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 post-coordinated 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, 2, 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 the format intended to be continually distributed for implementation.

  • Note that the information contained in the detailed Mapping and Modeling Guidelines section will be added to the SNOMED CT Editorial Guidance document.

• 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.

• Previous releases during the Alpha testing phase included two additional file formats (OWL and Excel) to assist in reviewing the content. Now that we are releasing the Production version, we will only publish the content in the official RF2 release format.

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 two content files: a LOINC Term to SNOMED CT Expression Reference Set and a LOINC Part to SNOMED CT 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 20170731 version of the International release of SNOMED CT and Version 2.58 of LOINC released December 2016.

This release is based on an updated list of LOINC Parts received after the last Technology Preview Alpha Release. 3M assisted us in mapping additional LOINC Parts to SNOMED CT concepts since the last Alpha release. This release includes a majority of the Top 2000 LOINC Lab Observations and LOINC Parts needed to represent these LOINC Terms. In addition, many LOINC Parts not used in the Top 2000 LOINC Lab Terms are included in this release. Some content has been excluded from the Production Release:

• We have not yet mapped all the LOINC Parts associated with the Top 2000 LOINC Terms to SNOMED CT concepts (or have not created the SNOMED CT concepts). The main reason for this exclusion is the requirement for further clarification with the Substance Project, RII, and Observable Model Redesign Project.

• There are Terms being discussed internally or with Regenstrief for modelling reconsiderations and possible modification:

  • Susceptibility testing

  • Genetic testing

  • Terms defined by LP Components containing “tested for”

  • Terms containing disjunction

• Physiological measurements and Vital signs Terms are not included because their scope is still being discussed with RII. Furthermore SNOMED International has not received the list of LOINC Parts from RII used to define these 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.

2.2 Content usage

The main purposes for the mapping 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 contains 21889 active LOINC Terms associated with post-coordinated SNOMED CT expressions. This refset 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 and see Figure 2 for a diagram of the Observables model used in this work.

• Section “Mapping and Modeling Guidelines” contains general rules on the mapping and exceptions.

• The majority of the expressions 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

• There are some known content issues in this reference set which are under discussion with the Observables and Investigation Modeling Project Group and Regenstrief Institute.

• See the SNOMED CT Technical Implementation Guide 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 post-coordinated 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.

A.

 B. 

Figure 2. Observables model showing the relationship of SNOMED CT attributes (in yellow) and values (in blue) used in creating the post-coordinated expressions in the LOINC Term to SNOMED CT Expression Refset. “A” shows the model for quality observables and “B” shows the model for process observables. Note that all the permissible value hierarchies are not shown in this diagram for brevity. See 6.3.3 Attributes for observable entities and evaluation procedures [6] in the SNOMED CT Editorial Guide for a complete list of approved hierarchies for values of each attribute.

2.3.2 LOINC Part to SNOMED CT Map Reference Set

• The LOINC Part to SNOMED CT Reference Set consists of 6627 LOINC Parts (LP) mapped to one or more SNOMED CT concepts.

• While the majority of the maps are one to one, occasionally one LP maps to more than one SNOMED CT concept or a combination of LPs map to one SNOMED CT concept or combination of SNOMED CT concepts. Additionally, a concept may be used as a value in more than one attribute.

• See section “Mapping and Modeling Guidelines” for general rules on the mapping and exceptions.

• See Table 2 for examples of Part maps.

A.

B.

Table 2.  Example of one LOINC Part mapped to a SNOMED CT concept to be used with two different attributes. LP15257-6 is a component part type in LOINC. The attributeId column indicates for which attribute in SNOMED CT this concept would be a value; in this case the concept is used as value for two different SNOMED CT attributes. 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 Part to SNOMED CT Complex Map Reference Set are included in this table.

3 Mapping and Modeling Guidelines

3.1 General Guidelines

• Mapping is performed from LOINC to SNOMED CT

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

• The list of attributes and values used in the SNOMED CT observable entity model is available in section 6.3.3 Attributes for observable entities and evaluation procedures [6] in the SNOMED CT Editorial Guide.

• In this Production Release we have modeled LOINC Terms as either a quality observable or a process observable. Definitions of these, provided in the Observables and Investigation procedures redesign Inception/Elaboration document [5], are below. See Figure 2 for a list of the attributes used to model quality and process observables.

  • 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

In general, we mapped from LOINC axis to SNOMED CT attribute as such:

• LOINC Component to SNOMED CT attributes

  • LOINC Component → 246093002 | Component (attribute) for quality observables. See Figure 2A for a list of the attributes used to model quality observables.

• LOINC Component → 704324001 | Process output (attribute) and 704321009 | Characterizes (attribute) (and optionally 704322002 | Process agent (attribute)) in process observables such as excretions. See Figure 2B for a list of the attributes used to model quality observables.

•  

  • When the LOINC Component contains additional information/qualifiers, we mapped 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 map the LOINC Components Appearance, Color, and Number to SNOMED CT concept. We instead use an appropriate SNOMED CT value from the property subhierarchy in the 704318007 | Property type (attribute).

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

      • Estimated Glomerular filtration rate, MDRD formula (eGFR)

      • RBC sedimentation rate

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

      • Base excess or Base deficit

    • For LOINC Parts that are anions and cations, we map to the electrolyte concept in SNOMED CT. The generic substance concept is considered to be a grouper for the electrolyte concept. See Table 2 for an example of a mapping.

    • 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.

    • 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 maps to 246501002 | Technique (attribute) in SNOMED CT. Example: LOINC Component Part Crystals.unidentified maps to 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) will be mapped as follows:

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

        • 246093002 | Component (attribute) = X organism

        • 246501002 | Technique (attribute) = serotyping, bacteriophage typing, biotyping, etc

    • Mapping for 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" maps to 44706009 | Lymphocyte antigen CD3 (substance).

      • LOINC Components that begin with HLA and include an asterisk are mapped 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 mapped 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 → 704318007 | Property type (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)

    • 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 aspiration 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.

    • Example mapping:

•  

  • 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 map 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 maps that are exact matches between LOINC Parts and SNOMED CT concepts. Where this is not possible, the map is given a designation other than “Exact match.”

  • Example: the LOINC Part “Leukocyte other” is mapped to “Leukocyte (cell)” and “Population of leukocytes in portion of fluid” with a correlation of “SNOMED CT Broader.”

  • Example: the LOINC Part “Beta lactamase.usual” is mapped to beta-Lactamase (substance) but this is not an exact match. However, since Beta lactamase.usual does not meet the inclusion criteria for SNOMED CT, we keep the map to the more general concept and label it as "LOINC Narrower/SNOMED CT Broader." LOINC Terms defined by this concept will be marked as primitive.

  • Example: 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, the map from LOINC Parts with NOS to SNOMED CT concepts will be “LOINC narrower.”

  • Example: LOINC Parts with “tissue” or “body fluid” will be “LOINC narrower.” 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.

• We mapped from one LOINC Part to one SNOMED CT concept where possible. In some cases a one to one map was not possible:

  • LOINC Part mapped to more than one SNOMED CT concept

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

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

    • LOINC Components containing typing will be mapped to an appropriate value in the 246093002 | Component (attribute) as well as to a typing technique concept such as biotyping, serotyping, etc. in 246501002 | Technique (attribute). If the LOINC Term is also defined by a Method in LOINC, a combination concept for the technique will be created and utilized.

    • 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 map 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).