fully Specified Name.
- Pieces of the LOINC term name (especially within the Component) have been labeled using these new Property relationships and an extended set of PartTypeName labels that make linkages to other extant terminologies more straightforward. For example, we can now clearly identify genes, chemicals, clinical drugs, etc.
- We have enabled direct reference to external vocabularies that represent the openly available, authoritative source for concepts in a particular domain by adding a field to carry the PartCodeSystem.
- We have defined several new collections of relationships that are gathered by new LinkTypeName, including: DetailedModel, SyntaxEnhancement, SemanticEnhancement, and Metadata. These new types join the previously used LinkTypeName labels of Primary, Search, DocumentOntology, and Radiology.
Please see the extended documentation, Release Notes, and Readme contained in this artifact for detailed reference information about this powerful resource and the ideas noted for future work. We welcome user feedback about these ideas, especially about the possible inclusion of an ordering sequence.
The mappings to and content from the RSNA Playbook are based on version 2.4 of that terminology, and Radiology Part mappings are based on RadLex version 3.15 and 4.0.
Some terms with multiple Aggregation values have one or more Aggregation values that are not being assigned the correct PartSequenceOrder number.
A small number of LOINC Radiology Parts do not have mappings to RadLex RIDs. We plan to address these issues for the next LOINC release.
REQUEST FOR COMMENT
We are contemplating adding a PartSequenceOrder field to the LoincPartLink.csv file that would be similar to the PartSequenceOrder field included in this file. We would appreciate feedback on the usefulness and format of this field to help inform our future efforts.
The license accompanying this release has been updated to Version 3.0 because we added references to our new release artifacts (LOINC Consumer Name File and LOINC Change Snapshot File), in accordance with the LOINC Versioning Policy.
In order to simplify the references to these (and future) release artifacts, we named specific collections of licensed artifacts (e.g. "Group 1 Artifacts") that are then referred to in subsequent sections of the license. This change reduces the "clutter" of having many long lists of file names without altering the intended licensing terms that apply to those files.
The global community of LOINC users continues to help produce a wonderful collection of translations. These linguistic variants (we support multiple translations of the same language) are available in RELMA, the online application, and in the LOINC Linguistic Variants File.
Updated Linguistic Variants in this release:
- es_ES_12 - Spanish (SPAIN)
- nl_NL_22 - Dutch (NETHERLANDS)
- fr_CA_8 - French (CANADA)
- fr_FR_18 - French (FRANCE)
- it_IT_16 - Italian (ITALY)
- zh_CN_5 - Chinese (CHINA)
Users should note that we intend to retire the translations produced by CUMUL in a future release. That translation effort was suspended many years ago and more comprehensive translations into French, German, and Italian have been produced by others.
We have implemented the following change to the LOINC Table (all formats):
Field Name: CONSUMER_NAME
Formal Definition: An experimental (beta) consumer friendly name for this item. The intent is to provide a test name that health care consumers will recognize; it will be similar to the names that might appear on a lab report and is not guaranteed to be unique because some elements of the LOINC name are likely to be omitted. We will continue to modify these names in future release, so do not expect it to be stable (or perfect). Feedback is welcome.
As noted above, we have begun a significant effort to expand and revise development of consumer-friendly names for LOINC terms. In this release we have published a new release artifact: the LOINC Consumer Name File. The existing entries in the CONSUMER_NAME field of the LOINC Table have been migrated into the separate release artifact. The separate artifact aids review and public comment. When such names reach a production level status, we intend to move them back into the CONSUMER_NAME field of the LOINC Table.
Notice of changes to the public LOINC data files for the December 2019 Release
LOINC Linguistic Variant File
Notice of upcoming changes to this artifact in the December 2019 release:
Field Name: TIME_ASPECT
Formal Definition: Third major axis-timing of the measurement (e.g., point in time vs 24 hours)
This field name will be updated to TIME_ASPCT (removing "E") to align with the naming of this column in the main LOINC table.
Web-based Panels and Forms browser
Clicking on the Panels, Forms & Surveys menu option will now open the panel browser on the LOINC website at http://loinc.org/panels instead of the RELMA internal panel browser. With this change, we now have the ability to make more dynamic changes to the categorization and layout of the panel browser.
The RELMA database and Lucene indexes contain LOINC Parts and Answer lists that may not be used by or linked to any LOINC terms, and you may see them returned in RELMA search results on the Part search tab and Answer list search tab. These Parts and Answer lists may have been used in the past or might not have ever been used. They are not included in the Part and Answer list release artifacts, and this discrepancy has been a source of confusion for some users. We are planning to remove these unused Parts and Answer lists from RELMA in a future release.
You will receive an error if you manually add a new local term and then delete a local term in the same session. As a work around, after you add a local term close and restart the program before manually deleting a local term.
The RELMA Export full panel structure function generates an Excel spreadsheet that represents a panel term and all its children. However, certain panel terms such as 50586-7 Glucose tolerance 3 hours panel - Serum or Plasma do not have an explicit list of child terms. Attempting to export these terms will result is an unexpected error. This issue should cause no harm and you can safely continue using the application. We will fix this issue in a future release.
Updated LOINC content available through the API
During our release process we have also updated our FHIR terminology server with the latest content. The server currently supports CodeSystem, ValueSet, and ConceptMap resources. Read more about the API at loinc.org/fhir.
We have also created several new collections of LOINC terms and published them as FHIR ValueSet resources, including: