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1		-Collabs.openminds.Documentation.WebHome
	1	+Collabs.openminds.openMINDS core.WebHome

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10	10	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.
11	11	)))
12	12
13		-=== The openMINDS umbrella ===
	13	+=== Overview of the openMINDS layout ===
14	14
15	15	(% style="text-align: justify;" %)
16	16	In summary, openMINDS is the overall umbrella for a set of distributed GitHub repositories, each defining a particular metadata model for neuroscience research products.
17	17
18		-(% style="text-align: justify;" %)
19		-The main (or central) [[openMINDS GitHub repository>>https://github.com/HumanBrainProject/openMINDS||rel="noopener noreferrer" target="_blank"]] ingests all these GitHub repositories as [[git-submodules>>https://git-scm.com/docs/git-submodule||rel="noopener noreferrer" target="_blank"]]. 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).
	18	+=== The openMINDS schema template syntax ===
20	20
21	21	(% style="text-align: justify;" %)
22		-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:
	21	+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##**.
23	23
24	24	(% style="text-align: justify;" %)
25		-**(1)** The openMINDS metadata model has to be located on a **public GitHub repository** and published under an **MIT license**.
	24	+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 it 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).
26	26
27	27	(% style="text-align: justify;" %)
28		-**(2)** The GitHub repository should have at least one **version branch** (e.g., "v1").
	27	+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 the key-value pairs need to be defined and interpreted.
29	29
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31		-**(3)** The version branch should have the following **main directory folders**: **##schemas##** (required), **##tests##** (recommended),  **##examples##** (recommended), and **##img##** (optional).
	30	+===== Target & context templates =====
32	32
33	33	(% style="text-align: justify;" %)
34		-**(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.
	33	+An openMINDS schema //HAS TO HAVE// a **##"_type"##** to be recognized as **target template**. In other words, the **##"_type"##** is used to define the openMINDS namespace of a corresponding schema using the following naming convention:
35	35
36		-(% style="text-align: justify;" %)
37		-**(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
38		-
39	39	(% style="text-align: center;" %)
40		-**##<<XXX>>-<<YYY>>.jsonld##**
	36	+**##"_type": "https:~/~/openminds.ebrains.eu/<<schema-model>>/<<schema-name>>"##**,
41	41
42	42	(% style="text-align: justify;" %)
43		-for files that should pass the tests, and
	39	+where **##<<schema-model>>##** has to be replaced with the label of the openMINDS metadata model the corresponding schema belongs to and **##<<schema-name>>##** exchanged with the label of that schema.
44	44
45		-(% style="text-align: center;" %)
46		-**##<<XXX>>-<<YYY>>-nok.jsonld##**
47		-
48	48	(% style="text-align: justify;" %)
49		-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##**).
	42	+If an openMINDS schema template file //DOES NOT// define a **##"_type"##**, it is interpreted as a **context template** which //HAS TO BE// extended to a target template with a corresponding openMINDS namespace. The context and corresponding target templates have to be located in the same openMINDS metadata model repository.
50	50
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52		-**(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.
	45	+Context templates are and should be used when multiple openMINDS schemas (target templates) have the same subset of properties. This 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.
53	53
54	54	(% style="text-align: justify;" %)
55		-**(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.
	48	+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.
56	56
57		-=== The openMINDS vocabulary ===
58		-
59	59	(% style="text-align: justify;" %)
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.
	51	+===== String properties =====
61	61
62	62	(% style="text-align: justify;" %)
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##**:
	54	+(//**coming soon**//)
64	64
65		-{{code language="json"}}
66		-{
67		- ...,
68		- "https://openminds.ebrains.eu/core/Person": {
69		- "description": "Structured information on a person (alive or dead).",
70		- "name": "Person",
71		- "translatableTo": [
72		- "https://schema.org/Person"
73		- ]
74		- },
75		- ...
76		-}
77		-{{/code}}
78		-
79		-... and a cutout of the **##properties.json##**:
80		-
81		-{{code language="json"}}
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",
88		- "sameAs": [
89		- "https://schema.org/givenName"
90		- ],
91		- "schemas": [
92		- "core/v3/actors/person.schema.tpl.json"
93		- ]
94		- },
95		- ...
96		-}
97		-{{/code}}
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).
	57	+===== Numerical properties =====
101	101
102	102	(% style="text-align: justify;" %)
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"##**).
	60	+(//**coming soon**//)
104	104
105	105	(% style="text-align: justify;" %)
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.
	63	+===== Object properties =====
107	107
108	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.
	66	+(//**coming soon**//)
110	110
111		-=== The openMINDS schema template syntax ===
112		-
113	113	(% style="text-align: justify;" %)
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##**.
	69	+===== Property arrays =====
115	115
116	116	(% style="text-align: justify;" %)
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).
	72	+(//**coming soon**//)
118	118
119		-(% style="text-align: justify;" %)
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.
121	121
122		-(% style="text-align: justify;" %)
123		-Let's start by going through the syntax of a simple openMINDS schema, the contactInformation.schema.tpl.json:
124		-
125		-{{code language="json"}}
126		-{
127		- "_type": "https://openminds.ebrains.eu/core/ContactInformation",
128		- "required": [
129		- "email"
130		- ],
131		- "properties": {
132		- "email": {
133		- "type": "string",
134		- "_formats": [
135		- "email"
136		- ],
137		- "_instruction": "Enter the email address of this person."
138		- }
139		- }
140		-}
141		-{{/code}}
142		-
143		-(% style="text-align: justify;" %)
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).
145		-
146	146	=== The openMINDS integration pipeline ===
147	147
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
149		-
150		-{{putFootnotes/}}
	77	+(//**coming soon**//)