Vocab. LOINC - OHDSI/Vocabulary-v5.0 GitHub Wiki

LOINC

Logical Observation Identifiers Names and Codes (LOINC) is a standardized coding system for laboratory and clinical tests, procedures, observations, surveys, and corresponding results.

Sources

All LOINC source information is obtained from the following:

1. LOINC Website that is supported by the Regenstrief Institute:

  • LOINC Table Core (Observations and Measurements)
  • LOINC Answers
  • LOINC Multiaxial Hierarchy
  • LOINC Document Ontology
  • LOINC Panels and Forms
  • LOINC Groups
  • LOINC to SNOMED mapping
  • LOINC Replacement Mapping

2. The National Library of Medicine (NLM) Website:

  • LOINC To CPT4 Mapping

3. LOINC Users' Guide:

  • Manual table of LOINC Classes

Concept Names

  • Values of a “long_common_name” field are considered to be preferred terms for concept names.
  • Values of “consumer_name”, “shortname” and “relatednames2” fields reside in the CONCEPT_SYNONYM table as synonyms.

Standard Concepts

Source Concept Type Standard Concept
LOINC Observations, Measurements and Procedures Standard
LOINC Answers Standard
LOINC Hierarchy Classification
LOINC Classes Classification
LOINC Categories Classification
LOINC Groups Classification
LOINC Parts (Component, Method, Property, Scale, System, Time) non-Standard

Domains and Concept Classes

LOINC Concepts are located in such domains as “Observation”, “Measurement”, “Procedure” and “Meas Value”.

Previously all concepts with a LOINC property of “classtype” with values “1” and “2” were considered to be Measurements. However, an initial analysis of such extended LOINC properties as “property”, system”, “scale_type”, “class”, “method_typ”, “definitiondescription” and “survey_quest_text” revealed that the LOINC domain distribution can be more accurate if used the combinations of LOINC properties. In turn, the Concept Class definition is connected with a defined Domain.

So, they were assigned pursuant to the following criteria:

Source Dependencies Domain Concept Class
Loinc core Table A “classtype” field value = 1 (Laboratory class) or 2 (Clinical class) AND:

1. A “survey_quest_text” field value contains a question mark, which always defines LOINC questions.

OR

2. A “scale_typ” field has “Set” value indicating concepts used for Clinical Attachments only.

OR

3. A “property” field value contains:

• “Hx” - History of different clinical and administrative events

• “Anat” - Anatomical sites, points, body structure descriptions

• “ClockTime”, “Date”, “TmStp”, “TmStpRange”, “DateRange” - time/date/date and time/ranges of different clinical and administrative events

• “Desc” - Description of procedures or clinical events

• “Instrct” - Instructions

• “Loc” - Location

• “Pn” - Person Name - administrative information about a person

• “Addr” - Address

• “EmailAddr” - Email Address

• “Tele” - Telephone Number

• “Xad” - also Address

• “Txt” - Text - notes and comments

• “URI” - Uniform Resource Identifier

• “Bib” - Bibliographic Citation

OR

4. A “property” field value is “ID” representing Identifiers such as serial numbers, codes and IDS while “system” field value in “BPU” (Blood Product Unit - additional information about a blood transfusion), “^Patient” (patient related codes), “Vaccine” (vaccination-related additional information).

OR

5. Values of a “system” field are represented by the following:

• “^Family member”,“Community”, “^Brother”,“^Daughter”, “^Sister”, “^Son” - observational particular person-related data

• “^CCD” - Continuity of Care Document

• “^Census tract” - information about people in a geographic region defined for the purpose of taking a census

• “^Clinical trial protocol” - Clinical trial protocol documentation and reports

• “*” - Mixed category defining sites, types, locations, device peculiarities, etc.

• “^Contact”, “^Emergency contact” - contact information

• “^Donor” - a donor type and ID

• “^Event” - information about incidents or events

• “^Facility” - information about services

• “Provider” - provider-related information

• “Report” - report specification

• “Repository” - health data repository

• “School” - a name of a school

• “Surgical procedure” - surgical specification

OR

6. values of a “system” filed are “^Patient” and “*^Patient” which contain observational data directly linked with a patient and, simultaneously, values of a “scale_typ” field are in:

• “Doc” - various types of documentation

• “Nar” - narrative text

• “Nom” - nominal or categorical responses that do not have a natural ordering

• “Ord” - ordered categorical responses, e.g. “Yes”, “No”.

while a “method_typ” field value is not “Apgar” (Apgar score is a screening test used to measure the vital signs of a newborn)

OR

7. values of a “property” field are in:

• “Imp” - impression/interpretation of a study - is used to represent a property when the evaluation is a mental abstraction based on one a collection of measurements and/or data.

• “Find” - findings (seem to be Observations in all cases regardless of the “system”, but not)

• “NRat” - number = count/time - e.g. “How many cigars are you smoking per week now?”

• “Num” - number - e.g. “[#] Pregnancies”

• “PrThr” - the presence of symptoms, historical facts, statuses, etc.

• “RelRto” - relative ratio - e.g. relative risk of developing a disease

• “Time” - time aspects - age, hours, years, etc.

• “Type” - a mixed category with a general notion of something

• “Arb” - arbitrary - a mixed category, e.g. “Informed consent obtained” or “RhoGam candidate”

while values of a “class” field are not “COAG” (it includes laboratory, tests related to hemostasis) and “PULM” (it is about measurements of respiratory function).

A general exclusion criterion: a “long_common_name” field value contains the words as “scale” or “score” (they indicate “Measurement” domain).

Observation Clinical Observation
OR

8. class = ‘RAD’ - radiology - represents radiology procedures like CT, XR, MR and so on

Exclusion: a “partnumber” field = LP7753-9 (Qn) or LP200093-5 (Calcium score) or LP200395-4 (Densitometry)

Procedure Clinical Observation
Other cases when a “classtype” field value = 1 (Laboratory class) Measurement Lab Test
Other cases when a “classtype” field value = 2 (Clinical class) Measurement Clinical Observation
A “classtype” field value = 3 (Claims attachment) Observation Claims Attachment
A “classtype” field value = 4 (Surveys) Observation Survey
LOINC Hierarchy A “Code text” field value contains the following:

• “identifier”, “ID”, “number”, “name”, “age”, “status”, “provider”, “subject”, “device”, “version”, “ICD code”, “coding system”, “priority”

• “time”, “date”, “date and time”, “term”

• “comment”, “narrative”, “note”, “directive”, “attachment”, “reference”, “interpretation”, “summary”, “information”, “suggestion”, “administration”, “route”, “instruction”, “intention”, “consent”, “report”, “flowsheet”,

• “recommended”, “reported”, “received”, “requested”, “reviewed”, “ordered”, “available”, “issued”, “performed”,

• “lifetime risk”, “risk factor” “alert”, “known exposure”, “not yet categorized”, “reason for”

At the same time a “code_text” field value does not contain: “thrombin time”, “clotting time”, “bleeding time”, “clot formation”, “kaolin activated time”, “closure time”, “protein feed time”, “Recalcification time”, “reptilase time” ,”russell viper venom time”, “implanted device”,” dosage.vial”, “isolate”, “within lymph node”, “cancer specimen”, “tumor”, “chromosome”, “inversion”, “bioavailable”.

Observation LOINC Hierarchy
A “path_to_root” field includes LP29684-5 (Radiology) Procedure LOINC Hierarchy
Other values of a “code_text” field Measurement LOINC Hierarchy
LOINC Classes LOINC Class name contains such the words as “history”, “report”, “document”, “miscellaneous”, “public health” Observation LOINC Class
Other cases Measurement LOINC Class
LOINC Group A “parentgroupid” field = LG85-3 (Radiology) or LG41849-7 (Region imaged: Lower extremity) or LG41814-1 (LG41814-1) Procedure LOINC Group
Other cases Measurement LOINC Group
LOINC Answer Independently Meas Value Answer

Relationships

Relationships are defined within LOINC and between LOINC and CPT, and LOINC and SNOMED:

I. Internal LOINC relationships

A purpose of Internal LOINC relationships is to build a LOINC Hierarchy, which makes it easier to sort and browse the database.

Relationship (reverse relationship) From To
Maps to

(Mapped from)

Each LOINC concept The same LOINC concept
Is a

(Subsumes)

Descendant LOINC Class Ancestor LOINC Class
Is a

(Subsumes)

LOINC Group LOINC Group Category
Is a

(Subsumes)

LOINC Measurement or Observation LOINC Class
Is a

(Subsumes)

LOINC Measurement or Observation LOINC Group
Is a

(Subsumes)

Descendant LOINC Measurement or Observation Ancestor LOINC Measurement or Observation
Panel contains

(Contained in panel)

LOINC Panel LOINC Measurement or Observation
Has Answer

(Answer of)

LOINC Question LOINC Answer
Has type of service

(Type of service of)

LOINC Measurement or Observation LOINC concept indicating a Type of Service (Document Ontology)
Has subject matter

(Subject matter of)

LOINC Measurement or Observation LOINC concept indicating a Subject Matter Domain (Document Ontology)
Has role

(Role of)

LOINC Measurement or Observation LOINC concept indicating a Role (Document Ontology)
Has setting

(Setting of)

LOINC Measurement or Observation LOINC concept indicating a Setting (Document Ontology)
Has kind

(Kind of)

LOINC Measurement or Observation LOINC concept indicating a Kind of Document (Document Ontology)
Concept replaced by

(Concept replaces)

Upgraded LOINC concept New LOINC concept
Has component

(Component of)
LOINC Measurement or Observation LOINC Component
Has method

(Method of)
LOINC Measurement or Observation LOINC Method
Has property

(Property of)
LOINC Measurement or Observation LOINC Property
Has scale type

(Scale type of)
LOINC Measurement or Observation LOINC Scale
Has system

(System of)
LOINC Measurement or Observation LOINC System
Has time aspect

(Time aspect of)
LOINC Measurement or Observation LOINC Time

II. External LOINC relationships

The purpose of External LOINC relationships is the following: to simplify a cross-analysis of clinical information systems, laboratory information, specifications or standards with a context of combined use of the LOINC and such a coding system as either the SNOMED or CPT4, or PPI.

Relationship From To Description Count
LOINC - SNOMED eq LOINC Lab Test SNOMED concept of 705114005 “LOINC Code System” (Qualifier Value) An identifier for a LOINC referenced component according to the "Using LOINC with SNOMED CT" guide. Note, this is not a mapping! 22560
LOINC - SNOMED eq LOINC Hierarchy SNOMED Body Structure (the “Spec Anatomic Site” domain) Defines a body structure observed or measured 26
LOINC - SNOMED eq LOINC Hierarchy SNOMED Morph Abnormality (the “Observation” domain) Indicates present in certain disease states structures which observed or measured 3
LOINC - SNOMED eq LOINC Hierarchy SNOMED Observable Entity (the “Observation” domain) Represents an entity observed or measured 8
LOINC - SNOMED eq LOINC Hierarchy SNOMED Organism (the “Observation” domain) Defines a microorganism measured 116
LOINC - SNOMED eq LOINC Hierarchy SNOMED Substance (domains of “Device” and “Observation”) Represents a biological substance or pharmacological agent measured 849
LOINC - SNOMED eq LOINC Hierarchy SNOMED Specimen (the “Specimen” domain) Indicates a specimen source observed or measured 4
LOINC - CPT4 eq LOINC Lab Test CPT4 Procedure or Measurement Defines link from a LOINC concept to a less granular CPT4 concept 1886
Mapped from LOINC Survey/Clinical Observation/Answer PPI Observation or Measurement Indicates an equivalent mapping from a concept of the PPI questionnaire-like vocabulary to a corresponding LOINC concept 2155

III. Hierarchy

All internal “Is a” and “Panel contains” relationships participate in the creation of the CONCEPT_ANCESTOR table, creating an internal hierarchy within the LOINC.

IIIa. OMOP CDM hierarchical crosswalk between LOINC and SNOMED was built by the following sequence of actions:

1. Assemblage of the pool of attributes for Standard fully-defined SNOMED Expressions of the Measurement Domain.

2. Connection of SNOMED Attributes to LOINC Laboratory Procedures using LOINC Parts and modified LOINC/SNOMED CT Collaborative Files.

3. Multi-axial matching of sharable attributes in different combinations for Standard LOINC and SNOMED Measurements (see Figure 1).

alt_text

Figure 1. The methodology of an automated hierarchical crosswalk between LOINC Laboratory tests and SNOMED CT Measurements.

The SQL script for the crosswalk creation is available in the OHDSI GitHub Repository as the part of the LOINC load stage (steps 17-22). As a result, there are 16,5K hierarchical links between LOINC Laboratory Tests and SNOMED Measurements.They are represented by “Is a” relationships (with reverse of “Subsumes”) which semantically embed LOINC Laboratory tests, as a descendant, “under” SNOMED Measurements in the OMOP Hierarchy of Measurements (see tables 1 and 2).

Table 1. The extract from the hierarchical crosswalk for more granular LOINC Laboratory tests, which are connected to a generic SNOMED Measurement through the “Is a” relationship.
loinc_code loinc_name relationship_id snomed_code snomed _name
69941-3 Glucose [Moles/volume] in Serum or Plasma --20 minutes post dose lactose PO Is a 33747003 Glucose measurement, blood
69942-1 Glucose [Moles/volume] in Serum or Plasma --40 minutes post dose lactose PO Is a 33747003 Glucose measurement, blood
69943-9 Glucose [Moles/volume] in Serum or Plasma --20 minutes post 50 g lactose PO Is a 33747003 Glucose measurement, blood
69944-7 Glucose [Moles/volume] in Serum or Plasma --40 minutes post 50 g lactose PO Is a 33747003 Glucose measurement, blood
70208-4 Glucose [Moles/volume] in Serum or Plasma --pre 100 g glucose PO Is a 33747003 Glucose measurement, blood
72895-6 Glucose [Moles/volume] in Serum or Plasma --2.5 hours post dose lactose PO Is a 33747003 Glucose measurement, blood
72896-4 Glucose [Moles/volume] in Serum or Plasma --15 minutes post dose lactose PO Is a 33747003 Glucose measurement, blood
74084-5 Glucose [Moles/volume] in Serum or Plasma --15 minutes post 50 g lactose PO Is a 33747003 Glucose measurement, blood
74774-1 Glucose [Mass/volume] in Serum, Plasma or Blood Is a 33747003 Glucose measurement, blood
75405-1 Glucose [Moles/volume] in Serum or Plasma --1.5 hours post dose triple bolus Is a 33747003 Glucose measurement, blood
75637-9 Glucose [Moles/volume] in Serum or Plasma --45 minutes post 50 g lactose PO Is a 33747003 Glucose measurement, blood
77677-3 Glucose [Moles/volume] in Serum, Plasma or Blood --2 hours post meal Is a 33747003 Glucose measurement, blood
77681-5 Glucose [Moles/volume] in Serum or Plasma --11 hour post XXX challenge Is a 33747003 Glucose measurement, blood
77135-2 Glucose [Moles/volume] in Serum, Plasma or Blood Is a 33747003 Glucose measurement, blood
93791-2 Glucose [Mass/volume] mean in Serum or Plasma Is a 33747003 Glucose measurement, blood

Table 2. The extract from the hierarchical crosswalk for the generic SNOMED Measurement, which is connected to more granular LOINC Laboratory tests through a “Subsumes” relationship.

snomed_code snomed _name relationship_id loinc_code loinc_name
33747003 Glucose measurement, blood Subsumes 93791-2 Glucose [Mass/volume] mean in Serum or Plasma
33747003 Glucose measurement, blood Subsumes 96799-2 Glucose [Mass/volume] in Serum or Plasma --30 minutes post dose arginine
33747003 Glucose measurement, blood Subsumes 96800-8 Glucose [Mass/volume] in Serum or Plasma --1 hour post dose arginine
33747003 Glucose measurement, blood Subsumes 96802-4 Glucose [Mass/volume] in Serum or Plasma --1.5 hours post dose arginine
33747003 Glucose measurement, blood Subsumes 6762-9 Glucose [Mass/volume] in Serum or Plasma --1.5 hours post 50 g lactose PO
33747003 Glucose measurement, blood Subsumes 2339-0 Glucose [Mass/volume] in Blood
33747003 Glucose measurement, blood Subsumes 13865-1 Glucose [Mass/volume] in Serum or Plasma --2.5 hours post 50 g lactose PO
33747003 Glucose measurement, blood Subsumes 6756-1 Glucose [Mass/volume] in Serum or Plasma --4.5 hours post 75 g glucose PO
33747003 Glucose measurement, blood Subsumes 12610-2 Glucose [Mass/volume] in Serum or Plasma --2 hours post XXX challenge
33747003 Glucose measurement, blood Subsumes 27432-4 Glucose [Mass/volume] in Serum or Plasma --8th specimen post XXX challenge
33747003 Glucose measurement, blood Subsumes 1539-6 Glucose [Mass/volume] in Serum or Plasma --4 hours post 75 g glucose PO
33747003 Glucose measurement, blood Subsumes 25669-3 Glucose [Moles/volume] in Serum or Plasma --3.5 hours post dose glucose
33747003 Glucose measurement, blood Subsumes 32359-2 Glucose [Moles/volume] in Serum or Plasma --10 minutes post dose glucose
33747003 Glucose measurement, blood Subsumes 14743-9 Glucose [Moles/volume] in Capillary blood by Glucometer
33747003 Glucose measurement, blood Subsumes 1548-7 Glucose [Mass/volume] in Serum or Plasma --pre 0.5 g/kg glucose IV

Future plans

As far SNOMED and LOINC put on hold the collaborative work, the hierarchy can be extended through the creation of hierarchical mappings for those LOINC Parts and SNOMED Attributes which do not exist yet, which can be incorporated into existing SQL-script. However, this approach looks time-consuming. Thus, we plan to review the status of Classification concepts of LOINC Hierarchy, which, becoming standard and being integrated into the LOINC-SNOMED Hierarchy as descendants of generic SNOMED concepts, can bring along all related Standard Measurements.

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