documentation:vocabulary:mapping
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| ===== Mapping of Concepts ===== | ===== Mapping of Concepts ===== | ||
| + | * **Mapping**, also known as **a map**, is an association between a particular concept in one code system or | ||
| + | * dataset and code in another, rarely the same, code system that has the same (or similar) meaning. | ||
| + | * Also, **Mapping** is the process to transform one concept into a Standard one. The Standardized Clinical Data Tables allow only Standard Concepts, thus all other codes used in the source databases have to be translated to Standard Concepts. | ||
| + | * Mapping is done through records in the CONCEPT_RELATIONSHIP table. They connect each Concept to a Standard Concept through a number of special relationship_id: | ||
| - | **Mapping** is the process to transform one Concept to another. The clinical data tables of the CDM allow only Standard Concepts. All other codes used in the source databases have to be translated to Standard Concepts. | + | ^ Relationship ID ^ Purpose ^ Features ^ |
| - | + | | **Maps to** | Mapping a Source Concept to a Standard Concept to be placed into the following fields of :[[https://github.com/OHDSI/CommonDataModel/wiki/Standardized-Clinical-Data-Tables|Standardized Clinical Data Tables]]:\\ • **condition_concept_id**\\ • **observation_concept_id**\\ • **measurement_concept_id**\\ • **drug_concept_id**\\ • **procedure_concept_id**\\ • **device_concept_id** etc. \\ \\ Note, that this relationship is also used for mapping of concepts to populate **value_as_concept_id**. | • stands for either a full equivalence or an “uphill” mapping (mapping to a more general semantic category)\\ \\ • can be single or multiple for each Source Concept | | |
| - | Mapping is done through records in the CONCEPT_RELATIONSHIP table. They connect each Concept to a Standard Concept through a number of special relationship_id: | + | | **Maps to value** | A special mapping between a Source Concept and a Standard Concept to be placed into the **value_as_concept_id** field of the MEASUREMENT and OBSERVATION tables | • points to a concept, indicating the value of Measurements or content of Observations\\ \\ • is used only in combination with a single “Maps to” | |
| - | + | ||
| - | ^ Relationship ID ^ Purpose ^ Features ^ | + | |
| - | | **Maps to** | Mapping a Source Concept to a Standard Concept to be placed into the following fields of :[[https://github.com/OHDSI/CommonDataModel/wiki/Standardized-Clinical-Data-Tables|Standardized Clinical Data Tables]]:\\ • **condition_concept_id**\\ • **observation_concept_id**\\ • **measurement_concept_id**\\ • **drug_concept_id**\\ • **procedure_concept_id**\\ • **device_concept_id** | • stands for either a full equivalence or an “uphill” mapping (mapping to a more general semantic category)\\ \\ • can be single or multiple for each Source Concept | | + | |
| - | | **Maps to value** | A special mapping between a Source Concept and a Standard Concept to be placed into the **value_as_concept_id** field of the MEASUREMENT and OBSERVATION tables | • points to a concept, indicating the value of Measurements or content of Observations\\ \\ • is used only in combination with a single “Maps to” | | + | |
| === "Maps to" Relationships === | === "Maps to" Relationships === | ||
| Line 14: | Line 14: | ||
| * Concepts participating in the “Maps to” mapping are Source (Non-standard) Concepts and Standard Concepts. | * Concepts participating in the “Maps to” mapping are Source (Non-standard) Concepts and Standard Concepts. | ||
| * The mapping always attempts to reflect the semantics of a Source Concept by an Equivalent Standard Concept. | * The mapping always attempts to reflect the semantics of a Source Concept by an Equivalent Standard Concept. | ||
| - | * Equivalent carries the same meaning, covers the same semantic space and, importantly, has the same parents and children in the hierarchy (if there are any) as well. If an equivalent Concept is not available, the mapping matches to a more generic Standard Concept(s). This ensures that a query in the target vocabulary will retrieve the same records as if they were queried in the original source vocabulary. | + | * Equivalent carries the same meaning, covers the same semantic space, and, importantly, has the same parents and children in the hierarchy (if there are any) as well. If an equivalent Concept is not available, the mapping matches to a more generic Standard Concept(s). This ensures that a query in the target vocabulary will retrieve the same records as if they were queried in the original source vocabulary. |
| * Source Concepts are mapped or may be mapped to one or several Standard Concepts. If they are mapped to more than one Standard Concept, in the resulting CDM table, there is more than one record for each record in the source. | * Source Concepts are mapped or may be mapped to one or several Standard Concepts. If they are mapped to more than one Standard Concept, in the resulting CDM table, there is more than one record for each record in the source. | ||
| * Standard Concepts are also mapped to Standard Concepts via "Maps to", this is a mapping to itself. | * Standard Concepts are also mapped to Standard Concepts via "Maps to", this is a mapping to itself. | ||
| + | * If there are 2 or more similar Standard concepts in the OMOP vocabulary, please, report about it at the [[https://forums.ohdsi.org/c/vocabulary-users|OHDSI Forum]] and unless it is fixed, as the first-line choice, use LOINC for Measurements and SNOMED for everything else. | ||
| + | * If there are 2 similar Standard concepts within SNOMED, look at the domain (Morphologic abnormality is an Observation, Clinical finding is a Condition), revise attributes and hierarchy of both concepts (its number, fullness, and correctness). It is not necessary to compare the amount of relationships/children precisely, just verify that all seems appropriate and the hierarchy is rich enough. If it does for both concepts, then choose concepts belonging to SNOMED International (short concept codes) rather than SNOMED US/UK Editions (long concept codes). If the length of concept codes is identical, then choose the one with a smaller number of concept_id. | ||
| //**NB!** Classification Concepts (standard_concept='C') do not have a mapping to a Standard Concept//. | //**NB!** Classification Concepts (standard_concept='C') do not have a mapping to a Standard Concept//. | ||
| Examples of usage: | Examples of usage: | ||
| - | ^ source concept code ^ source concept name ^ relationship ID ^ standard concept ID ^ standard concept code ^ standard concept name ^ | + | ^ source concept code ^ source concept name ^ relationship ID ^ standard concept ID ^ standard concept code ^ standard concept name ^ |
| - | ^ Single “Maps to” for a mapping to an Equivalent Standard Concept |||||| | + | ^ Single “Maps to” for mapping to an Equivalent Standard Concept |||||| |
| - | | M65.3 | Trigger finger | Maps to | 763891 | 448251000124102 | Trigger finger | | + | | M65.3 | Trigger finger | Maps to | 763891 | 448251000124102 | Trigger finger | |
| - | | A06 | Amebiasis | Maps to | 438959 | 111910009 | Amebic infection | | + | | A06 | Amebiasis | Maps to | 438959 | 111910009 | Amebic infection | |
| - | ^ Single “Maps to” for a mapping to a Non-equivalent Standard Concept |||||| | + | ^ Single “Maps to” for mapping to a Non-equivalent Standard Concept |||||| |
| - | | D46.5 | Refractory anaemia with multi-lineage dysplasia | Maps to | 4003185 | 109996008 | Refractory anemia | | + | | D46.5 | Refractory anaemia with multi-lineage dysplasia | Maps to | 4003185 | 109996008 | Refractory anemia | |
| - | | M81.50 | Idiopathic osteoporosis, multiple sites | Maps to | 81390 | 3345002 | Idiopathic osteoporosis | | + | | M81.50 | Idiopathic osteoporosis, multiple sites | Maps to | 81390 | 3345002 | Idiopathic osteoporosis | |
| - | ^ Multiple “Maps to” for a mapping to several Standard Concepts fully covering semantic space of a Source Concept |||||| | + | ^ Multiple “Maps to” for mapping to several Standard Concepts fully covering semantic space of a Source Concept |||||| |
| - | | S61.1 | Open wound of finger(s) with damage to nail | Maps to | 4054063 | 125653000 | Open wound of finger | | + | | S61.1 | Open wound of finger(s) with damage to nail | Maps to | 4054063 | 125653000 | Open wound of finger | |
| - | | ::: | ::: | Maps to | 4167909 | 275320004 | Injury of nail | | + | | ::: | ::: | Maps to | 4167909 | 275320004 | Injury of nail | |
| - | | I26.0 | Pulmonary embolism with mention of acute cor pulmonale | Maps to | 440417 | 59282003 | Pulmonary embolism | | + | | I26.0 | Pulmonary embolism with mention of acute cor pulmonale | Maps to | 440417 | 59282003 | Pulmonary embolism | |
| - | | ::: | ::: | Maps to | 312927 | 49584005 | Acute cor pulmonale | | + | | ::: | ::: | Maps to | 312927 | 49584005 | Acute cor pulmonale | |
| - | | G44.311 | Acute post-traumatic headache, intractable | Maps to | 42535403 | 290431000119101 | Intractable headache following trauma | | + | | G44.311 | Acute post-traumatic headache, intractable | Maps to | 42535403 | 290431000119101 | Intractable headache following trauma | |
| - | | ::: | ::: | Maps to | 44782681 | 122751000119105 | Acute posttraumatic headache | | + | | ::: | ::: | Maps to | 44782681 | 122751000119105 | Acute posttraumatic headache | |
| ^ Multiple “Maps to” for mapping to several Standard Concepts partially covering semantic space of a Source Concept |||||| | ^ Multiple “Maps to” for mapping to several Standard Concepts partially covering semantic space of a Source Concept |||||| | ||
| - | | V01.11 | Pedestrian on roller-skates injured in collision with pedal cycle in traffic accident | Maps to | 442247 | 215142005 | Pedal cycle accident involving collision between pedal cycle and pedestrian, pedestrian injured | | + | | V01.11 | Pedestrian on roller-skates injured in collision with pedal cycle in traffic accident | Maps to | 442247 | 215142005 | Pedal cycle accident involving collision between pedal cycle and pedestrian, pedestrian injured | |
| - | | ::: | ::: | Maps to | 441188 | 32906002 | Victim, pedestrian in vehicular AND/OR traffic accident | | + | | ::: | ::: | Maps to | 441188 | 32906002 | Victim, pedestrian in vehicular AND/OR traffic accident | |
| - | | T36.1x4 | Poisoning by cephalosporins and other beta-lactam antibiotics, undetermined | Maps to | 4303975 | 419347003 | Poisoning by antibacterial drug | | + | | T36.1x4 | Poisoning by cephalosporins and other beta-lactam antibiotics, undetermined | Maps to | 4303975 | 419347003 | Poisoning by antibacterial drug | |
| - | | ::: | ::: | Maps to | 4055774 | 242975003 | Poisoning of undetermined intent by drug | | + | | ::: | ::: | Maps to | 4055774 | 242975003 | Poisoning of undetermined intent by drug | |
| === "Maps to value" Relationships === | === "Maps to value" Relationships === | ||
| Line 52: | Line 54: | ||
| - Personal history of medical treatment or procedure | - Personal history of medical treatment or procedure | ||
| - Status of a transplant/prosthesis presence | - Status of a transplant/prosthesis presence | ||
| - | - Persons'encountering procedures, not carried out | + | - Patient encounter procedures, not carried out |
| Examples of usage: | Examples of usage: | ||
| Line 77: | Line 79: | ||
| ==== "Losses" in Mapping ==== | ==== "Losses" in Mapping ==== | ||
| - | **1. The hierarchical discrepancy between a Source and Standard Vocabularies** | + | **1. The hierarchical discrepancy between Source and Standard Vocabularies** |
| It is not uncommon for heavily pre-coordinated Concepts (complex and fine-grained Concepts that are combinations of different dimensions). The coordination depends on the structure of the topology of the vocabularies from and to which the Concept is mapped. If they are not equivalent, no direct mapping can be established. But in order to maintain the ability to retrieve these Concepts when searching using hierarchical Concepts, two or more mappings are provided instead. | It is not uncommon for heavily pre-coordinated Concepts (complex and fine-grained Concepts that are combinations of different dimensions). The coordination depends on the structure of the topology of the vocabularies from and to which the Concept is mapped. If they are not equivalent, no direct mapping can be established. But in order to maintain the ability to retrieve these Concepts when searching using hierarchical Concepts, two or more mappings are provided instead. | ||
| Line 94: | Line 96: | ||
| This is possible due to the following reasons: | This is possible due to the following reasons: | ||
| - | * Vague formulation of a Source Concept | + | | source concept code | source concept name | relationship ID | standard concept ID | standard concept code | standard concept name | |
| - | * Source Concept excessive granularity | + | ^ 1. Vague formulation of a Source Concept |||||| |
| - | * Classification difference between Source and Standard Vocabularies | + | | M99.9 | Biomechanical lesion, unspecified | Maps to | 4244662 | 928000 | Disorder of musculoskeletal system | |
| + | | A28.9 | Zoonotic bacterial disease, unspecified | Maps to | 432545 | 87628006 | Bacterial infectious disease | | ||
| + | ^ 2. Source Concept excessive granularity |||||| | ||
| + | | B33.4 | Hantavirus (cardio-)pulmonary syndrome [HPS] [HCPS] | Maps to | 441784 | 359761005 | Disease due to Hantavirus | | ||
| + | | I12.9 | Hypertensive renal disease without renal failure | Maps to | 201313 | 38481006 | Hypertensive renal disease | | ||
| + | | S06.4x9 | Epidural hemorrhage with loss of consciousness of unspecified duration | Maps to | 4306943 | 82999001 | Epidural hemorrhage | | ||
| + | | ::: | ::: | Maps to | 372448 | 419045004 | Loss of consciousness | | ||
| + | | S35.415 | Laceration of left renal vein | Maps to | 4124868 | 234084003 | Venous laceration | | ||
| + | | ::: | ::: | Maps to | 195125 | 5753006 | Injury of renal vein | | ||
| + | ^ 3. Classification difference between Source and Standard Vocabularies |||||| | ||
| + | | I48 | Atrial fibrillation and flutter | Maps to | 4068155 | 17366009 | Atrial arrhythmia | | ||
| + | | G06.0 | Intracranial abscess and granuloma | Maps to | 4181187 | 363176004 | Inflammatory disorder of head | | ||
| + | | J38.0 | Paralysis of vocal cords and larynx | Maps to | 4233244 | 89927005 | Paralysis of larynx | | ||
| + | | U82.1 | Resistance to methicillin | Maps to | 37017452 | 713728002 | Drug resistance to antibacterial agent | | ||
| **Other possible issues that one could encounter:** | **Other possible issues that one could encounter:** | ||
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| * Code irrelevant to the patient, for example, ICD-9-CM V65 “Other persons seeking consultation” | * Code irrelevant to the patient, for example, ICD-9-CM V65 “Other persons seeking consultation” | ||
| * Source code is ill-defined, for example, ICD-9-CM 799 “Other ill-defined and unknown causes of morbidity and mortality” | * Source code is ill-defined, for example, ICD-9-CM 799 “Other ill-defined and unknown causes of morbidity and mortality” | ||
| - | |||
| - | === CONDITION MAPPING ALGORITHM === | ||
| - | {{ :documentation:vocabulary:mapping_of_concepts_2_1_5_.png?600 |}} | ||
| === RULES FOR CONDITION MAPPING === | === RULES FOR CONDITION MAPPING === | ||
| Line 157: | Line 170: | ||
| **Conditions resulting from the use of Devices.** | **Conditions resulting from the use of Devices.** | ||
| Adverse or other outcomes of the exposure to a device are mapped to 473023007 "Complication associated with device and with another "Maps to value" relationship to the device itself, if possible. For example, ICD10 Y73.0 concept_id 45590664 "Gastroenterology and urology devices associated with adverse incidents, diagnostic and monitoring devices" has a "Maps to value" link to 45767866 "Gastro-urological device". | Adverse or other outcomes of the exposure to a device are mapped to 473023007 "Complication associated with device and with another "Maps to value" relationship to the device itself, if possible. For example, ICD10 Y73.0 concept_id 45590664 "Gastroenterology and urology devices associated with adverse incidents, diagnostic and monitoring devices" has a "Maps to value" link to 45767866 "Gastro-urological device". | ||
| + | |||
| + | |||
| + | === CONDITION MAPPING ALGORITHM === | ||
| + | {{ :documentation:vocabulary:mapping_of_concepts_2_1_5_.png?600 |}} | ||
| + | |||
documentation/vocabulary/mapping.1576259874.txt.gz · Last modified: 2019/12/13 17:57 by ptalapova
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