Changes for page Data Curation

Last modified by abonard on 2025/06/03 10:55
From version 221.2
edited by adavison
on 2024/07/05 18:30
Change comment: There is no comment for this version
To version 218.1
edited by lzehl
on 2024/05/06 09:51
Change comment: There is no comment for this version

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1 -XWiki.adavison
1 +XWiki.lzehl
Content
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29 29  
30 30  == **Information to get started** ==
31 31  
32 -**[[REQUEST CURATION>>https://nettskjema.no/a/386195]] to share data, simulations, computational models, and software, - or to add a new version of an existing one. **
32 +**[[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. **
33 33  
34 34  Have you already published your data somewhere else? You can increase the exposure and impact of your shared dataset by also listing it on EBRAINS.
35 35  
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92 92  
93 93  
94 94  
95 -(% style="margin-right:10px" %)[[image:https://lh3.googleusercontent.com/zh7TvO6w04YGW9jIhfhmdT6CexdGs-AWOLfJXKRq7-tdHOu6ar1rOQx8o4rZevrjXqgPZ7-Ejv4b6X9XpgXuHpdUXi-mBTHIUnv5Vz-DktHt0sP-PZ3gE8XgZid3TV3swV1uTCBhHx11ge0pjP7RVxswGQ=s2048||height="85px;" width="91px;"]](%%)** Fill in the [[EBRAINS Curation Request Form>>https://nettskjema.no/a/386195]]. **
95 +(% style="margin-right:10px" %)[[image:https://lh3.googleusercontent.com/zh7TvO6w04YGW9jIhfhmdT6CexdGs-AWOLfJXKRq7-tdHOu6ar1rOQx8o4rZevrjXqgPZ7-Ejv4b6X9XpgXuHpdUXi-mBTHIUnv5Vz-DktHt0sP-PZ3gE8XgZid3TV3swV1uTCBhHx11ge0pjP7RVxswGQ=s2048||height="85px;" width="91px;"]](%%)** Fill in the [[Curation request form>>https://nettskjema.no/a/277393#/]]. **
96 96  
97 -The form collects general information about your data, allowing us to assess whether the dataset fits within the scope of EBRAINS. The submission generates a curation ID allowing us to track and follow up on incoming requests.
97 +This form collects preliminary information about your data, allowing us to assess whether the dataset fits within the scope of EBRAINS. The submission generates a curation ID allowing us to track the case.
98 98  
99 -You will also be asked to fill in information related to ethics and regulatory compliance, so that we can evaluate whether we can ethically and legally share the data via EBRAINS (earlier, this was recorded via a [[separate form>>https://nettskjema.no/a/224765]]). See below for information about the ethical and legal aspects concerning sharing of human subject data.
100 100  
100 +(% style="margin-right:10px" %)[[image:https://lh6.googleusercontent.com/yw442oS6BwZOlY-_0BoVxyCW3DrdcJ5ogCes92iOD16_rgNEVk56aNMDaVWXFfBLYv24bHzmGgBF9wg0szjH70xzuRTqxoQAeuy3knNO7axCHoyZDXwtyTcMgFnYwbOYxOT29LK-zchrUKLW6Mle93kOkQ=s2048||height="94px;" width="94px;"]](%%)**Fill in the [[Ethics and Regulatory compliance form>>https://nettskjema.no/a/224765]]**.
101 101  
102 +This form collects the necessary information needed for us to evaluate whether we can ethically and legally share the data via EBRAINS.
103 +
104 +See below for information about the ethical and legal aspects concerning sharing of human subject data.
105 +
106 +
102 102  ==== **2. Upload data ** ====
103 103  
104 104  (% class="box floatinginfobox" id="share-data-infographic" %)
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210 210  
211 211  Alternatively, you can upload code to the Collab Drive or Bucket storage.
212 212  
213 -==== 4. Submit metadata ====
218 +==== 4.Submit metadata ====
214 214  
215 215  We recommend submitting metadata using the Model Catalog app, installed in your collab.
216 216  
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227 227  As development of your model proceeds, you can easily register new versions of the code,
228 228  and new parameterizations, by clicking "Add new version".
229 229  
230 -If you prefer not to use the app, you can instead fill in the [[EBRAINS Curation Request Form>>https://nettskjema.no/a/386195]].,
235 +If you prefer not to use the app, you can instead fill in the [[Curation request form>>https://nettskjema.no/a/277393#/]].,
231 231  and you will be contacted by e-mail with further instructions.
232 232  
233 233  ==== 5. Provide a reference dataset ====
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271 271  
272 272  === Step by Step - Software ===
273 273  
274 -1. Fill in the [[EBRAINS Curation 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.
279 +
280 +(% class="box floatinginfobox" id="software-curation-infographic" %)
281 +(((
282 +(% style="text-align:center" %)
283 +//Software curation at a glance//
284 +// //
285 +[[[[image:Thumb2.png||alt="EBRAINS-Share-Software.pdf" height="287" width="197"]]>>attach:EBRAINS-Share-Software-4.pdf]]
286 +)))
287 +
288 +(% 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"]]
289 +
290 +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.
275 275  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.
276 276  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.
277 277  
278 -If you want to add a new version to an already curated software, please request this via the [[EBRAINS Curation Request Form>>https://www.ebrains.eu/tools/ebrains-curation-request-form]].
294 +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]].
279 279  
280 280  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.
281 281  
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319 319  [[[[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]]
320 320  )))
321 321  
322 -openMINDS is a community-driven, open-source metadata framework for linked data, as used in graph database systems, such as the EBRAINS Knowledge Graph. It is composed of multiple metadata models with interlinked schemas, libraries of serviceable metadata instances, and supportive tooling (e.g., [[openMINDS Python>>https://github.com/openMetadataInitiative/openMINDS_Python]] or [[openMINDS Matlab>>https://github.com/openMetadataInitiative/openMINDS_MATLAB]]). A full documentation (for users and contributors) of the openMINDS framework can be found on [[ReadTheDocs>>https://openminds-documentation.readthedocs.io||rel="noopener noreferrer" target="_blank"]].
338 +openMINDS is a community-driven, open-source metadata framework for linked data, as used in graph database systems, such as the EBRAINS Knowledge Graph. It is composed of multiple metadata models with interlinked schemas, libraries of serviceable metadata instances, and supportive tooling (e.g., [[openMINDS Python>>https://github.com/openMetadataInitiative/openMINDS_Python]] or [[openMINDS Matlab>>https://github.com/openMetadataInitiative/openMINDS_MATLAB]]). A full documentation (for users and contributors) of the openMINDS framework can be found on [[ReadTheDocs>>https://openminds-documentation.readthedocs.io||target="_blank"]].
323 323  
324 324  For feedback, requests, or contributions, please get in touch with the openMINDS development team via
325 325  
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352 352  ==== **Add a tutorial or learning resource ** ====
353 353  
354 354  (% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
355 -(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
371 +(% style="--darkreader-inline-color:#e8e6e3; color:#000000" %)//More information will follow//
356 356  
357 357  
358 358  ==== **Create a workflow** ====
359 359  
360 360  (% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
361 -(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
377 +(% style="--darkreader-inline-color:#e8e6e3; color:#000000" %)//More information will follow//
362 362  
363 363  ----
364 364  
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368 368  
369 369  In EBRAINS, all datasets, models and software shared go through a streamlined curation process that ensures relevant annotation of the data using the [[openMINDS>>url:https://github.com/HumanBrainProject/openMINDS]] metadata framework and integration into the [[EBRAINS Knowledge Graph>>url:https://docs.kg.ebrains.eu/]] metadata management system. The research products are Findable and Accessible through the [[Knowledge Graph Search>>url:https://search.kg.ebrains.eu/?category=Dataset]] as dataset/model/software cards that display further information regarding the dataset's Interoperability and Reusability.
370 370  
371 -To further specify how EBRAINS aligns with the FAIR principles, we have assessed the FAIRness of datasets shared in the EBRAINS Knowledge Graph following the [[FAIRsFAIR Data Object Assessment Metrics>>https://zenodo.org/record/6461229||style="background-color: rgb(255, 255, 255); --darkreader-inline-bgcolor: #1c1e1f;"]]: see our **[[FAIR assessment of EBRAINS datasets>>doc:.FAIR assessment of EBRAINS datasets.WebHome]]. **
387 +To further specify how EBRAINS aligns with the FAIR principles, we have assessed the FAIRness of datasets shared in the EBRAINS Knowledge Graph following the [[FAIRsFAIR Data Object Assessment Metrics>>https://zenodo.org/record/6461229||style="background-color: rgb(255, 255, 255); --darkreader-inline-bgcolor: #181a1b;"]]: see our **[[FAIR assessment of EBRAINS datasets>>doc:.FAIR assessment of EBRAINS datasets.WebHome]]. **
372 372  
373 373  
374 374  ----
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414 414  
415 415  ----
416 416  
417 -== (% style="--darkreader-inline-color:#f1ede6; color:#1a202c; font-family:inherit; font-size:29px" %)**The curation team: meet the curators**(%%) ==
433 +== (% style="--darkreader-inline-color:#d2cec8; color:#1a202c; font-family:inherit; font-size:29px" %)**The curation team: meet the curators**(%%) ==
418 418  
419 419  The EBRAINS curators help researchers publish their research using the EBRAINS Research Infrastructure. A curator’s job is similar to the job of an editor of a scientific journal, checking the data is organized, understandable, accessible and sufficiently described.
420 420  
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430 430  
431 431  (% class="small" %)Curation Scientist
432 432  Neuroscience (PhD)(%%)
433 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Behavioral neuroscience and microscopy**
449 +(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Behavioral neuroscience and microscopy**
434 434  )))|(% style="width:303px" %)(((
435 435  [[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
436 436  
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439 439  (% class="small" %)Curation Scientist,
440 440  Phd Student
441 441  Neuroscience (M. Sc.)(%%)
442 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and data integration**
458 +(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Neuroanatomy and data integration**
443 443  )))|(% style="width:303px" %)(((
444 444  [[image:My project (1).jpg||height="209" width="167"]]
445 445  
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448 448  (% class="small" %)Curation Scientist,
449 449  Phd Student
450 450  Neuroscience (M. Sc.)(%%)
451 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and structural connectivity**
467 +(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Neuroanatomy and structural connectivity**
452 452  )))|(% style="width:303px" %)(((
453 453  [[image:My project1.jpg||height="209" width="167"]]
454 454  
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456 456  
457 457  (% class="small" %)Curation Scientist
458 458  Neurocognitive Psychology (M. Sc.)(%%)
459 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroimaging **
475 +(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Neuroimaging **
460 460  )))
461 461  
462 462  |(% style="width:303px" %)(((
... ... @@ -467,7 +467,7 @@
467 467  (% class="small" %)Curation Scientist,
468 468  Phd Student
469 469  Neuroscience (M. Sc.)(%%)
470 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and brain atlases**
486 +(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Neuroanatomy and brain atlases**
471 471  )))| | |
472 472  
473 473  
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481 481  (% class="small" %)Curation Scientist,
482 482  Phd Student
483 483  Sensors and Cognitive Psychology (M. Sc.)(%%)
484 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Human-Computer Interaction**
500 +(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Human-Computer Interaction**
485 485  )))|(% style="width:303px" %)(((
486 486  [[image:Lyuba.jpg||height="209" width="167"]]
487 487  
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489 489  
490 490  (% class="small" %)Knowledge Systems Engineer
491 491  Dr. rer. nat. (Systems Neuroscience)(%%)
492 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
508 +(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
493 493  )))|(% style="width:303px" %) |(% style="width:303px" %)
494 494  
495 495  ----
Public

Data Curation