Changes for page Working with HDC Datasets

Last modified by Dennis Segebarth on 2024/10/02 18:25
From version 1.3
edited by Susan Evans
on 2023/07/11 14:45
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To version 23.1
edited by Dennis Segebarth
on 2024/10/02 18:25
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1 -XWiki.sgevans
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2 2  {{toc depth="2"/}}
3 3  {{/box}}
4 4  
5 -Datasets extend Projects with comprehensive data management functionalities. Importantly, each Project can have multiple Datasets associated with it, but each Dataset can only be populated with data from a single Project.
5 +Datasets extend Projects with comprehensive data management functionalities. Importantly, each Project can have multiple Datasets associated with it, but each Dataset can only be populated with data from a single Project. Each Dataset can be viewed, accessed, and interacted with by the user who created it, as well as all users with the Project Administrator role in the Project the Dataset is associated with.
6 6  
7 7  In brief, Datasets are collections of related Project files, folders, and detailed metadata. The Dataset feature allows users to organize Project files, enrich with annotations, validate data structures, and publish controlled versions for sharing.
8 8  
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20 20  
21 21  = Creating a Dataset =
22 22  
23 -New Datasets are empty containers ready for you to add data files and/or folders from your Project Core. Your Dataset is private - only you can view and work with it until you download and share it with others.
23 +New Datasets are empty containers ready for you to add data files and/or folders from your Project Core. Each Dataset can be viewed, accessed, and interacted with by the user who created it, as well as all users with the Project Administrator role in the Project the Dataset is associated with.
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 -11. Define Dataset:
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 -1** //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.
37 -11.Description:
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>>url:http://github.com/HumanBrainProject/openMINDS]] standard.
40 -11* //Collection Method//: Based on the Human Brain Project [[OpenMINDS>>url:http://github.com/HumanBrainProject/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.**
43 -1. When you provided all required information, click **Create** in the upper right-hand corner to complete the Dataset creation.
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.
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.//
46 46  
48 +
47 47  = Adding Files to a Dataset =
48 48  
49 -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//).
51 +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//). Once this association between the Dataset and a Project has been established, the Dataset automatically becomes visible and accessible for all members of the Project that have the Project Administrator role.
50 50  
51 51  To add files to a Dataset,
52 52  
53 -[[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"]]
54 54  
55 55  1. Navigate your Project’s File Explorer and click **Core**.
56 56  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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62 62  
63 63  = Organizing and Validating Datasets =
64 64  
65 -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//).
66 66  
67 67  == Organizing Datasets ==
68 68  
69 69  Use the **Explorer** tab to organize and validate your Dataset.
70 70  
71 -[[image:Datasets Explorer v2.1.5 2023-01-24.png||height="10%" width="50%"]]
73 +[[image:1723802327251-439.png||height="182" width="897"]]
72 72  
73 73  1. Open the Dataset from the Datasets landing page, then select the **Explorer **tab.
74 74  1. Use **+ New Folder** or **Move to **to rearrange files and/or folders.
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87 87  
88 88  === BIDS Validation ===
89 89  
90 -[[image:BIDS_Logo.png||height="9%" width="20%"]]
92 +[[image:1723802339509-521.png||height="83" width="192"]]
91 91  
92 92  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]].
93 93  
94 94  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).
95 95  
96 -[[image:Datasets Validate BIDS v2.1.5 2023-01-24.png||height="13%" width="50%"]]
98 +[[image:1723802351811-730.png||height="230" width="878"]]
97 97  
98 98  1. Open the Dataset from the Datasets landing page and select the **Explorer **tab.
99 99  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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123 123  
124 124  Use the **Metadata** tab to annotate your Dataset.
125 125  
126 -[[image:Datasets Metadata v2.1.5 2023-01-24.png||height="10%" width="50%"]]
128 +[[image:1723802365719-520.png||height="176" width="876"]]
127 127  
128 128  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.
129 129  
130 130  1. Open the Dataset from the Datasets landing page and select the **Metadata **tab.
131 131  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.
132 -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).
133 133  
134 -[[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"]]
135 135  
136 -1. (((
137 137  Default schema categories include the following:
138 138  
139 139  * //Contributors//: Information about the persons or organizations who contributed to the Dataset.
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155 155  
156 156  1. Navigate to **Existing Schema**// //(left panel of the Metadata tab) and select the **Default Schemas** category.
157 157  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.
158 -1. (((
159 -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.
160 160  
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.
164 -)))
165 -
166 166  Any new changes are reflected in the Schemas view.
167 167  
168 168  == Creating a Custom Schema template ==
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171 171  
172 172  To create a Custom Schema,
173 173  
174 -[[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"]]
175 175  
176 176  1. Open the Dataset from the Datasets landing page and select the **Metadata **tab. Under **Existing Schema** (left panel), select **Default Schemas**.
177 177  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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200 200  
201 201  To manage a Custom Schema template that contains saved annotations,
202 202  
203 -[[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"]]
204 204  
205 205  1. Navigate to **Existing Schema**// //(left panel of the **Metadata **tab) and select the **Default Schema** category.
206 206  1. Click the Custom schema name, then click the **eye icon** to open the Schemas view (right side). The existing entries are displayed.
207 207  1. Click **Manage Template**.
208 -1. (((
209 -Make your desired edits. The following changes are possible:
210 -
211 -1. Add new fields
212 -1. Delete existing fields
213 -1. Change an existing field from required to optional
214 -)))
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
215 215  1. Give the updated Schema template a new name, e.g., {name} version 2.
216 216  1. Click **+ Create New Template**.
217 217  
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219 219  
220 220  == Annotating with OpenMINDS ==
221 221  
222 -[[image:openMINDS_logo.png||height="10%" width="20%"]]
218 +[[image:1723802431881-142.png||height="111" width="222"]]
223 223  
224 224  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.
225 225  
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227 227  
228 228  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]].
229 229  
230 -[[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"]]
231 231  
232 232  To upload an openMINDS JSON schema file,
233 233  
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248 248  
249 249  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.
250 250  
251 -[[image:Datasets Activity v2.1.5 2023-01-24.png||height="10%" width="50%"]]
247 +[[image:1723802458591-860.png||height="174" width="863"]]
252 252  
253 253  
254 254  == Anytime Dataset Download ==
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263 263  
264 264  To release a Dataset version,
265 265  
266 -[[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"]]
267 267  
268 268  
269 269  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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277 277  
278 278  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.
279 279  
280 -[[image:Datasets Versions v2.1.5 2023-01-26.png||height="24%" width="50%"]]
276 +[[image:1723802481440-617.png||height="234" width="488"]]
281 281  
282 282  ----
283 283  
284 -Copyright © 2023 [[Indoc Research>>url:https://www.indocresearch.org/]].
280 +Copyright © 2023-2024 [[Indoc Systems>>url:https://www.indocsystems.com]].
285 285  
286 -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]].
287 287  
288 288  
289 -
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