1 Introduction

1.1 Background

A cooperative agreement [3] was signed between the Regenstrief Institute (RII) and the SNOMED International (IHTSDO) in July 2013. The agreement details how SNOMED CT and LOINC will be linked through:

1. a map of LOINC Terms to postcoordinated SNOMED CT expressions

2. a map of LOINC Parts to SNOMED CT concepts

3. a map between LOINC Terms and existing pre-coordinated SNOMED CT concepts

4. LOINC Answer sets mapped to SNOMED CT codes

5. addition of new content in either terminology

See Figure 1 for an illustration of these connections. This Production Release includes artifacts related to items 1 and 5 above.

Open

Figure 1. Diagram showing an overview of maps, Expression Associations and content additions that form part of the Cooperative Works of the Agreement [3].

1.2 Purpose

• This document is intended to give a brief description, background context and explanatory notes on SNOMED International’s official RF2 release format of the LOINC - SNOMED CT Cooperative Project Production Release [1].

• This is not a detailed technical document about the release file formats, use cases, or on implementing LOINC and SNOMED CT together. See “Using LOINC with SNOMED CT” [2] for information about implementation of LOINC and SNOMED CT together.

• All content will be released by both SNOMED International and the Regenstrief Institute through their distribution channels, e.g. SNOMED International Confluence site, LOINC website.

1.3 Scope

This document is written for the purpose described above and is not intended to provide details of the technical specifications for SNOMED CT or encompass every change made during the release.

1.4 Audience

The audience includes National Release Centers, vendors of electronic health records, terminology developers and managers who wish to partake in the review of the LOINC - SNOMED CT Cooperative project edition Production release.

2 Content Development Activity

2.1 Overview

This Production release contains one content file: a LOINC Term to SNOMED CT Expression Reference Set. This Production release is RF2 compliant and it contains a full release file, a snapshot file and a delta file. The Production content is released under the 715515008 | LOINC - SNOMED CT Cooperation Project module (core metadata concept) with concept identifiers from the 20220131 version of the International release of SNOMED CT and Version 2.71 of LOINC released August 2021.

This release includes a majority of the Top 2000 LOINC Lab Observations needed to represent these LOINC Terms. Some content has been excluded from the Production Release:

• Physiological measurements and Vital signs Terms

• Veterinary specific terms are not considered in the scope of SNOMED CT and this project

• Although panel names are in the scope of the Cooperative Agreement, modeling of panel Terms is not. However, SNOMED International decided not to include the LOINC Term with panel names.

• LOINC Terms that have a status of "Discouraged"

The July 2017 Production release included another file - LOINC Part to SNOMED CT Reference Set - which is not part of this release.

2.2 Content usage

The main purposes for the alignment are to (a) link the laboratory coverage of LOINC with the SNOMED CT concept model to provide a consistent model rather than having divergent representation of similar concepts, (b) limit duplication of effort related to overlapping areas, and (c) focus resources on common and collaborative effort rather than the competing activities of the past. In practical terms there are a variety of ways to deploy and benefit from the resulting products. These are explored in the current draft of the document “Using LOINC with SNOMED CT.” It is available on Confluence at http://snomed.org/snomedloinc.

2.3 Content detail

2.3.1 LOINC Term to SNOMED CT Expression Reference Set

• The LOINC Term to SNOMED CT Expression Reference Set includes the majority of the LOINC Terms from the Top 2000 Laboratory LOINC list

• All of the LOINC Terms are subclasses of 363787002 | Observable entity (observable entity) in SNOMED CT and the expressions follow the latest version of the SNOMED CT Observables model. [4,5,6]

• See Table 1 for an example from the refset

• For a list of attributes from the Observables model used to create postcoordinated expressions in this work, see the generic quality observable entity template [4] and the generic process observable template [5]

• Section “Modeling Guidelines” contains general rules on the alignments and exceptions

• The majority of the expressions (~90%) included are fully defined and are an exact match with a LOINC Term, with some exceptions

• The expressions are represented in the stated form with no hierarchy included

• See the entry for "postcoordinated expression" in the SNOMED CT Glossary for more information about Expressions [7]

A.

B.

Table 1.  Example from the LOINC Term to SNOMED CT Expression Reference Set. This shows a LOINC term “Calcium:PrThr:Pt:Bld:Ord” (LOINC code 27182-5) with an equivalent postcoordinated expression. Note that “A” includes text labels for demonstration purposes; the actual refset will not contain the text descriptions (shown in “B”). For brevity, not all fields in the LOINC Term to SNOMED CT Expression Reference Set are included in this table.

3 Modeling Guidelines

3.1 General Guidelines

• Alignment is performed from LOINC to SNOMED CT

• As part of the LOINC - SNOMED CT Cooperation Project agreement, LOINC Terms are being defined with postcoordinated expressions using the Observable entity model

• The list of attributes and values used in the SNOMED CT observable entity model is available in section Observable Entity Attributes Summary [6] in the SNOMED CT Editorial Guide

• In this release we have modeled LOINC Terms as either a quality observable or a process observable. Definitions of these are below. 

  • Quality observable

    • An observable about a characteristic or feature, a quality, that is inherent in a person or a thing. Examples include the mass of a human being and the concentration of sodium in plasma.

      • Rate observables about the amount of output of a process (e.g., the volume of urine voided during a time interval, the volume of blood plasma that is cleared of creatinine per unit of time) are modeled as quality observables.

  • Process observable

    • An observable about a feature of a process or specific outcome of a process. Examples include durations and various kinds of rates such as secretion rate.

3.2 LOINC Part to SNOMED CT Concept and Attribute Alignment

While we are not releasing a LOINC Part to SNOMED CT Concept Refset at this time, the principles below illustrate the guidelines used when performing the original alignment and formation of expressions. In general, we aligned each LOINC axis to SNOMED CT attribute as such:

• LOINC Component to SNOMED CT attributes

  • LOINC Component → 246093002 | Component (attribute) for quality observables. See the template for generic quality observable entity for a list of the attributes used to model quality observables [4]

  • LOINC Component → 704324001 | Process output (attribute) and 704321009 | Characterizes (attribute) (and optionally 704322002 | Process agent (attribute)) in process observables such as excretions. See the template for generic process observable entity [5] for a list of the attributes used to model process observables. 

•  

  • When the LOINC Component contains additional information/qualifiers, we modeled as such:

    • LOINC Components containing divisors → 246093002 | Component (attribute) + 704325000 | Relative to (attribute)

    • LOINC Components containing challenges → 246093002 | Component (attribute) + 704326004 | Precondition (attribute)

    • LOINC Components containing adjustments → 246093002 | Component (attribute) + 246501002 | Technique (attribute)

      • Sometimes a new SNOMED CT concept containing a combination of techniques was needed

  • Exceptions, special cases and further information

    • We do not model the LOINC Components representing properties such as Appearance, Color, and Number to SNOMED CT concept. We instead use an appropriate SNOMED CT value from the 118598001 |Property (qualifier value)| subhierarchy in the 370130000 |Property (attribute)|.

    • The LOINC Property can determine if the LOINC Component is modeled with 246093002 | Component (attribute), 704324001 | Process output (attribute), or 704319004 | Inheres in (attribute) in the expression:

      • LOINC Property is a type of concentration, e.g., mass concentration, then LOINC Component → 246093002 | Component (attribute)

      • LOINC Property is a type of rate, e.g., mass rate, then LOINC Component → 704324001 | Process output (attribute)

      • LOINC Property is an inherent part of component, e.g., it is a type of identification such Type or PrID, then LOINC Component → 704319004 | Inheres in (attribute)

    • Observables entities are not allowed as values for the attributes in the observable entity model (and therefore LOINC postcoordinated expression). When a LOINC Component is an observable entity, it should be linked to the actual analyte being measured. Modeling additional attributes (e.g. technique) might become required. Some examples:

      • Erythrocyte sedimentation rate

      • Anion gap, Anion gap 3, and Anion gap 4

      • Base excess or Base deficit

    • For LOINC Parts that are anions and cations (generally calcium and magnesium) we link to the electrolyte concept in SNOMED CT (e.g., LOINC Terms with the Part "Calcium.ionized" are aligned with SNOMED CT concept 259295006 |Calcium electrolyte (substance)|). The generic substance concept is considered to be a grouper for the electrolyte concept (e.g., LOINC Terms with Part "Calcium" are aligned with SNOMED CT concept 5540006 |Calcium (substance)| which is the supertype of 259295006 |Calcium electrolyte (substance)|.) See Table 1 for an example of a LOINC Term with this modeling. 

    • Substance LOINC Components are in general aligned with concepts in the substance hierarchy rather than the product hierarchy in SNOMED CT. Concepts in the product hierarchy are defined by substance concepts via the “Has active ingredient (attribute)." In the measurement of drugs (or any product), what is actually being measured is the active ingredient. So while the range of “Component (attribute)” includes both products and substances, we align with substance hierarchy concepts in the vast majority of cases. This may differ in the future if: 1) additional changes in the substance hierarchy are performed, e.g., a substance concept representing a role is moved to the product hierarchy; 2) LOINC Terms representing susceptibility observables are added to the Expressions Refset. Susceptibility observables would be modeled with a concept from the product hierarchy as a value of 704320005 |Towards (attribute)|.

    • Some LOINC Components include “X organism species” such as “Salmonella species…” The use of terms of the form "X species" is routine in laboratory reporting, but in the context of the Linnaean organism hierarchy there is no difference between "Salmonella species" and simply "Salmonella" the genus. In the context of a laboratory report, the term "Salmonella species" sometimes is intended to convey additional information beyond the place of the identified organism in the Linnaean hierarchy, but the intended connotation may vary from lab to lab and from organism to organism. Since the organism code represents a class of organisms, it cannot also represent what was or was not done, or what will be done, to identify the organism. It also cannot properly represent other information about the result. If there is additional information that needs to be communicated, it should be in a separate statement or comment (e.g., "further species identification pending" or "sent to reference laboratory for further identification" or "further identification to be done if clinically indicated.")

    • From IUPAC (International Union Of Pure And Applied Chemistry) Gold Book: "Nor" used to denote the elimination of one methylene group from a side chain of a parent structure (including a methyl group). "Desmethyl" means the removal or absence of a methyl group from the parent compound. The LOINC User's Guide section 2.1.2.20: For drug metabolites we will use the "Nor" rather than the "Desmethyl", e.g., for instance Nordoxepin not Desmethyldoxepin. There are no desmethyl LOINC parts due to this approach.

    • Sometimes the LOINC Component also links to 246501002 | Technique (attribute) in SNOMED CT. Example: LOINC Component Part Crystals.unidentified aligns with 246093002 | Component (attribute) of "Crystal" and 246501002 | Technique (attribute) = "Detecting by light microscopy without classifying"

    • LOINC Components containing an organism name and a form of typing (e.g., serotype, phagetype, biotype) are handled as follows. These guidelines were needed to address inconsistencies in the terminologies.

      • Examples: X organism serotype, X organism phagetype, X organism biotype

        • 246093002 | Component (attribute) = X organism

        • No Technique (attribute) applied as the LOINC Term does not specify a method

        • Expression is marked as primitive

      • Examples: X organism serotype by Y explicit method (e.g., agglutination method)

        • 246093002 | Component (attribute) = X organism

        • 246501002 | Technique (attribute) = Y technique

        • Expression is marked as:

          • Fully defined if there are no LOINC Terms of the previous example type (e.g., X organism serotype with no specific method stated)

          • Primitive if there are LOINC Terms of the previous example type (e.g., X organism serotype with no specific method stated)

          • Primitive if there are other LOINC Parts with similar meaning, e.g., X organism serotype, X organism serovar, X organism identified).

    • Modeling HLA antigens, alleles and cells

      • LOINC Components containing “CDX” should be aligned with cell concepts, e.g., LP17730-0 "Cells.CD33" aligns with 116825007 | Cell positive for CD33 antigen (cell).

      • LOINC Components containing “CDX Ag” should be aligned with antigen substance concepts, e.g., LP LP37563-1 "CD3" aligns with 44706009 | Lymphocyte antigen CD3 (substance).

      • LOINC Components that begin with HLA and include an asterisk are linked to allele concepts.

    • As defined in the LOINC Users' Guide, "Peak" in LOINC refers to 'The time post drug dose at which the highest drug level is reached (differs by drug)' and "Trough" in LOINC refers to 'The time post drug dose at which the lowest drug level is reached (varies with drug).' Therefore these LPs are linked to 703764006 | At time of peak level (qualifier value) and 703765007 | At time of trough level (qualifier value), respectively, as they are only used in combination with substances. For example, the LP Component "Gentamicin^trough" includes the Component "Gentamicin" and a Challenge of "Trough." In SNOMED CT this would be modeled as 246093002 | Component (attribute) = Gentamicin (substance) and 704326004 | Precondition (attribute) = At time of trough level (qualifier value).

• LOINC Property to SNOMED CT attribute

  • LOINC Property → 370130000 |Property (attribute)|

• LOINC Scale to SNOMED CT attribute

  • LOINC Scale → 370132008 | Scale type (attribute)

• LOINC System to SNOMED CT attributes

  • LOINC System → 704327008 | Direct site (attribute) + 704319004 | Inheres in (attribute) (except when the LOINC Term has a property type of Prid, Type, Number of cells, ID)

    • Direct site is the equivalent of system in LOINC. Used for all specimen types except XXX.

    • Inheres in applies to all specimen types except “specimen”, XXX, Body fluid, tissue and aspirate specimen

    • Direct site and Inheres in definitions

      • The Direct site is the direct object of the observation action; the site or specimen where the observation takes place. This may be different from the value of Inheres in, since the property being observed may be inferred from a specimen or from a remote site. The intended object of the observation is the entity in which the observed property inheres; or the independent continuant which is ideally intended to be observed.

      • Example:

        • Serum specimen being used to determine body plasma sodium concentration. The concentration inheres in the plasma, but is being measured in a serum specimen

    • Note:

      • When the LOINC Term has a property of PRID and scale of NOM --> property inheres in organism (named in LOINC component)

• LOINC Time to SNOMED CT attributes

  • For quality observables:

    • LOINC Time Part Pt → 370134009 | Time aspect (attribute) = Single point in time in SNOMED CT

    • LOINC Time Part of X hours → 370134009 | Time aspect (attribute) = X hours in SNOMED CT

  • For process observables:

    • LOINC Time Part of X hours → 704323007 | Process duration (attribute) = X hours in SNOMED CT

• LOINC Method to SNOMED CT attribute

  • LOINC Method → 246501002 | Technique (attribute)

    • Some LOINC Terms contain references to techniques in both the LP Component name and the LP Method name. In some cases we have used a SNOMED CT technique concept which represents the LP Method and technique from the LP Component name or adjustment name.

• LOINC Units

  • LOINC Units → 246514001 | Units (attribute) in few cases

    • LOINC Units are example units or submitted units, and are not part of the 5-6 essential LOINC Parts that create LOINC Terms. Units of measure may change based on the setting and equipment, and can be standard or American units. We don't plan to include LOINC units unless they are absolutely required (for example, percentage was required to represent 100 cells). Percentage is understood and used the same everywhere.

3.3 Correlation between LOINC Part and SNOMED CT Concept and Attributes

• Our goal is to create exact alignment between LOINC Parts and SNOMED CT concepts. In some cases this is not possible. Some examples of this are:

  • The LOINC Part “Leukocyte other” is modeled as either “Leukocyte (cell)” and “Population of leukocytes in portion of fluid” depending on the property and we consider these SNOMED CT concepts to be broader than the LOINC Part.

  • We do not consider LOINC Parts with “NOS” equal to SNOMED CT concepts without “NOS.” “NOS” is specifically out of scope of SNOMED CT and would not be added. Therefore, LOINC Parts with NOS will be considered narrower than the modeled SNOMED CT concept.  

  • LOINC Parts with “tissue” or “body fluid” or "aspirate" are considered narrower than the modeled SNOMED CT concept. The "Body fluid" System really means fluids that are not otherwise defined in LOINC, and not a higher-level concept that encompasses all body fluids. Tissue LOINC Parts are defined similarly in LOINC. "Aspirate" in LOINC refers to a pathologic aspirate (e.g., abscess) so this is considered narrower than the included SNOMED CT concept.

• One LOINC Part is aligned to one SNOMED CT concept where possible. In some cases a one to one alignment was not possible:

  • LOINC Part aligned to more than one SNOMED CT concept

    • LOINC System Parts are aligned using two attribute-value pairs in SNOMED CT: 704327008 | Direct site (attribute) and 704319004 | Inheres in (attribute)

      • Example: LOINC Part “Ser/Plas” is aligned with SNOMED CT 704327008 | Direct site (attribute) = Acellular blood (serum or plasma) specimen and 704319004 | Inheres in (attribute) = Plasma

    • LOINC Parts for cells (e.g. Basophils) potentially align with two concepts in SNOMED CT: an individual X cell concept and a population of X cells in portion of fluid concept. The property type and scale of the associated LOINC Term will determine which alignment is appropriate for that LOINC Term. For example, the LP "Basophils" could align with 246093002 | Component (attribute) = 702963004 | Population of all basophils in portion of fluid (body structure) and/or 246093002 | Component (attribute) = 30061004 | Basophil, segmented (cell).

•  

  • Some LOINC Component Parts (generally substances) are aligned using the 246093002 | Component (attribute) and/or 704324001 | Process output (attribute) depending on the time aspect and property of a LOINC Term. When the Property type is MRat, SRat, VRat, and NRat, and Time = X hrs, then the 704324001 | Process output (attribute) carries the SNOMED CT concept equivalent to the LOINC Component. Otherwise, the 246093002 | Component (attribute) carries the SNOMED CT concept equivalent to the LOINC Component. A LOINC Term will generally only include a value for 246093002 | Component (attribute) OR for 704324001 | Process output (attribute) but not both. 

    • Example: Creatinine is used as a value of the 246093002 | Component (attribute) in LOINC Term Creatinine/Calcium [Mass Ratio] in Urine. Creatinine is used as a value of the 704324001 | Process output (attribute) in LOINC Term Creatinine [Mass/volume] in 24 hour Urine.

  • LOINC Divisor Parts are aligned to two attribute-value pairs in SNOMED CT: 704325000 | Relative to (attribute) and 246514001 | Units (attribute)

    • LOINC Part 100 Leukocytes is aligned with SNOMED CT 704325000 | Relative to (attribute) = Population of all leukocytes in portion of fluid and 246514001 | Units (attribute) = Percentage

• LOINC Part is not aligned with an equivalent SNOMED CT concept

  • LOINC Part that is not universal and reproducible is linked to a more general concept in SNOMED CT.

    • Example, the LOINC Part “Leukocyte other” is modeled as “Leukocyte (cell)” and “Population of leukocytes in portion of fluid” in SNOMED CT because the meaning of “Leukocyte other” cannot be specified.

• LOINC Part aligned with a different attribute in SNOMED CT concept

  • Example: The LOINC Component Part “Color” is modeled with the 370130000 |Property (attribute)| with a value of “Color” in SNOMED CT

• Two LOINC Parts are combined to align with two SNOMED CT concepts

  • LOINC Component Part Crystals.unidentified and LOINC Method Microscopy.light align with SNOMED CT 246093002 | Component (attribute) = Crystal and 246501002 | Technique (attribute) = Detecting by light microscopy without classifying

3.4 LOINC Term to SNOMED CT PostCoordinated Expression Alignment

• Our goal is to create a SNOMED CT expression equivalent to each LOINC Term and mark it as fully defined with a designation of “Exact match.” Where this is not possible, the expression is marked as primitive and/or a designation other than “Exact match” is utilized. In this Production Release, the only correlation beside “exact match” used is 447559001 | Broad to narrow map from SNOMED CT source code to target code (foundation metadata concept), i.e. the SNOMED CT expression is broader than the LOINC Term. To date, we have not created an expression that is narrower than the LOINC Term, and it is unlikely that we ever would.

  • LOINC Terms that utilize the following LOINC Parts will be marked as primitive because the LOINC Part will not have an exact match in SNOMED CT.

    • LP7641-6  Tiss

    • LP189537-6  XXX.tissue

    • LP61649-7  Tissue

    • LP7642-4  Tiss.FNA

    • LP29168-9  Soft tissue.FNA

    • LP7037-7 Asp

    • LP7593-9 Specimen

  • Example: the LOINC Term “Leukocytes other [#/volume] in Body fluid” is modeled with an expression that has 246093002 | Component (attribute) = Population of leukocytes in portion of fluid along with other attribute-value pairs. The expression is given a correlation of “LOINC narrower” and a designation of “Primitive.”

• An expression only needs to include the attributes necessary to specify the LOINC Term. It does not need to use every attribute in the Observables model.

• The LOINC Terms in this Production Release are modeled as either quality observables or process observables. See an example of a quality observable expression in the first row in the table below and a process observable in the second row of the table below. See definitions of quality and process observables in the General Guidelines section.

• LOINC Terms with Presence vs. Presence Identification: X in Y

  • PRID: e.g. 14475-8 | Bacteria identified in Cervix by Aerobe culture

    • Bacteria → 704319004 | Inheres in (attribute)

    • Cervix → 718497002 | Inherent location (attribute)

• If the expressions are classified, some more specific LOINC Terms are subsumed by more general LOINC Terms. We have verified the validity of the following subsumptions with Regenstrief Institute and the Observables and Investigation Model Project Group:

  • Subsumption of expressions due to SNOMED CT substance hierarchy organization:

    • Expressions containing SNOMED CT “Amino-acids” concepts subsume individual amino acid

    • Expressions containing SNOMED CT “Antibody” concepts subsume individual antibodies

    • Expressions containing SNOMED CT substances which include free, soluble, or unsaturated substances are subsumed by the generic substance concept

    • Expressions containing SNOMED CT substances which include organ/body part (e.g. Alkaline phosphatase.renal) are subsumed by the more general substance concept

  • Expressions for LOINC Terms with a technique are subsumed by expressions with a more generic method or methodless expressions

  • Expressions for LOINC Terms containing adjustments are subsumed by generic or unadjusted expressions

  • Expressions for LOINC Terms containing challenges are subsumed by generic expressions

  • Expressions for LOINC Terms with a more specific specimen are subsumed by more generic expressions, e.g. Arterial blood is necessarily a kind of Blood

  • Expressions for LOINC Terms with a more specific property are subsumed by expressions with a more generic property, e.g., NCnc subsuming LNCnc

    • Exception: Ratio in LOINC is a sibling to MRTO or SRTO and is interpreted as "other ratio." It is linked to Ratio in SNOMED CT, left primitive and does not subsume expressions which include MRTO or SRTO.

  • There is no subsumption of expressions when the LOINC Terms contain Point in time or timed measurements.

3.5 Additional Information

• Additional information is designated for each LOINC Term to SNOMED CT postcoordinated expression:

  • content origin (LOINC or SNOMED CT or both)

  • correlation (exact, narrower, broader)

  • definition status (primitive or fully defined)

  • refset identifier

  • module identifier

  • effective time of expression

  • expression status for active vs inactive

  • unique identifier of map row (GUID)

• Disjunctive substance LOINC Parts are not included in this Production file release because we there was no way to model them in SNOMED CT at the time of the original publication in 2017. 

• Active and trial LOINC Terms are included in the expression refset as some implementers are using these LOINC Terms. Deprecated and discouraged LOINC Terms are not included in the expressions refset.

• This file contains some LOINC Parts linked to the same SNOMED CT concept which need to be clarified to see if they are in fact duplicates

  • Example: 11-Ketoandrosterone and 11-Oxo-androsterone are both linked to 57244003 | 11-Ketoandrosterone (substance)

• This file contains some duplicate LOINC Parts which RII is planning on deprecating soon.

  • Example: E coli shiga-like and verotoxin are equivalent. RII indicated that they will deprecate the verotoxic term and link it to the shiga-like term.

• Some naming conventions in SNOMED CT concepts are not consistent

  • Example: "Immunoglobulin G antibody to Yersinia" vs "Immunoglobulin A antibody to Yersinia species"

• SNOMED CT utilizes multiple descriptions per concept, and some of the descriptions used may not be common parlance in laboratory medicine.

  • Examples: 

    • The LOINC Part for “Bacteria identified” is aligned with 409822003 |Domain Bacteria (organism)| in SNOMED CT. We agree that the fully specified SNOMED CT name for this concept is not used in most lab reports; the concept it signifies (“Bacteria”) is used in lab reports. This concept has a description/synonym of “Bacteria” in SNOMED CT.