Changes for page data-curation-copy

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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. **
... ... @@ -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  ----
... ... @@ -55,9 +55,19 @@
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 +(% class="box floatinginfobox" id="share-data-infographic" %)
77 +(((
78 +(% style="text-align:center" %)
79 +//Download our infographic//
80 +//with all you need to know//
81 +//to share data on EBRAINS: //
82 +// //
83 +[[[[image:image-20230324171114-2.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
59 59  
85 +
86 +)))
60 60  
88 +
61 61  ==== **1. Provide some general information about your dataset** ====
62 62  
63 63  
... ... @@ -70,7 +70,9 @@
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  
101 +See below for information about the ethical and legal aspects concerning sharing of human subject data.
73 73  
103 +
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**
123 +==== **3. Submit metadata** ====
94 94  
95 95  
96 96  [[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) **
... ... @@ -118,9 +118,17 @@
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// ====
151 +(% class="box floatinginfobox" id="data-descriptor-infographic" %)
152 +(((
153 +(% style="text-align:center" %)
154 +//Download our infographic: //
155 +//The EBRAINS Data//
156 +//Descriptor at a glance//
157 +// //
158 +[[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
159 +
160 +)))
122 122  
123 -
124 124  ==== **5. Preview and publish ** ====
125 125  
126 126  
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129 129  
130 130  ----
131 131  
132 -==== **Sharing human data ** ====
170 +==== **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:**
174 +**Human subject data that can be shared on EBRAINS:**
175 +// //
176 +// - Post-mortem data//
177 +// - Aggregated data//
178 +// - Strongly pseudonymized or de-identified subject data//
179 +// with a legal basis for sharing (e.g. Informed Consent)//
180 +// //
137 137  
138 -- Post-mortem data
139 -- Aggregated data
140 -- Strongly pseudonymized or de-identified subject data with a legal basis for sharing (e.g. Informed Consent)
141 -
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. //
182 +(% class="small" %)
183 +//If you have human data that does not qualify as any of the above,//
184 +//please [[get in touch>>https://www.ebrains.eu/contact/]] 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]].
187 +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"]]
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.
213 +(% class="box floatinginfobox" id="software-curation-infographic" %)
214 +(((
215 +(% style="text-align:center" %)
216 +//Software curation at a glance//
217 +// //
218 +[[[[image:Thumb2.png||alt="EBRAINS-Share-Software.pdf" height="287" width="197"]]>>attach:EBRAINS-Share-Software-4.pdf]]
219 +)))
173 173  
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.
221 +(% style="margin-left:15px" %)[[[[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"]]
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.
223 +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.
224 +1. 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.
225 +1. 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 below.
229 +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 on the right.
181 181  
182 -[[[[image:Thumb.png||alt="EBRAINS-Share-Software.pdf" height="203" style="float:left" width="139"]]>>attach:EBRAINS-Share-Software.pdf]]
183 183  
184 -
185 -==== //Software curation at a glance// ====
186 -
187 -
188 -
189 -
190 190  ----
191 191  
192 192  == **The openMINDS metadata framework** ==
... ... @@ -217,7 +217,7 @@
217 217  
218 218  (% class="small" %)Curation Scientist
219 219  Neuroscience (PhD)(%%)
220 -(% class="small" style="color:#4a5568" %)**Behavioral neuroscience and microscopy**
262 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Behavioral neuroscience and microscopy**
221 221  )))|(% style="width:303px" %)(((
222 222  [[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
223 223  
... ... @@ -226,7 +226,7 @@
226 226  (% class="small" %)Curation Scientist,
227 227  Phd Student
228 228  Neuroscience (M. Sc.)(%%)
229 -(% class="small" style="color:#4a5568" %)**Neuroanatomy and data integration**
271 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and data integration**
230 230  )))|(% style="width:303px" %)(((
231 231  [[image:My project (1).jpg||height="209" width="167"]]
232 232  
... ... @@ -235,7 +235,7 @@
235 235  (% class="small" %)Curation Scientist,
236 236  Phd Student
237 237  Neuroscience (M. Sc.)(%%)
238 -(% class="small" style="color:#4a5568" %)**Neuroanatomy and structural connectivity**
280 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and structural connectivity**
239 239  )))|(% style="width:303px" %)(((
240 240  [[image:My project1.jpg||height="209" width="167"]]
241 241  
... ... @@ -243,7 +243,7 @@
243 243  
244 244  (% class="small" %)Curation Scientist
245 245  Neurocognitive Psychology (M. Sc.)(%%)
246 -(% class="small" style="color:#4a5568" %)**Neuroimaging **
288 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroimaging **
247 247  )))
248 248  
249 249  |(% style="width:303px" %)(((
... ... @@ -254,7 +254,7 @@
254 254  (% class="small" %)Curation Scientist,
255 255  Phd Student
256 256  Neuroscience (M. Sc.)(%%)
257 -(% class="small" style="color:#4a5568" %)**Neuroanatomy and brain atlases**
299 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and brain atlases**
258 258  )))| | |
259 259  
260 260  
... ... @@ -268,8 +268,8 @@
268 268  (% class="small" %)Curation Scientist,
269 269  Phd Student
270 270  Sensors and Cognitive Psychology (M. Sc.)(%%)
271 -(% class="small" style="color:#4a5568" %)**Human-Computer Interaction**
272 -)))|(% style="width:303px" %)(((
313 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Human-Computer Interaction**
314 +)))|(% style="width:328px" %)(((
273 273  
274 274  
275 275  
... ... @@ -277,17 +277,12 @@
277 277  
278 278  
279 279  
280 -
281 -
282 -
283 -
284 -
285 285  **Lyuba Zehl**
286 286  
287 287  (% class="small" %)Knowledge Systems Engineer
288 288  Dr. rer. nat. (Systems Neuroscience)(%%)
289 -(% class="small" style="color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
290 -)))|(% style="width:303px" %) |
326 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
327 +)))|(% style="width:321px" %) |(% style="width:324px" %)
291 291  
292 292  ----
293 293  
... ... @@ -294,17 +294,6 @@
294 294  == **Add practical value to your shared data, model or software** ==
295 295  
296 296  
297 -==== **Add a tutorial or learning resource ** ====
298 -
299 -(% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
300 -(% style="color:#000000" %)//More information will follow//
301 -
302 -
303 -==== **Create a workflow** ====
304 -
305 -(% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
306 -(% style="color:#000000" %)//More information will follow//
307 -
308 308  ----
309 309  
310 310  === **Showcase shared data, models or software in other services** ===
... ... @@ -329,6 +329,19 @@
329 329  
330 330  ----
331 331  
358 +==== **Add a tutorial or learning resource ** ====
359 +
360 +(% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
361 +(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
362 +
363 +
364 +==== **Create a workflow** ====
365 +
366 +(% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
367 +(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
368 +
369 +----
370 +
332 332  === **The benefits of sharing data ** ===
333 333  
334 334  By sharing your data via EBRAINS, you gain access to the following benefits:
... ... @@ -337,7 +337,7 @@
337 337  
338 338  
339 339  
340 -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.
379 +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.
341 341  
342 342  ----
343 343  
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344 344  === **Frequently asked questions ** ===
345 345  
346 346  (((
347 -==== ====
386 +==== ====
348 348  
349 349  (((
350 ->The curation process is time consuming and difficult
389 +>Is the curation process time consuming and difficult?
351 351  )))
352 352  )))
353 353  
393 +
354 354  (% class="wikigeneratedid" id="HHowcanIshareA0models3F" %)
355 -Publishing your data naturally takes some time and effort but we will support you as much as possible. If communication is on a regular basis, we are able to finish basic curation - from the initial contact to dataset release - within two weeks.
395 +No, if communication is on a regular basis, we are able to finish curation within two weeks. Publishing your data naturally takes some effort but we will support you as much as possible.
356 356  
357 ->Sharing my data is not beneficial for me - only for others
397 +>Is sharing my data also beneficial for me or only for others?
358 358  
359 359  
360 360  When you publish your data via EBRAINS, we provide comprehensive data management support and safe long term storage - all free of charge. Additionally, your data can be cited, just like a scientific journal article. Sharing your data may even lead to new funding opportunities. Many funders specifically support projects that are part of the “Open Science” initiative.
361 361  
362 ->My data is too insignificant to share
402 +>Can my data be too insignificant to share?
363 363  
364 364  
365 -There is no such thing as insignificant data. Data that is considered insignificant for a given topic, may have great significance for another. By making “insignificant” data publicly available, other researchers may find something interesting that was off-topic for your own purposes.
405 +No, there is no such thing as insignificant data. Data that is considered insignificant for a given topic, may have great significance for another. By making “insignificant” data publicly available, other researchers may find something interesting that was off-topic for your own purposes.
366 366  
367 ->My data can easily be misused if I share it with the world
407 +>Can my data be easily misused if I share it?
368 368  
369 369  
370 -Your data will be covered by a Creative Commons license of your choice. There are a variety of licenses available, enabling you to prevent use for specific purposes, e.g. commercial use.
410 +No, your data will be covered by a Creative Commons license of your choice. There are a variety of licenses available, enabling you to prevent use for specific purposes, e.g. commercial use.
371 371  
372 ->I don't think I'm allowed to share my data
412 +>Can I share my data before my paper is published?
373 373  
374 374  
375 -Many institutions are still very careful about what can be shared and how, but the situation is constantly evolving. As a researcher providing data, you will be asked to fill out an ethics compliance survey which survey to ensure that data published through the EBRAINS platform has been collected according to EU regulations. We are working on solutions for sharing anonymised human data that complies with GDPR standards to protect the identity of research subjects.
415 +Yes, if you do not want to share your data before publishing the results in an article, you can publish your dataset with an embargo status. This will make it possible to find information about the data without making the data itself available, and give you a citeable DOI.
376 376  
377 ->I can't share my data before my paper is published
417 +>Can I lose my competitive edge if I share my data before I publish the associated paper?
378 378  
379 379  
380 -If you do not want to share your data before publishing the results in an article, you can publish your dataset with an embargo status. This will make it possible to find information about the data without making the data itself available, and give you a citeable DOI.
420 +No, publishing your data does not mean that others can use it however they want. Use of your data will require citation, and by choosing an appropriate Creative Commons licence you decide what others are allowed to do with it. If you still feel worried, you can publish your data under embargo, and in this way delay the date of data release, but still make it possible for others to find the information about the data.
381 381  
382 ->If I share my data before I publish the associated paper, I will lose my competitive edge
383 383  
384 -
385 -Publishing your data does not mean that others can use it however they want. Use of your data will require citation, and by choosing an appropriate Creative Commons licence you decide what others are allowed to do with it. If you still feel worried, you can publish your data under embargo, and in this way delay the date of data release, but still make it possible for others to find the information about the data.
386 -
387 -
388 388  ----
389 389  
390 390  == Contact ==
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