Changes for page data-curation-copy

Last modified by eapapp on 2023/07/04 16:46
From version 201.1
edited by ingrreit
on 2023/06/26 13:34
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To version 192.1
edited by eapapp
on 2023/06/13 10:26
Change comment: There is no comment for this version

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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  
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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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218 218  === Step by Step - Models ===
219 219  
220 220  
221 -==== 1. Start early ====
214 +~1. Request curation using the [[Curation request form>>https://nettskjema.no/a/277393#/]]. You will be contacted by a curator with more information.
222 222  
223 -It is not necessary to wait until you are ready to publish to register your model with EBRAINS.
224 224  
225 -By registering a model early in your project, you can take advantage of EBRAINS tools
226 -to keep track of simulations and to share them with your collaborators.
217 +//Additional information will be added soon.//
227 227  
228 -==== 2. Create/choose a Collab workspace ====
229 -
230 -We use EBRAINS Collaboratory "collab" workspaces to help manage the model curation process.
231 -
232 -In particular, we use collab membership (the "Team") to control who can view or edit your model metadata prior to publication.
233 -
234 -It is up to you whether you create a new collab for each model, or reuse an existing collab
235 -(it is no problem to have multiple models associated with a single collab).
236 -
237 -Collabs are also useful for storing simulation results, adding documentation for your model,
238 -and/or providing tutorials in Jupyter notebooks.
239 -
240 -==== 3. Upload code ====
241 -
242 -We recommend storing model code and/or configuration files in an online Git repository, for example on GitHub.
243 -This repository should be public when you publish the model, but a private repository can be used for model development.
244 -
245 -Alternatively, you can upload code to the Collab Drive or Bucket storage.
246 -
247 -==== 4.Submit metadata ====
248 -
249 -We recommend submitting metadata using the Model Catalog app, installed in your collab.
250 -
251 -To install it:
252 -
253 -1. click the "+ Create" button
254 -1. in the "Create Page" form, add a title, such as "Model Catalog", and select "Community App", then click "Create"
255 -1. scroll down until you find the "Model Catalog" app, click "Select", then "Save & View"
256 -
257 -You will then see a table of all the models and validation tests associated with this collab.
258 -If this is your first time using the app, the table will probably be empty.
259 -To add your model, click "+", fill in the form, then click "Add model".
260 -
261 -As development of your model proceeds, you can easily register new versions of the code,
262 -and new parameterizations, by clicking "Add new version".
263 -
264 -If you prefer not to use the app, you can instead fill in the [[Curation request form>>https://nettskjema.no/a/277393#/]].,
265 -and you will be contacted by e-mail with further instructions.
266 -
267 -==== 5. Provide a reference dataset ====
268 -
269 -Once you're ready to publish your model entry in the EBRAINS Knowledge Graph,
270 -we encourage you to provide a dataset containing the simulation results produced by your model,
271 -following the process under "Step by step - Data" above.
272 -
273 -These reference data will be linked to the model, and will be helpful to anyone trying to
274 -reuse your model.
275 -
276 -We will soon introduce a "Reproducible" badge for all models that include a reference dataset,
277 -and whose simulation results can be reproduced by an EBRAINS curator.
278 -
279 -==== 6. Request publication, preview and publish ====
280 -
281 -Until you request your model entry to be published in the EBRAINS Knowledge Graph,
282 -only members of the collab will be able to view the model entry, in the Model Catalog app
283 -or using the Model Validation Python client.
284 -
285 -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.
286 -
287 -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.
288 -
289 -
290 -Curators will then perform a number of checks:
291 -
292 -1. Does the model description provide sufficient context to understand the purpose and use of the model?
293 -1. Does the code repository contain a licence file, explaining the conditions for reusing the code?
294 -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.
295 -
296 -The curators will also take a snapshot of your model code.
297 -
298 -* 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"]].
299 -* 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.
300 -
301 -Once this is done, you will be invited to review a preview of how the model entry will appear in the KG Search,
302 -and will have the opportunity to request modifications prior to approval and publication.
303 -
304 304  ----
305 305  
306 306  === Step by Step - Software ===
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329 329  
330 330  == **The openMINDS metadata framework** ==
331 331  
332 -(% class="box floatinginfobox" %)
333 -(((
334 -[[[[image:https://github.com/HumanBrainProject/openMINDS/raw/main/img/light_openMINDS-logo.png||alt="openMINDS logo" height="87" width="164"]]>>https://github.com/HumanBrainProject/openMINDS]]
335 -)))
336 -
337 337  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]].
338 338  
339 339  For feedback, requests, or contributions, please get in touch with the openMINDS development team via
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412 412  Phd Student
413 413  Sensors and Cognitive Psychology (M. Sc.)(%%)
414 414  (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Human-Computer Interaction**
415 -)))|(% style="width:303px" %)(((
416 -[[image:Lyuba.jpg||height="209" width="167"]]
325 +)))|(% style="width:328px" %)(((
326 +
417 417  
328 +
329 +
330 +
331 +
332 +
333 +
334 +
418 418  **Lyuba Zehl**
419 419  
420 420  (% class="small" %)Knowledge Systems Engineer
421 421  Dr. rer. nat. (Systems Neuroscience)(%%)
422 422  (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
423 -)))|(% style="width:303px" %) |(% style="width:303px" %)
340 +)))|(% style="width:321px" %) |(% style="width:324px" %)
424 424  
425 425  ----
426 426  
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443 443  |(% colspan="2" %)**Use your research product in an interactive publication**
444 444  |[[image:LivePaper_screenshot.PNG]]|Add your data, models or software to a// Live paper. //Read more about [[Live papers on ebrains.eu>>https://www.ebrains.eu/data/live-papers/live-papers]].
445 445  
363 +
446 446  ----
447 447  
448 448  ==== **Add a tutorial or learning resource ** ====
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