Changes for page data-curation-copy

Last modified by eapapp on 2023/07/04 16:46
From version 192.1
edited by eapapp
on 2023/06/13 10:26
Change comment: There is no comment for this version
To version 200.1
edited by ingrreit
on 2023/06/21 12:15
Change comment: There is no comment for this version

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1 -XWiki.eapapp
1 +XWiki.ingrreit
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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 -
88 88  )))
89 89  
90 90  
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106 106  
107 107  ==== **2. Upload data ** ====
108 108  
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: //
109 109  
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 +
110 110  (% 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. **
111 111  
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.
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.
113 113  
114 114  (% 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).**
115 115  
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157 157  (% class="box floatinginfobox" id="data-descriptor-infographic" %)
158 158  (((
159 159  (% style="text-align:center" %)
160 -//Download our infographic: //
161 -//The EBRAINS Data//
162 -//Descriptor at a glance//
168 +//Download our infographic
169 +about the EBRAINS Data//
170 +//Descriptor//
163 163  // //
164 164  [[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
165 -
166 166  )))
167 167  
168 168  ==== **5. Preview and publish** ====
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211 211  === Step by Step - Models ===
212 212  
213 213  
214 -~1. Request curation using the [[Curation request form>>https://nettskjema.no/a/277393#/]]. You will be contacted by a curator with more information.
221 +==== 1. Start early ====
215 215  
223 +It is not necessary to wait until you are ready to publish to register your model with EBRAINS.
216 216  
217 -//Additional information will be added soon.//
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.
218 218  
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 +
219 219  ----
220 220  
221 221  === Step by Step - Software ===
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244 244  
245 245  == **The openMINDS metadata framework** ==
246 246  
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 +
247 247  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]].
248 248  
249 249  For feedback, requests, or contributions, please get in touch with the openMINDS development team via
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322 322  Phd Student
323 323  Sensors and Cognitive Psychology (M. Sc.)(%%)
324 324  (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Human-Computer Interaction**
325 -)))|(% style="width:328px" %)(((
326 -
415 +)))|(% style="width:303px" %)(((
416 +[[image:Lyuba.jpg||height="209" width="167"]]
327 327  
328 -
329 -
330 -
331 -
332 -
333 -
334 -
335 335  **Lyuba Zehl**
336 336  
337 337  (% class="small" %)Knowledge Systems Engineer
338 338  Dr. rer. nat. (Systems Neuroscience)(%%)
339 339  (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
340 -)))|(% style="width:321px" %) |(% style="width:324px" %)
423 +)))|(% style="width:303px" %) |(% style="width:303px" %)
341 341  
342 342  ----
343 343  
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360 360  |(% colspan="2" %)**Use your research product in an interactive publication**
361 361  |[[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]].
362 362  
363 -
364 364  ----
365 365  
366 366  ==== **Add a tutorial or learning resource ** ====
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