Wiki source code of Technical details

Version 69.1 by lzehl on 2021/06/27 12:46
Hide last authors
lzehl 3.1 1 (% class="box infomessage" %)
2 (((
lzehl 5.1 3 (% style="text-align: justify;" %)
lzehl 4.1 4 openMINDS is designed as modular as possible, in order to facilitate extensions and maintenance of existing, as well as development and integration of new metadata models and schemas. The layout and technical requirements for this modularity are described below.
5
lzehl 5.1 6 (% style="text-align: justify;" %)
lzehl 4.1 7 In parallel, openMINDS tries to consider the various programming skills present in the neuroscience research community. For this reason, openMINDS established an integration pipeline which gradually increases the level of technical detail: starting from a user-friendly, lightweight schema template and ending with established, highly technical metadata schema formats (e.g., JSON-Schema).
8
lzehl 5.1 9 (% style="text-align: justify;" %)
lzehl 8.1 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.
lzehl 3.1 11 )))
lzehl 5.2 12
lzehl 42.1 13 === The openMINDS umbrella ===
lzehl 5.2 14
lzehl 10.1 15 (% style="text-align: justify;" %)
lzehl 8.1 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.
lzehl 6.1 17
lzehl 42.1 18 (% style="text-align: justify;" %)
lzehl 49.1 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).
lzehl 42.1 20
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:
23
lzehl 54.1 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**.
lzehl 45.1 26
lzehl 54.1 27 (% style="text-align: justify;" %)
lzehl 53.1 28 **(2)** The GitHub repository should have at least one **version branch** (e.g., "v1").
29
lzehl 54.1 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).
lzehl 53.1 32
lzehl 54.1 33 (% style="text-align: justify;" %)
lzehl 53.1 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.
35
lzehl 54.1 36 (% style="text-align: justify;" %)
lzehl 55.1 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
lzehl 53.1 38
lzehl 55.1 39 (% style="text-align: center;" %)
40 **##<<XXX>>-<<YYY>>.jsonld##**
41
lzehl 54.1 42 (% style="text-align: justify;" %)
lzehl 55.1 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;" %)
lzehl 54.1 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.
lzehl 53.1 53
lzehl 54.1 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.
lzehl 53.1 56
lzehl 43.1 57 === The openMINDS vocabulary ===
58
59 (% style="text-align: justify;" %)
lzehl 68.2 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.
lzehl 43.1 61
lzehl 49.1 62 (% style="text-align: justify;" %)
lzehl 68.2 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:
lzehl 49.1 64
lzehl 57.1 65 {{code language="json"}}
lzehl 56.1 66 {
lzehl 68.2 67 "OPENMINDS_SCHEMA_TYPE": {
68 "description": "GENERAL_DESCRIPTION",
69 "name": "DISPLAY_LABEL",
lzehl 56.1 70 "translatableTo": [
lzehl 68.2 71 "REFERENCE_TO_RELATED_SCHEMA_OF_OTHER_INITIATIVE"
lzehl 56.1 72 ]
lzehl 68.2 73 }
lzehl 56.1 74 }
75 {{/code}}
76
lzehl 68.2 77 (% style="text-align: justify;" %)
lzehl 69.1 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.
lzehl 58.1 79
lzehl 68.2 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
lzehl 57.1 83 {{code language="json"}}
84 {
lzehl 68.2 85 "PROPERTY_NAME": {
86 "description": "GENERAL_DESCRIPTION",
87 "name": "DISPLAY_LABEL",
88 "nameForReverseLink": "DISPLAY_LABEL_OF_REVERSED_LINK",
lzehl 57.1 89 "sameAs": [
lzehl 68.2 90 "REFERENCE_TO_MATCHING_SCHEMA-PROPERTY_OF_OTHER_INITIATIVE"
lzehl 57.1 91 ],
92 "schemas": [
lzehl 68.2 93 "RELATIVE_PATH_TO_SCHEMA_USING_THIS_PROPERTY"
lzehl 57.1 94 ]
lzehl 68.2 95 }
lzehl 57.1 96 }
97 {{/code}}
98
lzehl 49.1 99 (% style="text-align: justify;" %)
lzehl 69.1 100 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.
lzehl 49.1 101
102 (% style="text-align: justify;" %)
lzehl 50.1 103 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.
lzehl 49.1 104
lzehl 7.1 105 === The openMINDS schema template syntax ===
lzehl 6.1 106
lzehl 9.1 107 (% style="text-align: justify;" %)
lzehl 68.1 108 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.
lzehl 6.1 109
lzehl 10.1 110 (% style="text-align: justify;" %)
lzehl 68.1 111 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.
112
113 (% style="text-align: justify;" %)
lzehl 67.1 114 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:
lzehl 9.1 115
lzehl 67.1 116 {{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}}
lzehl 10.1 129
lzehl 67.1 130 (% style="text-align: justify;" %)
lzehl 68.1 131 **##"_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.
lzehl 18.1 132
lzehl 67.1 133 (% style="text-align: justify;" %)
lzehl 68.1 134 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.
lzehl 61.1 135
lzehl 67.1 136 (% 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
lzehl 68.1 139 (% style="text-align: justify;" %)
lzehl 68.2 140 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"##**.
lzehl 68.1 141
lzehl 6.1 142 === The openMINDS integration pipeline ===
143
lzehl 61.1 144 (//**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/}}
Public

openMINDS