documentation:vocabulary:loinc
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documentation:vocabulary:loinc [2019/05/02 12:39] ptalapova [Table] |
documentation:vocabulary:loinc [2019/05/24 11:00] ptalapova [Table] |
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| * LOINC Replacement 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]]: | 2. [[https://www.nlm.nih.gov/research/umls/mapping_projects/loinc_to_cpt_map.html|The National Library of Medicine (NLM) Website]]: | ||
| - | * LOINC To CPT Mapping | + | * LOINC To CPT4 Mapping |
| 3. [[https://loinc.org/file-access/download-id/9031/|LOINC Users' Guide]]: | 3. [[https://loinc.org/file-access/download-id/9031/|LOINC Users' Guide]]: | ||
| * Manual table of LOINC Classes | * Manual table of LOINC Classes | ||
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| ==== Concept Names ==== | ==== Concept Names ==== | ||
| * Values of a “**long_common_name**” field are considered to be preferred terms for 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. | + | * Values of “**consumer_name**”, “**shortname**” and “**relatednames2**” fields reside in the CONCEPT_SYNONYM table as synonyms. |
| ==== Standard Concepts ==== | ==== Standard Concepts ==== | ||
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| ^ Source ^ Dependencies ^ Domain ^ Concept Class ^ | ^ 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 **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 | | | 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 | | ||
| - | | | 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), “**^Patient**” (patient related codes), “**Vaccine**” (vaccination-related codes).\\ \\ 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\\ 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 | |
| - | | | 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). | | | | + | | | 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 | |
| | | Other cases when a “classtype” field value = 1 (Laboratory class) | Measurement | Lab Test | | | | 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 | | | | Other cases when a “classtype” field value = 2 (Clinical class) | Measurement | Clinical Observation | | ||
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| ^Relationship^From^To^ | ^Relationship^From^To^ | ||
| + | |Maps to|Each LOINC concept|The same LOINC concept| | ||
| |Is a|Descendant LOINC Class|Ancestor LOINC Class| | |Is a|Descendant LOINC Class|Ancestor LOINC Class| | ||
| |Is a|LOINC Group|LOINC Group Category| | |Is a|LOINC Group|LOINC Group Category| | ||
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| ^Reverse Relationship^From^To^ | ^Reverse Relationship^From^To^ | ||
| + | |Mapped from|Each LOINC concept|The same LOINC concept| | ||
| |Subsumes|Ancestor LOINC Class|Descendant LOINC Class| | |Subsumes|Ancestor LOINC Class|Descendant LOINC Class| | ||
| |Subsumes|LOINC Group Category|LOINC Group| | |Subsumes|LOINC Group Category|LOINC Group| | ||
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| |Concept replaces|New LOINC concept|Updated LOINC concept| | |Concept replaces|New LOINC concept|Updated LOINC concept| | ||
| - | ===2. LOINC to SNOMED relationships === | + | ===2. External LOINC relationships === |
| - | 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%) is currently mapped. Also, note that some of the mappings seem to confuse the testing for drugs with the drugs themselves. | + | 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. | ||
| - | ===3. LOINC to CPT relationships === | + | ^ Relationship ^ From ^ To ^ Description ^ Count ^ |
| - | These relationships are defined as "LOINC - CPT4 eq" between LOINC Lab Test Concepts and SNOMED Concepts. Note that only a small fraction (2%) is mapped. | + | | 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 === | === Hierarchy === | ||
| - | 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. | + | 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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