Wiki source code of Technical details

Version 61.1 by lzehl on 2021/06/24 12:28
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 49.1 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.
lzehl 43.1 61
lzehl 49.1 62 (% style="text-align: justify;" %)
lzehl 58.1 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##**:
lzehl 49.1 64
lzehl 57.1 65 {{code language="json"}}
lzehl 56.1 66 {
67 ...,
68 "https://openminds.ebrains.eu/core/Person": {
lzehl 58.1 69 "description": "Structured information on a person (alive or dead).",
lzehl 56.1 70 "name": "Person",
71 "translatableTo": [
72 "https://schema.org/Person"
73 ]
74 },
75 ...
76 }
77 {{/code}}
78
lzehl 59.1 79 ... and a cutout of the **##properties.json##**:
lzehl 58.1 80
lzehl 57.1 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
lzehl 49.1 99 (% style="text-align: justify;" %)
lzehl 60.1 100 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).
lzehl 49.1 101
102 (% style="text-align: justify;" %)
lzehl 60.1 103 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"##**).
104
105 (% style="text-align: justify;" %)
lzehl 52.1 106 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.
lzehl 49.1 107
108 (% style="text-align: justify;" %)
lzehl 50.1 109 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.
lzehl 49.1 110
lzehl 7.1 111 === The openMINDS schema template syntax ===
lzehl 6.1 112
lzehl 9.1 113 (% style="text-align: justify;" %)
lzehl 39.1 114 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##**.
lzehl 6.1 115
lzehl 10.1 116 (% style="text-align: justify;" %)
lzehl 61.1 117 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).
lzehl 9.1 118
lzehl 11.1 119 (% style="text-align: justify;" %)
lzehl 61.1 120 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.
lzehl 10.1 121
lzehl 12.1 122 (% style="text-align: justify;" %)
lzehl 61.1 123 Let's start by going through the syntax of a simple openMINDS schema, the contactInformation.schema.tpl.json:
lzehl 18.1 124
lzehl 61.1 125 {{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
lzehl 18.1 143 (% style="text-align: justify;" %)
lzehl 61.1 144 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).
lzehl 10.1 145
lzehl 6.1 146 === The openMINDS integration pipeline ===
147
lzehl 61.1 148 (//**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/}}
Public

openMINDS