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 77.2
edited by lzehl
on 2021/06/27 15:22
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -57,10 +57,10 @@
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 +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 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 +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 64  
65 65  {{code language="json"}}
66 66  {
... ... @@ -75,10 +75,10 @@
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 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.
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.
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. 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:
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:
82 82  
83 83  {{code language="json"}}
84 84  {
... ... @@ -90,33 +90,27 @@
90 90   "REFERENCE_TO_MATCHING_SCHEMA-PROPERTY_OF_OTHER_INITIATIVE"
91 91   ],
92 92   "schemas": [
93 - "RELATIVE_PATH_TO_SCHEMA_USING_THIS_PROPERTY"
93 + "RELATIVE_PATH_TO_OPENMINDS-SCHEMA_USING_THIS_PROPERTY"
94 94   ]
95 - }
95 + }
96 96  }
97 97  {{/code}}
98 98  
99 99  (% style="text-align: justify;" %)
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).
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.
101 101  
102 -(% style="text-align: justify;" %)
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;" %)
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.
107 -
108 -(% style="text-align: justify;" %)
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.
110 -
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.
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.
115 115  
116 116  (% style="text-align: justify;" %)
117 117  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.
118 118  
119 119  (% style="text-align: justify;" %)
111 +==== Basic openMINDS schema structure ====
112 +
113 +(% style="text-align: justify;" %)
120 120  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:
121 121  
122 122  {{code language="json"}}
... ... @@ -134,7 +134,7 @@
134 134  {{/code}}
135 135  
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.
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.
138 138  
139 139  (% style="text-align: justify;" %)
140 140  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.
... ... @@ -143,8 +143,29 @@
143 143  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.
144 144  
145 145  (% 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"##**.
140 +==== Schemas extending a context-schema ====
147 147  
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.
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 +
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 +(% style="text-align: justify;" %)
161 +If the expected data **##"type"##** is a **##"string"##** the expected number of characters, the format or a regular expression pattern of the string can be further defined.
162 +
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