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18 -
19 -
20 20  == Publishing neuroscience data, models and software via EBRAINS ==
21 21  
22 22  
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27 27  {{toc depth="3" start="2"/}}
28 28  {{/box}}
29 29  
11 +
30 30  == **Information to get started** ==
31 31  
32 32  **[[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. **
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48 48  
49 49  (% class="box successmessage" %)
50 50  (((
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]]
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
52 52  )))
53 53  
54 54  ----
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73 73  
74 74  [[image:image-20230326054341-1.png]]
75 75  
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.// ====
58 +==== ====
77 77  
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. //
78 78  
79 79  ==== **1. Provide some general information about your dataset** ====
80 80  
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88 88  
89 89  This form collects the necessary information needed for us to evaluate whether we can ethically and legally share the data via EBRAINS.
90 90  
91 -See below for information about the ethical and legal aspects concerning sharing of human subject data.
92 92  
93 -
94 94  ==== **2. Upload data ** ====
95 95  
96 96  
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110 110  If a data collection is already uploaded elsewhere, we may link to the already existing repository.
111 111  
112 112  
113 -==== **3. Submit metadata** ====
97 +(% style="color:#1a202c; font-family:inherit; font-size:23px" %)**3. Submit metadata**
114 114  
115 115  
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) **
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) **
117 117  
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
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
119 119  
120 120  //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:
121 121  
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126 126  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.
127 127  
128 128  
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 +
129 129  ==== **4. Write a Data Descriptor ** ====
130 130  
131 131  [[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]]** . **
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138 138  
139 139  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.
140 140  
141 -==== [[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]//The EBRAINS Data descriptor at-a-glance// ====
142 142  
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
143 143  
144 144  ==== **5. Preview and publish ** ====
145 145  
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149 149  
150 150  ----
151 151  
152 -==== **Sharing human subject data ** ====
147 +==== **Sharing human data ** ====
153 153  
154 154  (% class="box floatinginfobox" %)
155 155  (((
156 -**Human subject data that can be shared on EBRAINS:**
151 +**Human subject data that can be shared on EBRAINS consists of:**
157 157  
158 158  - Post-mortem data
159 159  - Aggregated data
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162 162  (% 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. //
163 163  )))
164 164  
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]].
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]].
166 166  
167 167  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).
168 168  
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187 187  
188 188  === Step by Step - Software ===
189 189  
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"]]
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"]]
191 191  
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.
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.
193 193  
194 194  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.
195 195  
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.
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]]
197 197  
198 198  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]].
199 199  
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.
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.
201 201  
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]] ====
204 204  
205 -----
206 206  
207 -== **The openMINDS metadata framework** ==
208 208  
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]].
210 210  
211 -For feedback, requests, or contributions, please get in touch with the openMINDS development team via
212 212  
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]]
216 216  
203 +
217 217  ----
218 218  
219 219  == **The curation team: meet the curators** ==
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232 232  
233 233  (% class="small" %)Curation Scientist
234 234  Neuroscience (PhD)(%%)
235 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Behavioral neuroscience and microscopy**
222 +(% class="small" style="color:#4a5568" %)**Behavioral neuroscience and microscopy**
236 236  )))|(% style="width:303px" %)(((
237 237  [[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
238 238  
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241 241  (% class="small" %)Curation Scientist,
242 242  Phd Student
243 243  Neuroscience (M. Sc.)(%%)
244 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and data integration**
231 +(% class="small" style="color:#4a5568" %)**Neuroanatomy and data integration**
245 245  )))|(% style="width:303px" %)(((
246 246  [[image:My project (1).jpg||height="209" width="167"]]
247 247  
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250 250  (% class="small" %)Curation Scientist,
251 251  Phd Student
252 252  Neuroscience (M. Sc.)(%%)
253 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and structural connectivity**
240 +(% class="small" style="color:#4a5568" %)**Neuroanatomy and structural connectivity**
254 254  )))|(% style="width:303px" %)(((
255 255  [[image:My project1.jpg||height="209" width="167"]]
256 256  
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258 258  
259 259  (% class="small" %)Curation Scientist
260 260  Neurocognitive Psychology (M. Sc.)(%%)
261 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroimaging **
248 +(% class="small" style="color:#4a5568" %)**Neuroimaging **
262 262  )))
263 263  
264 264  |(% style="width:303px" %)(((
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269 269  (% class="small" %)Curation Scientist,
270 270  Phd Student
271 271  Neuroscience (M. Sc.)(%%)
272 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and brain atlases**
259 +(% class="small" style="color:#4a5568" %)**Neuroanatomy and brain atlases**
273 273  )))| | |
274 274  
275 275  
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283 283  (% class="small" %)Curation Scientist,
284 284  Phd Student
285 285  Sensors and Cognitive Psychology (M. Sc.)(%%)
286 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Human-Computer Interaction**
273 +(% class="small" style="color:#4a5568" %)**Human-Computer Interaction**
287 287  )))|(% style="width:303px" %)(((
288 288  
289 289  
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301 301  
302 302  (% class="small" %)Knowledge Systems Engineer
303 303  Dr. rer. nat. (Systems Neuroscience)(%%)
304 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
291 +(% class="small" style="color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
305 305  )))|(% style="width:303px" %) |
306 306  
307 307  ----
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309 309  == **Add practical value to your shared data, model or software** ==
310 310  
311 311  
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 +
312 312  ----
313 313  
314 314  === **Showcase shared data, models or software in other services** ===
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333 333  
334 334  ----
335 335  
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 -
349 349  === **The benefits of sharing data ** ===
350 350  
351 351  By sharing your data via EBRAINS, you gain access to the following benefits:
... ... @@ -354,14 +354,17 @@
354 354  
355 355  
356 356  
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.
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.
358 358  
344 +
359 359  ----
360 360  
347 +=== ===
348 +
361 361  === **Frequently asked questions ** ===
362 362  
363 363  (((
364 -==== ====
352 +==== ====
365 365  
366 366  (((
367 367  >The curation process is time consuming and difficult
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