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 stores the openMINDS vocabulary (vocab), providing general definitions and references for types and properties used in schemas across all openMINDS repositories (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:

(1) The openMINDS metadata model has to be located on a public GitHub repository and published under an MIT license.

(2) The GitHub repository should have at least one version branch (e.g., "v1").

(3) The version branch should have the following main directory folders: schemas (required), tests (recommended),  examples (recommended), and img (optional).

(4) 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.

(5) 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-withoutCI.jsonld).

(6) 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 or flat.

(7) The img folder should contain image files used on that GitHub repository (e.g., the logo of the new openMINDS metadata model). The directory of the images can be further structured or flat.

The openMINDS vocabulary

Through the integration pipeline of the openMINDS generator, the openMINDS vocabulary is automatically gathered and stored in the main openMINDS GitHub in order to centrally maintain general definitions and references for types and properties used in schemas across all openMINDS repositories. How this works is explained in the following.

Schema types and properties are stored in dedicated JSON files (types.json and properties.json) under the folder vocab located in the main openMINDS GitHub directory. Each schema type and property occurring in the openMINDS metadata models is automatically represented in those files as nested dictionaries. Here a cutout of the types.json:

... and a cutout of the properties.json:

The keywords of those nested dictionaries are pre-defined to consistently capture for all schema types and properties their namespace, their occurrence (cf. "schemas" in properties.json), their general description (cf. "description" in types.json and properties.json), and possible references to related or matching schema types (cf. "translatableTo" in types.json) and properties  (cf. ""sameAs"" in properties.json) of other metadata initiatives (e.g., schema.org). 

This setup also allows us to define some values/entries to be automatically filled in by the openMINDS integration pipeline with each commit to one of the openMINDS repositories ("name", "schemas") and others to be manually editable later on ("description", "translatableTo", "sameAs", "nameForReverseLink"). 

For security, outdated entries in those openMINDS vocabulary files (e.g., because the namespace of the schema type or property changed or the schema type or property was deleted) are not automatically deleted, but kept and marked as being deprecated. After evaluation, deprecated schema types or properties can be deleted manually from openMINDS vocabulary.

With that, the openMINDS vocab reflects always an up-to-date status of the schema types and properties in use across all openMINDS metadata models, while providing the opportunity to centrally review and maintain their consistency and references. 

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 making the openMINDS schemas 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.

Let's start by going through the syntax of a simple openMINDS schema, the contactInformation.schema.tpl.json:

The "_type" identifies the schema type or namespace for the particular schema. In "required" all property names have to be listed¹ that must be provided and filled out in a valid instance of this schema type (here, only the property "email" is required). Under "properties", information about the expected value for each property defining the particular schema is given in a nested dictionary² (here, the only property is "email"). In this nested dictionary the "type" of the expected value should be specified (here, a value of type "string"³ is expected). For values of type "string" it is further possible to list the accepted formats of the "string" under "_formats" (here, the expected "string" value has to be an email).

The openMINDS integration pipeline

(coming soon) If you'd like to learn more about the openMINDS integration pipeline, especially if you'd like to contribute to it, please get in touch with us (the openMINDS development team) via the issues on the openMINDS or openMINDS_generator GitHub or the support email: openminds@ebrains.eu

1. ^ A list is a data structure that is an ordered sequence of elements. Each element inside of a list is typically called an item. Lists are defined by having values between square brackets [ ].
2. ^ A dictionary is a data structure that consists of an unordered collection of key:value pairs. Dictionaries are defined by having these key:value pairs between curly brackets {...}.
3. ^ Strings are defined as characters between quotes "...".