Enriched linkages between LOINC terms and LOINC Parts

Overview

Beginning with LOINC version 2.66, we enhanced our model of how LOINC terms relate to LOINC Parts and published these enhanced linkages in the LoincPartLink.csv file.

The first key aspect of this effort was clearly labeling the specialized aspects of our names into defined relationships. The second key aspect was labeling pieces of the LOINC term name (especially Components) to make linkages to other extant terminologies more straightforward.

We have previously used PartTypeName and LinkTypeName to identify different kinds of parts and relationships. The new approach extends this model further and organizes certain kinds of Part Types into groups that would be identified as a specific LinkType. We have now defined 8 groups of LinkTypes as described below. Note that not all LOINC terms will have all of these LinkTypes.

1. Primary: the six key Parts that comprise the LOINC Fully Specified Name;
2. DetailedModel: compositional subparts defined by the official LOINC semantic model (specified in Chapter 2 of the LOINC Users’ Guide);
3. SyntaxEnhancement: more detailed Parts that represent useful pieces of the LOINC term name that are NOT officially part of the semantic model;
4. SemanticEnhancement: relationships that enhance the semantics of the LOINC term by providing additional sub-typing and/or special linkages to external ontologies and vocabularies;
5. Metadata: accessory term attributes that are coded but not part of the official semantic model;
6. Radiology: the specialized properties defined by the LOINC/RSNA Radiology Playbook;
7. DocumentOntology: the specialized properties defined by LOINC Document Ontology;
8. Search: synonyms, fragments, and other Parts that are linked to a term to enable more encompassing search results.

Since the LOINC 2.68 release, the LoincPartLink.csv file has been split into two separate files – LoincPartLink_Primary.csvand LoincPartLink_Supplementary.csv. The first includes the Primary properties plus DocumentOntology and Radiology properties. All of the other properties are included in the LoincPartLink_Supplementary.csv file. We did this for two reasons: one, the original file was extremely big, and two, we think it is important to clearly identify the most important (i.e., Primary, DocumentOntology, and Radiology) attributes that should be implemented for each term. Note that the supplementary file still exceeds the row capacity of Excel and LibreOffice.

Rather than exploding the number of PartTypeNames (and having too many duplicate Part concepts across various types) to handle the more complex set of attributes we want to represent, we included a field that describes the specific attribute (or “property” as FHIR calls them). Here, we will follow the pattern already established, of using URIs to identify the property. We reuse the URIs we’ve already defined, and create new ones in the common FHIR style that uses dashes to separate words (e.g., http://loinc.org/property/rad-modality-subtype).

The last major enhancement we enabled borrows from the open ontology style with a model that allows the direct reference to other external vocabularies where they represent the definitive or authoritative source for concepts in a particular domain. This may not ever obviate the need for LOINC Parts, but we can start laying a path that makes it easier to connect LOINC to these other sources. To do this we added a new attribute to describe the CodeSystem for the “Part”. This is a work in progress and currently is only enabled for GENE type Parts, which are linked to terms with a LinkType of SemanticEnhancement. Looking ahead, we can imagine a scenario where for some domains (e.g. chemicals, bacteria, anatomy, etc) we explicitly draw from another reference terminology (e.g. CHEBI, UBERON, etc) as the basis for creating some of our Parts.

For the LOINC 2.68 release, we implemented the supplementary links as part of our FHIR terminology services.

A comprehensive model for linking LOINC Parts to LOINC Terms

Primary

This LinkType identifies the key six Parts that comprise the LOINC Fully Specified Name. Every LOINC term has 5 (or 6 if Method is specified) Parts that represent the full contents of the corresponding field in the LOINC Table. For a given LOINC term, this set of Parts will have names that exactly match the contents of the LOINC Table. Based on conventions established a few years ago and documented in the LOINC Users’ Guide, we have already defined these Properties and have published them in the loinc.xml FHIR specification.

Primary Properties

Examples

Example rows from LoincPartLink_Primary.csv for 10000-8

Example rows from LoincPartLink_Primary.csv for 3097-3

Example rows from LoincPartLink_Primary.csv for 17876-4

Special Notes

• There should be a minimum of 5 and a maximum of 6 Primary linkages for any LOINC term, depending on whether Method is specified.
• We recommend that all FHIR terminology servers implementing LOINC as a CodeSystem include these “core” attributes for every term and deploy them as coded entities.
• In Loinc_2.65_PartFile_2.65-Beta.2 and prior, the linkage to the CLASS PartTypeName was as LinkTypeName Primary. Beginning in 2.66, these links were re-labeled as as LinkTypeName Metadata as described below.

DetailedModel

This LinkType identifies the more detailed compositional subparts defined by the official LOINC semantic model, which is specified in Chapter 2 of the LOINC Users’ Guide. In the LOINC Table, the main Parts are divided further into subparts by separation with the carat (^) character.

Not all of these detailed subparts are required for a particular term, and in fact, LOINC terms representing radiology procedures and terms in the LOINC Document Ontology do not include the DetailedModel LinkTypes. These terms have their own specialized semantic models with Radiology and DocumentOntology LinkTypes, respectively, which are described below.

DetailedModel Links, Properties, and PartTypeNames

Footnotes

† In cases where we have not defined a “sub” Part in the LOINC semantic model, we reuse the main Properties because they correspond exactly in meaning. While a little redundant, putting them together in both LinkTypes ensures you can grab the full set of relationships you want via LinkType.

Special Notes

• Overall, this set contains the Parts that comprise the detailed Fully-Specified Name. It does NOT contain divisors, suffixes, “method subtypes”, or other special pieces that we have not documented as official parts of the name. As such, the definition here for Analyte corresponds exactly to the whole “first subpart” described in the LOINC User’s Guide. It does not strip out suffixes or divisors. Those extra details will be characterized in other relationships (described below).
• The collection of strings (with delimiters) identified by Primary LinkTypes will equal exactly the collection of strings (with delimiters) identified by DetailedModel LinkTypes, and these both will add up to the exact string name corresponding to our Fully Specified Name.

Examples

Example rows from LoincPartLink_Supplementary.csv for 3097-3

Example rows from LoincPartLink_Supplementary.csv for 66134-8

Syntax Enhancement

This LinkType identifies more detailed Parts that represent useful pieces of the LOINC term name that are not officially part of the semantic model. Historically, many of these linkages have not been obvious to most LOINC users. The main purpose of these links is further decompose the structure of the LOINC name into defined fragments. Behind the scenes, they are used for several things, including synonym linkages, language translation, and linking descriptive text.

Here, we use a naming style with the DetailedModel PropertyLabels as the first piece of the name (e.g. analyte). This helps organize where these little bits fit into the overall LOINC model.

SyntaxEnhancement Links, Properties, and PartTypeNames

Special Notes

• [Future Work] For now, we are keeping the current model for DIVISORs, which internally uses a specialized PartTypeName (called DIVISOR) and postfixes the relevant System. For example, consider [LOINC:48149-9] Osmolality.urine/Osmolality.serum. In the long run, we are considering getting rid of the DIVISOR PartType. These could all be regular Component parts, if we had a model that supported grouped relationships. Such a term could instead be modeled as:
  • 48149-9 | analyte-core = Osmolality
  • 48149-9 | analyte-divisor = Osmolality
  • 48149-9 | system-core = Urine
  • 48149-9 | system-divisor = Ser/Plas
• [Future Work] In several places of the LOINC name we use a dot “.” to indicate subclass and other relationships. For example, Calcium.ionized or RR interval.standard deviation. Additional SyntaxEnhancement LinkType associations could be considered to make these terms more computable.

Examples

Example rows from LoincPartLink_Supplementary.csv for 50995-0

Example rows from LoincPartLink_Supplementary.csv for 3097-3

Example rows from LoincPartLink_Supplementary.csv for 48149-9

Semantic Enhancement

This LinkType identifies relationships that enhance semantics of the LOINC term by providing additional sub-typing and/or special linkages to external ontologies and vocabularies. These linkages are not officially part of the LOINC naming model that defines a term, but they can be extremely helpful for advanced processing of LOINC-coded data. For example, they help separate the different kinds of entities (chemicals, organisms, etc) that can serve as a Component.

As before, we use a naming style that includes the DetailedModel PropertyLabel as the first piece of the name. This helps organize where these little bits fit into the overall LOINC model. With this LinkType, we do allow repeat linkages within a particular term. For example, a LOINC term may represent testing about multiple genes.

This is a work in progress and currently is only implemented for GENE type Parts, but several examples are included in the table below for illustrative purposes.

SemanticEnhancement Links, Properties, and PartTypeNames

Special Notes

• We are considering implementing some kind of ordering/sequence to help group and order blocks or repeats of relationships. For example, a given LOINC term may contain multiple genes in its Component.

Examples

Example rows from LoincPartLink_Supplementary.csv for 50995-0

Metadata

This new LinkType will identify accessory term attributes that are coded but not part of the concept model (a.k.a. the structured term name).

Metadata Links, Properties, and PartTypeNames

Examples

Example rows from LoincPartLink_Supplementary.csv for 40443-4

Radiology

This LinkType identifies the specialized properties defined by the LOINC/RSNA Radiology Playbook. A full description of these attributes is given in the Annex LOINC/RSNA Radiology Playbook User Guide.

Radiology PartTypeNames and their Properties

Special Notes

• These properties were already identified in our loinc.xml FHIR code system resource, so we use the same URIs here.
• LOINC terms for which Radiology LinkType relationships defined will NOT have DetailedModel LinkType relationships defined because the Radiology model supersedes.

Examples

Example rows from LoincPartLink_Primary.csv for 36283-0

DocumentOntology

This LinkType identifies the specialized properties defined by LOINC Document Ontology. A full description of these attributes is given in the LOINC Document Ontology chapter of the LOINC Users’ Guide.

DocumentOntology PartTypeNames and their Properties

Special Notes

• These properties were already identified in our loinc.xml FHIR code system resource, so we use the same URIs here.
• LOINC terms for which DocumentOntology LinkType relationships defined will NOT have DetailedModel LinkType relationships defined because the Document Ontology model supersedes.

Examples

Example rows from LoincPartLink_Primary.csv for 11508-9

Discussion

Known Issues

Future Work

• [Future work] To be maximally useful, this file should specify a Sequence that allows for ordering and grouping sets of links. We do this now in the LoincRsnaRadiologyPlaybook File.
• [Future work] Consider replacing the linkages to LOINC Parts in some SemanticEnhancement LinkTypeName relationships with concepts from domain-specific ontologies.
• [Future Work] Consider replacing the current model for DIVISORs with a model that supports grouped relationships.
• [Future Work] In several places of the LOINC name we use a dot “.” to indicate subclass and other relationships. For example, Calcium.ionized or RR interval.standard deviation. Additional SyntaxEnhancement LinkType associations could be considered to make these terms more computable.
• [Future Work] Expand linkages of categories to LOINC terms.
• [Future Work] Explore use of Tag LinkType associations for special purposes (e.g terms representing tests performed only in a veterinary or public health context).