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--- documentation:vocabulary:general_structure_and_use [2015/01/24 14:33]
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+++ documentation:vocabulary:general_structure_and_use [2015/09/18 18:32] (current)
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 ===== General Structure and Use =====
-The Standardized Vocabularies are organized into Domains and Vocabularies. Domains refer to the nature of type of a clinical entity, which also defines the CDM data table where a data record is stored, while Vocabularies are sets of Concepts imported from external national or international existing standards, or created by the Standardized Vocabularies Team if no suitable standard is available.
-There is no one-to-one relationship between Domains and Vocabularies. Some Vocabularies are very broad, such as SNOMED-CT or Read, and contain Concepts of all medical Domains. Other vocabularies are specific for a certain Domain, such as RxNorm for Drugs or ICD-9-Proc for Procedures. In many cases Vocabularies are generally assumed in the community to be of a single Domain, when in fact they are not: For example, CPT-4 and HCPCS, are expected by their name to contain Procedure codes, only, but contain Observation, Condition, Device and Drug Concepts:
-{{ :documentation:vocabulary:domainsandvocabs.jpg?nolink&800 |Domains and Vocabularies}}
-Within a Domain, codes come from a number of Vocabularies, and their codes have often identical or overlapping meanings. To bring order to this situation, each of them is assigned one of three designations:
-  * **Standard Concept** (standard_concept = 'S'). Among the codes of the various vocabularies with the same meaning, these are the concepts which "officially" represent the meaning in the OMOP CDM. They are used to represent the data in the Standardized Clinical Data Tables and their Concept ID is written to the respective *_concept_id fields. Usually, Standard Concept are sourced from a well-established Vocabulary that has a comprehensive coverage of the Domain and the Concepts are well-defined. For example in the Condition Domain this is achieved through the SNOMED-CT Vocabulary. An example for the other extreme is the Device Domain, where there is no comprehensive list of available Devices used in healthcare, and therefore Standard Concepts come from a variety of different Vocabularies. Same is true for the Procedure Domain.
-  * **Classification Concept** (standard_concept = 'C'). These Concepts are not used to represent the data uniquely in the CDM data tables, but provide hierarchical classes where the Standard Concepts are members. For example, the MedDRA concept for "COPD" has hierarchical relationships to the Standard SNOMED-CT Concepts that are all forms of this disease. Classification Concepts are sourced from different Vocabularies. Note that Classification Concepts are not unique. For example, there are Concepts for the Drug Class "Anticoagulants" coming from the NDF-RT, VA Class, ETC and ATC Vocabularies. Also note that the membership depends on the Vocabulary. In most cases the membership list of equivalent Classification Concepts are similar or identical, but the Medical Science does not provide a generally agreed upon standard definition of these classes.
-  * **Source Concepts** (standard_concept = NULL). These are all remaining Concepts that are not Standard or Classification Concepts. Note that Concepts can change their designation over time: if they are deprecated (valid_end_date is less than 2099-12-31 and invalid_reason = 'D' or 'U'), formerly Standard or Classification Concepts will turn into Source Concepts.
-For all Concepts in a Domain, this creates the following logical structure:
-{{ :documentation:vocabulary:structure.jpg?nolink |}}
-Source Concepts are mapped through a [[documentation:vocabulary:mappings|mapping mechanism]] to Standard Concepts, and these have relationships of various semantic natures to each other. In addition, they have hierarchical relationships to each other and the Classification Concepts, in this case derived from the Vocabularies A, B and C. Hierarchical relationships amongst Classification Concepts generally are only happening between Concepts of the same Vocabulary.
-All Concepts are stored in the [[documentation:cdm:concept|CONCEPT]] table, all relationships in the [[documentation:cdm:concept_relationship|CONCEPT_RELATIONSHP]] table and all generation-spanning hierarchical relationships in the [[documentation:cdm:concept_ancestor|CONCEPT_ANCESTOR]] table. The latter are only defined between Standard and Classification Concepts, Source Concepts do not participate in this hierarchical tree structure.
+The OMOP Standardized Vocabularies combine a number of different vocabularies that are used for different aspects of recording healthcare information. These different purposes cause the vocabularies to come with different formats, quality, comprehensiveness and coverage, and life cycle. In order to bring some order into this variability, a number of structural elements were introduced and exposed to the vocabularies, which are described in the following.
+**Note:** Even though the content of the vocabularies are left intact, the new format and structural elements will result in a different representation of each vocabulary than its native form. If you need a vocabulary in its native form, do not use the OMOP Standardized Vocabularies.

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