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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
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To version 229.2
edited by abonard
on 2025/06/03 10:55
Change comment: There is no comment for this version

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1 -XWiki.adavison
1 +XWiki.abonard
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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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208 208  We recommend storing model code and/or configuration files in an online Git repository, for example on GitHub.
209 209  This repository should be public when you publish the model, but a private repository can be used for model development.
210 210  
211 -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.
212 212  
213 213  ==== 4. Submit metadata ====
214 214  
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261 261  
262 262  The curators will also take a snapshot of your model code.
263 263  
264 -* 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"]].
263 +* 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"]] (via the updateSWH extension).
265 265  * 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.
266 266  
267 267  Once this is done, you will be invited to review a preview of how the model entry will appear in the KG Search,
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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.
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 -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.
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.
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]].
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.
279 279  
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.
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.
281 281  
282 -
283 283  ----
284 284  
285 285  === Sharing human subject data ===
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316 316  
317 317  (% class="box floatinginfobox" %)
318 318  (((
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]]
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]]
320 320  )))
321 321  
322 322  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"]].
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339 339  
340 340  
341 341  |(% colspan="2" %)**Viewer for 2D images**
342 -|[[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.
343 343  |(% colspan="2" %)**Viewer for sequential atlas-registered 2D images with annotation options**
344 344  |[[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]].
345 345  |(% colspan="2" %)**Interactive 3D atlas viewer with options for data visualization**
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412 412  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.
413 413  
414 414  
415 -----
416 -
417 -== (% style="--darkreader-inline-color:#f1ede6; color:#1a202c; font-family:inherit; font-size:29px" %)**The curation team: meet the curators**(%%) ==
418 -
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 -
421 -The curators in EBRAINS are located in Oslo, Jülich, Trier and Paris. 
422 -
423 -
424 -**Located in Norway**
425 -
426 -|(% style="width:303px" %)(((
427 -[[image:My project2.jpg||height="209" width="167"]]
428 -
429 -**Archana Golla**
430 -
431 -(% class="small" %)Curation Scientist
432 -Neuroscience (PhD)(%%)
433 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Behavioral neuroscience and microscopy**
434 -)))|(% style="width:303px" %)(((
435 -[[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
436 -
437 -**Camilla H. Blixhavn**
438 -
439 -(% class="small" %)Curation Scientist,
440 -Phd Student
441 -Neuroscience (M. Sc.)(%%)
442 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and data integration**
443 -)))|(% style="width:303px" %)(((
444 -[[image:My project (1).jpg||height="209" width="167"]]
445 -
446 -**Ingrid Reiten**
447 -
448 -(% class="small" %)Curation Scientist,
449 -Phd Student
450 -Neuroscience (M. Sc.)(%%)
451 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and structural connectivity**
452 -)))|(% style="width:303px" %)(((
453 -[[image:My project1.jpg||height="209" width="167"]]
454 -
455 -**Sophia Pieschnik**
456 -
457 -(% class="small" %)Curation Scientist
458 -Neurocognitive Psychology (M. Sc.)(%%)
459 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroimaging **
460 -)))
461 -
462 -|(% style="width:303px" %)(((
463 -[[image:My project.jpg||height="209" width="167"]]
464 -
465 -**Heidi Kleven**
466 -
467 -(% class="small" %)Curation Scientist,
468 -Phd Student
469 -Neuroscience (M. Sc.)(%%)
470 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and brain atlases**
471 -)))| | |
472 -
473 -
474 -\\**Located in Germany**
475 -
476 -|(% style="width:303px" %)(((
477 -[[image:My project (2).jpg||height="209" width="167"]]
478 -
479 -**Jan Gündling**
480 -
481 -(% class="small" %)Curation Scientist,
482 -Phd Student
483 -Sensors and Cognitive Psychology (M. Sc.)(%%)
484 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Human-Computer Interaction**
485 -)))|(% style="width:303px" %)(((
486 -[[image:Lyuba.jpg||height="209" width="167"]]
487 -
488 -**Lyuba Zehl**
489 -
490 -(% class="small" %)Knowledge Systems Engineer
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**
493 -)))|(% style="width:303px" %) |(% style="width:303px" %)
494 -
495 -----
496 -
497 -
498 -
499 -----
500 -
501 501  == Contact ==
502 502  
503 503  [[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
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510 510  
511 511  //Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Germany (PI: Timo Dicksheid)//
512 512  
426 +//Paris-Saclay Institute of Neuroscience, CNRS, Université Paris-Saclay, France (PI: Andrew P. Davison)//
427 +
513 513  ----
514 514  
515 515  == References ==
EBRAINS-Share-Software-4.pdf
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EBRAINS-Share-Software.pdf
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Data Curation