Overview of the openMINDS layout

In summary, openMINDS is the overall umbrella for a set of distributed GitHub repositories, each defining a particular metadata model for neuroscience research products.

The openMINDS schema template syntax

All openMINDS metadata models use a light-weighted schema template syntax for defining the expected metadata. The correspondingly formatted schema files use the extension: .schema.tpl.json.

Although, as the file extension suggests, this openMINDS schema template syntax is inspired by JSON-Schema, it facilitates or even excludes technical aspects that are generally expected for the openMINDS schemas making them more human-readable, especially for untrained eyes. Behind the scenes, within the openMINDS integration pipeline (cf. below), this schema template syntax is then interpreted and flexibly translated to various formal metadata formats (e.g., JSON-Schema).

Despite the simplification in comparison to JSON-Schema, the openMINDS schema templates are also, at the core, specially formatted JSON files using a particular syntax, meaning special key-value pairs that define the validation rules of a schema.

Please find in the following a full documentation of the openMINDS schema template syntax and how it's key-value pairs need to be defined and interpreted.

Target & concept templates

Same as in JSON-Schema, all openMINDS schema templates define the expected name (written in lowerCamelCase) and value of the metadata, typically called property, under the key properties as nested dictionaries. Furthermore, the names of obligatory metadata can be listed under the key required. Here a generalized example:

In addition, an openMINDS schema has to have a key "_type" to be recognized as target template. In other words, the "_type" is used to define the openMINDS namespace of a corresponding schema using a particular naming convention. Here again a generalized example:

Note that <<schema-model>> has to be replaced with the label of the openMINDS metadata model to which the corresponding schema belongs to, and <<schema-name>> has to be replaced with the corresponding name of the schema (written in CamelCase).

If an openMINDS schema template does not define a key "_type" (as in the first example above), it is interpreted as a concept template which has to be extended to a target template.

Concept templates are and should be used when multiple target templates have the same subset of properties, because they facilitate the long-term maintenance of those shared properties: Instead of defining the same properties repeatedly within multiple target templates, the common subset can be defined within a single concept template and passed on to all extending target templates.

To define that a target template is the extension of a concept template, the target template can state under "_extends" the relative path to the concept template. For example, the openMINDS core target template Dataset extends the core concept template researchProduct as indicated here:

Note that this convention requires the concept and corresponding target templates to be located in the same openMINDS metadata model repository. Note also that for properties, the following rules apply for target and concept template:  

1. A concept template has to define some properties which will be inherited by all extending target templates.
2. If a concept template additionally states that some of these properties are required, all extending target templates will require the same properties.  
3. A target template can require properties of the concept template, that are not explicitly required within the concept template. In such a case, the other target templates extending the same concept template will not require those properties.
4. A target template can (but does not have to) define and require additional properties that were not defined and required in the concept template. These additionally defined and required properties will not be shared with the other target templates extending the same concept template.

How to define the expected value of a property will be explained for the different property types in the following sections.

Defining expected values

The expected value of a property can be defined in large parts in the same way as in JSON-Schema, with some openMINDS syntax specific simplifications and modifications.

On the first level, the "type" of the expected property value needs to be defined. In principle, the openMINDS template syntax supports the same value types as JSON-Schema Draft 7.0, meaning:  
+ "string"  
+ "number"  
+ "integer"  
+ "array"  
+ "boolean"  
+ "null"  
+ "object"  

Also very similar to JSON-Schema, additional type-specific keys can be used to set further requirements for the expected value. H

The openMINDS integration pipeline

(coming soon)