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Changes for page Technical details

Last modified by lzehl on 2021/07/05 18:57
From version 76.3
edited by lzehl
on 2021/06/27 13:52
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To version 22.1
edited by lzehl
on 2021/03/08 20:51
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Summary

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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.
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 the 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 +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:
38 38  
39 -(% style="text-align: center;" %)
40 -**##<<XXX>>-<<YYY>>.jsonld##**
41 -
42 -(% style="text-align: justify;" %)
43 -for files that should pass the tests, and
44 -
45 -(% style="text-align: center;" %)
46 -**##<<XXX>>-<<YYY>>-nok.jsonld##**
47 -
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##**).
50 -
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.
53 -
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.
56 -
57 -=== The openMINDS vocabulary ===
58 -
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##**>>https://raw.githubusercontent.com/HumanBrainProject/openMINDS/v2/vocab/types.json||rel="noopener noreferrer" target="_blank"]] and [[**##properties.json##**>>https://raw.githubusercontent.com/HumanBrainProject/openMINDS/v2/vocab/properties.json||rel="noopener noreferrer" target="_blank"]]). 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.
61 -
62 -(% style="text-align: justify;" %)
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 -
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 - }
40 + "_type": "https:~/~/openminds.ebrains.eu/<<schema-model>>/<<schema-name>>"
74 74  }
75 75  {{/code}}
76 76  
77 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.
45 +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.
79 79  
80 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 (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:
48 +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.
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_OPENMINDS-SCHEMA_USING_THIS_PROPERTY"
94 - ]
95 - }
96 -}
97 -{{/code}}
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"##** 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.
51 +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.
101 101  
102 -=== The openMINDS schema template syntax ===
103 -
104 104  (% style="text-align: justify;" %)
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 by the openMINDS integration pipeline, making the openMINDS schemas more human-readable, especially for untrained eyes.
54 +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. Note that this requires the context and corresponding target templates to be located in the same openMINDS metadata model repository.
106 106  
107 107  (% style="text-align: justify;" %)
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.
57 +===== String properties =====
109 109  
110 110  (% style="text-align: justify;" %)
111 -==== Basic openMINDS schema structure ====
60 +(//**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:
63 +===== Numerical 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. **##"ContactInformation"##**) have to be specified. Obviously, the schema name should be meaningful and provide some insides into what metadata content the schema covers.
66 +(//**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.
69 +===== Object properties =====
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.
72 +(//**coming soon**//)
138 138  
139 139  (% style="text-align: justify;" %)
140 -==== Schemas extending a context-schema ====
75 +===== Property arrays =====
141 141  
142 142  (% style="text-align: justify;" %)
143 -In the case that several schemas are highly related and contain a common set of properties, it is possible to define a non-type context-schema with these common properties that can be extended and modified by the group of related schemas.
78 +(//**coming soon**//)
144 144  
145 -(% style="text-align: justify;" %)
146 -All properties and constraints (e.g. required properties, expected data types) defined in the context-schema are passed on to the schemas extending this context-schema. Each of these schemas can define additional properties, or (if necessary) can overwrite the constraints of the context-schema (incl. **##"_instructions"##**). In order to state that a schema is extending a context-schema, the following additional key-value pair has to be added to the schema template above:
147 147  
148 -(% style="text-align: center;" %)
149 -**##"_extends": "RELATIVE_PATH_TO_OPENMINDS-CONTEXT-SCHEMA"##**
150 -
151 -(% style="text-align: justify;" %)
152 -This design not only makes it easier to identify highly related schemas, but also facilitates the maintenance of the commonly used properties. A good hands-on example, is the context-schema [[ResearchProduct>>https://raw.githubusercontent.com/HumanBrainProject/openMINDS_core/v3/schemas/products/researchProduct.schema.tpl.json||rel="noopener noreferrer" target="_blank"]] which is extended by the following schema set: [[Dataset>>https://raw.githubusercontent.com/HumanBrainProject/openMINDS_core/v3/schemas/products/dataset.schema.tpl.json||rel="noopener noreferrer" target="_blank"]], [[MetaDataModel>>https://raw.githubusercontent.com/HumanBrainProject/openMINDS_core/v3/schemas/products/metaDataModel.schema.tpl.json]], [[Model>>https://raw.githubusercontent.com/HumanBrainProject/openMINDS_core/v3/schemas/products/model.schema.tpl.json||rel="noopener noreferrer" target="_blank"]], and [[Software>>https://raw.githubusercontent.com/HumanBrainProject/openMINDS_core/v3/schemas/products/software.schema.tpl.json||rel="noopener noreferrer" target="_blank"]].
153 -
154 -(% style="text-align: justify;" %)
155 -==== Data type depending constraints ====
156 -
157 -(% style="text-align: justify;" %)
158 -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"##**.
159 -
160 160  === The openMINDS integration pipeline ===
161 161  
162 -(//**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
163 -
164 -{{putFootnotes/}}
83 +(//**coming soon**//)
Public

openMINDS