Changes for page Technical details

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

From 67.1 to 68.1 From 78.5 to 79.1

From version 68.1

edited by lzehl
on 2021/06/24 19:11

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To version 78.5

edited by lzehl
on 2021/07/05 10:21

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@@ -13,12 +13,24 @@
  === The openMINDS umbrella ===
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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.
++openMINDS is the overall umbrella for a set of integrated metadata models for describing neuroscience research products in graph databases. The correct integration of these metadata models as well as the provision of a central access point is handled by an integration pipeline. All metadata models are developed on separate GitHub repositories, in order to facilitate extensions and maintenance of existing, as well as development and integration of new openMINDS metadata models and schemas. The integration pipeline ensures that the central openMINDS GitHub repository ingests all these GitHub repositories as [[git-submodules>>https://git-scm.com/docs/git-submodule||rel="noopener noreferrer" target="_blank"]], integrates the respective metadata models and builds the openMINDS GitHub pages, as well as ZIP files containing the respective openMINDS schemas in the supported formats, such as the openMINDS syntax (cf. below), JSON-Schema, or HTML. In the following we will summarize the contents and requirements for the central openMINDS GitHub repository as well as all metadata model git-submodules. The openMINDS integration pipeline will be handled in a separate chapter (cf. below).
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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).
++Let us start with the [[central openMINDS GitHub repository>>https://github.com/HumanBrainProject/openMINDS||rel="noopener noreferrer" target="_blank"]] which has a **main branch**, a **documentation branch**, and **version branches** (naming convention: vX; e.g., v1). Official releases (naming convention: vX.Y; e.g., v1.0) are tagged and provided as release packages.
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++The **main branch** hosts the general README, the LICENSE document, the CONTRIBUTING document, and the general openMINDS logo. In addition, it maintains the openMINDS vocabulary (vocab; cf. below) which provides general definitions and references for schema types and properties used across all openMINDS metadata models and their versions, as well as the bash script that builds the content of the documentation and version branches.
++
++(% style="text-align: justify;" %)
++The **documentation** branch hosts the HTML files that build the [[openMINDS GitHub pages>>https://humanbrainproject.github.io/openMINDS/||rel="noopener noreferrer" target="_blank"]], as well as a ZIP file for each version branch and official release containing the respective openMINDS schemas in the currently supported formats, such as the openMINDS syntax (`.schema.tpl.json`; cf. below), JSON-Schema (`.schema.json`), or HTML (`.html`).
++
++(% style="text-align: justify;" %)
++The **version** branches host the respective openMINDS schemas of a major version by ingesting the corresponding metadata models as git-submodules. Note that these version branches can have official release tags. If a version branch has an official release tag, only backwards compatible changes can be merged on this branch. This can include corrections of typos in instructions, introduction of additional properties to schemas, loosening constraints on expected value numbers or formats, granting additional relations between schemas, and adding new schemas (if they do not require relational changes in existing schemas). Except for typo corrections, these changes are typically tagged as sub-releases for the respective major version (e.g., v1.1). If a version branch does not have an official release tag, yet, also non-backwards compatible changes can be merged on this branch. This can include renaming of existing properties, increasing constraints on expected value numbers or formats, removing relations between schemas and adding new schemas, if they cause relational changes in existing schemas. In case all version branches have official release tags, a new non-backwards compatible change would lead to the creation of a new version branch (with a respectively increased major version number).
++
++(% style="text-align: justify;" %)
++As mentioned already above, the setup of the central openMINDS GitHub repository is maintained by the openMINDS integration pipeline (cf. below). Note that the pipeline is configured in such a way, that each commit on one of the openMINDS submodules will trigger a new build of the central openMINDS repository ensuring that its content is always up-to-date.
++
++(% style="text-align: justify;" %)
  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:
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@@ -25,16 +25,23 @@
  **(1)** The openMINDS metadata model has to be located on a **public GitHub repository** and published under an **MIT license**.
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--**(2)** The GitHub repository should have at least one **version branch** (e.g., "v1").
++**(2)** The GitHub repository of such a metadata model should have at least one **version branch** (naming convention: vX, where X is a major version number).
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--**(3)** The version branch should have the following **main directory folders**: **##schemas##** (required), **##tests##** (recommended),  **##examples##** (recommended), and **##img##** (optional).
++**(3)** The version branch should have the following **folders** & **files**:
--(% style="text-align: justify;" %)
--**(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.
++* **##schemas/##** (required) - contains the schemas of that metadata model implemented in the reduced openMINDS syntax (cf. below). The sub-directory of the "schemas" folder can be further structured or flat.
++* **##tests/##** (recommended) - contains test-instances (JSON-LDs) for checking the constraints defined in the schemas of the metadata model. The sub-directory of the "tests" folder should follow the same structure as the "schemas" folder. The file names of the test-instances should state in lowerCamelCase first the name of the respectively tested schema and second, separated with an underscore, what schema constrain is tested (e.g., **##contactInformation_validEmail.jsonld##**). If a test-instance is expected to fail the schema validation the file name should receive the postfix **##"_nok"##** (e.g., **##contactInformation_invalidEmail_nok.jsonld##**).
++* **##examples/##** (recommended)
++* **##img/##** (optional) - contains typically the logo of the openMINDS submodule.
++* **##instances/##** (optional) - contains the controlled metadata instances (JSON-LDs) for selected schemas of the metadata model. The sub-directory of the "instances" folder should follow the same structure as the "schemas" folder.
++* **##version.txt##** (required)
++* **##README.md##** (required)
++* **##LICENSE.txt##** (required)
++
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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
++**(5)** The **##tests##** folder should for the schemas in a flat directory. The file names for these test-instances should follow the convention of
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  **##<<XXX>>-<<YYY>>.jsonld##**
@@ -57,66 +57,60 @@
  === The openMINDS vocabulary ===
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--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.
++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.
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--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##**:
++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:
  {{code language="json"}}
  {
--  ...,
--  "https://openminds.ebrains.eu/core/Person": {
--    "description": "Structured information on a person (alive or dead).",
--    "name": "Person",
++  "OPENMINDS_SCHEMA_TYPE": {
++    "description": "GENERAL_DESCRIPTION",
++    "name": "DISPLAY_LABEL",
      "translatableTo": [
--      "https://schema.org/Person"
++      "REFERENCE_TO_RELATED_SCHEMA_OF_OTHER_INITIATIVE"
      ]
--  },
--  ...
++  }
  }
  {{/code}}
--... and a cutout of the **##properties.json##**:
++(% style="text-align: justify;" %)
++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.
++(% style="text-align: justify;" %)
++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:
++
  {{code language="json"}}
  {
--  ...,
--  "givenName": {
--    "description": "Name given to a person, including all potential middle names, but excluding the family name.",
--    "name": "Given name",
--    "nameForReverseLink": "Is given name of",
++  "PROPERTY_NAME": {
++    "description": "GENERAL_DESCRIPTION",
++    "name": "DISPLAY_LABEL",
++    "nameForReverseLink": "DISPLAY_LABEL_OF_REVERSED_LINK",
      "sameAs": [
--      "https://schema.org/givenName"
++      "REFERENCE_TO_MATCHING_SCHEMA-PROPERTY_OF_OTHER_INITIATIVE"
      ],
      "schemas": [
--      "core/v3/actors/person.schema.tpl.json"
++      "RELATIVE_PATH_TO_OPENMINDS-SCHEMA_USING_THIS_PROPERTY"
      ]
--    },
--  ...
++  }
  }
  {{/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).
++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.
--(% style="text-align: justify;" %)
--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"##**).
++=== The openMINDS syntax ===
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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.
++All openMINDS metadata models are defined using a light-weighted schema syntax. Although this schema 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.
  (% style="text-align: justify;" %)
--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 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.
--=== 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.
++==== Basic openMINDS schema structure ====
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--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"}}
@@ -134,7 +134,7 @@
  {{/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.
++**##"_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.
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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.
@@ -143,8 +143,29 @@
  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.
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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"##**.
++==== Schemas extending a context-schema ====
++(% style="text-align: justify;" %)
++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.
++
++(% style="text-align: justify;" %)
++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:
++
++(% style="text-align: center;" %)
++**##"_extends": "RELATIVE_PATH_TO_OPENMINDS-CONTEXT-SCHEMA"##**
++
++(% style="text-align: justify;" %)
++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"]].
++
++(% style="text-align: justify;" %)
++==== Data type depending constraints ====
++
++(% style="text-align: justify;" %)
++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"##**.
++
++(% style="text-align: justify;" %)
++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.
++
  === The openMINDS integration pipeline ===
  (//**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