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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##**>>https://raw.githubusercontent.com/HumanBrainProject/openMINDS/v2/vocab/types.json]] and [[**##properties.json##**>>https://raw.githubusercontent.com/HumanBrainProject/openMINDS/v2/vocab/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. With that, the openMINDS vocab reflects always an up-to-date status of the general attributes of existing **schemas** and **properties** 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. How this works in detail 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 (via their type). For each openMINDS schema, a small list of general attributes are provided in a nested associative array. Currently, the following attributes are captured:
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 predefined 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-value pair; **##"deprecated": true##**). It only can be permanently removed from the **##types.json##** file, if the entry is manually deleted.
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	81	+Similar to the **##types.json##** file, the **##properties.json##** file is an associative array listing all properties across all existing openMINDS schemas (via the property name). For each openMINDS property, a small list of general attributes are provided in a nested associative array. Currently, the following attributes are captured:
	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_OPENMINDS-SCHEMA_USING_THIS_PROPERTY"
93	93	]
94		- },
95		- ...
	95	+ }
96	96	}
97	97	{{/code}}
98	98
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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-value pair; **##"deprecated": true##**). It only can be permanently removed from the **##properties.json##** file, if the entry is manually deleted.
101	101
	102	+=== The openMINDS schema template syntax ===
	103	+
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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"##**).
	105	+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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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.
	108	+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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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.
	111	+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:
110	110
111		-=== The openMINDS schema template syntax ===
	113	+{{code language="json"}}
	114	+{
	115	+ "_type": "https://openminds.ebrains.eu/LABEL_OF_METADATA_MODEL/SCHEMA_NAME",
	116	+ "properties": {
	117	+ "PROPERTY_NAME": {
	118	+ "type": "DATA_TYPE",
	119	+ "_instruction": "METADATA_ENTRY_INSTRUCTION"
	120	+ },
	121	+ "required": [
	122	+ "PROPERTY_NAME"
	123	+ ]
	124	+}
	125	+{{/code}}
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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##**.
	128	+**##"_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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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).
	131	+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.
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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.
	134	+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.
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123		-For the more inexperienced programmers, let's start by explaining first some general terms that will be later used in the openMINDS schema template syntax specification. More experienced programmers can of course skip these explanations and jump directly further down to Specifications.
	137	+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"##**.
124	124
125		-**What are strings, integers, floats or booleans?** Generally speaking strings, integers, floats or booleans are derived **data types**. A **string** is defined as a sequence of characters between quotes (e.g., ##"Is this a string? YES!"## or ##'thisIsAlsoAString'##). For a string, openMINDS accepts Unicode characters. An **integer** is a whole number, positive or negative, without decimals, of unlimited length (e.g., ##5##, ##-5## or ##1238921234##). A **float** represents a real number, written with a decimal point dividing the integer and fractional part, both of unlimited length (e.g., ##5.15##, ##-5.15## or ##1238921234.1345##). A **boolean** represents a logical proposition by means of the binary digits ##0## (##false##) and ##1## (##true##), especially in computing and electronics. How a boolean is written depends highly on the format or computational language.
126		-
127		-**What is a list or array?** A **list** is a data structure that is a mutable ordered sequence of values (also called items). The values of a list are typically defined between square brackets (e.g., ##[value1, value2, value3]##). Note that the values within a list do not have to have the same data type. In contrast, an **array** is a data structure that is a mutable unordered sequence of values of the same data type. What data types are accepted for values in a list or in an array is highly depending on the format or computational language.
128		-
129		-**What is a key-value pair or an associative array?** A **key-value pair** (sometimes also called name-value pair, attribute-value pair, property-value pair, or field-value pair) is a basic data representation and standard language feature in computing languages, systems and applications. In most cases this concept is used to build an **associative array** (also called **dictionary**), meaning an unordered list of unique keys with associated values typically defined within curly brackets (e.g., ##{key1: value1, key3: value3, key2:value2}##). What data types are accepted for keys and values highly depends on the format or computational language. Note that a value could also be a data structure, such as a list, an array or an associative array.
130		-
131		-**What is JSON?** JSON is short for **J**ava**S**cript **O**bject **N**otation, a lightweight data-interchange format which is built on associative arrays with key-value pairs and lists. Each JSON document/file begins as associative array. The keys are separated from the values via a colon and key-value pairs are separated by a comma. While a key always has to be a string in double quotes, a value can be a string in double quotes, an integer, a float, a boolean (written as true or false), null, a list or an associative array. Nesting of these structures is unlimited. For more information please go to the official webpage: [[https:~~/~~/www.json.org/>>https://www.json.org/]]. Several serialisation formats have been built on the JSON specification, such as JSON-LD (cf.[[ Application details: JSON-LD - the openMINDS serialization format>>doc:Collabs.openminds.Documentation.Application details.WebHome||target="_blank"]]). In addition, several schema languages have been developed to annotate and validate JSON documents, such as JSON-Schema and SHACL (cf. The openMINDS integration pipeline).
132		-
133		-==== Specifications ====
134		-
135		-(coming soon)
136		-
137	137	=== The openMINDS integration pipeline ===
138	138
139	139	(//**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