Changes for page Working with HDC Datasets

Last modified by Dennis Segebarth on 2024/10/02 18:25
From version 1.7
edited by Susan Evans
on 2023/07/11 14:53
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edited by Dennis Segebarth
on 2024/08/16 10:01
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1 -XWiki.sgevans
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24 24  
25 25  Datasets are created from the Main Menu. To create a new dataset,
26 26  
27 -[[image:Main Menu Datasets NonAdmin v2.26 2023-04-12.png||height="5%" width="50%"]]
27 +[[image:1723802288344-928.png||height="92" width="859"]]
28 28  
29 +
29 29  1. Click **Datasets** from the Main Menu to open the Datasets landing page. Datasets you previously created are displayed in this page in the “My Datasets” tab, and you can continue working on them as described in the following sections of this article, e.g. see //Adding Files to a Dataset//.
30 30  1. Click **+ Create New** in the upper right-hand corner. You will be prompted to provide some essential metadata information about your dataset in two sections (“Define Dataset” and “Description”, see the following list for more details):
31 31  Note: this information is stored in the Dataset’s Essential schema and is visible in the Dataset Home tab, and can be changed later (with the exception of Dataset Code) - see //Reviewing and Editing Metadata Annotations//. Mandatory fields are denoted by a red asterisk ( * ).
32 32  11. Define Dataset
33 33  11*. //Title//*: A short title for the Dataset (max. 100 characters). This entry can be changed later.
34 -11*. //Dataset Code//*: A distinct, immutable code defined by you to uniquely identify your Dataset. This entry cannot be changed later.
35 -11*. //Authors//*: One or more authors. Hit Enter after each entry. These entries can be changed later.
36 -11*. //Dataset Type//: Use the default GENERAL or, if your Dataset uses the Brain Imaging Data Structure (BIDS) standard and you wish to use the built-in BIDS validation tool, select BIDS from the dropdown menu. This entry can be changed later.
35 +11*. //Dataset Code//*: A distinct, immutable code defined by you to uniquely identify your Dataset. This entry __cannot__ be changed later.
36 +11*. //Authors//*: One or more authors. Hit **Enter** after each entry. These entries can be changed later.
37 +11*. //Dataset Type//: Use the default **GENERAL** or, if your Dataset uses the Brain Imaging Data Structure (BIDS) standard and you wish to use the built-in BIDS validation tool, select **BIDS** from the dropdown menu. This entry can be changed later.
37 37  11. Description:
38 38  11*. //Dataset Description//*: A longer description of the dataset. Please remember to comply with the Platform Terms of Use, Privacy Policy, and do not enter sensitive personal information in this field.
39 -11*. //Modality: Based on the Human Brain Project OpenMINDS standard.
40 -11*. Collection Method: Based on the Human Brain Project OpenMINDS standard.
41 -11*. License: License under which you want to share your Dataset (e.g., Creative Commons). A License is not required, yet highly recommended if you want to share your Dataset in compliance with the FAIR criteria.
42 -11*. Tags: Custom keywords you create for your Dataset. Tags are displayed on the Datasets landing page and information bar.
40 +11*. //Modality//: Based on the Human Brain Project [[OpenMINDS>>http://github.com/HumanBrainProject/openMINDS]] standard.
41 +11*. //Collection Method//: Based on the Human Brain Project [[OpenMINDS>>http://github.com/HumanBrainProject/openMINDS]] standard.
42 +11*. //License//: License under which you want to share your Dataset (e.g., Creative Commons). A License is not required, yet highly recommended if you want to share your Dataset in compliance with the FAIR criteria.
43 +11*. //Tags//: Custom keywords you create for your Dataset. Tags are displayed on the Datasets landing page and information bar.
43 43  1. When you provided all required information, click Create in the upper right-hand corner to complete the Dataset creation.
44 44  
45 45  Your Dataset is now saved and is visible in the Datasets landing page under My Dataset. Next, you can go to a Project and begin copying files into the Dataset, as described below in the section //Adding Files to a Dataset.//
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51 51  
52 52  To add files to a Dataset,
53 53  
54 -[[image:Datasets Add to Datasets v2.1.5 2023-01-24.png||height="11%" width="50%"]]
55 +[[image:1723802315115-691.png||height="191" width="870"]]
55 55  
56 56  1. Navigate your Project’s File Explorer and click **Core**.
57 57  1. Select one or more files and/or folders by clicking the checkbox beside each one, then click **Add to Datasets** in the File Explorer menu.
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63 63  
64 64  = Organizing and Validating Datasets =
65 65  
66 -After copying Project files into a Dataset, you can perform a variety of tasks including moving, previewing, renaming or deleting files and folders, and validating the file structure against a supported external specification (currently, the [[Brain Imaging Data Structure (BIDS)>>url:https://bids.neuroimaging.io/specification.html]] standard is supported). You can also add metadata (see //Annotating Datasets with Metadata//).
67 +After copying Project files into a Dataset, you can perform a variety of tasks including moving, previewing, renaming or deleting files and folders, and validating the file structure against a supported external specification (currently, the [[Brain Imaging Data Structure (BIDS)>>url:https://bids.neuroimaging.io/specification.html]] standard is supported). You can also add metadata (see //Annotating Datasets with Metadata//) and share these with members of your Project by first creating a Space in the [[EBRAINS Knowledge Graph>>url:https://docs.kg.ebrains.eu/]], and then uploading the metadata to it (see //Interacting with the EBRAINS Knowledge Graph//).
67 67  
68 68  == Organizing Datasets ==
69 69  
70 70  Use the **Explorer** tab to organize and validate your Dataset.
71 71  
72 -[[image:Datasets Explorer v2.1.5 2023-01-24.png||height="10%" width="50%"]]
73 +[[image:1723802327251-439.png||height="182" width="897"]]
73 73  
74 74  1. Open the Dataset from the Datasets landing page, then select the **Explorer **tab.
75 75  1. Use **+ New Folder** or **Move to **to rearrange files and/or folders.
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88 88  
89 89  === BIDS Validation ===
90 90  
91 -[[image:BIDS_Logo.png||height="9%" width="20%"]]
92 +[[image:1723802339509-521.png||height="83" width="192"]]
92 92  
93 93  The **Validate BIDS** tool allows you to check your Dataset for conformation with the [[Brain Imaging Data Structure (BIDS)>>url:https://bids.neuroimaging.io/specification.html]] standard. The tool uses the open-source [[bids-validator 1.8.4 Python Package>>url:https://pypi.org/project/bids-validator/#quickstart]].
94 94  
95 95  Before running the Validate BIDS tool, ensure that the Dataset Type is set to BIDS (defined at Dataset creation or modified in the **Metadata **tab under Schemas > Essential).
96 96  
97 -[[image:Datasets Validate BIDS v2.1.5 2023-01-24.png||height="13%" width="50%"]]
98 +[[image:1723802351811-730.png||height="230" width="878"]]
98 98  
99 99  1. Open the Dataset from the Datasets landing page and select the **Explorer **tab.
100 100  1. Click **Validate BIDS**. If the Validate BIDS button isn’t visible, make sure your Dataset Type is set to BIDS (see above).
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124 124  
125 125  Use the **Metadata** tab to annotate your Dataset.
126 126  
127 -[[image:Datasets Metadata v2.1.5 2023-01-24.png||height="10%" width="50%"]]
128 +[[image:1723802365719-520.png||height="176" width="876"]]
128 128  
129 129  These steps describe how to annotate your dataset using the Default Schema. If you have created a Custom Schema (see the section titled //Creating a Custom Schema// in this article), you can follow the same steps described here, selecting your Custom Schema name instead of Default Schema in Step 2.
130 130  
131 131  1. Open the Dataset from the Datasets landing page and select the **Metadata **tab.
132 132  1. Under **Existing Schema**, select **Default Schemas**. The schemas that have already been completed in part or full are listed in the left panel, and their details are displayed in the right panel. This includes the Essential schema template with the information you entered at the time the Dataset was created.
133 -1. In the **Schemas **section on the right panel, click the **Select schema to complete **dropdown menu and select one of the Default schema templates or a Custom Schema created by you (see the section //Creating a Custom Schema //in this article).
134 +1. (((
135 +In the **Schemas **section on the right panel, click the **Select schema to complete **dropdown menu and select one of the Default schema templates or a Custom Schema created by you (see the section //Creating a Custom Schema //in this article).
134 134  
135 -[[image:Datasets Metadata Default Schema v2.1.5 2023-01-25.png||height="38%" width="50%"]]
137 +[[image:1723802376639-303.png||height="246" width="326"]]
136 136  
137 -1. (((
138 138  Default schema categories include the following:
139 139  
140 140  * //Contributors//: Information about the persons or organizations who contributed to the Dataset.
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156 156  
157 157  1. Navigate to **Existing Schema**// //(left panel of the Metadata tab) and select the **Default Schemas** category.
158 158  1. Click the schema name, then click the eye icon to open the Schemas view (right side). The existing entries are displayed in the **Schemas **panel at the right side.
159 -1. (((
160 -To edit the entries, click **Edit** and make the changes, and.
160 +1. To edit the entries, click **Edit** and make the changes, and
161 +1*. **X Reset** to return all entries to their original values.
162 +1*. **Cancel **to exit without saving changes.
163 +1*. **Update** to save the changes and return to the schema view.
161 161  
162 -1. **X Reset** to return all entries to their original values.
163 -1. **Cancel **to exit without saving changes.
164 -1. **Update** to save the changes and return to the schema view.
165 -)))
166 -
167 167  Any new changes are reflected in the Schemas view.
168 168  
169 169  == Creating a Custom Schema template ==
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172 172  
173 173  To create a Custom Schema,
174 174  
175 -[[image:Datasets Metadata Create Custom Schema v2.1.5 2023-01-25.png||height="24%" width="50%"]]
173 +[[image:1723802393964-978.png||height="237" width="485"]]
176 176  
177 177  1. Open the Dataset from the Datasets landing page and select the **Metadata **tab. Under **Existing Schema** (left panel), select **Default Schemas**.
178 178  1. In the **Schemas **panel (right side), click the **Select schema to complete **dropdown menu and select **+ Create Custom Schema** to open the Custom Schema Template creation window.
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201 201  
202 202  To manage a Custom Schema template that contains saved annotations,
203 203  
204 -[[image:Datasets Metadata Manage Custom Schema Template v2.1.5 2023-01-25.png||height="17%" width="50%"]]
202 +[[image:1723802410617-147.png||height="163" width="481"]]
205 205  
206 206  1. Navigate to **Existing Schema**// //(left panel of the **Metadata **tab) and select the **Default Schema** category.
207 207  1. Click the Custom schema name, then click the **eye icon** to open the Schemas view (right side). The existing entries are displayed.
208 208  1. Click **Manage Template**.
209 -1. (((
210 -Make your desired edits. The following changes are possible:
211 -
212 -1. Add new fields
213 -1. Delete existing fields
214 -1. Change an existing field from required to optional
215 -)))
207 +1. Make your desired edits. The following changes are possible:
208 +1*. Add new fields
209 +1*. Delete existing fields
210 +1*. Change an existing field from required to optional
216 216  1. Give the updated Schema template a new name, e.g., {name} version 2.
217 217  1. Click **+ Create New Template**.
218 218  
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220 220  
221 221  == Annotating with OpenMINDS ==
222 222  
223 -[[image:openMINDS_logo.png||height="10%" width="20%"]]
218 +[[image:1723802431881-142.png||height="111" width="222"]]
224 224  
225 225  The **open** **M**etadata **I**nitiative for **N**euroscience **D**ata **S**tructures ([[openMINDS>>url:https://github.com/HumanBrainProject/openMINDS]])// //is an open-source, community-driven research infrastructure initiative powered by EBRAINS and the Human Brain Project. The openMINDS schema gathers a set of metadata models that can be used for describing heterogeneous neuroscience data. The data can originate from human, animal or simulated studies, computational models, and software tools, as well as metadata or data models.
226 226  
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228 228  
229 229  Community tools are offered to help generate openMINDS JSON schemas, including a [[wizard>>url:https://wizard.kg-ppd.ebrains.eu/]] and a [[python package>>url:https://pypi.org/project/openMINDS/]]. For information or support, please contact the [[openMINDS team>>url:https://github.com/HumanBrainProject/openMINDS]].
230 230  
231 -[[image:Datasets Metadata openMINDS Schemas v2.1.5 2023-01-25.png||height="18%" width="50%"]]
226 +[[image:1723802444445-662.png||height="320" width="864"]]
232 232  
233 233  To upload an openMINDS JSON schema file,
234 234  
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249 249  
250 250  To view Activity, open the Dataset from the Datasets landing page and select the **Activity **tab. Use the date filters to narrow the range of activities displayed.
251 251  
252 -[[image:Datasets Activity v2.1.5 2023-01-24.png||height="10%" width="50%"]]
247 +[[image:1723802458591-860.png||height="174" width="863"]]
253 253  
254 254  
255 255  == Anytime Dataset Download ==
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264 264  
265 265  To release a Dataset version,
266 266  
267 -[[image:Datasets Release new version v2.1.5 2023-01-26.png||height="10%" width="50%"]]
262 +[[image:1723802471096-883.png||height="169" width="864"]]
268 268  
269 269  
270 270  1. Open the Dataset from the **Datasets **landing page and ensure you have made all the desired updates to the files, folder structure and metadata.
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278 278  
279 279  To view all released Dataset versions, click **Versions **in the Dataset information bar located next to the Dataset title. This opens the **Versions **sidebar where you can browse and download the Versions you have created.
280 280  
281 -[[image:Datasets Versions v2.1.5 2023-01-26.png||height="24%" width="50%"]]
276 +[[image:1723802481440-617.png||height="234" width="488"]]
282 282  
283 283  ----
284 284  
285 -Copyright © 2023 [[Indoc Research>>url:https://www.indocresearch.org/]].
280 +Copyright © 2023-2024 [[Indoc Systems>>url:https://www.indocsystems.com]].
286 286  
287 -HealthDataCloud is powered by Pilot technology, a product of [[Indoc Research>>url:https://www.indocresearch.org/]].
282 +HealthDataCloud is powered by Pilot technology, a product of [[Indoc Systems>>url:https://www.indocsystems.com]].
288 288  
289 289  
290 290  
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