The openMINDS umbrella

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 main (or central) openMINDS GitHub repository ingests all these GitHub repositories as git-submodules. Furthermore it defines the openMINDS vocabulary (vocab) used for types and properties across all schemas independent of their original repository (cf. below). And last but not least, it holds the schema representations for all supported metadata formats created by the openMINDS integration pipeline (cf. below).

For this to work smoothly for the existing, but also for all new openMINDS metadata models, the corresponding openMINDS submodules (GitHub repositories) have to meet the following requirements:

• The openMINDS metadata model has to be located on a public GitHub repository and published under an MIT license.
• The GitHub repository should have at least one version branch (e.g. "v1").
• The version branch should have the following main directory folders: schemas (required), tests (recommended),  examples (recommended), and img (optional).
• The schemas folder should contain the schemas of that metadata model implemented in the openMINDS schema template syntax (cf. below). The directory of the schemas can be further structured or flat.
• The tests folder should contain test-instances (JSON-LDs) for the schemas in a flat directory. The file names for these test-instances should follow the convention of <<XXX>>-<<YYY>>.jsonld for files that should pass the tests, and <<XXX>>-<<YYY>>-nok.jsonld for files that should fail the test. In both cases, <<XXX>> should be replaced with the label of the schema that is tested, and <<YYY>> with a user defined label for what aspect is tested (e.g., person-withoutContactInfo.jsonld).
• The examples folder should contain examples for valid instance collections for that metadata model. Each example should receive its own directory (folder) with a README.md describing the example, and an metadataCollection subfolder containing the openMINDS instances (JSON-LDs). This subfolder can be further structured to group related instances.

The openMINDS vocabulary

(coming soon) 

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)