Changes for page data-curation-copy

Last modified by eapapp on 2023/07/04 16:46
From version 151.1
edited by ingrreit
on 2023/06/05 10:37
Change comment: There is no comment for this version
To version 166.1
edited by eapapp
on 2023/06/06 11:30
Change comment: There is no comment for this version

Summary

Details

Page properties
Author
... ... @@ -1,1 +1,1 @@
1 -XWiki.ingrreit
1 +XWiki.eapapp
Content
... ... @@ -1,3 +1,22 @@
1 +{{html clean="false"}}
2 +<div style="float:right;margin-left:1em;margin-bottom:1em">
3 + <form title="Search in this collab" target="_blank" action="https://wiki.ebrains.eu/bin/view/Main/Search">
4 + <input type="hidden" name="sort" value="score">
5 + <input type="hidden" name="sortOrder" value="desc">
6 + <input type="hidden" name="highlight" value="true">
7 + <input type="hidden" name="facet" value="true">
8 + <input type="hidden" name="r" value="1">
9 + <input type="hidden" name="f_locale" value="en">
10 + <input type="hidden" name="f_space_facet" value="1/Collabs.test-ir2.">
11 + <input type="hidden" name="l_space_facet" value="100">
12 + <input type="hidden" name="f_type" value="DOCUMENT">
13 + <input type="text" name="text" placeholder="Search here..." size="25" id="searchbox" />
14 + <input type="submit" value="&#x1F50E;&#xFE0E;" id="submit"/>
15 + </form>
16 +</div>
17 +{{/html}}
18 +
19 +
1 1  == Publishing neuroscience data, models and software via EBRAINS ==
2 2  
3 3  
... ... @@ -8,7 +8,6 @@
8 8  {{toc depth="3" start="2"/}}
9 9  {{/box}}
10 10  
11 -
12 12  == **Information to get started** ==
13 13  
14 14  **[[REQUEST CURATION>>https://nettskjema.no/a/277393#/]] to share data, simulations, computational models, and software, - or to add a new version of an existing one. **
... ... @@ -30,7 +30,7 @@
30 30  
31 31  (% class="box successmessage" %)
32 32  (((
33 -**Particular needs? Contact us! **The workflows for sharing can be modified for researchers or research groups aiming to frequently publish larger numbers of their research products through EBRAINS. Please contact the curation service team in such cases
51 +**Particular needs? Contact us! **The workflows for sharing can be modified for researchers or research groups aiming to frequently publish larger numbers of their research products through EBRAINS. Please contact the curation service team in such cases. Reach us at [[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
34 34  )))
35 35  
36 36  ----
... ... @@ -55,12 +55,8 @@
55 55  
56 56  [[image:image-20230326054341-1.png]]
57 57  
58 -==== ====
76 +==== [[[[image:image-20230324171114-2.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]//All you need to know to share data on EBRAINS.// ====
59 59  
60 -(% style="width:1841.22px" %)
61 -|(% style="width:344px" %)(((
62 -[[[[image:image-20230324171114-2.png||height="219" width="155"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
63 -)))|(% style="width:1493px" %)//We have collected 'all you need to know to share data on EBRAINS' in an infographic. //
64 64  
65 65  ==== **1. Provide some general information about your dataset** ====
66 66  
... ... @@ -74,7 +74,9 @@
74 74  
75 75  This form collects the necessary information needed for us to evaluate whether we can ethically and legally share the data via EBRAINS.
76 76  
91 +See below for information about the ethical and legal aspects concerning sharing of human subject data.
77 77  
93 +
78 78  ==== **2. Upload data ** ====
79 79  
80 80  
... ... @@ -94,12 +94,12 @@
94 94  If a data collection is already uploaded elsewhere, we may link to the already existing repository.
95 95  
96 96  
97 -(% style="color:#1a202c; font-family:inherit; font-size:23px" %)**3. Submit metadata**
113 +==== **3. Submit metadata** ====
98 98  
99 99  
100 -[[image:https://lh5.googleusercontent.com/WS4T2LhF9znWWChn3Z550agLrrb-KTWdYVsJSv0lh4cGjKbjuN1WV68WER9xkYqi1UqN7KYZz7bImYz3_TpOuTuvma7T192QUiUZoyJVPk1fj5NSDSQh_kpIeBufAOdDtsDRpPKK_P5EDPqRCTAaOTNyCw=s2048||height="91px;" width="91px;"]]**Submit metadata using our **[[EBRAINS Metadata wizard>>https://ebrains-metadata-wizard.apps.hbp.eu/]]** (opt. 1), or through direct interaction with the Knowledge Graph (opt. 2) **
116 +[[image:https://lh5.googleusercontent.com/WS4T2LhF9znWWChn3Z550agLrrb-KTWdYVsJSv0lh4cGjKbjuN1WV68WER9xkYqi1UqN7KYZz7bImYz3_TpOuTuvma7T192QUiUZoyJVPk1fj5NSDSQh_kpIeBufAOdDtsDRpPKK_P5EDPqRCTAaOTNyCw=s2048||height="91px;" width="91px;"]]**Submit metadata using the **[[EBRAINS Wizard>>https://ebrains-metadata-wizard.apps.hbp.eu/]]** (opt. 1), or through direct interaction with the Knowledge Graph (opt. 2) **
101 101  
102 -//Opt. 1.// Manually submit the minimal required metadata via the [[EBRAINS Metadata wizard>>https://ebrains-metadata-wizard.apps.hbp.eu/]]. The minimal required metadata covers extended bibliographic information necessary to publish your dataset on EBRAINS. The submitted information, including uploaded files, will be sent to the Curation team automatically
118 +//Opt. 1.// Manually submit the minimal required metadata via the [[EBRAINS Wizard>>https://ebrains-metadata-wizard.apps.hbp.eu/]]. The minimal required metadata covers extended bibliographic information necessary to publish your dataset on EBRAINS. The submitted information, including uploaded files, will be sent to the Curation team automatically
103 103  
104 104  //Opt. 2.// To go beyond the minimal required metadata, you can directly interact with the Knowledge Graph (KG) in your private space. Within the private space, you can upload metadata and interact with them, moreover you can connect your metadata to existing publicly accessible entries. Access to your private space is granted upon the initiation of the curation process. You can access your private space via:
105 105  
... ... @@ -110,17 +110,6 @@
110 110  Datasets published through the EBRAINS Knowledge Graph have to be registered using **openMINDS compliant metadata** delivered as JSON-LD files. See this summary table for an overview of [[the minimally required openMINDS properties for publishing>>https://drive.ebrains.eu/lib/47995dbc-f576-4008-a76c-eefbfd818529/file/ebrains-minimum-required-metadata.xlsx]] on EBRAINS.
111 111  
112 112  
113 -**The openMINDS metadata framework**
114 -
115 -openMINDS (open Metadata Initiative for Neuroscience Data Structures) is a community-driven, open-source metadata framework for graph database systems, such as the EBRAINS Knowledge Graph. It is composed of linked metadata models, libraries of serviceable metadata instances, and supportive tooling ([[openMINDS Python>>url:https://pypi.org/project/openMINDS/]], openMINDS Matlab). For exploring the openMINDS schemas, go to the [[HTML documentation>>url:https://humanbrainproject.github.io/openMINDS/]]. For a full overview of the framework, go to [[the openMINDS collab>>url:https://wiki.ebrains.eu/bin/view/Collabs/openminds/]] or the [[GitHub repository>>https://github.com/HumanBrainProject/openMINDS]].
116 -
117 -For feedback, requests, or contributions, please get in touch with the openMINDS development team via
118 -
119 -* the support-email: [[openminds@ebrains.eu>>path:mailto:openminds@ebrains.eu]]
120 -* the [[GitHub issue tracker>>url:https://github.com/HumanBrainProject/openMINDS/issues]]
121 -* the INCF NeuroStars [[openMINDS Community Forum>>url:https://neurostars.org/t/openminds-community-forum-virtual/20156]]
122 -
123 -
124 124  ==== **4. Write a Data Descriptor ** ====
125 125  
126 126  [[image:https://lh4.googleusercontent.com/lMYEKOXzejbBydOdotWWteXQo7j363xRyntBGjcPZVEdtIU1CJYX7q1STpdr2JPZK4hpWWXk20UlkUOqDGL5kX6vnQVBSdrfUo6EGfXOwpuGq1Uygv0tTZJ0lRO6voJvg56QC2mufvjAcRXGfAKFOjtc6w=s2048||height="94px;" width="94px;"]]**Write a data descriptor by filling in **[[this template>>https://drive.ebrains.eu/f/a2e07c95b1a54090bbbc/?dl=1]]** . **
... ... @@ -133,8 +133,8 @@
133 133  
134 134  Journal publications sufficiently describing the shared data, such as made available through [[Nature Scientific Data>>http://www.nature.com/sdata/about]], [[Elsevier Data in Brief>>http://www.journals.elsevier.com/data-in-brief/]], [[BMC Data note>>https://bmcresnotes.biomedcentral.com/submission-guidelines/preparing-your-manuscript/data-note]] and more, can replace the EBRAINS Data Descriptor.
135 135  
141 +==== [[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]//The EBRAINS Data descriptor at-a-glance// ====
136 136  
137 -|(% style="width:175px" %)[[[[image:image-20230324171109-1.png||height="154" width="109"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]|(% style="width:1662px" %)The EBRAINS Data descriptor at-a-glance
138 138  
139 139  ==== **5. Preview and publish ** ====
140 140  
... ... @@ -144,11 +144,11 @@
144 144  
145 145  ----
146 146  
147 -==== **Sharing human data ** ====
152 +==== **Sharing human subject data ** ====
148 148  
149 149  (% class="box floatinginfobox" %)
150 150  (((
151 -**Human subject data that can be shared on EBRAINS consists of:**
156 +**Human subject data that can be shared on EBRAINS:**
152 152  
153 153  - Post-mortem data
154 154  - Aggregated data
... ... @@ -157,7 +157,7 @@
157 157  (% class="small" %)//If you have human data that does not classify as any of the above, please get in touch and we will clarify the available options. //
158 158  )))
159 159  
160 -Human data shared on EBRAINS must comply with [[GDPR >>https://gdpr-info.eu/]]and [[EU directives>>https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=celex%3A32010L0063]]. The information we need to assess this is collected via our [[Ethics and Regulatory Compliance Survey>>https://nettskjema.no/a/224765]].
165 +Human subject data shared on EBRAINS must comply with [[GDPR >>https://gdpr-info.eu/]]and [[EU directives>>https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=celex%3A32010L0063]]. The information we need to assess this is collected via our [[Ethics and Regulatory Compliance Survey>>https://nettskjema.no/a/224765]].
161 161  
162 162  Post-mortem and aggregated human data can be shared openly, given direct identifiers in the metadata are removed. Strongly pseudonymized and de-identified data can be shared via the Human Data Gateway (HDG).
163 163  
... ... @@ -182,25 +182,33 @@
182 182  
183 183  === Step by Step - Software ===
184 184  
185 -[[[[image:swc-flow-no-header.png||alt="swc-flow.png"]]>>https://www.ebrains.eu/tools/ebrains-curation-request-form||rel="noopener noreferrer" target="_blank"]]
190 +[[[[image:Screenshot 2023-06-06 1122082.png||alt="swc-flow.png" height="136" width="637"]]>>https://www.ebrains.eu/tools/ebrains-curation-request-form||rel="noopener noreferrer" target="_blank"]]
186 186  
187 -~1. Fill in the [[request form>>https://www.ebrains.eu/tools/ebrains-curation-request-form]]. You'll be contacted by a curator with further instructions. In these instructions you will find the links to your software and software version entries in the Knowledge Graph.
192 +~1. Fill in the [[request form>>https://www.ebrains.eu/tools/ebrains-curation-request-form]]. You'll be contacted by a curator with further instructions. In these instructions, you will find the links to your software and software version entries in the Knowledge Graph.
188 188  
189 189  2. Enter the metadata of your software in your private space of the [[Knowledge Graph Editor>>url:https://editor.kg.ebrains.eu/]] by using the links provided by the curator. Please provide the metadata for your software as complete as possible. This makes it easier for users to find and use your software. If you have questions feel free to contact the curation support. After you have finished editing your entries, please let the curators know by replying to your ticket. We curate your metadata and get back to you, if necessary.
190 190  
191 -3. After a quality check, we integrate and publish the information to the Knowledge Graph. Your software is then searchable and usable for the neuroscience community.[[[[image:Thumb.png||alt="EBRAINS-Share-Software.pdf" height="315" style="float:right" width="215"]]>>attach:EBRAINS-Share-Software.pdf]]
196 +3. After a quality check, we integrate and publish the information to the Knowledge Graph. Your software is then searchable and usable for the neuroscience community.
192 192  
193 193  If you want to add a new version to an already curated software, please request this via the [[curation request form>>https://nettskjema.no/a/277393]].
194 194  
195 -For more information, visit our [[Guide to Software Curation in the EBRAINS Knowledge Graph>>url:https://wiki.ebrains.eu/bin/view/Collabs/swc-guide]] or see our infographic.
200 +For more information, visit our [[Guide to Software Curation in the EBRAINS Knowledge Graph>>url:https://wiki.ebrains.eu/bin/view/Collabs/swc-guide]] or see our infographic below.
196 196  
202 +(% style="text-align: right;" %)
203 +==== //Software curation at a glance          //[[[[image:Thumb2.png||alt="EBRAINS-Share-Software.pdf" height="287" width="197"]]>>attach:EBRAINS-Share-Software-4.pdf]] ====
197 197  
205 +----
198 198  
207 +== **The openMINDS metadata framework** ==
199 199  
209 +openMINDS (open Metadata Initiative for Neuroscience Data Structures) is a community-driven, open-source metadata framework for graph database systems, such as the EBRAINS Knowledge Graph. It is composed of linked metadata models, libraries of serviceable metadata instances, and supportive tooling ([[openMINDS Python>>url:https://pypi.org/project/openMINDS/]], openMINDS Matlab). For exploring the openMINDS schemas, go to the [[HTML documentation>>url:https://humanbrainproject.github.io/openMINDS/]]. For a full overview of the framework, go to [[the openMINDS collab>>url:https://wiki.ebrains.eu/bin/view/Collabs/openminds/]] or the [[GitHub repository>>https://github.com/HumanBrainProject/openMINDS]].
200 200  
211 +For feedback, requests, or contributions, please get in touch with the openMINDS development team via
201 201  
213 +* the support-email: [[openminds@ebrains.eu>>path:mailto:openminds@ebrains.eu]]
214 +* the [[GitHub issue tracker>>url:https://github.com/HumanBrainProject/openMINDS/issues]]
215 +* the INCF NeuroStars [[openMINDS Community Forum>>url:https://neurostars.org/t/openminds-community-forum-virtual/20156]]
202 202  
203 -
204 204  ----
205 205  
206 206  == **The curation team: meet the curators** ==
... ... @@ -219,7 +219,7 @@
219 219  
220 220  (% class="small" %)Curation Scientist
221 221  Neuroscience (PhD)(%%)
222 -(% class="small" style="color:#4a5568" %)**Behavioral neuroscience and microscopy**
235 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Behavioral neuroscience and microscopy**
223 223  )))|(% style="width:303px" %)(((
224 224  [[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
225 225  
... ... @@ -228,7 +228,7 @@
228 228  (% class="small" %)Curation Scientist,
229 229  Phd Student
230 230  Neuroscience (M. Sc.)(%%)
231 -(% class="small" style="color:#4a5568" %)**Neuroanatomy and data integration**
244 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and data integration**
232 232  )))|(% style="width:303px" %)(((
233 233  [[image:My project (1).jpg||height="209" width="167"]]
234 234  
... ... @@ -237,7 +237,7 @@
237 237  (% class="small" %)Curation Scientist,
238 238  Phd Student
239 239  Neuroscience (M. Sc.)(%%)
240 -(% class="small" style="color:#4a5568" %)**Neuroanatomy and structural connectivity**
253 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and structural connectivity**
241 241  )))|(% style="width:303px" %)(((
242 242  [[image:My project1.jpg||height="209" width="167"]]
243 243  
... ... @@ -245,7 +245,7 @@
245 245  
246 246  (% class="small" %)Curation Scientist
247 247  Neurocognitive Psychology (M. Sc.)(%%)
248 -(% class="small" style="color:#4a5568" %)**Neuroimaging **
261 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroimaging **
249 249  )))
250 250  
251 251  |(% style="width:303px" %)(((
... ... @@ -256,7 +256,7 @@
256 256  (% class="small" %)Curation Scientist,
257 257  Phd Student
258 258  Neuroscience (M. Sc.)(%%)
259 -(% class="small" style="color:#4a5568" %)**Neuroanatomy and brain atlases**
272 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and brain atlases**
260 260  )))| | |
261 261  
262 262  
... ... @@ -270,7 +270,7 @@
270 270  (% class="small" %)Curation Scientist,
271 271  Phd Student
272 272  Sensors and Cognitive Psychology (M. Sc.)(%%)
273 -(% class="small" style="color:#4a5568" %)**Human-Computer Interaction**
286 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Human-Computer Interaction**
274 274  )))|(% style="width:303px" %)(((
275 275  
276 276  
... ... @@ -288,7 +288,7 @@
288 288  
289 289  (% class="small" %)Knowledge Systems Engineer
290 290  Dr. rer. nat. (Systems Neuroscience)(%%)
291 -(% class="small" style="color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
304 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
292 292  )))|(% style="width:303px" %) |
293 293  
294 294  ----
... ... @@ -296,17 +296,6 @@
296 296  == **Add practical value to your shared data, model or software** ==
297 297  
298 298  
299 -==== **Add a tutorial or learning resource ** ====
300 -
301 -(% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
302 -(% style="color:#000000" %)//More information will follow//
303 -
304 -
305 -==== **Create a workflow** ====
306 -
307 -(% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
308 -(% style="color:#000000" %)//More information will follow//
309 -
310 310  ----
311 311  
312 312  === **Showcase shared data, models or software in other services** ===
... ... @@ -331,6 +331,19 @@
331 331  
332 332  ----
333 333  
336 +==== **Add a tutorial or learning resource ** ====
337 +
338 +(% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
339 +(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
340 +
341 +
342 +==== **Create a workflow** ====
343 +
344 +(% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
345 +(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
346 +
347 +----
348 +
334 334  === **The benefits of sharing data ** ===
335 335  
336 336  By sharing your data via EBRAINS, you gain access to the following benefits:
... ... @@ -339,17 +339,14 @@
339 339  
340 340  
341 341  
342 -We support you to better follow the FAIR^^ ^^guiding principles for data management and stewardship{{footnote}}Wilkinson, M., Dumontier, M., Aalbersberg, I. et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data 3, 160018 (2016). https://doi.org/10.1038/sdata.2016.18 {{/footnote}}.  Publishing data, models or code via EBRAINS will provide you with a citeable [[DataCite DOI>>https://www.doi.org/the-identifier/resources/handbook/]] for your research product.
357 +We support you to better follow the [[FAIR^^ ^^guiding principles>>https://www.nature.com/articles/sdata201618]] for data management and stewardship{{footnote}}Wilkinson, M., Dumontier, M., Aalbersberg, I. et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data 3, 160018 (2016). https://doi.org/10.1038/sdata.2016.18 {{/footnote}}.  Publishing data, models or code via EBRAINS will provide you with a citeable [[DataCite DOI>>https://www.doi.org/the-identifier/resources/handbook/]] for your research product.
343 343  
344 -
345 345  ----
346 346  
347 -=== ===
348 -
349 349  === **Frequently asked questions ** ===
350 350  
351 351  (((
352 -==== ====
364 +==== ====
353 353  
354 354  (((
355 355  >The curation process is time consuming and difficult
EBRAINS-Share-Software-4.pdf
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.jan
Size
... ... @@ -1,0 +1,1 @@
1 +1.2 MB
Content
Screenshot 2023-06-06 112208.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.jan
Size
... ... @@ -1,0 +1,1 @@
1 +138.1 KB
Content
Screenshot 2023-06-06 1122082.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.jan
Size
... ... @@ -1,0 +1,1 @@
1 +123.6 KB
Content
Thumb2.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.jan
Size
... ... @@ -1,0 +1,1 @@
1 +165.5 KB
Content