Changes for page data-curation-copy

Last modified by eapapp on 2023/07/04 16:46
From version 200.1
edited by ingrreit
on 2023/06/21 12:15
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To version 190.1
edited by eapapp
on 2023/06/08 17:08
Change comment: There is no comment for this version

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1 -XWiki.ingrreit
1 +XWiki.eapapp
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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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433 433  
434 434  Below is a list of additional services that data, models or software shared via EBRAINS can benefit from. EBRAINS is continuously looking to increase the number of interoperable services.
435 435  
353 +(% cellpadding="15" style="margin-right:auto" %)
354 +|(% colspan="2" %)**Viewer for 2D images**|(% colspan="2" rowspan="1" %)**Viewer for sequential atlas-registered 2D images with annotation options**
355 +|(% style="white-space:nowrap; width:320px" %)[[image:MIO_screenshot.PNG||alt="MIO viewer" height="242" style="float:left" width="300"]]|Integrate image data with //the Mio viewer//: EBRAINS Multi-Image OpenSeadragon viewer provides an intuitive way of navigating high-resolution 2D image series. It has browser-based classic pan and zoom capabilities. A collection can be displayed as a filmstrip (Filmstrip Mode) or as a table (Collection Mode) with adjustable number of row and columns. See [[Mio viewer links available for this dataset>>https://search.kg.ebrains.eu/?category=Dataset&q=nr2f1#9677359c-73fa-4425-b8fa-3de794e9017a]] as an example. MioViewer user manual is found [[here>>https://multi-image-osd.readthedocs.io/en/latest/index.html]].|(% style="white-space:nowrap; width:320px" %)**[[image:LZ_screenshot.PNG||alt="LocaliZoom viewer" height="250" style="float:left" width="300"]]**|Integrate atlas-registered 2D image data with //the LocaliZoom viewer//: The EBRAINS LocaliZoom serial section viewer displays series of registered 2D section images with atlas overlay, allowing the users to zoom into high-resolution images and have information about the brain regions. See the [[LocaliZoom links available for this dataset>>https://doi.org/10.25493/T686-7BX]] as an example. LocaliZoom user manual is found [[here>>https://localizoom.readthedocs.io/en/latest/index.html]].
356 +|(% colspan="2" rowspan="1" %)**Use your research product in an interactive publication**|(% colspan="2" rowspan="1" %)**Interactive 3D atlas viewer with options for data visualization**
357 +|[[image:LivePaper_screenshot.PNG||alt="LivePaper" height="341" style="float:left" width="300"]]|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]].|[[image:3Datlas_screenshot.PNG||alt="Siibra explorer" height="204" style="float:left" width="300"]]|Upload your data to //the Siibra//-explorer: The siibra-explorer is used for visualizing volumetric brain data in all the brain atlases provided by EBRAINS (Human, Monkey, Rat and Mouse). The siibra-explorer viewer uses siibra-api to enable navigation of brain region hierarchies, maps in different coordinate spaces, and linked regional data features. Furthermore, it is connected with the siibra toolsuite providing several analytical workflows. To learn more about how to register your data to atlases, read about the [[Atlas services on ebrains.eu>>https://ebrains.eu/services/atlases#Integratedatatoanatlas]].
436 436  
437 -|(% colspan="2" %)**Viewer for 2D images**
438 -|[[image:MIO_screenshot.PNG]]|Integrate image data with //the Mio viewer//: EBRAINS Multi-Image OpenSeadragon viewer provides an intuitive way of navigating high-resolution 2D image series. It has browser-based classic pan and zoom capabilities. A collection can be displayed as a filmstrip (Filmstrip Mode) or as a table (Collection Mode) with adjustable number of row and columns. See [[Mio viewer links available for this dataset>>https://search.kg.ebrains.eu/?category=Dataset&q=nr2f1#9677359c-73fa-4425-b8fa-3de794e9017a]] as an example. MioViewer user manual is found [[here>>https://multi-image-osd.readthedocs.io/en/latest/index.html]].
439 -|(% colspan="2" %)**Viewer for sequential atlas-registered 2D images with annotation options**
440 -|[[image:LZ_screenshot.PNG]]|Integrate atlas-registered 2D image data with //the LocaliZoom viewer//: The EBRAINS LocaliZoom serial section viewer displays series of registered 2D section images with atlas overlay, allowing the users to zoom into high-resolution images and have information about the brain regions. See the [[LocaliZoom links available for this dataset>>https://doi.org/10.25493/T686-7BX]] as an example. LocaliZoom user manual is found [[here>>https://localizoom.readthedocs.io/en/latest/index.html]].
441 -|(% colspan="2" %)**Interactive 3D atlas viewer with options for data visualization**
442 -|[[image:3Datlas_screenshot.PNG]]|Upload your data to the //Siibra-explorer//: The siibra-explorer is used for visualizing volumetric brain data in all the brain atlases provided by EBRAINS (Human, Monkey, Rat and Mouse). The siibra-explorer viewer uses siibra-api to enable navigation of brain region hierarchies, maps in different coordinate spaces, and linked regional data features. Furthermore, it is connected with the siibra toolsuite providing several analytical workflows. To learn more about how to register your data to atlases, read about the [[Atlas services on ebrains.eu>>https://ebrains.eu/services/atlases#Integratedatatoanatlas]].
443 -|(% colspan="2" %)**Use your research product in an interactive publication**
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 -
446 446  ----
447 447  
448 448  ==== **Add a tutorial or learning resource ** ====
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