2. PhenoDB overview

Schematic overview of entities (slightly simplified)

Schema description

• met Metadata schema. Holds metadata of the individual level data in the coh and sec schemas, and of the summary level data in the sum schema.
• coh Cohort data schema. Holds individual level data.
• sec Secure cohort data schema. Holds more sensitive individual level data that is always deemed to be hidden from a standard extraction. This can be individual identifiable identifiers such as study participant ID's, personal contact information etc.
• sum Summary data schema. This schema holds non-individual level data and aggregated summary statistics such as phenotype population prevalences and genotype association dataset specific data.

Standardised table description

The Metadata Schema 'met'

Tables and views in this schema are generally friendly to interact with manually, in contrast to the tables in the coh schema. The tables are named and created to model most entities and relations of the database.

• assessment Assessments, characterised by a code and version code. Corresponds to a typical standardised questionnaire, but can capture anything of the sort from other kinds of assessments. Different types of assessments are modelled by the assessment_type. Each version of assessment will have its own row and identifier.
• assessment_item Assessment items, characterised by an assessment, assessment_item_type and an item code. Assessment items groups assessment_item_variables into groups that generally corresponds to an item in a questionnaire or the corresponding for other assessment_types (has its own question text or description, but multiple pieces of data).
• assessment_item_type Assessment item types; an entity created to characterise assessment_items to allow for multiple different types in one assessment. Characterised by an assessment_type (describing the typical assessment type that this item type may be associated with), and a code. An example of this would be an assessment that combined questionnaire type items and interview or imaging items. A typical use would be to be able to filter among multiple items across assessments.
• assessment_item_variable Assessment item variables, characterised by an assessment_item and a code, is the entity modelling the most granular piece of individual cohort data in the database. Each assessment item variable should correspond to a column in a table under the 'coh' schema.
• assessment_type Assessment types, characterised by a code, describes the top sorting category for an assessment. An assessment can only have one assessment type, which may make it more useful to create detailed assessment item types instead. The default assessment types are:

• Questionnaire - A questionnaire type of assessment, either on paper or digitally distributed.
• Interview - An interview type of assessment.
• Imaging - An imaging type assessment.
• Biological sample - An assessment made on a biological sample.
• Cognitive test - A cognitive test performed using either a technical platform or other means to assess the result.
• Probe - Any kind of non-imaging technical measurement.