documentation:vocabulary:mapping
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documentation:vocabulary:mapping [2019/12/13 17:58] ptalapova ["Losses" in Mapping] |
documentation:vocabulary:mapping [2020/12/09 09:34] ptalapova [Table] |
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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 21: | Line 21: | ||
| 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 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 52: | ||
| - 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 94: | Line 94: | ||
| 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 168: | ||
| **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.txt · Last modified: 2020/12/09 10:56 by ptalapova
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