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--- documentation:vocabulary:mesh [2015/06/17 04:29]
cgreich created
+++ documentation:vocabulary:mesh [2016/06/05 18:52] (current)
cgreich
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-Only codes that can be mapped.
+===== MeSH =====
+MeSH stands for Medical Subject Heading and is a vocabulary used for indexing articles for [[https://www.ncbi.nlm.nih.gov/pubmed/|PubMed]], the US National Library of Medicine (NLM's) bibliographic database of biomedical literature. Each abstract in Pubmed has a set of search keywords assigned to it that are relevant to the content of the publication. These keywords are organized in MeSH.
+MeSH is very large, and therefore only those Concepts are imported to the OMOP Standardized Vocabulary System that have a mapping to a Standard Concept in one of the vocabularies RxNorm, SNOMED, CPT4 and HCPCS. This is in contrast to all other vocabularies, which are loaded completely, including legacy Concepts.
+The purpose of having MeSH Concepts in the OMOP Standard Vocabularies is exclusively for mapping scientific literature to relevant Standard Concepts to support research.
+==== Transformation =====
+The procedures for transforming Concepts from the source to the OMOP Standard Vocabularies can be found [[https://github.com/OHDSI/Vocabulary-v5.0/tree/master/MeSH|here]].
+==== Concept Names ====
+Concept Names are taken from the "str" field of the MRCONSO table of the UMLS metathesaurus.
+==== Concept Codes ====
+Concept Codes are taken from the "code" field of the MRCONSO table of the UMLS metathesaurus.
+==== Standard Concepts ====
+All MeSH Concepts are non-Standard.
+==== Concept Classes ====
+Two types of MeSH Concepts are incorporated into the vocabularies: Main Headings and Supplementary Concepts. Maing Headings, also known as Descriptors, are used to index the abstracts in Pubmed. Supplementary Concepts are used to index chemicals, drugs, and other concepts such as rare diseases.
+^Concept Class^Notes^
+|Main Heading|The concept_code always starts with D|
+|Suppl Concept|The concept_code always starts with C|
+|Condition|Only deprecated legacy concepts|
+|Drug|Only deprecated legacy concepts|
+|Measurement|Only deprecated legacy concepts|
+|Observation|Only deprecated legacy concepts|
+|Procedure|Only deprecated legacy concepts|
+==== Domains ====
+For each MeSH Concept, the Domain is inferred from the Concept it is mapped to.
+^Domain^Count (May 2016)^
+|Condition|5022|
+|Drug|3991|
+|Measurement|217|
+|Procedure|749|
+==== Concept Relationships ====
+There are only mapping relationships defined for MeSH.
+==== Hierarchy ====
+MeSH Concepts are non-Standard Concepts and therefore do not participate in the hierarchy of the CONCEPT_ANCESTOR table. The hierarchical relationships MeSH Concepts have to each other, in particular the Supplementary Concepts have to the Main Headings, are not reproduced in the OMOP Standard Vocabularies.

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