Changes for page Data Curation

Last modified by abonard on 2025/06/03 10:55
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edited by lzehl
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To version 229.1
edited by abonard
on 2025/05/22 15:11
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1 -XWiki.lzehl
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29 29  
30 30  == **Information to get started** ==
31 31  
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. **
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. **
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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84 84  //with all you need to know//
85 85  //to share data on EBRAINS: //
86 86  // //
87 -[[[[image:image-20230324171114-2.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
87 +[[~[~[image:image-20230324171114-2.png~|~|height="150" width="106"~]~]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
88 88  )))
89 89  
90 90  
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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 [[Curation request form>>https://nettskjema.no/a/277393#/]]. **
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]]. **
96 96  
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.
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.
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.
99 99  
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 -
107 107  ==== **2. Upload data ** ====
108 108  
109 109  (% class="box floatinginfobox" id="share-data-infographic" %)
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113 113  //with guidelines
114 114  on data organization: //
115 115  
116 -(% style="text-align:center" %)
117 -[[[[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/]]
111 +[[~[~[image:image-20230621121014-1.png~|~|data-xwiki-image-style-alignment="center" height="150" width="106"~]~]>>https://drive.ebrains.eu/lib/f5cf4964-f095-49bd-8c34-e4ffda05a497/file/ebrains-infographic-data-organisation.pdf/]]
118 118  )))
119 119  
120 120  (% 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. **
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128 128  **Opt. 2. **For larger datasets or datasets with a large amount of files, we recommend using a programmatic approach. The [[python script>>https://github.com/eapapp/ebrains-data-storage/tree/main/data-proxy]] is interactive and does not require any additional programming.
129 129  
130 130  
131 -EBRAINS offers secure, long-term storage at [[CSCS Swiss National Supercomputing Centre>>url:https://www.cscs.ch/]], with currently no upper limit of storage capacity. 
125 +EBRAINS offers secure, long-term storage at FENIX Supercomputing Centres in Europe.
132 132  
133 133  If a data collection is already uploaded elsewhere, we may link to the already existing repository.
134 134  
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171 171  about the EBRAINS Data//
172 172  //Descriptor//
173 173  // //
174 -[[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
168 +[[~[~[image:image-20230324171109-1.png~|~|height="150" width="106"~]~]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
175 175  )))
176 176  
177 177  ==== **5. Preview and publish** ====
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213 213  We recommend storing model code and/or configuration files in an online Git repository, for example on GitHub.
214 214  This repository should be public when you publish the model, but a private repository can be used for model development.
215 215  
216 -Alternatively, you can upload code to the Collab Drive or Bucket storage.
210 +Alternatively, you can upload code to the Collab Drive (in this case, curators will copy it to a read-only Bucket upon publication) or Bucket storage.
217 217  
218 -==== 4.Submit metadata ====
212 +==== 4. Submit metadata ====
219 219  
220 220  We recommend submitting metadata using the Model Catalog app, installed in your collab.
221 221  
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232 232  As development of your model proceeds, you can easily register new versions of the code,
233 233  and new parameterizations, by clicking "Add new version".
234 234  
235 -If you prefer not to use the app, you can instead fill in the [[Curation request form>>https://nettskjema.no/a/277393#/]].,
229 +If you prefer not to use the app, you can instead fill in the [[EBRAINS Curation Request Form>>https://nettskjema.no/a/386195]].,
236 236  and you will be contacted by e-mail with further instructions.
237 237  
238 238  ==== 5. Provide a reference dataset ====
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276 276  
277 277  === Step by Step - Software ===
278 278  
273 +We ask software developers to provide their metadata in the "CodeMeta" format. [[CodeMeta>>https://codemeta.github.io/]] is a common format for software metadata, supported by GitHub, Zenodo, FigShare, DataCite, and the US National Science Foundation.
279 279  
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 -)))
275 +1. Create a codemeta.json file for your software. There are several [[tools>>https://codemeta.github.io/tools/]] to help you do this, for example the [[CodeMeta generator>>https://codemeta.github.io/codemeta-generator]] app. Please fill in as many of the fields as possible.
276 +1. Place this file in the root folder of your code repository.
277 +1. Contact [[EBRAINS support>>https://www.ebrains.eu/contact/]] to request curation of your software, letting us know the URL of your code repository. If you need help hosting your code online, please also let us know.
278 +1. After a quality check, we integrate and publish the information contained in your codemeta.json file to the Knowledge Graph. Your software is then searchable and usable for the neuroscience community.
287 287  
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"]]
280 +When you release a new version of your software, just update the codemeta.json file in your repository. We will check the repository on a regular basis, and if the version identifier has changed the Knowledge Graph will be updated accordingly.
289 289  
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.
291 -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.
292 -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.
293 -
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]].
295 -
296 -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.
297 -
298 -
299 299  ----
300 300  
301 301  === Sharing human subject data ===
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332 332  
333 333  (% class="box floatinginfobox" %)
334 334  (((
335 -[[[[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]]
318 +[[~[~[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]]
336 336  )))
337 337  
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"]].
321 +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"]].
339 339  
340 340  For feedback, requests, or contributions, please get in touch with the openMINDS development team via
341 341  
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355 355  
356 356  
357 357  |(% colspan="2" %)**Viewer for 2D images**
358 -|[[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]].
341 +|[[image:MIO_screenshot.PNG]]|Integrate image data with //SeriesZoom viewer//: EBRAINS 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 [[viewer links available for this dataset>>https://search.kg.ebrains.eu/?category=Dataset&q=nr2f1#9677359c-73fa-4425-b8fa-3de794e9017a]] as an example.
359 359  |(% colspan="2" %)**Viewer for sequential atlas-registered 2D images with annotation options**
360 360  |[[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]].
361 361  |(% colspan="2" %)**Interactive 3D atlas viewer with options for data visualization**
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368 368  ==== **Add a tutorial or learning resource ** ====
369 369  
370 370  (% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
371 -(% style="--darkreader-inline-color:#e8e6e3; color:#000000" %)//More information will follow//
354 +(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
372 372  
373 373  
374 374  ==== **Create a workflow** ====
375 375  
376 376  (% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
377 -(% style="--darkreader-inline-color:#e8e6e3; color:#000000" %)//More information will follow//
360 +(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
378 378  
379 379  ----
380 380  
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384 384  
385 385  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.
386 386  
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]]. **
370 +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]]. **
388 388  
389 389  
390 390  ----
... ... @@ -428,92 +428,6 @@
428 428  No, publishing your data does not mean that others can use it however they want. Use of your data will require citation, and by choosing an appropriate Creative Commons licence you decide what others are allowed to do with it. If you still feel worried, you can publish your data under embargo, and in this way delay the date of data release, but still make it possible for others to find the information about the data.
429 429  
430 430  
431 -----
432 -
433 -== (% style="--darkreader-inline-color:#d2cec8; color:#1a202c; font-family:inherit; font-size:29px" %)**The curation team: meet the curators**(%%) ==
434 -
435 -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.
436 -
437 -The curators in EBRAINS are located in Oslo, Jülich, Trier and Paris. 
438 -
439 -
440 -**Located in Norway**
441 -
442 -|(% style="width:303px" %)(((
443 -[[image:My project2.jpg||height="209" width="167"]]
444 -
445 -**Archana Golla**
446 -
447 -(% class="small" %)Curation Scientist
448 -Neuroscience (PhD)(%%)
449 -(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Behavioral neuroscience and microscopy**
450 -)))|(% style="width:303px" %)(((
451 -[[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
452 -
453 -**Camilla H. Blixhavn**
454 -
455 -(% class="small" %)Curation Scientist,
456 -Phd Student
457 -Neuroscience (M. Sc.)(%%)
458 -(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Neuroanatomy and data integration**
459 -)))|(% style="width:303px" %)(((
460 -[[image:My project (1).jpg||height="209" width="167"]]
461 -
462 -**Ingrid Reiten**
463 -
464 -(% class="small" %)Curation Scientist,
465 -Phd Student
466 -Neuroscience (M. Sc.)(%%)
467 -(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Neuroanatomy and structural connectivity**
468 -)))|(% style="width:303px" %)(((
469 -[[image:My project1.jpg||height="209" width="167"]]
470 -
471 -**Sophia Pieschnik**
472 -
473 -(% class="small" %)Curation Scientist
474 -Neurocognitive Psychology (M. Sc.)(%%)
475 -(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Neuroimaging **
476 -)))
477 -
478 -|(% style="width:303px" %)(((
479 -[[image:My project.jpg||height="209" width="167"]]
480 -
481 -**Heidi Kleven**
482 -
483 -(% class="small" %)Curation Scientist,
484 -Phd Student
485 -Neuroscience (M. Sc.)(%%)
486 -(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Neuroanatomy and brain atlases**
487 -)))| | |
488 -
489 -
490 -\\**Located in Germany**
491 -
492 -|(% style="width:303px" %)(((
493 -[[image:My project (2).jpg||height="209" width="167"]]
494 -
495 -**Jan Gündling**
496 -
497 -(% class="small" %)Curation Scientist,
498 -Phd Student
499 -Sensors and Cognitive Psychology (M. Sc.)(%%)
500 -(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Human-Computer Interaction**
501 -)))|(% style="width:303px" %)(((
502 -[[image:Lyuba.jpg||height="209" width="167"]]
503 -
504 -**Lyuba Zehl**
505 -
506 -(% class="small" %)Knowledge Systems Engineer
507 -Dr. rer. nat. (Systems Neuroscience)(%%)
508 -(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
509 -)))|(% style="width:303px" %) |(% style="width:303px" %)
510 -
511 -----
512 -
513 -
514 -
515 -----
516 -
517 517  == Contact ==
518 518  
519 519  [[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
... ... @@ -526,6 +526,8 @@
526 526  
527 527  //Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Germany (PI: Timo Dicksheid)//
528 528  
426 +//Paris-Saclay Institute of Neuroscience, CNRS, Université Paris-Saclay, France (PI: Andrew P. Davison)//
427 +
529 529  ----
530 530  
531 531  == References ==
EBRAINS-Share-Software-4.pdf
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Data Curation