Changes for page data-curation-copy

Last modified by eapapp on 2023/07/04 16:46
From version 205.1
edited by ingrreit
on 2023/07/04 14:27
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To version 194.2
edited by adavison
on 2023/06/14 14:59
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17 17  {{/html}}
18 18  
19 19  
20 -(% class="wikigeneratedid" id="HPublishingneurosciencedata2CmodelsandsoftwareviaEBRAINS" %)
21 -(% style="font-size:2em" %)**Publishing neuroscience data, models and software via EBRAINS**
20 +== Publishing neuroscience data, models and software via EBRAINS ==
22 22  
22 +
23 23  (% class="wikigeneratedid" %)
24 24  The aim of this collab is to provide you with detailed information about publishing data, simulations, computational models, and software via EBRAINS. If you want a quick overview of the sharing process, see [[https:~~/~~/ebrains.eu/service/share-data>>https://ebrains.eu/service/share-data]].
25 25  
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83 83  //to share data on EBRAINS: //
84 84  // //
85 85  [[[[image:image-20230324171114-2.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
86 +
87 +
86 86  )))
87 87  
88 88  
... ... @@ -104,20 +104,10 @@
104 104  
105 105  ==== **2. Upload data ** ====
106 106  
107 -(% class="box floatinginfobox" id="share-data-infographic" %)
108 -(((
109 -(% style="text-align:center" %)
110 -//Download our infographic//
111 -//with guidelines
112 -on data organization: //
113 113  
114 -(% style="text-align:center" %)
115 -[[[[image:image-20230621121014-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/lib/f5cf4964-f095-49bd-8c34-e4ffda05a497/file/ebrains-infographic-data-organisation.pdf/]]
116 -)))
117 -
118 118  (% style="margin-right:10px" %)[[image:https://lh5.googleusercontent.com/sieKO-kW8O18iPaUyonwyo4UfHBmtc2E9BDnjbx52j6J_uGmm-OzGAo7sloMk3sYwKa6QW3hYQsOA9N4H7uGQpca088Wrk0Nurpt_J3B0-NSbcaPNdZIh21otQcG6jnAxLGiKoEvkTyaDGTMk3fu7me8mQ=s2048||height="94px;" width="94px;"]](%%)**Ensure data is structured consistently prior to upload. **
119 119  
120 -We look for organized data, not organized according to our standard. This is to support the broadest degree of sharing possible. We do however require that the data is organized in a consistent and precise manner. Please see our// //[[guidelines on data organization>>https://drive.ebrains.eu/smart-link/25299f04-c4e5-4028-8f5f-3b8208f9a532/]] for further guidance.
112 +We look for organized data, not organized according to our standard. This is to support the broadest degree of sharing possible. We do however require that the data is organized in a consistent and precise manner. Please see our// //[[collection of guidelines on data organization>>https://drive.ebrains.eu/smart-link/25299f04-c4e5-4028-8f5f-3b8208f9a532/]] for further guidance.
121 121  
122 122  (% style="margin-right:10px" %)[[image:https://lh5.googleusercontent.com/EWtYwfVlbeC-jqPasgmzidqc50GrkKIEgwXeUeql8aaMHIukmFdWEy0nufVWWATbxDDK3XwwZEDmASrbpCsBk1u0HpAd8x4ZgAMsMPRcWyrb9etlV6FgKE_QN2e6SqKxHE0rzkR8uI1rRW_5z21TFGYVnw=s2048||height="91px;" width="91px;"]](%%)**Upload data to EBRAINS Storage, either using a drag-and-drop solution (opt. 1) or an interactive python script (opt. 2).**
123 123  
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165 165  (% class="box floatinginfobox" id="data-descriptor-infographic" %)
166 166  (((
167 167  (% style="text-align:center" %)
168 -//Download our infographic
169 -about the EBRAINS Data//
170 -//Descriptor//
160 +//Download our infographic: //
161 +//The EBRAINS Data//
162 +//Descriptor at a glance//
171 171  // //
172 172  [[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
165 +
173 173  )))
174 174  
175 175  ==== **5. Preview and publish** ====
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180 180  Once a Curator has assembled the dataset in the EBRAINS Knowledge Graph, combining the data, metadata and data descriptor, the data provider will receive a private URL for previewing the dataset prior to release. We need an official approval from the data custodian{{footnote}}The Data Custodian is responsible for the content and quality of the Data and metadata, and is the person to be contacted by EBRAINS CS in case of any misconduct related to the Data. It is the obligation of a Data Custodian to keep EBRAINS informed about changes in the contact information of the authors of the Datasets provided by them ([[EBRAINS Data Provision Protocol - version 1.1>>https://strapi-prod.sos-ch-dk-2.exo.io/EBRAINS_Data_Provision_Protocol_dfe0dcb104.pdf]]).{{/footnote}} to release the dataset. Once released, a [[DataCite DOI>>https://datacite.org/]] will be generated for the dataset. If the identical data collection has received a DOI elsewhere, we recommend re-using the already issued DOI.
181 181  
182 182  
176 +----
183 183  
178 +==== ====
184 184  
180 +==== **Sharing human subject data** ====
181 +
182 +(% class="box floatinginfobox" %)
183 +(((
184 +**Human subject data that can be shared on EBRAINS:**
185 +// //
186 +// - Post-mortem data//
187 +// - Aggregated data//
188 +// - Strongly pseudonymized or de-identified subject data//
189 +// with a legal basis for sharing (e.g. Informed Consent)//
190 +// //
191 +
192 +(% class="small" %)
193 +//If you have human data that does not qualify as any of the above,//
194 +//please [[get in touch>>https://www.ebrains.eu/contact/]] and we will clarify the available options.//
195 +)))
196 +
197 +
198 +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]].
199 +
200 +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).
201 +
202 +The Human Data Gateway (HDG) was introduced in February 2021 as a response to the needs of multiple data providers who are bringing human subject data to EBRAINS. HDG covers the sharing of strongly pseudonymized or de-identified data, a limited range human subject data without direct identifiers and with very few indirect identifiers.
203 +
204 +The HDG adds an an authentication layer on top of the data. This means that **data users **must request access to the data (via their EBRAINS account) and will receive access provided they actively accept the [[EBRAINS Access Policy>>https://ebrains.eu/terms#access-policy]], the [[EBRAINS General Terms of Use>>https://ebrains.eu/terms#general-terms-of-use]], and the [[EBRAINS Data Use Agreement>>https://ebrains.eu/terms#data-use-agreement]]. The account holder also have to accept that information about their request and access to specific data under HDG is being tracked and stored. **Data owners** must be aware that sharing under the HDG affects the legal responsibilities for the data. They must agree to joint control of the data (see the [[Data Provision Protocol v1>>url:https://strapi-prod.sos-ch-dk-2.exo.io/EBRAINS_Data_Provision_Protocol_dfe0dcb104.pdf]], section 1.4 - 1.5) and the Data Protection Officers of the responsible institutions must have accepted that the data can be shared under HDG.
205 +
206 +The HDG is an extension of the existing services and does not replace the future EBRAINS Service for sensitive data (planned for 2024) which is outside the domain of the current EBRAINS Data and Knowledge services.
207 +
208 +
185 185  ----
186 186  
187 187  === Step by Step - Models ===
188 188  
189 189  
214 +
215 +
190 190  ==== 1. Start early ====
191 191  
192 192  It is not necessary to wait until you are ready to publish to register your model with EBRAINS.
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206 206  Collabs are also useful for storing simulation results, adding documentation for your model,
207 207  and/or providing tutorials in Jupyter notebooks.
208 208  
209 -==== 3. Upload code ====
210 210  
211 -We recommend storing model code and/or configuration files in an online Git repository, for example on GitHub.
212 -This repository should be public when you publish the model, but a private repository can be used for model development.
213 213  
214 -Alternatively, you can upload code to the Collab Drive or Bucket storage.
215 215  
216 -==== 4.Submit metadata ====
238 +~1. Request curation using the [[Curation request form>>https://nettskjema.no/a/277393#/]]. You will be contacted by a curator with more information.
217 217  
218 -We recommend submitting metadata using the Model Catalog app, installed in your collab.
219 219  
220 -To install it:
241 +//Additional information will be added soon.//
221 221  
222 -1. click the "+ Create" button
223 -1. in the "Create Page" form, add a title, such as "Model Catalog", and select "Community App", then click "Create"
224 -1. scroll down until you find the "Model Catalog" app, click "Select", then "Save & View"
225 -
226 -You will then see a table of all the models and validation tests associated with this collab.
227 -If this is your first time using the app, the table will probably be empty.
228 -To add your model, click "+", fill in the form, then click "Add model".
229 -
230 -As development of your model proceeds, you can easily register new versions of the code,
231 -and new parameterizations, by clicking "Add new version".
232 -
233 -If you prefer not to use the app, you can instead fill in the [[Curation request form>>https://nettskjema.no/a/277393#/]].,
234 -and you will be contacted by e-mail with further instructions.
235 -
236 -==== 5. Provide a reference dataset ====
237 -
238 -Once you're ready to publish your model entry in the EBRAINS Knowledge Graph,
239 -we encourage you to provide a dataset containing the simulation results produced by your model,
240 -following the process under "Step by step - Data" above.
241 -
242 -These reference data will be linked to the model, and will be helpful to anyone trying to
243 -reuse your model.
244 -
245 -We will soon introduce a "Reproducible" badge for all models that include a reference dataset,
246 -and whose simulation results can be reproduced by an EBRAINS curator.
247 -
248 -==== 6. Request publication, preview and publish ====
249 -
250 -Until you request your model entry to be published in the EBRAINS Knowledge Graph,
251 -only members of the collab will be able to view the model entry, in the Model Catalog app
252 -or using the Model Validation Python client.
253 -
254 -After publication, the model will appear in the [[EBRAINS public search results>>https://search.kg.ebrains.eu/?category=Model||rel="noopener noreferrer" target="_blank"]], and will receive a DOI.
255 -
256 -To request publication, [[contact EBRAINS support>>https://ebrains.eu/support||rel="noopener noreferrer" target="_blank"]], providing the collab name and the model name or ID.
257 -
258 -
259 -Curators will then perform a number of checks:
260 -
261 -1. Does the model description provide sufficient context to understand the purpose and use of the model?
262 -1. Does the code repository contain a licence file, explaining the conditions for reusing the code?
263 -1. Does the model have a clearly defined version identifier (e.g. v1.0)? For models in a Git repository, the version identifier should match the name of a tag or release.
264 -
265 -The curators will also take a snapshot of your model code.
266 -
267 -* For models in public Git repositories, we archive a copy of the repository in [[Software Heritage>>https://www.softwareheritage.org/||rel="noopener noreferrer" target="_blank"]].
268 -* For models in a collab Bucket or Drive, we make a read-only copy of the code in a public container in the EBRAINS repository.
269 -
270 -Once this is done, you will be invited to review a preview of how the model entry will appear in the KG Search,
271 -and will have the opportunity to request modifications prior to approval and publication.
272 -
273 273  ----
274 274  
275 275  === Step by Step - Software ===
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296 296  
297 297  ----
298 298  
299 -=== Sharing human subject data ===
300 -
301 -(% class="box floatinginfobox" %)
302 -(((
303 -**Human subject data that can be shared on EBRAINS:**
304 -// //
305 -// - Post-mortem data//
306 -// - Aggregated data//
307 -// - Strongly pseudonymized or de-identified subject data//
308 -// with a legal basis for sharing (e.g. Informed Consent)//
309 -// //
310 -
311 -(% class="small" %)
312 -//If you have human data that does not qualify as any of the above,//
313 -//please [[get in touch>>https://www.ebrains.eu/contact/]] and we will clarify the available options.//
314 -)))
315 -
316 -
317 -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]].
318 -
319 -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).
320 -
321 -The Human Data Gateway (HDG) was introduced in February 2021 as a response to the needs of multiple data providers who are bringing human subject data to EBRAINS. HDG covers the sharing of strongly pseudonymized or de-identified data, a limited range human subject data without direct identifiers and with very few indirect identifiers.
322 -
323 -The HDG adds an an authentication layer on top of the data. This means that **data users **must request access to the data (via their EBRAINS account) and will receive access provided they actively accept the [[EBRAINS Access Policy>>https://ebrains.eu/terms#access-policy]], the [[EBRAINS General Terms of Use>>https://ebrains.eu/terms#general-terms-of-use]], and the [[EBRAINS Data Use Agreement>>https://ebrains.eu/terms#data-use-agreement]]. The account holder also have to accept that information about their request and access to specific data under HDG is being tracked and stored. **Data owners** must be aware that sharing under the HDG affects the legal responsibilities for the data. They must agree to joint control of the data (see the [[Data Provision Protocol v1>>url:https://strapi-prod.sos-ch-dk-2.exo.io/EBRAINS_Data_Provision_Protocol_dfe0dcb104.pdf]], section 1.4 - 1.5) and the Data Protection Officers of the responsible institutions must have accepted that the data can be shared under HDG.
324 -
325 -The HDG is an extension of the existing services and does not replace the future EBRAINS Service for sensitive data (planned for 2024) which is outside the domain of the current EBRAINS Data and Knowledge services.
326 -
327 -----
328 -
329 329  == **The openMINDS metadata framework** ==
330 330  
331 331  (% class="box floatinginfobox" %)
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350 350  The curators in EBRAINS are located in Oslo, Jülich, Trier and Paris. 
351 351  
352 352  
353 -**Located in Norway**
293 +**Located in Norway:**
354 354  
355 355  |(% style="width:303px" %)(((
356 356  [[image:My project2.jpg||height="209" width="167"]]
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400 400  )))| | |
401 401  
402 402  
403 -\\**Located in Germany**
343 +\\**Located in Germany:**
404 404  
405 405  |(% style="width:303px" %)(((
406 406  [[image:My project (2).jpg||height="209" width="167"]]
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411 411  Phd Student
412 412  Sensors and Cognitive Psychology (M. Sc.)(%%)
413 413  (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Human-Computer Interaction**
414 -)))|(% style="width:303px" %)(((
415 -[[image:Lyuba.jpg||height="209" width="167"]]
354 +)))|(% style="width:328px" %)(((
355 +
416 416  
357 +
358 +
359 +
360 +
361 +
362 +
363 +
417 417  **Lyuba Zehl**
418 418  
419 419  (% class="small" %)Knowledge Systems Engineer
420 420  Dr. rer. nat. (Systems Neuroscience)(%%)
421 421  (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
422 -)))|(% style="width:303px" %) |(% style="width:303px" %)
369 +)))|(% style="width:321px" %) |(% style="width:324px" %)
423 423  
424 424  ----
425 425  
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509 509  [[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
510 510  
511 511  
512 -== Affiliated laboratories ==
513 -
514 -
515 -//Institute of Basic Medical Sciences,** **University of Oslo, Norway (PI: Jan G. Bjaalie, Trygve B. Leergaard)//
516 -
517 -//Human-Computer Interaction, University of Trier, Germany  //
518 -
519 -//Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Germany (PI: Timo Dicksheid)//
520 -
521 -
522 522  == References ==
523 523  
524 524  {{putFootnotes/}}
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