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Last modified by lzehl on 2021/10/13 13:11
From version 45.1
edited by lzehl
on 2021/05/02 14:27
Change comment: Renamed back-links.
To version 51.1
edited by lzehl
on 2021/10/13 13:11
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... ... @@ -44,7 +44,7 @@
44 44  where **##XXX##** and **##YYY##** should be replaced with the openMINDS sub-module (e.g., **##core##**) and corresponding schema-name (e.g., **##ContactInformation##**), respectively.
45 45  
46 46  (% style="text-align: justify;" %)
47 -In return, the JSON-LD property **##"@id"##** defines the particular metadata instance (node). For this reason, the **##"@id"##** also expects an entry (value) of type string with the format of an IRI. In particular when you plan to submit your metadata collection later to the EBRAINS Knowledge Graph, we recommend you use the following naming convention on your local machine for this identifier:
47 +In return, the JSON-LD property **##"@id"##** defines the particular metadata instance (i.e., graph database node). For this reason, the **##"@id"##** also expects an entry (value) of type string with the format of an IRI. In particular when you plan to submit your metadata collection later to the EBRAINS Knowledge Graph, we recommend you use the following naming convention on your local machine for this identifier:
48 48  
49 49  (% style="text-align: center;" %)
50 50  **##"@id": "http:~/~/localhost/YYY/ZZZ"##**
... ... @@ -71,17 +71,18 @@
71 71  {{/code}}
72 72  
73 73  (% style="text-align: justify;" %)
74 -Note that we do not use all properties defined for the schema (cf. the [[Person HTML>>https://humanbrainproject.github.io/openMINDS/core/schemas/v3/actors/person.html||rel="noopener noreferrer" target="_blank"]]), but that we only used the required property **##"givenName"##** and two optional properties **##"familyName"##** and **##"ContactInformation"##**. Please also note, that a person is allowed to link to multiple contact information instances, hence it expects a list of dictionaries, instead of a single dictionary (which would be valid if only a single link is expected).
74 +Note that we do not use all properties defined for the schema (cf. the [[Person HTML>>https://humanbrainproject.github.io/openMINDS/core/schemas/v3/actors/person.html||rel="noopener noreferrer" target="_blank"]]), but that we only used the required property **##"givenName"##** and two optional properties **##"familyName"##** and **##"contactInformation"##**. This means, optional properties, if not known, do not have to be defined in the respective JSON-LD, but they could also be listed with a **##null##** value. Please note in addition, that values for properties which expect an array should always be provided as such (cf. property **##"contactInformation"##**), even if only one item is defined.
75 75  
76 76  (% style="text-align: justify;" %)
77 77  You learned now how a valid JSON-LD for an openMINDS metadata instance looks like and how linkages between openMINDS instances are defined. In the following sections you will learn about the different tools that support you to create your own openMINDS JSON-LD metadata collection.
78 78  
79 -=== The openMINDS Python API ===
79 +=== openMINDS Python ===
80 80  
81 -One possible way to write openMINDS conform JSON-LDs is to use the openMINDS Python API which will help you to interact with the EBRAINS openMINDS metadata models and schemas. It consists of two sub-modules: 
81 +(% style="text-align: justify;" %)
82 +openMINDS Python is a small library that allows you the dynamic usage of openMINDS metadata models and schemas in your Python application for generating your own collection of openMINDS conform metadata representations (instances) as JSON-LDs.
82 82  
83 -The **openMINDS.generator** (coming soon) facilitates the translation of the openMINDS schema template syntax to other established formats, such as HTML and JSON-Schema (cf. also [[Technical details>>doc:Collabs.openminds.Documentation.Implementation details.WebHome]]).
84 -\\The **openMINDS.compiler** allows you the dynamic usage of openMINDS metadata models and schemas in your Python application for generating your own collection of openMINDS conform metadata representations (instances) as JSON-LDs (as described above). Please note that the openMINDS.compiler only helps you to generate correctly formatted JSON-LD metadata instances - the preparation on how you want to describe your research product with openMINDS is still up to you. If you need support in designing your own openMINDS metadata collection, check out the [[Tutorials>>openminds@ebrains.eu||target="_blank"]] which might give you hints on how to tackle your individual case or, of course, get in touch with us via [[openminds@ebrains.eu>>mailto:openminds@ebrains.eu]].
84 +(% style="text-align: justify;" %)
85 +Please note that openMINDS Python only helps you to generate correctly formatted JSON-LD metadata instances - the preparation on how you want to describe your research product with openMINDS is still up to you. If you need support in designing your own openMINDS metadata collection, check out the [[Tutorials>>doc:Collabs.openminds.Tutorials.WebHome||target="_blank"]] which might give you hints on how to tackle your individual case or, of course, get in touch with us directly via our support-email ([[openminds@ebrains.eu>>mailto:openminds@ebrains.eu]]).
85 85  
86 86  ===== Installation =====
87 87  
... ... @@ -88,33 +88,40 @@
88 88  The official versions are available at the [[Python Package Index>>https://pypi.org/project/openMINDS/]] and can be installed using `pip install` in your console:
89 89  
90 90  {{code language="console"}}
91 -pip install openminds
92 +pip install openMINDS
92 92  {{/code}}
93 93  
94 94  The latest development version is available on the [[openMINDS generator GitHub>>https://github.com/HumanBrainProject/openMINDS_generator]].
95 95  
96 -===== openMINDS.compiler documentation =====
97 +===== Usage =====
97 97  
98 -As stated above, the openMINDS.compiler allows you the dynamic usage of openMINDS metadata models and schemas in your Python application for generating your own collection of openMINDS conform metadata representations (instances) as JSON-LDs. Here a small example:
99 +As stated above, the openMINDS Python allows you the dynamic usage of openMINDS metadata models and schemas in your Python application for generating your own collection of openMINDS conform metadata representations (instances) as JSON-LDs. Here a small example:
99 99  
100 100  {{code language="python"}}
101 -import openMINDS.compiler
102 +import openMINDS
103 +import openMINDS.version_manager
102 102  
105 +# Initialise the local copy of openMINDS
106 +openMINDS.version_manager.init()
107 +
108 +# Select which version of openMINDS to use
109 +openMINDS.version_manager.version_selection('v2.0.0')
110 +
103 103  # initiate the helper class for the dynamic usage of a specific openMINDS version
104 -helper = openMINDS.compiler.Helper(version="v1.0")
112 +helper = openMINDS.Helper()
105 105  
106 106  # initiate the collection into which you will store all metadata instances
107 -mycollection = helper.get_collection()
115 +mycollection = helper.create_collection()
108 108  
109 109  # create a metadata instance for (e.g.) the openMINDS Person schema
110 -lyuba = mycollection.add_core_person(givenName="Lyuba")
118 +person_open = mycollection.add_core_person(givenName="open")
111 111  
112 112  # add more metadata to a created instance
113 -mycollection.get(lyuba).familyName = "Zehl"
121 +mycollection.get(person_open).familyName = "MINDS"
114 114  
115 115  # add connections to other metadata instances
116 -email_lyuba = mycollection.add_core_contactInformation(email="openminds@ebrains.eu")
117 -mycollection.get(lyuba).contactInformation = email_lyuba
124 +email_openminds = mycollection.add_core_contactInformation(email="openminds@ebrains.eu")
125 +mycollection.get(person_open).contactInformation = email_openminds
118 118  
119 119  # save your collection
120 120  mycollection.save("./myFirstOpenMINDSMetadataCollection/")
... ... @@ -126,13 +126,12 @@
126 126  Interactively you can also get an overview of the requirement of a schema and all its properties by using the **##help_##** function of the openMINDS.compiler. Here an example:
127 127  
128 128  {{code language="python"}}
129 -mycollection.help_core_person()
137 +# Getting help for properties
138 +mycollection.help_core_actors_person()
130 130  {{/code}}
131 131  
132 -
141 +=== openMINDS spreadsheet templates ===
133 133  
134 -=== The openMINDS spreadsheet templates ===
135 -
136 136  (% style="text-align: justify;" %)
137 137  ((% style="color:#7f8c8d" %)**//coming soon//**(%%)) For users with no programming experience, it is possible to provide at least openMINDS conform metadata by using the openMINDS spreadsheet templates.
138 138  
... ... @@ -139,4 +139,19 @@
139 139  === The EBRAINS Knowledge Graph Editor ===
140 140  
141 141  (% style="text-align: justify;" %)
142 -For curators of the EBRAINS Data & Knowledge service, it is possible to register openMINDS conform metadata into the EBRAINS Knowledge Graph database by using the EBRAINS Knowledge Graph Editor.
149 +For curators of the EBRAINS Data & Knowledge service and users with an EBRAINS account, it is possible to register openMINDS conform metadata into the EBRAINS Knowledge Graph database by using the EBRAINS Knowledge Graph Editor. This editor not only allows the manual registration of openMINDS conform metadata, but also has many project management related features establishing a controlled and secured environment for curating metadata of submitted research products that should be published via the EBRAINS Knowledge Graph database (including the assignment of an EBRAINS DOI if requested).
150 +
151 +(% style="text-align: justify;" %)
152 +To guarantee the latter, the EBRAINS Data & Knowledge service has its own EBRAINS Knowledge Graph Editor environment which reserves the rights of publicly releasing metadata and assigned EBRAINS DOIs via the EBRAINS Knowledge Graph for the members of the curation team. Nonetheless, users with an EBRAINS account can receive access to a separate EBRAINS Knowledge Graph Editor environment through a private Collab in the EBRAINS Collaboratory. All members of such a private Collab can then manually register openMINDS conform metadata through the EBRAINS Knowledge Graph Editor to a restricted space of the Knowledge Graph database that is not accessible to any user outside of the respective Collab. In order to publicly release these privately registered metadata, an official curation request has to be made through the EBRAINS Data & Knowledge service.
153 +
154 +(% style="text-align: justify;" %)
155 +Independent of the different user environments, the EBRAINS Knowledge Graph Editor has the following features to facilitate the manual registration of openMINDS conform metadata:
156 +
157 +(% style="text-align: justify;" %)
158 +(1) Input masks for all openMINDS metadata schemas. New metadata instances can be easily created through an intuitive input mask that validates the user entries already against the respective openMINDS schema.
159 +
160 +(% style="text-align: justify;" %)
161 +(2) Facilitation of correct linkages between metadata instances. In accordance with the openMINDS metadata models, registered metadata instances can be linked with each other. Establishing these linkages is facilitated by jumping via dedicated properties to new input masks of matching schema types.
162 +
163 +(% style="text-align: justify;" %)
164 +(3) Drop down menus for existing metadata instances. Establishing linkages between instances in accordance with the openMINDS metadata models is further facilitated by providing drop down menus for the dedicated properties for selecting existing instances of matching schema types.
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