Changes for page Data Curation

Last modified by abonard on 2025/06/03 10:55
From version 227.1
edited by spieschnik
on 2025/03/06 10:52
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To version 217.3
edited by eapapp
on 2024/01/17 17:05
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1 -XWiki.spieschnik
1 +XWiki.eapapp
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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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140 140  * [[Fairgraph>>https://fairgraph.readthedocs.io/en/stable/]]: This is the recommended software tool for programmatic interaction with the KG. It allows you to programmatically upload openMINDS compliant metadata into your KG space and interact with existing metadata.
141 141  * [[KG Core Python SDK>>https://github.com/HumanBrainProject/kg-core-sdks]]: This python package gives you full freedom in interacting with he KG. It allows you to upload any JSON-LD with metadata into your private space. Note, for dataset publications in EBRAINS, the JSON-LD metadata files have to comply to openMINDS.
142 142  
143 -Datasets published through the EBRAINS Knowledge Graph have to be registered using **openMINDS compliant metadata** delivered as JSON-LD files. See this summary table for an overview of [[the minimally required openMINDS properties for publishing>>https://drive.ebrains.eu/f/3e226ad165054b35b456/||rel="noopener noreferrer" target="_blank"]] on EBRAINS.
149 +Datasets published through the EBRAINS Knowledge Graph have to be registered using **openMINDS compliant metadata** delivered as JSON-LD files. See this summary table for an overview of [[the minimally required openMINDS properties for publishing>>https://drive.ebrains.eu/f/3e226ad165054b35b456/||rel=" noopener noreferrer" target="_blank"]] on EBRAINS.
144 144  
145 145  
146 146  ==== **4. Write a Data Descriptor** ====
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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 (open Metadata Initiative for Neuroscience Data Structures) is a community-driven, open-source metadata framework for graph database systems, such as the EBRAINS Knowledge Graph. It is composed of linked metadata models, libraries of serviceable metadata instances, and supportive tooling ([[openMINDS Python>>url:https://pypi.org/project/openMINDS/]], openMINDS Matlab). For exploring the openMINDS schemas, go to the [[HTML documentation>>url:https://humanbrainproject.github.io/openMINDS/]]. For a full overview of the framework, go to [[the openMINDS collab>>url:https://wiki.ebrains.eu/bin/view/Collabs/openminds/]] or the [[GitHub repository>>https://github.com/HumanBrainProject/openMINDS]].
322 322  
323 323  For feedback, requests, or contributions, please get in touch with the openMINDS development team via
324 324  
325 -* [[support@openmetadatainitiative.org>>mailto:mailto:support@openmetadatainitiative.org]]
326 -* [[GitHub Issues>>https://github.com/openMetadataInitiative/openMINDS/issues]] (for metadata schemas)
327 -* [[GitHub Issues>>https://github.com/openMetadataInitiative/openMINDS_instances/issues]] (for metadata instances)
328 -* [[openMINDS Community Forum>>https://neurostars.org/t/openminds-community-forum-virtual]]
342 +* the support-email: [[openminds@ebrains.eu>>path:mailto:openminds@ebrains.eu]]
343 +* the [[GitHub issue tracker>>url:https://github.com/HumanBrainProject/openMINDS/issues]]
344 +* the INCF NeuroStars [[openMINDS Community Forum>>url:https://neurostars.org/t/openminds-community-forum-virtual/20156]]
329 329  
330 330  ----
331 331  
... ... @@ -351,13 +351,13 @@
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//
370 +(% 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//
376 +(% 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]]. **
386 +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  
430 +----
431 +
432 +== (% style="--darkreader-inline-color:#d2cec8; color:#1a202c; font-family:inherit; font-size:29px" %)**The curation team: meet the curators**(%%) ==
433 +
434 +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.
435 +
436 +The curators in EBRAINS are located in Oslo, Jülich, Trier and Paris. 
437 +
438 +
439 +**Located in Norway**
440 +
441 +|(% style="width:303px" %)(((
442 +[[image:My project2.jpg||height="209" width="167"]]
443 +
444 +**Archana Golla**
445 +
446 +(% class="small" %)Curation Scientist
447 +Neuroscience (PhD)(%%)
448 +(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Behavioral neuroscience and microscopy**
449 +)))|(% style="width:303px" %)(((
450 +[[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
451 +
452 +**Camilla H. Blixhavn**
453 +
454 +(% class="small" %)Curation Scientist,
455 +Phd Student
456 +Neuroscience (M. Sc.)(%%)
457 +(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Neuroanatomy and data integration**
458 +)))|(% style="width:303px" %)(((
459 +[[image:My project (1).jpg||height="209" width="167"]]
460 +
461 +**Ingrid Reiten**
462 +
463 +(% class="small" %)Curation Scientist,
464 +Phd Student
465 +Neuroscience (M. Sc.)(%%)
466 +(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Neuroanatomy and structural connectivity**
467 +)))|(% style="width:303px" %)(((
468 +[[image:My project1.jpg||height="209" width="167"]]
469 +
470 +**Sophia Pieschnik**
471 +
472 +(% class="small" %)Curation Scientist
473 +Neurocognitive Psychology (M. Sc.)(%%)
474 +(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Neuroimaging **
475 +)))
476 +
477 +|(% style="width:303px" %)(((
478 +[[image:My project.jpg||height="209" width="167"]]
479 +
480 +**Heidi Kleven**
481 +
482 +(% class="small" %)Curation Scientist,
483 +Phd Student
484 +Neuroscience (M. Sc.)(%%)
485 +(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Neuroanatomy and brain atlases**
486 +)))| | |
487 +
488 +
489 +\\**Located in Germany**
490 +
491 +|(% style="width:303px" %)(((
492 +[[image:My project (2).jpg||height="209" width="167"]]
493 +
494 +**Jan Gündling**
495 +
496 +(% class="small" %)Curation Scientist,
497 +Phd Student
498 +Sensors and Cognitive Psychology (M. Sc.)(%%)
499 +(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Human-Computer Interaction**
500 +)))|(% style="width:303px" %)(((
501 +[[image:Lyuba.jpg||height="209" width="167"]]
502 +
503 +**Lyuba Zehl**
504 +
505 +(% class="small" %)Knowledge Systems Engineer
506 +Dr. rer. nat. (Systems Neuroscience)(%%)
507 +(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
508 +)))|(% style="width:303px" %) |(% style="width:303px" %)
509 +
510 +----
511 +
512 +
513 +
514 +----
515 +
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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Public

Data Curation