Changes for page Technical details

Last modified by lzehl on 2021/07/05 18:57

From 40.1 to 39.1 From 69.1 to 68.2

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edited by lzehl
on 2021/06/27 12:38

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--Collabs.openminds.Documentation.WebHome
++Collabs.openminds.openMINDS core.WebHome

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  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.
  )))
--=== The openMINDS umbrella ===
++=== Overview of the openMINDS layout ===
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  In summary, openMINDS is the overall umbrella for a set of distributed GitHub repositories, each defining a particular metadata model for neuroscience research products.
++=== The openMINDS schema template syntax ===
++
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--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).
++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##**.
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--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:
++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).
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--**(1)** The openMINDS metadata model has to be located on a **public GitHub repository** and published under an **MIT license**.
++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.
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--**(2)** The GitHub repository should have at least one **version branch** (e.g., "v1").
++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.
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--**(3)** The version branch should have the following **main directory folders**: **##schemas##** (required), **##tests##** (recommended),  **##examples##** (recommended), and **##img##** (optional).
++===== Target & concept templates =====
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--**(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.
++Same as in JSON-Schema, all openMINDS schema templates define the expected name (written in **##lowerCamelCase##**) and value of the metadata, typically called property, under the key **##properties##** as nested dictionaries. Furthermore, the names of obligatory metadata can be listed under the key **##required##**. Here a generalized example:
++{{code language="json"}}
++{
++ "properties": {
++   "propertyNameA": {},
++   "propertyNameB": {},
++   "propertyNameC": {}
++ },
++ "required": [
++   "propertyNameA",
++   "propertyNameC"
++ ]
++}
++{{/code}}
++
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--**(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
++In addition, an openMINDS schema //has to have// a key **##"_type"##** to be recognized as **target template**. In other words, the **##"_type"##** is used to define the openMINDS namespace of a corresponding schema using a particular naming convention. Here again a generalized example:
--(% style="text-align: center;" %)
--**##<<XXX>>-<<YYY>>.jsonld##**
++{{code language="json"}}
++{
++ "_type": "https:~/~/openminds.ebrains.eu/<<schema-model>>/<<schema-name>>",
++ "properties": {}
++}
++{{/code}}
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--for files that should pass the tests, and
++Note that **##<<schema-model>>##** has to be replaced with the label of the openMINDS metadata model to which the corresponding schema belongs to, and **##<<schema-name>>##** has to be replaced with the corresponding name of the schema (written in **##CamelCase##**).
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--**##<<XXX>>-<<YYY>>-nok.jsonld##**
++(% style="text-align: justify;" %)
++If an openMINDS schema template //does not// define a key **##"_type"##** (as in the first example above), it is interpreted as a **concept template** which //has to be// extended to a target template.
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--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##**).
++Concept templates are and should be used when multiple target templates have the same subset of properties, because they facilitate the long-term maintenance of those shared properties: Instead of defining the same properties repeatedly within multiple target templates, the common subset can be defined within a single concept template and passed on to all extending target templates.
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--**(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.
++To define that a target template is the extension of a concept template, the target template can state under **##"_extends"##** the relative path to the concept template. For example, the openMINDS core target template **##Dataset##** extends the core concept template **##researchProduct##** as indicated here:
++{{code language="json"}}
++{
++  "_type": "https:~/~/openminds.ebrains.eu/core/Dataset",
++  "_extends": "products/researchProduct.schema.tpl.json"
++}
++{{/code}}
++
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--**(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.
++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:
--=== The openMINDS vocabulary ===
++1. A concept template has to define some properties which will be inherited by all extending target templates.
++1. If a concept template additionally states that some of these properties are required, all extending target templates will require the same properties.
++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.
++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.
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--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.
++How to define the expected value of a property will be explained for the different property types in the following sections.
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--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:
++===== Properties expecting a string value =====
++(% style="text-align: justify;" %)
++Properties that expect values of type string can be defined in large parts in the same way as in JSON-Schema. Without any further formatting requirements the definition of such a property looks like this:
++
  {{code language="json"}}
  {
--  "OPENMINDS_SCHEMA_TYPE": {
--    "description": "GENERAL_DESCRIPTION",
--    "name": "DISPLAY_LABEL",
--    "translatableTo": [
--      "REFERENCE_TO_RELATED_SCHEMA_OF_OTHER_INITIATIVE"
--    ]
++  "properties": {
++    "freeStringProperty": {
++      "type": "string"
++    }
    }
  }
  {{/code}}
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--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.
++In accordance with JSON-Schema, it is possible, though, to further define a selected list of built-in formats that are accepted for the expected string. Supported are all [[built-in formats of JSON-Schema Draft 7.0>>https://json-schema.org/understanding-json-schema/reference/string.html#built-in-formats||rel="noopener noreferrer" target="_blank"]]. Assuming that my string property only accepts a value of format "email", the openMINDS syntax is the following:
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--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:
--
  {{code language="json"}}
  {
--  "PROPERTY_NAME": {
--    "description": "GENERAL_DESCRIPTION",
--    "name": "DISPLAY_LABEL",
--    "nameForReverseLink": "DISPLAY_LABEL_OF_REVERSED_LINK",
--    "sameAs": [
--      "REFERENCE_TO_MATCHING_SCHEMA-PROPERTY_OF_OTHER_INITIATIVE"
--    ],
--    "schemas": [
--      "RELATIVE_PATH_TO_SCHEMA_USING_THIS_PROPERTY"
--    ]
++  "properties": {
++    "emailProperty": {
++      "type": "string",
++      "_formats": [
++        "email"
++      ]
      }
++  }
  }
  {{/code}}
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--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).
++Also like JSON-Schema, it is possible to define a customized regular expression pattern for the expected string, supporting the [[ECMA-262  regex-dialect>>https://www.ecma-international.org/publications-and-standards/standards/ecma-262/]]. Assuming that my string property only accepts a Gregorian calendar year, the corresponding openMINDS syntax look like this:
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--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"##**).
--
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--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.
--
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--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.
--
--=== The openMINDS schema template syntax ===
--
--(% style="text-align: justify;" %)
--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.
--
--(% style="text-align: justify;" %)
--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.
--
--(% style="text-align: justify;" %)
--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:
--
  {{code language="json"}}
  {
--  "_type": "https://openminds.ebrains.eu/LABEL_OF_METADATA_MODEL/SCHEMA_NAME",
    "properties": {
--    "PROPERTY_NAME": {
--      "type": "DATA_TYPE",
--      "_instruction": "METADATA_ENTRY_INSTRUCTION"
--  },
--  "required": [
--    "PROPERTY_NAME"
--  ]
++    "yearProperty": {
++      "type": "string",
++      "pattern": "([0-9]{4})"
++    }
++  }
  }
  {{/code}}
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--**##"_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.
++===== Properties expecting a numerical value =====
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--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.
++(//**coming soon**//)
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--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.
++===== Properties expecting another object =====
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--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"##**.
++(//**coming soon**//)
--=== The openMINDS integration pipeline ===
++(% style="text-align: justify;" %)
++===== Properties expecting an array of values =====
--(//**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
++(% style="text-align: justify;" %)
++(//**coming soon**//)
--{{putFootnotes/}}
++
++=== The openMINDS integration pipeline ===
++
++(//**coming soon**//)