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57	57	=== The openMINDS vocabulary ===
58	58
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60		-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.
	60	+Located under the folder **##vocab##** in the main openMINDS GitHub directory, the openMINDS vocabulary is semi-automatically gathered and stored in dedicated JSON files (**##types.json##** and **##properties.json##**). The openMINDS integration pipeline makes sure that both files are updated with each commit to any of the GitHub repositories for the openMINDS metadata models. For this reason, the files always contain an up-to-date list of all schemas and properties in use. This setup not only allows us to centrally maintain general definitions and references for schema **types** and **properties** across all openMINDS metadata models, but also to keep several technical aspects for the openMINDS schemas hidden from the naive user. How this works is explained in the following.
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63		-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##**:
	63	+The **##types.json##** file is an associative array listing all existing openMINDS schemas. For each openMINDS schema a nested associative array is created providing the respective display label, the general description, and a list of references to corresponding schemas of other initiatives:
64	64
65	65	{{code language="json"}}
66	66	{
67		- ...,
68		- "https://openminds.ebrains.eu/core/Person": {
69		- "description": "Structured information on a person (alive or dead).",
70		- "name": "Person",
	67	+ "OPENMINDS_SCHEMA_TYPE": {
	68	+ "description": "GENERAL_DESCRIPTION",
	69	+ "name": "DISPLAY_LABEL",
71	71	"translatableTo": [
72		- "https://schema.org/Person"
	71	+ "REFERENCE_TO_RELATED_SCHEMA_OF_OTHER_INITIATIVE"
73	73	]
74		- },
75		- ...
	73	+ }
76	76	}
77	77	{{/code}}
78	78
79		-... and a cutout of the **##properties.json##**:
	77	+(% style="text-align: justify;" %)
	78	+With each new schema committed to one of the openMINDS metadata models, a new entry is appended to the **##types.json##** file, with the display label automatically derived from the respective schema type and the remaining attributes provided with a null value. Once an entry for a schema is made in the **##types.json##** file, the values of all attributes (**##"name"##**, **##"description"##**, and **##"translatableTo"##**) can be manually edited. All manual editions will be preserved and not overwritten when the file is updated again with a new commit. In case a schema is deleted from the openMINDS metadata models, the corresponding entry in the **##types.json##** file is marked as being deprecated (additional attribute; **##"deprecated": true##**). It only can be permanently removed from the **##types.json##** file, if the entry is manually deleted.
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	80	+(% style="text-align: justify;" %)
	81	+Similar to the **##types.json##** file, the **##properties.json##** file is an associative array listing all properties across all existing openMINDS schemas. For each openMINDS property a nested associative array is created providing the respective display label, the general description, the label for displaying the reversed link of that property, the list of schemas in which the property is used, and a list of references to matching schema properties of other initiatives:
	82	+
81	81	{{code language="json"}}
82	82	{
83		- ...,
84		- "givenName": {
85		- "description": "Name given to a person, including all potential middle names, but excluding the family name.",
86		- "name": "Given name",
87		- "nameForReverseLink": "Is given name of",
	85	+ "PROPERTY_NAME": {
	86	+ "description": "GENERAL_DESCRIPTION",
	87	+ "name": "DISPLAY_LABEL",
	88	+ "nameForReverseLink": "DISPLAY_LABEL_OF_REVERSED_LINK",
88	88	"sameAs": [
89		- "https://schema.org/givenName"
	90	+ "REFERENCE_TO_MATCHING_SCHEMA-PROPERTY_OF_OTHER_INITIATIVE"
90	90	],
91	91	"schemas": [
92		- "core/v3/actors/person.schema.tpl.json"
	93	+ "RELATIVE_PATH_TO_SCHEMA_USING_THIS_PROPERTY"
93	93	]
94		- },
95		- ...
	95	+ }
96	96	}
97	97	{{/code}}
98	98
99	99	(% style="text-align: justify;" %)
100		-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).
	100	+With each new property committed to a schema of one of the openMINDS metadata models, a new entry is appended to the **##properties.json##** file, with the display label and list of schemas in which this property occurs automatically derived. The remaining attributes are initially provided with a null value. Once an entry for a property is made in the **##properties.json##** file, the values of all attributes (**##"name"##**, **##"description"##**, **##"nameForReversedLink"##**, and **##"sameAs"##**) can be manually edited, except for **##"schemas"##** which will be always automatically updated. All those manual editions will be preserved and not overwritten when the file is updated again with a new commit. In case a property is not used anymore in any of the schemas from the openMINDS metadata models, the corresponding entry in the **##properties.json##** file is marked as being deprecated (additional attribute; ##"deprecated": true##). It only can be permanently removed from the **##properties.json##** file, if the entry is manually deleted.
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103		-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"##**).
	103	+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. In addition, this design allows us to centrally define and maintain multiple references to related schemas and matching schema properties of other metadata initiatives.
104	104
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106		-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.
107		-
108		-(% style="text-align: justify;" %)
109		-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.
110		-
111	111	=== The openMINDS schema template syntax ===
112	112
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114		-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##**.
	108	+All openMINDS metadata models are defined using a light-weighted schema template syntax. Although this schema template syntax is inspired by JSON-Schema, it outsources most schema technicalities to be handled in the openMINDS integration pipeline, making the openMINDS schemas more human-readable, especially for untrained eyes.
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117		-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).
	111	+The few remaining customized technical properties which need additional interpretation or translation to a formal schema languages (e.g. JSON-Schema) have an underscore as prefix (e.g., **##"_type"##**). Within the openMINDS integration pipeline (cf. below), the schema template syntax is interpreted, extended and flexibly translated to various formal schema languages. All further specifications of the openMINDS schema template syntax are described below.
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120		-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.
	114	+All openMINDS schemas need to have the extension **##.schema.tpl.json##** and each schema is defined as a nested associative array (dictionary) with the following conceptual structure:
121	121
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123		-Let's start by going through the syntax of a simple openMINDS schema, the contactInformation.schema.tpl.json:
124		-
125	125	{{code language="json"}}
126	126	{
127		- "_type": "https://openminds.ebrains.eu/core/ContactInformation",
128		- "required": [
129		- "email"
130		- ],
	118	+ "_type": "https://openminds.ebrains.eu/LABEL_OF_METADATA_MODEL/SCHEMA_NAME",
131	131	"properties": {
132		- "email": {
133		- "type": "string",
134		- "_formats": [
135		- "email"
136		- ],
137		- "_instruction": "Enter the email address of this person."
138		- }
139		- }
	120	+ "PROPERTY_NAME": {
	121	+ "type": "DATA_TYPE",
	122	+ "_instruction": "METADATA_ENTRY_INSTRUCTION"
	123	+ },
	124	+ "required": [
	125	+ "PROPERTY_NAME"
	126	+ ]
140	140	}
141	141	{{/code}}
142	142
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144		-The **##"_type"##** identifies the schema type or namespace for the particular schema. In **##"required"##** all property names have to be listed{{footnote}}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 **##[ ]##**.{{/footnote}} 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 dictionary{{footnote}}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 **##{...}##**.{{/footnote}} (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"##**{{footnote}}Strings are defined as characters between quotes **##"..."##**.{{/footnote}} 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).
	131	+**##"_type"##** defines the schema type (or namespace) with the depicted naming convention, where the label of the respective openMINDS metadata model (e.g., **##"core"##**) and the schema name (format: UpperCamelCase; e.g. **##"Person"##**) have to be specified. Obviously, the schema name should be meaningful and provide some insides into what metadata content the schema covers.
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	133	+(% style="text-align: justify;" %)
	134	+Under **##"properties"##** a nested associative array is defined, where each key defines the property name (format: lowerCamelCase; e.g. **##"givenName"##**). The corresponding value is again a nested associative array defining the expected data **##"type"##** (cf. below) and the **##"_instructions"##** for entering the correct metadata for the respective property.
	135	+
	136	+(% style="text-align: justify;" %)
	137	+Under **##"required"##** a list of property names can be provided that are obligatory to be present in a correctly instantiated metadata instance of the respective schema. If none of the properties are required, this key-value pair does not have to be specified.
	138	+
	139	+(% style="text-align: justify;" %)
	140	+Now, depending on the expected data type additional constraints can be made for the metadata entry of a respective property. Currently, the openMINDS schema template syntax supports the following data types: **##"string"##**, ##**"integer"**##, **##"float"##**, **##"boolean"##**, **##"array"##** and **##"object"##**.
	141	+
146	146	=== The openMINDS integration pipeline ===
147	147
148	148	(//**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