documentation:vocabulary:mapping
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documentation:vocabulary:mapping [2018/07/09 11:06] dimshitc1 |
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| ===== Mapping of Concepts ===== | ===== Mapping of Concepts ===== | ||
| - | 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. | + | |
| + | **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. | ||
| 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 done through records in the CONCEPT_RELATIONSHIP table. They connect each Concept to a Standard Concept through a number of special relationship_id: | ||
| - | ^Relationship ID^Purpose^ | + | ^ Relationship ID ^ Purpose ^ Features ^ |
| - | |Maps to|Mapping Concept to Standard Concept to be placed in the *_concept_id| | + | | **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|Special mapping between a Concept and a Standard Concept to be placed into the value_as_concept field of the MEASUREMENT and OBSERVATION tables| | + | | **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 === | ||
| - | Concepts participating in the "Maps to" mapping are Source Concepts and Standard Concepts. The mapping attempts to map to the equivalent target Concept. Equivalent means it carries the same meaning, and, importantly, the children in the hierarchy (if there are any) are equivalent as well or cover the same semantic space. If an equivalent Concept is not available, the mapping attempts a match to a broader Concept. This ensures that a query in the target vocabulary will retrieve the same records as if they were queried in the original source vocabulary. | ||
| - | Generally, source Concepts and Standard Concepts are mapped: | + | * 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. | ||
| + | * 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. | ||
| + | * Standard Concepts are also mapped to Standard Concepts via "Maps to", this is a mapping to itself. | ||
| - | * Source Concepts concepts are mapped to one or several Standard Concepts. If they are mapped to more than one Standard Concept, then in the resulting CDM table more than one record is written for each record in the source. | + | //**NB!** Classification Concepts (standard_concept='C') do not have a mapping to a Standard Concept//. |
| - | * Standard Concepts are also mapped to Standard Concepts, usually this is a map to itself. | + | |
| - | Classification Concepts (standard_concept='S') do not have a mapping to a Standard Concept. | + | Examples of usage: |
| + | ^ source concept code ^ source concept name ^ relationship ID ^ standard concept ID ^ standard concept code ^ standard concept name ^ | ||
| + | ^ Single “Maps to” for mapping to an Equivalent Standard Concept |||||| | ||
| + | | M65.3 | Trigger finger | Maps to | 763891 | 448251000124102 | Trigger finger | | ||
| + | | A06 | Amebiasis | Maps to | 438959 | 111910009 | Amebic infection | | ||
| + | ^ 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 | | ||
| + | | M81.50 | Idiopathic osteoporosis, multiple sites | Maps to | 81390 | 3345002 | Idiopathic osteoporosis | | ||
| + | ^ 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 | | ||
| + | | ::: | ::: | Maps to | 4167909 | 275320004 | Injury of nail | | ||
| + | | I26.0 | Pulmonary embolism with mention of acute cor pulmonale | Maps to | 440417 | 59282003 | Pulmonary embolism | | ||
| + | | ::: | ::: | Maps to | 312927 | 49584005 | Acute cor pulmonale | | ||
| + | | G44.311 | Acute post-traumatic headache, intractable | Maps to | 42535403 | 290431000119101 | Intractable headache following trauma | | ||
| + | | ::: | ::: | Maps to | 44782681 | 122751000119105 | Acute posttraumatic headache | | ||
| + | ^ 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 | | ||
| + | | ::: | ::: | 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 | | ||
| + | | ::: | ::: | Maps to | 4055774 | 242975003 | Poisoning of undetermined intent by drug | | ||
| === "Maps to value" Relationships === | === "Maps to value" Relationships === | ||
| - | These relationships are designed to distinguish between Observation and Measurements, and their results. For example, ICD9CM V12.71 concept_id 44820383 "Personal history of peptic ulcer disease" has a relationship "Maps to" to SNOMED 4214956 "History of clinical finding in subject" (Observation Domain) and another relationship "Maps to value" to SNOMED 4027663 "Peptic ulcer" (Condition Domain). | ||
| - | ==== "Losses" due to Mapping ==== | + | To preserve the meaning of Source concepts indicating values of Measurements or content of Observations, “Maps to” are complemented with a comprehensive set of “Maps to value” relationships. Such mappings are considered to be equivalent. There are the following semantic groups of Source concepts which are mapped in such a way: |
| - | There is significant concern about the effect of mapping from one vocabulary to another on the quality of the data and the ability to reliably identify patients for a cohort given inclusion and exclusion criteria. This effect can have a variety of reasons: | + | - Conditions indicating abnormal levels of tests |
| + | - Encounter for a procedure and an aftercare | ||
| + | - Conditions resulting from the use of devices | ||
| + | - Need for an immunization | ||
| + | - Personal history of a condition | ||
| + | - Family history of a condition | ||
| + | - Personal history of medical treatment or procedure | ||
| + | - Status of a transplant/prosthesis presence | ||
| + | - Patient encounter procedures, not carried out | ||
| + | |||
| + | Examples of usage: | ||
| + | ^ case # ^ source concept code ^ source concept name ^ relationship ID ^ standard concept code ^ standard concept name ^ standard concept domain ID ^ | ||
| + | | 1 | R77.0 | Abnormality of albumin | Maps to | 26758005 | Albumin measurement | Measurement | | ||
| + | | ::: | ::: | ::: | Maps to value | 263654008 | Abnormal | Spec Disease Status | | ||
| + | | 2 | Z47.0 | Follow-up care involving removal of fracture plate and other internal fixation device | Maps to | 390906007 | Follow-up encounter | Observation | | ||
| + | | ::: | ::: | ::: | Maps to value | 72010008 | Removal of internal fixation device | Procedure | | ||
| + | | 3 | Y71 | Cardiovascular devices associated with adverse incidents | Maps to | 269691005 | Medical accidents to patients during surgical and medical care | Observation | | ||
| + | | ::: | ::: | ::: | Maps to value | 303476002 | Cardiovascular equipment | Device | | ||
| + | | 4 | Z23.2 | Need for immunization against tuberculosis [BCG] | Maps to | 723620004 | Requires vaccination | Observation | | ||
| + | | ::: | ::: | ::: | Maps to value | 42284007 | BCG vaccination | Procedure | | ||
| + | | 5 | Z86.4 | Personal history of psychoactive substance abuse | Maps to | 417662000 | History of clinical finding in subject | Observation | | ||
| + | | ::: | ::: | ::: | Maps to value | 91388009 | Psychoactive substance abuse | Condition | | ||
| + | | 6 | Z84.1 | Family history of disorders of kidney and ureter | Maps to | 416471007 | Family history of clinical finding | Observation | | ||
| + | | ::: | ::: | ::: | Maps to value | 443820000 | Disorder of kidney and/or ureter | Condition | | ||
| + | | 7 | Z92.2 | Personal history of long-term (current) use of other medicaments | Maps to | 416940007 | Past history of procedure | Observation | | ||
| + | | ::: | ::: | ::: | Maps to value | 266713003 | Long-term drug therapy | Procedure | | ||
| + | | 8 | Z96.3 | Presence of artificial larynx | Maps to | 416940007 | Past history of procedure | Observation | | ||
| + | | ::: | ::: | ::: | Maps to value | 27926003 | Construction of artificial larynx | Procedure | | ||
| + | | 9 | Z53.2 | Procedure not carried out because of patient's decision for other and unspecified reasons | Maps to | 416237000 | Procedure not done | Observation | | ||
| + | | ::: | ::: | ::: | Maps to value | 105480006 | Refusal of treatment by patient | Observation | | ||
| + | |||
| + | ==== "Losses" in Mapping ==== | ||
| + | |||
| + | **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. | ||
| + | |||
| + | For example, in ICD-10-CM diabetic complications are a part of the disorder of Diabetes Mellitus, while in SNOMED Diabetes Mellitus and its complications reside in distinct hierarchical branches. | ||
| + | |||
| + | {{ :documentation:vocabulary:5_-_diabetes-related_case_3_.png?400 |}} | ||
| + | |||
| + | As another example, ICD-10 codes indicating complications of pregnancy are in the chapter of "Pregnancy, childbirth and the puerperium" that has a semantic relation to the fact of pregnancy, while in SNOMED denoting pregnancy conditions and their complications are in the separate hierarchical branches. | ||
| - | * Mapping is missing. Please report missing mappings to the [[http://forums.ohdsi.org/c/cdm-builders|OHDSI Forum]], so they can be added. | + | {{ :documentation:vocabulary:6_-_pregnancy-related_case_1_.png?400 |}} |
| - | * Source code is ill-defined, for example ICD9CM 799 "Other ill-defined and unknown causes of morbidity and mortality" | + | |
| - | * Negative assertion, for example ICD9CM V64.0 "Vaccination not carried out" | + | |
| - | * Code irrelevant to the patient, for example ICD9CM V65 "Other persons seeking consultation" | + | |
| - | * Source and target hierarchies incongruent | + | |
| - | The latter effect 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 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. | + | The solution for both examples is to map Non-standard concepts to several standard ones. Even though there is no distinct equivalent in SNOMED, hierarchical queries will retrieve the correct records. |
| - | For example, ICD10 Concept 45755355 "Non-insulin-dependent diabetes mellitus with coma" (code E10.0) cannot directly map to SNOMED: | + | **2. Missing Source Concept equivalent** |
| - | {{ :documentation:vocabulary:diabetesmapping.png?nolink |Mapping of ICD10 E10.0}} | + | This is possible due to the following reasons: |
| + | * Vague formulation of a Source Concept | ||
| + | * Source Concept excessive granularity | ||
| + | * Classification difference between Source and Standard Vocabularies | ||
| - | The target hierarchy in SNOMED has a different topology to the organizational structure in ICD10. Here, type 1 (insulin-dependent, E10) and type 2 (insulin-independent, E11) diabetes are the primary distinctive features. The combination of type 2 diabetes with its combination coma E11.0 defines type 2 diabetes with its complication coma. In SNOMED, diabetic complications has its own hierarchy, which branches into the Concept of diabetes with coma, or type 1 or 2 diabetes with complication. On the next level the distinctive forms of coma (hypoglycemic, hyperosmolar and ketoacidotic) are distinguished. However, there is no combination of diabetes type 2 with coma. | + | **Other possible issues that one could encounter:** |
| + | * Mapping has to exist and it can be built, but it is missing. Please report to [[https://forums.ohdsi.org/|the OHDSI Forum]], so it can be added. | ||
| + | * 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” | ||
| - | The solution is to map E11.0 to both 44054006 Type 2 diabetes mellitus and 420662003 Coma associated with diabetes mellitus. Even though there is no distinct equivalent in SNOMED, hierarchical queries for either diabetes 2 in combination with coma will retrieve the correct records. | + | === CONDITION MAPPING ALGORITHM === |
| + | {{ :documentation:vocabulary:mapping_of_concepts_2_1_5_.png?600 |}} | ||
| - | === Rules for Condition Mapping === | + | === RULES FOR CONDITION MAPPING === |
| - | In general, Conditions are records suggesting the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom. However, there are a lot of conditions that are not originating in the biological function of the human body, but still require medical attention. Or they are true Conditions, but not at the time of the recording (History of) or in the person itself (Family history of). The mapping rules for these are as follows: | + | In general, Conditions are records suggesting the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom. However, there are a lot of conditions that are not originating in the biological function of the human body but still require medical attention. Or they are true Conditions, but not at the time of the recording (History of) or in the person itself (Family history of). The mapping rules for these are as follows: |
| **Aftercare after procedures.** | **Aftercare after procedures.** | ||
| - | Those are mapped to a single concept 413467001 "Aftercare", and with a second "Maps to value" relationship to the adequante procedure. For example, ICD10CM Z47.1 "Aftercare following joint replacement surgery" maps to both 413467001 "Aftercare" and to the procedure 4189532 "Implantation of joint prosthesis". Note that "Aftercare" is itself not a condition, but belons to the Observation Domain. | + | Those are mapped to a single concept 413467001 "Aftercare", and with a second "Maps to value" relationship to the adequate procedure. For example, ICD10CM Z47.1 "Aftercare following joint replacement surgery" maps to both 413467001 "Aftercare" and to the procedure 4189532 "Implantation of joint prosthesis". Note that "Aftercare" is itself not a condition, but belongs to the Observation Domain. |
| **Late effects or sequelae of other conditions.** | **Late effects or sequelae of other conditions.** | ||
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| **Family history of a condition.** | **Family history of a condition.** | ||
| - | These, too, have a dual mapping to 4167217 "Family history of clinical finding" and a to the actual condition through a "Maps to value" relationship. For example, ICD10/ICD10CM Z80.0 concept_id 45542462 "Family history of malignant neoplasm of digestive organs" maps to 4167217 "Family history of clinical finding" as well as 443568 "Malignant neoplasm of gastrointestinal tract". | + | These, too, have a dual mapping to 4167217 "Family history of clinical finding" and a to the actual condition through a "Maps to value" relationship. For example, ICD10/ICD10CM Z80.0 concept_id 45542462 "Family history of malignant neoplasm of digestive organs" maps to 4167217 "Family history of clinical finding" as well as 443568 "Malignant neoplasm of the gastrointestinal tract". |
| **History of medical treatment.** | **History of medical treatment.** | ||
| - | Similary, these are mapped to Observation Concept 4207283 "History of drug therapy", and through a "Maps to value" link to the actual therapy. For example, ICD10 Z92.0 concept_id 45605174 "Personal history of contraception" goes to 4207283 "History of drug therapy" history of drug therapy and 4027509 "Contraception". If the exact Ingredient or Clinical/Branded Drug is known, the map would direct to these Drug Concepts. But that is not typical. | + | Similarly, these are mapped to Observation Concept 4207283 "History of drug therapy", and through a "Maps to value" link to the actual therapy. For example, ICD10 Z92.0 concept_id 45605174 "Personal history of contraception" goes to 4207283 "History of drug therapy" history of drug therapy and 4027509 "Contraception". If the exact Ingredient or Clinical/Branded Drug is known, the map would direct to these Drug Concepts. But that is not typical. |
| **Adverse effect of medication.** | **Adverse effect of medication.** | ||
| - | If possible, these are mapped to a direct equivalent. However, that usually does not exist, and then they are treated like the above history of medical treatments. For example, both ICD10CM T36.8X5A concept_id 45551127 "Adverse effect of other systemic antibiotics, initial encounter" and T36.8X5D "Adverse effect of other systemic antibiotics, subsequent encounter" map to 437191 "Antibacterial drug adverse reaction", while ICD10CM T36.8X5S concept_id 45560654 "Adverse effect of other systemic antibiotics, sequela" maps to 4207283 "History of drug therapy". | + | If possible, these are mapped to a direct equivalent. However, that usually does not exist, and then they are treated as the above history of medical treatments. For example, both ICD10CM T36.8X5A concept_id 45551127 "Adverse effect of other systemic antibiotics, initial encounter" and T36.8X5D "Adverse effect of other systemic antibiotics, subsequent encounter" map to 437191 "Antibacterial drug adverse reaction", while ICD10CM T36.8X5S concept_id 45560654 "Adverse effect of other systemic antibiotics, sequela" maps to 4207283 "History of drug therapy". |
| **Underdosing of medication.** | **Underdosing of medication.** | ||
| This information is handled similarly to the adverse effects, and the equivalent SNOMED concepts generally do not exist. For example, ICD10CM T36.0X6A concept_id 45565479 "Underdosing of penicillins, initial encounter" and T36.0X6D concept_id 45565480 "Underdosing of penicillins, subsequent encounter" go to 40488434 "Medication dose too low", while T36.0X6S concept_id 45565481 "Underdosing of penicillins, sequela" points at 4207283 "History of drug therapy". | This information is handled similarly to the adverse effects, and the equivalent SNOMED concepts generally do not exist. For example, ICD10CM T36.0X6A concept_id 45565479 "Underdosing of penicillins, initial encounter" and T36.0X6D concept_id 45565480 "Underdosing of penicillins, subsequent encounter" go to 40488434 "Medication dose too low", while T36.0X6S concept_id 45565481 "Underdosing of penicillins, sequela" points at 4207283 "History of drug therapy". | ||
| - | **Status of organ absence or transplant/prostetic presence.** | + | **Status of organ absence or transplant/prosthetic presence.** |
| Absent organs are due to a procedure having removed them (unless they are inborn conditions, which are mapped as such). Therefore, they are mapped to 4215685 "Past history of procedure" and the appropriate procedure that removed the organ through a "Maps to value" link. For example, ICD10CM Z94.0 concept_id 35225404 "Kidney transplant status" maps to 4215685 "Past history of procedure" and 4322471 "Transplant of kidney". Z95.5 concept_id 35225418 "Presence of coronary angioplasty implant and graft" is pointed to 4215685 "Past history of procedure" and 4184832 "Coronary angioplasty". | Absent organs are due to a procedure having removed them (unless they are inborn conditions, which are mapped as such). Therefore, they are mapped to 4215685 "Past history of procedure" and the appropriate procedure that removed the organ through a "Maps to value" link. For example, ICD10CM Z94.0 concept_id 35225404 "Kidney transplant status" maps to 4215685 "Past history of procedure" and 4322471 "Transplant of kidney". Z95.5 concept_id 35225418 "Presence of coronary angioplasty implant and graft" is pointed to 4215685 "Past history of procedure" and 4184832 "Coronary angioplasty". | ||
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| - To the most common ancestor | - To the most common ancestor | ||
| - | Examples for these 3 possibilites are: | + | Examples for these 3 possibilities are: |
| - ICD10 A01 concept_id 45576225 "Typhoid and paratyphoid fevers" has a single "Maps to" relationship to 4022808 "Human typhoid AND/OR paratyphoid fever". | - ICD10 A01 concept_id 45576225 "Typhoid and paratyphoid fevers" has a single "Maps to" relationship to 4022808 "Human typhoid AND/OR paratyphoid fever". | ||
| - | - IC10 M07.47 concept_id 42616699 "Arthropathy in Crohn disease [regional enteritis], ankle and foot" has two "Maps to" relationships to 4116143 "Arthropathy in Crohn's disease" and 4117687 "Rheumatoid arthritis - ankle and/or foot". | + | - IC10CM F12.22 concept_id 45591098 "Cannabis dependence with intoxication" has two "Maps to" relationships to 4052690 "Cannabis intoxication" and 440387 "Cannabis dependence". |
| - ICD10 L02.0 concept_id 45596354 "Cutaneous abscess, furuncle and carbuncle of face" has a single "Maps to" relationship_id to 400082007 Disorder of skin of head. | - ICD10 L02.0 concept_id 45596354 "Cutaneous abscess, furuncle and carbuncle of face" has a single "Maps to" relationship_id to 400082007 Disorder of skin of head. | ||
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| **Need for immunization.** | **Need for immunization.** | ||
| - | These Concepts are mapped to an Observation indicating such immunity gap. A second mapping with the relationship_id "Maps to value" is then directed to the Condition (represented as a SNOMED Concept) the immunization is inocculating against. Note that it is not mapped to the vaccine itself (which would be represented as a RxNorm Concept). For example, ICD10 Z23 concept_id 45556822 "Need for immunization against single bacterial diseases" maps to 170536002 "Vaccination required" and maps to value 87628006 "Bacterial infectious disease". | + | These Concepts are mapped to an Observation indicating such an immunity gap. A second mapping with the relationship_id "Maps to value" is then directed to the Condition (represented as a SNOMED Concept) the immunization is inoculating against. Note that it is not mapped to the vaccine itself (which would be represented as a RxNorm Concept). For example, ICD10 Z23 concept_id 45556822 "Need for immunization against single bacterial diseases" maps to 170536002 "Vaccination required" and maps to value 87628006 "Bacterial infectious disease". |
| **Conditions indicating abnormal levels of a test.** | **Conditions indicating abnormal levels of a test.** | ||
documentation/vocabulary/mapping.txt · Last modified: 2020/12/09 10:56 by ptalapova
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