Changes for page Technical details

Last modified by lzehl on 2021/07/05 18:57
From version 45.1
edited by lzehl
on 2021/03/18 11:46
Change comment: There is no comment for this version
To version 36.1
edited by lzehl
on 2021/03/08 22:33
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -10,34 +10,15 @@
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 defines the openMINDS vocabulary (**##vocab##**) used for **##types##** and **##properties##** across all schemas independent of their original repository (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).
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 -
24 -(% style="text-align:justify" %)
25 -* The openMINDS metadata model has to be located on a **public GitHub repository** and published under an **MIT license**.
26 -* The GitHub repository should have at least one **version branch** (e.g. "v1").
27 -* The version branch should have the following **main directory folders**: **##schemas##** (required), **##tests##** (recommended),  **##examples##** (recommended), and **##img##** (optional).
28 -* 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.
29 -* 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 **##<<XXX>>-<<YYY>>.jsonld##** for files that should pass the tests, and **##<<XXX>>-<<YYY>>-nok.jsonld##** 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-withoutContactInformation.jsonld##**).
30 -* 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 to group related instances.
31 -
32 -=== The openMINDS vocabulary ===
33 -
34 -(% style="text-align: justify;" %)
35 -((% style="color:#7f8c8d" %)//**coming soon**//(%%))
36 -
37 37  === The openMINDS schema template syntax ===
38 38  
39 39  (% style="text-align: justify;" %)
40 -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##**.
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##**.
41 41  
42 42  (% style="text-align: justify;" %)
43 43  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).
... ... @@ -57,13 +57,13 @@
57 57  {{code language="json"}}
58 58  {
59 59   "properties": {
60 - "propertyNameA": {},
61 - "propertyNameB": {},
62 - "propertyNameC": {}
41 + "propertyNameA": {},
42 + "propertyNameB": {},
43 + "propertyNameC": {}
63 63   },
64 64   "required": [
65 - "propertyNameA",
66 - "propertyNameC"
46 + "propertyNameA",
47 + "propertyNameC"
67 67   ]
68 68  }
69 69  {{/code}}
... ... @@ -97,7 +97,6 @@
97 97  }
98 98  {{/code}}
99 99  
100 -(% style="text-align: justify;" %)
101 101  Note that this convention requires the concept and corresponding target templates to be located in the same openMINDS metadata model repository. Note also that for properties, the following rules apply for target and concept template: 
102 102  
103 103  1. A concept template has to define some properties which will be inherited by all extending target templates.
... ... @@ -105,28 +105,33 @@
105 105  1. A target template can require properties of the concept template, that are not explicitly required within the concept template. In such a case, the other target templates extending the same concept template will not require those properties.
106 106  1. A target template can (but does not have to) define and require additional properties that were not defined and required in the concept template. These additionally defined and required properties will not be shared with the other target templates extending the same concept template.
107 107  
108 -(% style="text-align: justify;" %)
109 109  How to define the expected value of a property will be explained for the different property types in the following sections.
110 110  
111 111  (% style="text-align: justify;" %)
112 -===== Defining expected values =====
91 +===== String properties =====
113 113  
114 114  (% style="text-align: justify;" %)
115 -The expected value of a property can be defined in large parts in the same way as in JSON-Schema, with some openMINDS syntax specific simplifications and modifications.
94 +(//**coming soon**//)
116 116  
117 117  (% style="text-align: justify;" %)
118 -On the first level, the **##"type"##** of the expected property value needs to be defined. In principle, the openMINDS template syntax supports the same value types as JSON-Schema Draft 7.0, meaning:
119 -+ **##"string"##**
120 -+ **##"number"##**
121 -+ **##"integer"##**
122 -+ **##"array"##**
123 -+ **##"boolean"##**
124 -+ **##"null"##**
125 -+ **##"object"##** 
97 +===== Numerical properties =====
126 126  
127 -Also very similar to JSON-Schema, additional type-specific keys can be used to set further requirements for the expected value. H
99 +(% style="text-align: justify;" %)
100 +(//**coming soon**//)
128 128  
102 +(% style="text-align: justify;" %)
103 +===== Object properties =====
129 129  
105 +(% style="text-align: justify;" %)
106 +(//**coming soon**//)
107 +
108 +(% style="text-align: justify;" %)
109 +===== Property arrays =====
110 +
111 +(% style="text-align: justify;" %)
112 +(//**coming soon**//)
113 +
114 +
130 130  === The openMINDS integration pipeline ===
131 131  
132 132  (//**coming soon**//)
Public

openMINDS