Vocab. CTD

Comparative Toxicogenomics Database - Chemicals

The CTD vocabulary contains all chemicals derived from the Comparative Toxicogenomics Database.

Sources

The chemicals data file is downloaded from here

Transformation

The procedures for transforming Concepts from the source to the OMOP Standard Vocabularies can be found on the OHDSI GitHub.

Concept Names

All Concepts are assigned the longest of all available names.

Concept Code

The CAS registration number is used as the concept code.

Standard Concepts

All concepts are non-Standard which means that they are mapped to the respective Standard concepts defined by the vocabulary team. Technically, they have single (1-to-1) or several (1-to-many) "Maps to" relationships in the concept_relationship_table. The primary target concepts are RxNorm or RxExtension ingredients.

Domains

sample text: For each Concept, the Domain is inferred from the SNOMED Concept it is mapped to. If a Source Concept is mapped to more than one target SNOMED Concept, a combination Domain is assigned. If a Concept has no mappings the Domain is inferred from its neighboring codes.

Domain	Notes
Drug

Concept Classes

As we are only using chemical substances from CTD, the only concept class needed is Ingredient.

Class	Notes
Ingredient

Concept Relationships

There are only mapping relationships defined for CTD.

CTD to RxNorm

Mappings are derived from external sources and only if no such relationships can be found, string matching is employed.

The mappings establish one-to-one equivalence between the Concepts. All these cases are properly handled as described in the Mapping description.

Hierarchy

The CTD Concepts are non-Standard Concepts and therefore do not participate in the hierarchy of the CONCEPT_ANCESTOR table.

Instructions for ETL

If CAS codes are present in a source vocabulary / data, they can be crosslinked to identify the correct RxNorm ingredient.