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--- documentation:vocabulary:principles [2016/06/18 22:50]
cgreich
+++ documentation:vocabulary:principles [2016/06/20 10:27] (current)
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 The Standardized Vocabularies are constructed with a few principles in mind. Not every principle has been executed to perfection, but it represents a general motivation and direction of the ongoing improvement and development process:
-  - **Standardization:** Multiple Vocabularies used in observational data consolidated into a common format. This relieves the researchers from having to understand and handle multiple different formats and life cycle conventions of the Vocabularies.
+  - **Standardization:** Multiple Vocabularies used in observational data are consolidated into a common format. This relieves the researchers from having to understand and handle multiple different formats and life cycle conventions of the originating Vocabularies.
-  - **Unique Standard Concepts**: For each Clinical Entity, there is only one Concepts representing it, called the Standard Concept. Other equivalent or similar Concepts are designated non-Standard and mapped to the Standard ones.
+  - **Unique Standard Concepts**: For each Clinical Entity there is only one Concept representing it, called the Standard Concept. Other equivalent or similar Concepts are designated non-Standard and mapped to the Standard ones.
-  - **Domains:** Each Concept is assigned a Domain, and it is done so correctly. This also defines in which CDM table a clinical entity should be placed into or looked up in at query time.
+  - **Domains:** Each Concept is assigned a Domain. "Dirty" Non-Standard Concepts can also belong to more than one Domain. This also defines in which CDM table a clinical entity should be placed into or looked up in at query time.
-  - **Comprehensive coverage:** The Standardized Vocabularies intend to capture every event that is relevant to the patient's clinical experience (e.g. Conditions, Procedures, Exposures to Drug, etc.) and some of the administrative artifacts of the healthcare system (e.g. Visits, Care Sites, etc.). This means that in many cases a single Vocabulary is not sufficient to cover a Domain.
+  - **Comprehensive coverage:** Every event that is relevant to the patient's healthcare experience (e.g. Conditions, Procedures, Exposures to Drug, etc.) and some of the administrative artifacts of the healthcare system (e.g. Visits, Care Sites, etc.) are covered by the Concepts of a Domain.
-  - **Hierarchy:** Within a Domain all Concepts are organized in a hierarchical structure. This allows to researcher to query for all Concepts (e.g. drug products) that are hierarchically subsumed under a higher level Concept (e.g. a drug class). This entails the solution of two separate problems:
+  - **Hierarchy:** Within a Domain all Concepts are organized in a hierarchical structure. This allows to query for all Concepts (e.g. drug products) that are hierarchically subsumed under a higher level Concept (e.g. a drug class). This entails addressing two separate problems:
     * Each Concepts should have one or more classifications (bottom up).
     * Each Classification should contain all the relevant Concepts (top down).
-  - **Relationships** between Concepts within and acros Vocabularies and **Mappings** from non-Standard to Standard Concepts.
+  - **Relationships** between Concepts within and across Vocabularies and **Mappings** from non-Standard to Standard Concepts.
-  - **Life cycle** keeping data representation up to date but supporting the processing of deprecated Concepts. This means that for each deprecated Concept a replacement Concept has to be assigned capturing the meaning of the clinical entity.
+  - **Life cycle** keeping data representation up to date but supporting the processing of deprecated and upgraded Concepts.
-It is important to note that these critera are followed strictly for the purpose of observational research. In that regard the Standardized Vocabularies differ from large collections with equivalence mapping of concepts such as the [[http://www.nlm.nih.gov/research/umls|UMLS]], which supports indexing and searching the entire biomedical literature. UMLS resources have been used heavily as a basis for constructing many of the Standardized Vocabulary components, but significant additional efforts have been made to the make the framework for for purpose:
+It is important to note that these critera have the purpose to serve observational research. In that regard the Standardized Vocabularies differ from large collections with equivalence mappings of concepts such as the [[http://www.nlm.nih.gov/research/umls|UMLS]], which supports indexing and searching of the entire biomedical literature. UMLS resources have been used heavily as a basis for constructing many of the Standardized Vocabulary components, but significant additional efforts have been made to adjust the framework:
-  * Additional Vocabularies were created, mostly for metadata purposes.
-  * Mappings and relationships were added to achieve comprehensive coverage. If equivalence cannot be achieved, "uphill" relationships from more granular non-standard to higher level Standard Concepts are created.
+  * Additional Vocabularies, mostly for metadata purposes, are established.
-  * A comprehensive domain structure was established and each Concepts was assigned a Domain (or combination of Domains).
+  * Mappings and relationships are being added to achieve comprehensive coverage. If equivalence cannot be achieved, "uphill" relationships from more granular non-standard to higher level Standard Concepts are created.
+  * A comprehensive domain structure is established and each Concepts was assigned a Domain (or combination of Domains).
   * A hierarchical tree within Domains was built representing classifications used in medical science and clinical practice.
 However, significant work needs to be done to achieve all the criteria in all of the Domains. Currently, for the complex and non-administrative Domains we can achieve the following compliance:
-^Domain^Standardization^Unique Concepts^Reliable Domains^Comprehensive Coverage^Hierarchy^Mapping
+^Domain^Standardization^  Unique Concepts  ^  Reliable Domains  ^  Comprehensive Coverage  ^  Hierarchy  ^  Mapping  ^
-|Drug|  x  |  x  |  x  |  In US, other countries in process  |  x  |  x  |
+|Drug|  x  |  x  |  In US, other countries in process  |  x  |  x  |  x  |
-|Condition|  x  |  x  |  x  |  x  |  x  |  x  |
+|Condition|  x  |  x  |  mostly  |  x  |  x  |  mostly  |
-|Procedure|  x  |  heavily overlapping  |  x  |  x  | |
+|Procedure|  x  |  heavily overlapping  |  x  |  x  | |  x  |
 |Measurement|  x  |  somewhat  |  mostly  |  x  |  minimal  | |
 |Device| | |  mostly  | | | |
 |Unit|  x  |  x  |  x  |  x  | | |
-The Life Cycle is implemented for all Concepts, and its rules are described
+The Life Cycle is implemented for all Concepts, and its rules are described in the CONCEPT table [[documentation:cdm:concept|description]] and in the discussion of the individual vocabularies (if there are specific rules, but this is rare).

Observational Health Data Sciences and Informatics

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