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edited by eapapp
on 2023/06/06 11:30
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1 1  == Publishing neuroscience data, models and software via EBRAINS ==
2 2  
3 3  
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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. **
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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  ----
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55 55  
56 56  [[image:image-20230326054341-1.png]]
57 57  
58 -==== [[[[image:image-20230324171114-2.png||height="176" width="125"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]//All you need to know to share data on EBRAINS.// ====
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 60  
61 61  ==== **1. Provide some general information about your dataset** ====
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70 70  
71 71  This form collects the necessary information needed for us to evaluate whether we can ethically and legally share the data via EBRAINS.
72 72  
91 +See below for information about the ethical and legal aspects concerning sharing of human subject data.
73 73  
93 +
74 74  ==== **2. Upload data ** ====
75 75  
76 76  
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90 90  If a data collection is already uploaded elsewhere, we may link to the already existing repository.
91 91  
92 92  
93 -(% style="color:#1a202c; font-family:inherit; font-size:23px" %)**3. Submit metadata**
113 +==== **3. Submit metadata** ====
94 94  
95 95  
96 -[[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) **
97 97  
98 -//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
99 99  
100 100  //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:
101 101  
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118 118  
119 119  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.
120 120  
121 -[[[[image:image-20230324171109-1.png||height="191" width="135"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]The EBRAINS Data descriptor at-a-glance
141 +==== [[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]//The EBRAINS Data descriptor at-a-glance// ====
122 122  
123 123  
124 124  ==== **5. Preview and publish ** ====
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129 129  
130 130  ----
131 131  
132 -==== **Sharing human data ** ====
152 +==== **Sharing human subject data ** ====
133 133  
134 134  (% class="box floatinginfobox" %)
135 135  (((
136 -**Human subject data that can be shared on EBRAINS consists of:**
156 +**Human subject data that can be shared on EBRAINS:**
137 137  
138 138  - Post-mortem data
139 139  - Aggregated data
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142 142  (% 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. //
143 143  )))
144 144  
145 -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]].
146 146  
147 147  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).
148 148  
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167 167  
168 168  === Step by Step - Software ===
169 169  
170 -[[[[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"]]
171 171  
172 -~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.
173 173  
174 174  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.
175 175  
176 -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.
177 177  
178 178  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]].
179 179  
180 -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.
181 181  
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]] ====
182 182  
183 -
184 -
185 -
186 -
187 -
188 -
189 189  ----
190 190  
191 191  == **The openMINDS metadata framework** ==
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216 216  
217 217  (% class="small" %)Curation Scientist
218 218  Neuroscience (PhD)(%%)
219 -(% class="small" style="color:#4a5568" %)**Behavioral neuroscience and microscopy**
235 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Behavioral neuroscience and microscopy**
220 220  )))|(% style="width:303px" %)(((
221 221  [[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
222 222  
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225 225  (% class="small" %)Curation Scientist,
226 226  Phd Student
227 227  Neuroscience (M. Sc.)(%%)
228 -(% class="small" style="color:#4a5568" %)**Neuroanatomy and data integration**
244 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and data integration**
229 229  )))|(% style="width:303px" %)(((
230 230  [[image:My project (1).jpg||height="209" width="167"]]
231 231  
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234 234  (% class="small" %)Curation Scientist,
235 235  Phd Student
236 236  Neuroscience (M. Sc.)(%%)
237 -(% class="small" style="color:#4a5568" %)**Neuroanatomy and structural connectivity**
253 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and structural connectivity**
238 238  )))|(% style="width:303px" %)(((
239 239  [[image:My project1.jpg||height="209" width="167"]]
240 240  
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242 242  
243 243  (% class="small" %)Curation Scientist
244 244  Neurocognitive Psychology (M. Sc.)(%%)
245 -(% class="small" style="color:#4a5568" %)**Neuroimaging **
261 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroimaging **
246 246  )))
247 247  
248 248  |(% style="width:303px" %)(((
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253 253  (% class="small" %)Curation Scientist,
254 254  Phd Student
255 255  Neuroscience (M. Sc.)(%%)
256 -(% class="small" style="color:#4a5568" %)**Neuroanatomy and brain atlases**
272 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and brain atlases**
257 257  )))| | |
258 258  
259 259  
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267 267  (% class="small" %)Curation Scientist,
268 268  Phd Student
269 269  Sensors and Cognitive Psychology (M. Sc.)(%%)
270 -(% class="small" style="color:#4a5568" %)**Human-Computer Interaction**
286 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Human-Computer Interaction**
271 271  )))|(% style="width:303px" %)(((
272 272  
273 273  
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285 285  
286 286  (% class="small" %)Knowledge Systems Engineer
287 287  Dr. rer. nat. (Systems Neuroscience)(%%)
288 -(% 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**
289 289  )))|(% style="width:303px" %) |
290 290  
291 291  ----
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293 293  == **Add practical value to your shared data, model or software** ==
294 294  
295 295  
296 -==== **Add a tutorial or learning resource ** ====
297 -
298 -(% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
299 -(% style="color:#000000" %)//More information will follow//
300 -
301 -
302 -==== **Create a workflow** ====
303 -
304 -(% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
305 -(% style="color:#000000" %)//More information will follow//
306 -
307 307  ----
308 308  
309 309  === **Showcase shared data, models or software in other services** ===
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328 328  
329 329  ----
330 330  
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 +
331 331  === **The benefits of sharing data ** ===
332 332  
333 333  By sharing your data via EBRAINS, you gain access to the following benefits:
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336 336  
337 337  
338 338  
339 -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.
340 340  
341 -
342 342  ----
343 343  
344 -=== ===
345 -
346 346  === **Frequently asked questions ** ===
347 347  
348 348  (((
349 -==== ====
364 +==== ====
350 350  
351 351  (((
352 352  >The curation process is time consuming and difficult
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