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Changes for page Data Curation

Last modified by abonard on 2025/06/03 10:55
From version 219.1
edited by eapapp
on 2024/06/20 12:30
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To version 227.1
edited by spieschnik
on 2025/03/06 10:52
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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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108 108  //with guidelines
109 109  on data organization: //
110 110  
111 -(% style="text-align:center" %)
112 -[[[[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/]]
113 113  )))
114 114  
115 115  (% 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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123 123  **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.
124 124  
125 125  
126 -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.
127 127  
128 128  If a data collection is already uploaded elsewhere, we may link to the already existing repository.
129 129  
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166 166  about the EBRAINS Data//
167 167  //Descriptor//
168 168  // //
169 -[[[[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/]]
170 170  )))
171 171  
172 172  ==== **5. Preview and publish** ====
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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 ====
212 +==== 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 [[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]].,
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  
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.
274 274  
275 -(% class="box floatinginfobox" id="software-curation-infographic" %)
276 -(((
277 -(% style="text-align:center" %)
278 -//Software curation at a glance//
279 -// //
280 -[[[[image:Thumb2.png||alt="EBRAINS-Share-Software.pdf" height="287" width="197"]]>>attach:EBRAINS-Share-Software-4.pdf]]
281 -)))
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.
282 282  
283 -(% 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.
284 284  
285 -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.
286 -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.
287 -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.
288 -
289 -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]].
290 -
291 -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.
292 -
293 -
294 294  ----
295 295  
296 296  === Sharing human subject data ===
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327 327  
328 328  (% class="box floatinginfobox" %)
329 329  (((
330 -[[[[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]]
331 331  )))
332 332  
333 333  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"]].
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423 423  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.
424 424  
425 425  
426 -----
427 -
428 -== (% style="--darkreader-inline-color:#f1ede6; color:#1a202c; font-family:inherit; font-size:29px" %)**The curation team: meet the curators**(%%) ==
429 -
430 -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.
431 -
432 -The curators in EBRAINS are located in Oslo, Jülich, Trier and Paris. 
433 -
434 -
435 -**Located in Norway**
436 -
437 -|(% style="width:303px" %)(((
438 -[[image:My project2.jpg||height="209" width="167"]]
439 -
440 -**Archana Golla**
441 -
442 -(% class="small" %)Curation Scientist
443 -Neuroscience (PhD)(%%)
444 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Behavioral neuroscience and microscopy**
445 -)))|(% style="width:303px" %)(((
446 -[[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
447 -
448 -**Camilla H. Blixhavn**
449 -
450 -(% class="small" %)Curation Scientist,
451 -Phd Student
452 -Neuroscience (M. Sc.)(%%)
453 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and data integration**
454 -)))|(% style="width:303px" %)(((
455 -[[image:My project (1).jpg||height="209" width="167"]]
456 -
457 -**Ingrid Reiten**
458 -
459 -(% class="small" %)Curation Scientist,
460 -Phd Student
461 -Neuroscience (M. Sc.)(%%)
462 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and structural connectivity**
463 -)))|(% style="width:303px" %)(((
464 -[[image:My project1.jpg||height="209" width="167"]]
465 -
466 -**Sophia Pieschnik**
467 -
468 -(% class="small" %)Curation Scientist
469 -Neurocognitive Psychology (M. Sc.)(%%)
470 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroimaging **
471 -)))
472 -
473 -|(% style="width:303px" %)(((
474 -[[image:My project.jpg||height="209" width="167"]]
475 -
476 -**Heidi Kleven**
477 -
478 -(% class="small" %)Curation Scientist,
479 -Phd Student
480 -Neuroscience (M. Sc.)(%%)
481 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and brain atlases**
482 -)))| | |
483 -
484 -
485 -\\**Located in Germany**
486 -
487 -|(% style="width:303px" %)(((
488 -[[image:My project (2).jpg||height="209" width="167"]]
489 -
490 -**Jan Gündling**
491 -
492 -(% class="small" %)Curation Scientist,
493 -Phd Student
494 -Sensors and Cognitive Psychology (M. Sc.)(%%)
495 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Human-Computer Interaction**
496 -)))|(% style="width:303px" %)(((
497 -[[image:Lyuba.jpg||height="209" width="167"]]
498 -
499 -**Lyuba Zehl**
500 -
501 -(% class="small" %)Knowledge Systems Engineer
502 -Dr. rer. nat. (Systems Neuroscience)(%%)
503 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
504 -)))|(% style="width:303px" %) |(% style="width:303px" %)
505 -
506 -----
507 -
508 -
509 -
510 -----
511 -
512 512  == Contact ==
513 513  
514 514  [[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
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521 521  
522 522  //Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Germany (PI: Timo Dicksheid)//
523 523  
426 +//Paris-Saclay Institute of Neuroscience, CNRS, Université Paris-Saclay, France (PI: Andrew P. Davison)//
427 +
524 524  ----
525 525  
526 526  == References ==
EBRAINS-Share-Software-4.pdf
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Data Curation