documentation:vocabulary:loinc
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documentation:vocabulary:loinc [2015/10/11 21:59] cgreich [Concept Classes] |
documentation:vocabulary:loinc [2019/05/24 11:00] ptalapova [Table] |
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| ===== LOINC ===== | ===== LOINC ===== | ||
| - | LOINC is a coding system for lab tests, but also for surveys, tests and other clinical procedures or activities that create a result, usually for a diagnostic purpose. | + | **Logical Observation Identifiers Names and Codes (LOINC)** is a standardized coding system for laboratory and clinical tests, procedures, observations, surveys, and corresponding results. |
| ==== Sources ==== | ==== Sources ==== | ||
| - | All LOINC source information is obtained from the LOINC websites that is supported by the Regenstrief institute, except the mapping between LOINC and CPT4, which is provided by the NLM: | + | All LOINC source information is obtained from the following: |
| - | Generic LOINC Concept | + | |
| - | - LOINC Multiaxial Hierarchy | + | 1. [[https://loinc.org/downloads/|LOINC Website]] that is supported by the Regenstrief Institute: |
| - | - LOINC Forms and LOINC Answers | + | * LOINC Table Core (Observations and Measurements) |
| - | - LOINC Panel | + | * LOINC Answers |
| - | - LOINC Class | + | * LOINC Multiaxial Hierarchy |
| - | - LOINC to CPT mapping | + | * LOINC Document Ontology |
| - | - LOINC to SNOMED mapping | + | * LOINC Panels and Forms |
| + | * LOINC Groups | ||
| + | * LOINC to SNOMED mapping | ||
| + | * LOINC Replacement Mapping | ||
| + | 2. [[https://www.nlm.nih.gov/research/umls/mapping_projects/loinc_to_cpt_map.html|The National Library of Medicine (NLM) Website]]: | ||
| + | * LOINC To CPT4 Mapping | ||
| + | 3. [[https://loinc.org/file-access/download-id/9031/|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 ==== | ==== Standard Concepts ==== | ||
| - | All LOINC Concepts are Standard Concepts, while Concepts of the Source LOINC Class, LOINC Hierarchy are Classification Concepts. | + | ^Source Concept Type^Standard Concept^ |
| + | |LOINC Observations and Measurements|Standard| | ||
| + | |LOINC Answers|Standard| | ||
| + | |LOINC Hierarchy|Classification| | ||
| + | |LOINC Classes|Classification| | ||
| + | |LOINC Categories|Classification| | ||
| + | |LOINC Groups|Classification| | ||
| - | ==== Concept Classes ==== | + | ==== Domains and Concept Classes ==== |
| - | Concepts in the LOINC vocabulary are assigned Concept Class as following: | + | LOINC Concepts are located in such domains as “Observation”, “Measurement”, or “Meas Value”. |
| - | ^Source^Resourced^Concept Class^Description^ | + | |
| - | |LOINC|CLASSTYPE=1|Lab Test|The Universal Lab Order Codes Value Set contains the most frequent lab orders| | + | |
| - | | |CLASSTYPE=2|Clinical Observation|Anything that can be tested, measured, or observed about a patient without removing a specimen| | + | |
| - | | |CLASSTYPE=3|Claims Attachment|Information necessary to adjudicate claims for ambulance, rehabilitation, or emergency room services| | + | |
| - | | |CLASSTYPE=4|Survey|Set of questions on a survey or form| | + | |
| - | | |CLASS|LOINC Class|Similar to the Concept Classes of each LOINC Concept, but more detailed and hierarchical| | + | |
| - | |LOINC Hierarchy|CODE|LOINC Hierarchy|Similar to LOINC Class, but separate hierarchical system| | + | |
| - | |LOINC Answer|AnswerStringID|Answer|Observation result value as an answer to a LOINC Concept| | + | |
| - | ==== Domains ==== | + | 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 interconnected with a defined Domain. |
| - | LOINC Concepts can have a Measurement or Observation Domain. This is assigned as following: | + | |
| - | ^Source^Depending on ^Domain^ | + | So, they were assigned pursuant to the following criteria: |
| - | |LOINC|CLASSTYPE=1 or 2|Measurement| | + | |
| - | ||CLASSTYPE=3 or 4|Observation| | + | ^ Source ^ Dependencies ^ Domain ^ Concept Class ^ |
| - | |LOINC Hierarchy|Concept_code>'LP76352-1'|Observation| | + | | LOINC Core Table | A “**classtype**” field value = 1 (Laboratory class) or 2 (Clinical class) AND:\\ 1. A “**survey_quest_text**” field value contains **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 | Observation | Clinical Observation | |
| - | ||Concept_code>='LP76352-1'|Measurement| | + | | | 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 | Observation | Clinical Observation | |
| - | |LOINC Class|Manual|Observation or Measurement| | + | | | 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\\ 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 | |
| - | |LOINC Answer||Meas Value| | + | | | 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 | | ||
| + | | | 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 Answer | Independently | Meas Value | Answer | | ||
| ==== Relationships ==== | ==== Relationships ==== | ||
| - | Relationships are defined within LOINC and between LOINC and CPT and LOINC and SNOMED: | + | Relationships are defined within LOINC and between LOINC and CPT, and LOINC and SNOMED: |
| - | === Internal LOINC relationships === | + | ===1. Internal LOINC relationships === |
| - | - "Is a" relationships between LOINC Concepts and LOINC Hierarchy and LOINC Class Concepts | + | A purpose of Internal LOINC relationships is to build a LOINC Hierarchy, which makes it easier to sort and browse the database. |
| - | - "Has Answer" relationships between LOINC Concepts and LOINC Answer Concepts | + | |
| - | - "Panel contains" relationships between LOINC Concepts | + | |
| - | === LOINC to SNOMED relationships === | + | ^Relationship^From^To^ |
| - | These relationships are defined as "LOINC - SNOMED eq" between "LOINC Hierarchy" Concepts and SNOMED Concepts representing the entity that is measured. Note that only a small fraction (1% as of late 2015) are currently mapped. Also, note that some of the mappings seem to confuse the testing for drugs with the drugs themselves. | + | |Maps to|Each LOINC concept|The same LOINC concept| |
| + | |Is a|Descendant LOINC Class|Ancestor LOINC Class| | ||
| + | |Is a|LOINC Group|LOINC Group Category| | ||
| + | |Is a|LOINC Measurement or Observation|LOINC Class| | ||
| + | |Is a|LOINC Measurement or Observation|LOINC Group| | ||
| + | |Is a|Descendant LOINC Measurement or Observation|Ancestor LOINC Measurement or Observation| | ||
| + | |Panel contains|LOINC Panel|LOINC Measurement or Observation| | ||
| + | |Has Answer|LOINC Question|LOINC Answer| | ||
| + | |Has type of service|LOINC Measurement or Observation|LOINC concept indicating a Type of Service (Document Ontology)| | ||
| + | |Has subject matter|LOINC Measurement or Observation|LOINC concept indicating a Subject Matter Domain (Document Ontology)| | ||
| + | |Has role|LOINC Measurement or Observation|LOINC concept indicating a Role (Document Ontology)| | ||
| + | |Has setting|LOINC Measurement or Observation|LOINC concept indicating a Setting (Document Ontology)| | ||
| + | |Has kind|LOINC Measurement or Observation|LOINC concept indicating a Kind of Document (Document Ontology)| | ||
| + | |Concept replaced by|Updated LOINC concept|New LOINC concept| | ||
| - | === LOINC to CPT relationships === | + | ^Reverse Relationship^From^To^ |
| - | These relationships are defined as "LOINC - CPT4 eq" between LOINC Lab Test Concepts and SNOMED Concepts. Note that only a small franction (2% as of late 2015) are mapped. | + | |Mapped from|Each LOINC concept|The same LOINC concept| |
| + | |Subsumes|Ancestor LOINC Class|Descendant LOINC Class| | ||
| + | |Subsumes|LOINC Group Category|LOINC Group| | ||
| + | |Subsumes|LOINC Class|LOINC Measurement or Observation| | ||
| + | |Subsumes|LOINC Group|LOINC Measurement or Observation| | ||
| + | |Subsumes|Ancestor LOINC Measurement or Observation|Descendant LOINC Measurement or Observation| | ||
| + | |Contained in panel|LOINC Measurement or Observation|LOINC Panel| | ||
| + | |Answer of|LOINC Answer|LOINC Question| | ||
| + | |Type of service of|LOINC concept indicating a Type of Service (Document Ontology)|LOINC Measurement or Observation| | ||
| + | |Subject matter of|LOINC concept indicating a Subject Matter Domain (Document Ontology)|LOINC Measurement or Observation| | ||
| + | |Role of|LOINC concepts indicating a Role (Document Ontology)|LOINC Measurement or Observation| | ||
| + | |Setting of|LOINC concepts indicating a Setting (Document Ontology)|LOINC Measurement or Observation| | ||
| + | |Kind of|LOINC concepts indicating Kinds of Document (Document Ontology)|LOINC Measurement or Observation| | ||
| + | |Concept replaces|New LOINC concept|Updated LOINC concept| | ||
| - | === Hierarchy === | + | ===2. External LOINC relationships === |
| - | All internal "Is a" and "Panel contains" relationships participate in the creation of the CONCEPT_ANCESTOR table, creating an internal hierarchy within LOINC not connected to the larger Measurement or Observation Domain space. | + | The purpose of External LOINC relationships is the following: |
| + | to simplify s 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 [[https://confluence.ihtsdotools.org/download/attachments/38260209/doc_LoincWithSnomed_Current-en-US_INT_20170403.pdf?api=v2|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 | | ||
| + | === 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. Note, the LOINC hierarchy is not connected to the SNOMED hierarchy which is the core Domain space for Measurement and Observation in OHDSI vocabularies. | ||
documentation/vocabulary/loinc.txt · Last modified: 2022/01/27 10:49 by adavydov
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