Changes for page Data Curation

Last modified by abonard on 2025/06/03 10:55
From version 217.3
edited by eapapp
on 2024/01/17 17:05
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To version 222.1
edited by adavison
on 2024/07/05 18:47
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1 -XWiki.eapapp
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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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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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146 146  * [[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.
147 147  * [[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.
148 148  
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 +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.
150 150  
151 151  
152 152  ==== **4. Write a Data Descriptor** ====
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215 215  
216 216  Alternatively, you can upload code to the Collab Drive or Bucket storage.
217 217  
218 -==== 4.Submit metadata ====
213 +==== 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#/]].,
230 +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  
274 +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 -)))
276 +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.
277 +1. Place this file in the root folder of your code repository.
278 +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.
279 +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"]]
281 +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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335 335  [[[[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]]
336 336  )))
337 337  
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 +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  
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]]
326 +* [[support@openmetadatainitiative.org>>mailto:mailto:support@openmetadatainitiative.org]]
327 +* [[GitHub Issues>>https://github.com/openMetadataInitiative/openMINDS/issues]] (for metadata schemas)
328 +* [[GitHub Issues>>https://github.com/openMetadataInitiative/openMINDS_instances/issues]] (for metadata instances)
329 +* [[openMINDS Community Forum>>https://neurostars.org/t/openminds-community-forum-virtual]]
345 345  
346 346  ----
347 347  
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367 367  ==== **Add a tutorial or learning resource ** ====
368 368  
369 369  (% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
370 -(% style="--darkreader-inline-color:#e8e6e3; color:#000000" %)//More information will follow//
355 +(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
371 371  
372 372  
373 373  ==== **Create a workflow** ====
374 374  
375 375  (% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
376 -(% style="--darkreader-inline-color:#e8e6e3; color:#000000" %)//More information will follow//
361 +(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
377 377  
378 378  ----
379 379  
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383 383  
384 384  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.
385 385  
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 +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]]. **
387 387  
388 388  
389 389  ----
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429 429  
430 430  ----
431 431  
432 -== (% style="--darkreader-inline-color:#d2cec8; color:#1a202c; font-family:inherit; font-size:29px" %)**The curation team: meet the curators**(%%) ==
417 +== (% style="--darkreader-inline-color:#f1ede6; color:#1a202c; font-family:inherit; font-size:29px" %)**The curation team: meet the curators**(%%) ==
433 433  
434 434  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.
435 435  
... ... @@ -445,7 +445,7 @@
445 445  
446 446  (% class="small" %)Curation Scientist
447 447  Neuroscience (PhD)(%%)
448 -(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Behavioral neuroscience and microscopy**
433 +(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Behavioral neuroscience and microscopy**
449 449  )))|(% style="width:303px" %)(((
450 450  [[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
451 451  
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454 454  (% class="small" %)Curation Scientist,
455 455  Phd Student
456 456  Neuroscience (M. Sc.)(%%)
457 -(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Neuroanatomy and data integration**
442 +(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and data integration**
458 458  )))|(% style="width:303px" %)(((
459 459  [[image:My project (1).jpg||height="209" width="167"]]
460 460  
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463 463  (% class="small" %)Curation Scientist,
464 464  Phd Student
465 465  Neuroscience (M. Sc.)(%%)
466 -(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Neuroanatomy and structural connectivity**
451 +(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and structural connectivity**
467 467  )))|(% style="width:303px" %)(((
468 468  [[image:My project1.jpg||height="209" width="167"]]
469 469  
... ... @@ -471,7 +471,7 @@
471 471  
472 472  (% class="small" %)Curation Scientist
473 473  Neurocognitive Psychology (M. Sc.)(%%)
474 -(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Neuroimaging **
459 +(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroimaging **
475 475  )))
476 476  
477 477  |(% style="width:303px" %)(((
... ... @@ -482,7 +482,7 @@
482 482  (% class="small" %)Curation Scientist,
483 483  Phd Student
484 484  Neuroscience (M. Sc.)(%%)
485 -(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Neuroanatomy and brain atlases**
470 +(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and brain atlases**
486 486  )))| | |
487 487  
488 488  
... ... @@ -496,7 +496,7 @@
496 496  (% class="small" %)Curation Scientist,
497 497  Phd Student
498 498  Sensors and Cognitive Psychology (M. Sc.)(%%)
499 -(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Human-Computer Interaction**
484 +(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Human-Computer Interaction**
500 500  )))|(% style="width:303px" %)(((
501 501  [[image:Lyuba.jpg||height="209" width="167"]]
502 502  
... ... @@ -504,7 +504,7 @@
504 504  
505 505  (% class="small" %)Knowledge Systems Engineer
506 506  Dr. rer. nat. (Systems Neuroscience)(%%)
507 -(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
492 +(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
508 508  )))|(% style="width:303px" %) |(% style="width:303px" %)
509 509  
510 510  ----
Public

Data Curation