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ObjectiveDevelop an extract, transform, load (ETL) framework for the conversion of health databases to the Observational Medical Outcomes Partnership Common Data Model (OMOP CDM) that supports transparency of the mapping process, readability, refactoring, and maintainability.Materials and MethodsWe propose an ETL framework that is metadata-driven and generic across source datasets. The ETL framework reads mapping logic for OMOP tables from YAML files, which organize SQL snippets in key-value pairs that define the extract and transform logic to populate OMOP columns.ResultsWe developed a data manipulation language (DML) for writing the mapping logic from health datasets to OMOP, which defines mapping operations on a column-by-column basis. A core ETL pipeline converts the DML in YAML files and generates an ETL script. We provide access to our ETL framework via a web application, allowing users to upload and edit YAML files and obtain an ETL SQL script that can be used in development environments.DiscussionThe structure of the DML and the mapping operations defined in column-by-column operations maximizes readability, refactoring, and maintainability, while minimizing technical debt, and standardizes the writing of ETL operations for mapping to OMOP. Our web application allows institutions and teams to reuse the ETL pipeline by writing their own rules using our DML.ConclusionThe research community needs tools that reduce the cost and time effort needed to map datasets to OMOP. These tools must support transparency of the mapping process for mapping efforts to be reused by different institutions.

The discussion centered initially on the possibilities for and limitations of performing laboratory animal science research in the central animal units (CAU). Many such units are very small, often with only one or a few scientifically qualified member/s. It was agreed upon the necessity ofa minimum ”critical mass” of qualified people for the unit to be able to successfully conduct research and develop work within the field of laboratory animal science. It was pointed out, however, that it is necessary also for the small CAUs to get started, at whatever modest scale, to work and produce some publishable results, and thus slowly grow on their own merits. This was backed up by the firm belief that the laboratory animal scientists should be able/allowed to contribute to the advancement of knowledge. Implicit in this is that it is vital for the development of the CAUs to have resources e.g. space, for research of their own. Next to be discussed was the publication strategies within the CAUs. It was agreed upon that the scientific as well as the technical staff of the CAU could be co-authors on any publication arising as a result of work being done in the CAU. This should, however, be based upon an active scientific contribution from the CAU member, such as being an active part in the planning of the experimental series and/or contributing actively to its conduct. It must be remembered that a CAU, from the point of view of scientists in general, is a service unit, similar to other kinds of service laboratories. Finally it was emphasised that the director of a CAU has considerable ethical obligations, covering all the work being done on animals in the unit. This could also mean that ”negative” results or problems arising in a particular project e.g. the modifying effect of an intercurrent infection on experimental results, might be turned into useful information for the field of laboratory animal science., Scandinavian Journal of Laboratory Animal Sciences, Vol. 17 No. 3 (1990)