Summary

• Page properties (1 modified, 0 added, 0 removed)

Details

Page properties

Content

...	...	@@ -13,44 +13,47 @@
13	13	=== The openMINDS umbrella ===
14	14
15	15	(% style="text-align: justify;" %)
16		-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).
	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	18	(% style="text-align: justify;" %)
19		-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.
	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 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).
20	20
21	21	(% style="text-align: justify;" %)
22		-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.
	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	23
24	24	(% style="text-align: justify;" %)
25		-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`).
	25	+**(1)** The openMINDS metadata model has to be located on a **public GitHub repository** and published under an **MIT license**.
26	26
27	27	(% style="text-align: justify;" %)
28		-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).
	28	+**(2)** The GitHub repository should have at least one **version branch** (e.g., "v1").
29	29
30	30	(% style="text-align: justify;" %)
31		-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.
	31	+**(3)** The version branch should have the following **main directory folders**: **##schemas##** (required), **##tests##** (recommended),  **##examples##** (recommended), and **##img##** (optional).
32	32
33	33	(% style="text-align: justify;" %)
34		-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:
	34	+**(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.
35	35
36	36	(% style="text-align: justify;" %)
37		-**(1)** The openMINDS metadata model has to be located on a **public GitHub repository** and published under an **MIT license**.
	37	+**(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
38	38
	39	+(% style="text-align: center;" %)
	40	+**##<<XXX>>-<<YYY>>.jsonld##**
	41	+
39	39	(% style="text-align: justify;" %)
40		-**(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).
	43	+for files that should pass the tests, and
41	41
	45	+(% style="text-align: center;" %)
	46	+**##<<XXX>>-<<YYY>>-nok.jsonld##**
	47	+
42	42	(% style="text-align: justify;" %)
43		-**(3)** The version branch should have the following **folders** & **files**:
	49	+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##**).
44	44
45		-* **##schemas/##** (required) - contains the schemas of the respective metadata model implemented in the reduced openMINDS syntax (cf. below). The sub-directory of the "schemas" folder can be further structured or flat.
46		-* **##tests/##** (recommended) - contains test-instances (JSON-LDs) for checking the constraints defined in the schemas of the respective metadata model. The sub-directory of the "tests" folder should follow the same structure as the "schemas" folder with an additional sub-directory for each schema. The file names of the test-instances should be written in lowerCamelCase and state 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##**).
47		-* **##examples/##** (recommended) - contains examples for valid instance collections for the respective 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.
48		-* **##img/##** (optional) - contains typically the logo of the openMINDS submodule.
49		-* **##instances/##** (optional) - contains the controlled metadata instances (JSON-LDs) for selected schemas of the respective metadata model. The sub-directory of the "instances" folder should follow the same structure as the "schemas" folder with an additional sub-directory for each schema. The file names of the controlled instances should be written in lowerCamelCase and state the simple, human-readable identifier of the instance (e.g., **##homoSapiens.jsonld##** for the controlledTerms schema **##Species##**).
50		-* **##version.txt##** (required) - states the identifier of the version branch (e.g., **##v1##**) of the respective metadata model.
51		-* **##README.md##** (required) - contains a short content description of the respective metadata model.
52		-* **##LICENSE.txt##** (required) - states the license for the respective metadata model (has to be MIT).
	51	+(% style="text-align: justify;" %)
	52	+**(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.
53	53
	54	+(% style="text-align: justify;" %)
	55	+**(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.
	56	+
54	54	=== The openMINDS vocabulary ===
55	55
56	56	(% style="text-align: justify;" %)
...	...	@@ -89,7 +89,7 @@
89	89	"schemas": [
90	90	"RELATIVE_PATH_TO_OPENMINDS-SCHEMA_USING_THIS_PROPERTY"
91	91	]
92		- }
	95	+ }
93	93	}
94	94	{{/code}}
95	95
...	...	@@ -96,18 +96,15 @@
96	96	(% style="text-align: justify;" %)
97	97	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.
98	98
99		-=== The openMINDS syntax ===
	102	+=== The openMINDS schema template syntax ===
100	100
101	101	(% style="text-align: justify;" %)
102		-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.
	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.
103	103
104	104	(% style="text-align: justify;" %)
105	105	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.
106	106
107	107	(% style="text-align: justify;" %)
108		-==== Basic openMINDS schema structure ====
109		-
110		-(% style="text-align: justify;" %)
111	111	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:
112	112
113	113	{{code language="json"}}
...	...	@@ -134,29 +134,14 @@
134	134	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.
135	135
136	136	(% style="text-align: justify;" %)
137		-==== Schemas extending a context-schema ====
	137	+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. 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. 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:
138	138
139		-(% style="text-align: justify;" %)
140		-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.
141		-
142		-(% style="text-align: justify;" %)
143		-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:
144		-
145	145	(% style="text-align: center;" %)
146	146	**##"_extends": "RELATIVE_PATH_TO_OPENMINDS-CONTEXT-SCHEMA"##**
147	147
148	148	(% style="text-align: justify;" %)
149		-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"]].
150		-
151		-(% style="text-align: justify;" %)
152		-==== Data type depending constraints ====
153		-
154		-(% style="text-align: justify;" %)
155	155	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"##**.
156	156
157		-(% style="text-align: justify;" %)
158		-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.
159		-
160	160	=== The openMINDS integration pipeline ===
161	161
162	162	(//**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