Changes for page Working with HDC Datasets

Last modified by Dennis Segebarth on 2024/10/02 18:25
From version 1.1
edited by Susan Evans
on 2023/07/11 14:41
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To version 22.1
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 -1. (((
31 -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 +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):
32 32  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 ( * ).
33 +11. Define Dataset
34 +11*. //Title//*: A short title for the Dataset (max. 100 characters). 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.
38 +11. Description:
39 +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.
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.
44 +1. When you provided all required information, click Create in the upper right-hand corner to complete the Dataset creation.
33 33  
34 -1. Define Dataset:
35 -1.
36 -1*. //Title*//: A short title for the Dataset (max. 100 characters). This entry can be changed later.
37 -1*. //Dataset Code*//: A distinct, immutable code defined by you to uniquely identify your Dataset. This entry cannot be changed later.
38 -1*. //Authors*//: One or more authors. Hit **Enter** after each entry. These entries can be changed later.
39 -1*. //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.
40 -1.
41 -
42 -Description:
43 -
44 -1.
45 -1*. //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.
46 -1*. //Modality//: Based on the Human Brain Project [[OpenMINDS>>url:http://github.com/HumanBrainProject/openMINDS]] standard.
47 -1*. //Collection Method//: Based on the Human Brain Project [[OpenMINDS>>url:http://github.com/HumanBrainProject/openMINDS]] standard.
48 -1*. //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.
49 -1*. //Tags//: Custom keywords you create for your Dataset.  Tags are displayed on the Datasets landing page and information bar.
50 -)))
51 -1. When you provided all required information, click **Create** in the upper right-hand corner to complete the Dataset creation.
52 -
53 53  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.//
54 54  
48 +
55 55  = Adding Files to a Dataset =
56 56  
57 57  As mentioned above, each Dataset is associated to a single Project. Therefore, files can be added to a Dataset only from the Core of the respective Project. This will create a copy of the file so the original file in the Core is unaffected by subsequent manipulations inside the Dataset. The Dataset must have already been created before files can be added (see //Creating a Dataset//).
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58 58  
59 59  To add files to a Dataset,
60 60  
61 -[[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"]]
62 62  
63 63  1. Navigate your Project’s File Explorer and click **Core**.
64 64  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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70 70  
71 71  = Organizing and Validating Datasets =
72 72  
73 -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//).
74 74  
75 75  == Organizing Datasets ==
76 76  
77 77  Use the **Explorer** tab to organize and validate your Dataset.
78 78  
79 -[[image:Datasets Explorer v2.1.5 2023-01-24.png||height="10%" width="50%"]]
73 +[[image:1723802327251-439.png||height="182" width="897"]]
80 80  
81 81  1. Open the Dataset from the Datasets landing page, then select the **Explorer **tab.
82 82  1. Use **+ New Folder** or **Move to **to rearrange files and/or folders.
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95 95  
96 96  === BIDS Validation ===
97 97  
98 -[[image:BIDS_Logo.png||height="9%" width="20%"]]
92 +[[image:1723802339509-521.png||height="83" width="192"]]
99 99  
100 100  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]].
101 101  
102 102  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).
103 103  
104 -[[image:Datasets Validate BIDS v2.1.5 2023-01-24.png||height="13%" width="50%"]]
98 +[[image:1723802351811-730.png||height="230" width="878"]]
105 105  
106 106  1. Open the Dataset from the Datasets landing page and select the **Explorer **tab.
107 107  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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131 131  
132 132  Use the **Metadata** tab to annotate your Dataset.
133 133  
134 -[[image:Datasets Metadata v2.1.5 2023-01-24.png||height="10%" width="50%"]]
128 +[[image:1723802365719-520.png||height="176" width="876"]]
135 135  
136 136  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.
137 137  
138 138  1. Open the Dataset from the Datasets landing page and select the **Metadata **tab.
139 139  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.
140 -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).
141 141  
142 -[[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"]]
143 143  
144 -1. (((
145 145  Default schema categories include the following:
146 146  
147 147  * //Contributors//: Information about the persons or organizations who contributed to the Dataset.
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163 163  
164 164  1. Navigate to **Existing Schema**// //(left panel of the Metadata tab) and select the **Default Schemas** category.
165 165  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.
166 -1. (((
167 -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.
168 168  
169 -1. **X Reset** to return all entries to their original values.
170 -1. **Cancel **to exit without saving changes.
171 -1. **Update** to save the changes and return to the schema view.
172 -)))
173 -
174 174  Any new changes are reflected in the Schemas view.
175 175  
176 176  == Creating a Custom Schema template ==
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179 179  
180 180  To create a Custom Schema,
181 181  
182 -[[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"]]
183 183  
184 184  1. Open the Dataset from the Datasets landing page and select the **Metadata **tab. Under **Existing Schema** (left panel), select **Default Schemas**.
185 185  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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208 208  
209 209  To manage a Custom Schema template that contains saved annotations,
210 210  
211 -[[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"]]
212 212  
213 213  1. Navigate to **Existing Schema**// //(left panel of the **Metadata **tab) and select the **Default Schema** category.
214 214  1. Click the Custom schema name, then click the **eye icon** to open the Schemas view (right side). The existing entries are displayed.
215 215  1. Click **Manage Template**.
216 -1. (((
217 -Make your desired edits. The following changes are possible:
218 -
219 -1. Add new fields
220 -1. Delete existing fields
221 -1. Change an existing field from required to optional
222 -)))
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
223 223  1. Give the updated Schema template a new name, e.g., {name} version 2.
224 224  1. Click **+ Create New Template**.
225 225  
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227 227  
228 228  == Annotating with OpenMINDS ==
229 229  
230 -[[image:openMINDS_logo.png||height="10%" width="20%"]]
218 +[[image:1723802431881-142.png||height="111" width="222"]]
231 231  
232 232  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.
233 233  
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235 235  
236 236  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]].
237 237  
238 -[[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"]]
239 239  
240 240  To upload an openMINDS JSON schema file,
241 241  
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256 256  
257 257  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.
258 258  
259 -[[image:Datasets Activity v2.1.5 2023-01-24.png||height="10%" width="50%"]]
247 +[[image:1723802458591-860.png||height="174" width="863"]]
260 260  
261 261  
262 262  == Anytime Dataset Download ==
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271 271  
272 272  To release a Dataset version,
273 273  
274 -[[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"]]
275 275  
276 276  
277 277  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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285 285  
286 286  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.
287 287  
288 -[[image:Datasets Versions v2.1.5 2023-01-26.png||height="24%" width="50%"]]
276 +[[image:1723802481440-617.png||height="234" width="488"]]
289 289  
290 290  ----
291 291  
292 -Copyright © 2023 [[Indoc Research>>url:https://www.indocresearch.org/]].
280 +Copyright © 2023-2024 [[Indoc Systems>>url:https://www.indocsystems.com]].
293 293  
294 -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]].
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