Technical details

Version 30.1 by lzehl on 2021/03/08 22:10

openMINDS is designed as modular as possible, in order to facilitate extensions and maintenance of existing, as well as development and integration of new metadata models and schemas. The layout and technical requirements for this modularity are described below.

In parallel, openMINDS tries to consider the various programming skills present in the neuroscience research community. For this reason, openMINDS established an integration pipeline which gradually increases the level of technical detail: starting from a user-friendly, lightweight schema template and ending with established, highly technical metadata schema formats (e.g., JSON-Schema).

Please find below a documentation of the layout and requirements needed to keep the openMINDS modularity, the syntax of the openMINDS schema template, as well as the openMINDS integration pipeline.

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 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 & context templates

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

{
"properties": {
  "propertyNameA": {},
  "propertyNameB": {},
  "propertyNameC": {}
},
"required": [
  "propertyNameA",
  "propertyNameC"
]
}

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:

{
"_type": "https:~/~/openminds.ebrains.eu/<<schema-model>>/<<schema-name>>",
"properties": {}
}

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 context template which has to be extended to a target template.

Context templates are and should be used when multiple openMINDS schemas (target templates) have the same subset of properties. Such a common subset of properties can then be defined within a single context schema instead of each target template which facilitates the long-term maintenance of these properties.

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

{
"_type": "https:~/~/openminds.ebrains.eu/core/Dataset",
"_extends": "products/researchProduct.schema.tpl.json"
}

Note that this convention requires the context 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:

A concept template has to define some properties which will be inherited by all extending target templates.
If a concept template additionally states that some of these properties are required, all extending target templates will require the same properties.
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.
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.