Changes for page Technical details

Last modified by lzehl on 2021/07/05 18:57
From version 68.2
edited by lzehl
on 2021/06/27 12:38
Change comment: There is no comment for this version
To version 64.1
edited by lzehl
on 2021/06/24 15:34
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -57,42 +57,42 @@
57 57  === The openMINDS vocabulary ===
58 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.
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.
61 61  
62 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:
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##**:
64 64  
65 65  {{code language="json"}}
66 66  {
67 - "OPENMINDS_SCHEMA_TYPE": {
68 - "description": "GENERAL_DESCRIPTION",
69 - "name": "DISPLAY_LABEL",
67 + ...,
68 + "https://openminds.ebrains.eu/core/Person": {
69 + "description": "Structured information on a person (alive or dead).",
70 + "name": "Person",
70 70   "translatableTo": [
71 - "REFERENCE_TO_RELATED_SCHEMA_OF_OTHER_INITIATIVE"
72 + "https://schema.org/Person"
72 72   ]
73 - }
74 + },
75 + ...
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, 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 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.
79 +... and a cutout of the **##properties.json##**:
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:
82 -
83 83  {{code language="json"}}
84 84  {
85 - "PROPERTY_NAME": {
86 - "description": "GENERAL_DESCRIPTION",
87 - "name": "DISPLAY_LABEL",
88 - "nameForReverseLink": "DISPLAY_LABEL_OF_REVERSED_LINK",
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",
89 89   "sameAs": [
90 - "REFERENCE_TO_MATCHING_SCHEMA-PROPERTY_OF_OTHER_INITIATIVE"
89 + "https://schema.org/givenName"
91 91   ],
92 92   "schemas": [
93 - "RELATIVE_PATH_TO_SCHEMA_USING_THIS_PROPERTY"
92 + "core/v3/actors/person.schema.tpl.json"
94 94   ]
95 - }
94 + },
95 + ...
96 96  }
97 97  {{/code}}
98 98  
... ... @@ -111,40 +111,30 @@
111 111  === The openMINDS schema template syntax ===
112 112  
113 113  (% style="text-align: justify;" %)
114 -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.
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##**.
115 115  
116 116  (% style="text-align: justify;" %)
117 -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.
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).
118 118  
119 119  (% style="text-align: justify;" %)
120 -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:
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.
121 121  
122 -{{code language="json"}}
123 -{
124 - "_type": "https://openminds.ebrains.eu/LABEL_OF_METADATA_MODEL/SCHEMA_NAME",
125 - "properties": {
126 - "PROPERTY_NAME": {
127 - "type": "DATA_TYPE",
128 - "_instruction": "METADATA_ENTRY_INSTRUCTION"
129 - },
130 - "required": [
131 - "PROPERTY_NAME"
132 - ]
133 -}
134 -{{/code}}
135 -
136 136  (% style="text-align: justify;" %)
137 -**##"_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.
123 +For the more inexperienced programmers, let's start by explaining first some general terms that will be later used in the openMINDS schema template syntax specification. More experienced programmers can of course skip these explanations and jump directly further down.
138 138  
139 -(% style="text-align: justify;" %)
140 -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.
125 +**What are strings, integers, floats or booleans?** Generally speaking strings, integers, floats or booleans are derived **data types**. A **string** is defined as a sequence of characters between quotes (e.g., ##"Is this a string? YES!"## or ##'thisIsAlsoAString'##). For a string, openMINDS accepts Unicode characters. An **integer** is a whole number, positive or negative, without decimals, of unlimited length (e.g., ##5##, ##-5## or ##1238921234##). A **float** represents a real number, written with a decimal point dividing the integer and fractional part, both of unlimited length (e.g., ##5.15##, ##-5.15## or ##1238921234.1345##). A **boolean** represents a logical proposition by means of the binary digits ##0## (##false##) and ##1## (##true##), especially in computing and electronics. How a boolean is written depends highly on the format or computational language.
141 141  
142 -(% style="text-align: justify;" %)
143 -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.
127 +**What is a list or array?** A **list** is a data structure that is a mutable ordered sequence of values (also called items). The values of a list are typically defined between square brackets (e.g., ##[value1, value2, value3]##). Note that the values within a list do not have to have the same data type. In contrast, an **array** is a data structure that is a mutable unordered sequence of values of the same data type. What data types are accepted for values in a list or in an array is highly depending on the format or computational language.
144 144  
145 -(% style="text-align: justify;" %)
146 -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"##**.
129 +**What is a key-value pair or an associative array?** A **key-value pair** (sometimes also called name-value pair, attribute-value pair, property-value pair, or field-value pair) is a basic data representation and standard language feature in computing languages, systems and applications. In most cases this concept is used to build an **associative array**, meaning an unordered list of unique keys with associated values typically defined within curly brackets (e.g., ##{key1: value1, key3: value3, key2:value2}##). What data types are accepted for keys and values highly depends on the format or computational language. Note that a value could also be a data structure, such as a list, an array or an associative array.
147 147  
131 +**What is a dictionary and what is JSON?**
132 +
133 +
134 +==== Specification of the openMINDS schema template syntax ====
135 +
136 +(coming soon)
137 +
148 148  === The openMINDS integration pipeline ===
149 149  
150 150  (//**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
Public

openMINDS