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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 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).
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.
29 29  
30 30  (% style="text-align: justify;" %)
31 -**(3)** The version branch should have the following **main directory folders**: **##schemas##** (required), **##tests##** (recommended),  **##examples##** (recommended), and **##img##** (optional).
30 +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.
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 +===== Target & context templates =====
35 35  
36 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
36 +Same as in JSON-Schema, all openMINDS schemas define the name and value of the metadata they expect under the key **##properties##** as nested dictionaries, and which of those properties is obligatory under the key **##required##** listing the corresponding property names, as depicted here:
38 38  
39 -(% style="text-align: center;" %)
40 -**##<<XXX>>-<<YYY>>.jsonld##**
38 +{{code language="json"}}
39 +{
40 + "properties": {
41 + "propertyNameA": {},
42 + "propertyNameB": {},
43 + "propertyNameC": {}
44 + },
45 + "required": [
46 + "propertyNameA",
47 + "propertyNameC"
48 + ]
49 +}
50 +{{/code}}
41 41  
42 42  (% style="text-align: justify;" %)
43 -for files that should pass the tests, and
53 +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, as depicted here:
44 44  
45 -(% style="text-align: center;" %)
46 -**##<<XXX>>-<<YYY>>-nok.jsonld##**
55 +{{code language="json"}}
56 +{
57 + "_type": "https:~/~/openminds.ebrains.eu/<<schema-model>>/<<schema-name>>",
58 + "properties": {},
59 + "required": []
60 +}
61 +{{/code}}
47 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##**).
64 +where **##<<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 that schema (written in **##CamelCase##**).
50 50  
51 51  (% style="text-align: justify;" %)
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.
67 +If an openMINDS schema template //does not// define a key **##"_type"##** (as in the first example above), it is interpreted as a **context template** which //has to be// extended to a target template.
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.
70 +Context templates are and should be used when multiple openMINDS schemas (target templates) have the same subset of properties. Such a 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.
56 56  
57 -=== The openMINDS vocabulary ===
58 -
59 59  (% style="text-align: justify;" %)
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.
73 +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. For example, the openMINDS core target template **##Dataset##** extends the core concept template **##researchProduct##**:
61 61  
62 -(% style="text-align: justify;" %)
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 -
65 65  {{code language="json"}}
66 66  {
67 - "OPENMINDS_SCHEMA_TYPE": {
68 - "description": "GENERAL_DESCRIPTION",
69 - "name": "DISPLAY_LABEL",
70 - "translatableTo": [
71 - "REFERENCE_TO_RELATED_SCHEMA_OF_OTHER_INITIATIVE"
72 - ]
73 - }
77 + "_type": "https:~/~/openminds.ebrains.eu/core/Dataset",
78 + "_extends": "products/researchProduct.schema.tpl.json",
79 + "properties": []
74 74  }
75 75  {{/code}}
76 76  
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.
83 +Note that this convention requires the context and corresponding target templates to be located in the same openMINDS metadata model repository. Note also that both, target and concept template, can or cannot define required properties. In this context, the following rules apply: 
79 79  
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:
85 +1. If a concept template requires properties, the target templates extending this concept template require the same properties.
86 +1. A target template can require properties of the concept template, that are not explicitly required within the concept template. Other target templates extending the same concept template will not require those properties.
87 +1. A target template can define and require additional properties that were not defined and required in the concept template. These properties are not shared with the other target templates that extend the same concept template.
82 82  
83 -{{code language="json"}}
84 -{
85 - "PROPERTY_NAME": {
86 - "description": "GENERAL_DESCRIPTION",
87 - "name": "DISPLAY_LABEL",
88 - "nameForReverseLink": "DISPLAY_LABEL_OF_REVERSED_LINK",
89 - "sameAs": [
90 - "REFERENCE_TO_MATCHING_SCHEMA-PROPERTY_OF_OTHER_INITIATIVE"
91 - ],
92 - "schemas": [
93 - "RELATIVE_PATH_TO_SCHEMA_USING_THIS_PROPERTY"
94 - ]
95 - }
96 -}
97 -{{/code}}
89 +How to define the expected value of a property will be explained for the different property types in the following sections.
98 98  
99 99  (% style="text-align: justify;" %)
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##**. All manual editions of those attribute values 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.
92 +===== String properties =====
101 101  
102 102  (% style="text-align: justify;" %)
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 and references.
95 +(//**coming soon**//)
104 104  
105 -=== The openMINDS schema template syntax ===
106 -
107 107  (% style="text-align: justify;" %)
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.
98 +===== Numerical properties =====
109 109  
110 110  (% style="text-align: justify;" %)
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.
101 +(//**coming soon**//)
112 112  
113 113  (% style="text-align: justify;" %)
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:
104 +===== Object properties =====
115 115  
116 -{{code language="json"}}
117 -{
118 - "_type": "https://openminds.ebrains.eu/LABEL_OF_METADATA_MODEL/SCHEMA_NAME",
119 - "properties": {
120 - "PROPERTY_NAME": {
121 - "type": "DATA_TYPE",
122 - "_instruction": "METADATA_ENTRY_INSTRUCTION"
123 - },
124 - "required": [
125 - "PROPERTY_NAME"
126 - ]
127 -}
128 -{{/code}}
129 -
130 130  (% style="text-align: justify;" %)
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.
107 +(//**coming soon**//)
132 132  
133 133  (% 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.
110 +===== Property arrays =====
135 135  
136 136  (% 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.
113 +(//**coming soon**//)
138 138  
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"##**.
141 141  
142 142  === The openMINDS integration pipeline ===
143 143  
144 -(//**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
145 -
146 -{{putFootnotes/}}
118 +(//**coming soon**//)
Public

openMINDS