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.

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.

• 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).

• Some LOINC Component Parts (generally substances) are mapped 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. The Part map may include a value for 246093002 | Component (attribute) and 704324001 | Process output (attribute).

• 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 mapped to two attribute-value pairs in SNOMED CT: 704325000 | Relative to (attribute) and 246514001 | Units (attribute)

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

• LOINC Part is not mapped to an equivalent SNOMED CT concept

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

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

• LOINC Part mapped to a different attribute in SNOMED CT concept

• Example: The LOINC Component Part “Color” is mapped to the 704318007 | Property type (attribute) with a value of “Color” in SNOMED CT

• Two LOINC Parts are combined to map to two SNOMED CT concepts

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

3.4 LOINC Term to SNOMED CT Post Coordinated 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 map 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 mapped to an expression that has 246093002 | Component (attribute) = Population of leukocytes in portion of fluid along with other attribute-value pairs. The map is given a correlation of “LOINC narrower” and a designation of “Primitive.”

• 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, when linking the related LOINC Terms to SNOMED CT expressions, we set the definition status for the expressions containing "NOS" to “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 and a process observable in the second row of the table. 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)

• 704319004 | Inheres in (attribute) and 718497002 | Inherent location (attribute) are required in pair (except when specimen is XXX, aspiration, specimen, tissue, soft tissue).

• Presence: e.g. 21262-1 | Escherichia coli shiga-like [Presence] in Stool by Immunoassay

• Escherichia coli shiga-like → SNOMED CT Component

• Stool → SNOMED CT Inheres In

• • Note: Identity (or type or taxon) is a property of the bacteria while presence is a property of the system where the bacteria were found. For example, the type of bacteria might be Escherichia coli but it's a property of the abscess to contain or not contain bacteria.

• Modeling of Time in LOINC Terms

  • LOINC Terms modeled as quality observables will utilize the Time aspect attribute to represent time with a value of Single point in time, 24 hours, 2 hours, etc.

  • LOINC Terms modeled as process observables will utilize the Process duration attribute to represent time with a value of X hours.

  • See the table below for examples of expressions modeled as process observable (first row) and quality observables (second and third rows).

• 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 subsumbed 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 mapped 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 Part to SNOMED CT value/attribute map:

• content origin (LOINC or SNOMED CT or both)

• correlation (exact, narrower, broader)

• attribute (where a Part is used in an expression)

• refset identifier

• module identifier

• effective time of map

• map status for active vs inactive

• unique identifier of map row (GUID)

• Additional information is designated for each LOINC Term to SNOMED CT post coordinated 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)

• Some SNOMED CT Concepts included in the file do not specifically map to one LOINC Part, e.g. some specimen concepts and some technique concepts

• Disjunctive substance LOINC Parts are not included in this Production file release because we do not have a way to model them in SNOMED CT at this time. Therefore they are on hold until a solution is provided. These LOINC Parts were included in previous Alpha releases but have been removed from the Production Release as a result of this recent decision.

• Active, discouraged and trial LOINC Terms are included in the mapping as some implementers are using these LOINC Terms. Deprecated LOINC Terms and Parts are not included in the mapping.

• This file contains some LOINC Parts mapped to the same SNOMED CT concept which are being reviewed by Regenstrief to see if they are in fact duplicates

• Example: 11-Ketoandrosterone and 11-Oxoandrosterone are both mapped to 57244003 | 11-Ketoandrosterone (substance)

• Example: Macroglobulin and IgM are both mapped to

• 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 map 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.

• Example: The LOINC Part for “Bacteria identified” is mapped to Superkingdom 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.

• Example: The LOINC Part for “Fungus identified” Is mapped to Kingdom Fungi (organism) in SNOMED CT. This concept currently has a description of “Fungi.” Although another SNOMED CT - Fungus (organism) - would appear to be a more accurate match, there has been a recent recommendation by the Organism and Infectious Disease Model Project Group to retire 23496000 | Fungus (organism) | as a duplicate of 414561005 | Kingdom Fungi (organism) |. When this occurs we will add a description/synonym of “Fungus” to this concept.

The SNOMED International Microbiology Reporting Project Group discussed similar topics and posted guidelines in the SNOMED CT Editorial Guide in section 6.3.5. Observables and results for microbiology tests (https://confluence.ihtsdotools.org/x/fYu2AQ). These guidelines can be applied to Superkingdom Bacteria vs. Bacteria identified as well.