Changes for page Data Curation

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edited by puchades
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To version 218.1
edited by lzehl
on 2024/05/06 09:51
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1 -XWiki.puchades
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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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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 [[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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108 108  //with guidelines
109 109  on data organization: //
110 110  
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/]]
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/]]
112 112  )))
113 113  
114 114  (% 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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122 122  **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.
123 123  
124 124  
125 -EBRAINS offers secure, long-term storage at FENIX Supercomputing Centres in Europe.
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. 
126 126  
127 127  If a data collection is already uploaded elsewhere, we may link to the already existing repository.
128 128  
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165 165  about the EBRAINS Data//
166 166  //Descriptor//
167 167  // //
168 -[[~[~[image:image-20230324171109-1.png~|~|height="150" width="106"~]~]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
174 +[[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
169 169  )))
170 170  
171 171  ==== **5. Preview and publish** ====
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209 209  
210 210  Alternatively, you can upload code to the Collab Drive or Bucket storage.
211 211  
212 -==== 4. Submit metadata ====
218 +==== 4.Submit metadata ====
213 213  
214 214  We recommend submitting metadata using the Model Catalog app, installed in your collab.
215 215  
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226 226  As development of your model proceeds, you can easily register new versions of the code,
227 227  and new parameterizations, by clicking "Add new version".
228 228  
229 -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#/]].,
230 230  and you will be contacted by e-mail with further instructions.
231 231  
232 232  ==== 5. Provide a reference dataset ====
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270 270  
271 271  === Step by Step - Software ===
272 272  
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 -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.
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 +)))
279 279  
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.
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"]]
281 281  
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 +
282 282  ----
283 283  
284 284  === Sharing human subject data ===
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315 315  
316 316  (% class="box floatinginfobox" %)
317 317  (((
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]]
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]]
319 319  )))
320 320  
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"]].
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"]].
322 322  
323 323  For feedback, requests, or contributions, please get in touch with the openMINDS development team via
324 324  
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338 338  
339 339  
340 340  |(% colspan="2" %)**Viewer for 2D images**
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.
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]].
342 342  |(% colspan="2" %)**Viewer for sequential atlas-registered 2D images with annotation options**
343 343  |[[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]].
344 344  |(% colspan="2" %)**Interactive 3D atlas viewer with options for data visualization**
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351 351  ==== **Add a tutorial or learning resource ** ====
352 352  
353 353  (% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
354 -(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
371 +(% style="--darkreader-inline-color:#e8e6e3; color:#000000" %)//More information will follow//
355 355  
356 356  
357 357  ==== **Create a workflow** ====
358 358  
359 359  (% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
360 -(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
377 +(% style="--darkreader-inline-color:#e8e6e3; color:#000000" %)//More information will follow//
361 361  
362 362  ----
363 363  
... ... @@ -367,7 +367,7 @@
367 367  
368 368  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.
369 369  
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]]. **
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]]. **
371 371  
372 372  
373 373  ----
... ... @@ -411,6 +411,92 @@
411 411  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.
412 412  
413 413  
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 +
414 414  == Contact ==
415 415  
416 416  [[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
... ... @@ -423,8 +423,6 @@
423 423  
424 424  //Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Germany (PI: Timo Dicksheid)//
425 425  
426 -//Paris-Saclay Institute of Neuroscience, CNRS, Université Paris-Saclay, France (PI: Andrew P. Davison)//
427 -
428 428  ----
429 429  
430 430  == References ==
EBRAINS-Share-Software-4.pdf
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EBRAINS-Share-Software.pdf
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Data Curation