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Changes for page Data Curation

Last modified by abonard on 2025/06/03 10:55
From version 212.1
edited by ingrreit
on 2023/08/07 13:21
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To version 221.1
edited by eapapp
on 2024/06/20 12:34
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1 -XWiki.ingrreit
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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/lib/47995dbc-f576-4008-a76c-eefbfd818529/file/ebrains-minimum-required-metadata.xlsx]] 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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287 287  
288 288  (% 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"]]
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.
285 +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.
291 291  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.
292 292  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.
293 293  
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]].
289 +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]].
295 295  
296 296  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.
297 297  
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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]].
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"]].
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]]
337 +* [[support@openmetadatainitiative.org>>mailto:mailto:support@openmetadatainitiative.org]]
338 +* [[GitHub Issues>>https://github.com/openMetadataInitiative/openMINDS/issues]] (for metadata schemas)
339 +* [[GitHub Issues>>https://github.com/openMetadataInitiative/openMINDS_instances/issues]] (for metadata instances)
340 +* [[openMINDS Community Forum>>https://neurostars.org/t/openminds-community-forum-virtual]]
345 345  
346 346  ----
347 347  
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377 377  
378 378  ----
379 379  
376 +== **EBRAINS commits to the FAIR principles** ==
377 +
378 +In 2016, the 'FAIR Guiding Principles for the management and guardianship of scientific data'{{footnote}}Wilkinson, M., Dumontier, M., Aalbersberg, I. et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data 3, 160018 (2016). https://doi.org/10.1038/sdata.2016.18 {{/footnote}} were introduced to the scientific community. The objective of the authors was to provide a set of general recommendations aimed at enhancing the Findability, Accessibility, Interoperability, and Reusability of digital resources (data). They emphasize the importance of making data more open, discoverable, and usable, ultimately facilitating collaboration and knowledge sharing within the scientific community. Today, the FAIR principles are widely recognized and adopted as best practices in data management and stewardship across scientific fields.
379 +
380 +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.
381 +
382 +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]]. **
383 +
384 +
385 +----
386 +
380 380  == **General benefits of sharing data ** ==
381 381  
382 382  By sharing your data via EBRAINS, you gain access to the following benefits:
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385 385  
386 386  
387 387  
388 -We support you to better follow the [[FAIR^^ ^^guiding principles>>https://www.nature.com/articles/sdata201618]] for data management and stewardship{{footnote}}Wilkinson, M., Dumontier, M., Aalbersberg, I. et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data 3, 160018 (2016). https://doi.org/10.1038/sdata.2016.18 {{/footnote}}.  Publishing data, models or code via EBRAINS will provide you with a citeable [[DataCite DOI>>https://www.doi.org/the-identifier/resources/handbook/]] for your research product.
395 +We support you to better follow the [[FAIR^^ ^^guiding principles>>https://www.nature.com/articles/sdata201618]] for data management and stewardship. Publishing data, models or code via EBRAINS will provide you with a citeable [[DataCite DOI>>https://www.doi.org/the-identifier/resources/handbook/]] for your research product.
389 389  
390 390  ----
391 391  
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418 418  
419 419  ----
420 420  
421 -== (% style="color:#1a202c; font-family:inherit; font-size:29px" %)**The curation team: meet the curators**(%%) ==
428 +== (% style="--darkreader-inline-color:#f1ede6; color:#1a202c; font-family:inherit; font-size:29px" %)**The curation team: meet the curators**(%%) ==
422 422  
423 423  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.
424 424  
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434 434  
435 435  (% class="small" %)Curation Scientist
436 436  Neuroscience (PhD)(%%)
437 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Behavioral neuroscience and microscopy**
444 +(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Behavioral neuroscience and microscopy**
438 438  )))|(% style="width:303px" %)(((
439 439  [[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
440 440  
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443 443  (% class="small" %)Curation Scientist,
444 444  Phd Student
445 445  Neuroscience (M. Sc.)(%%)
446 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and data integration**
453 +(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and data integration**
447 447  )))|(% style="width:303px" %)(((
448 448  [[image:My project (1).jpg||height="209" width="167"]]
449 449  
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452 452  (% class="small" %)Curation Scientist,
453 453  Phd Student
454 454  Neuroscience (M. Sc.)(%%)
455 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and structural connectivity**
462 +(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and structural connectivity**
456 456  )))|(% style="width:303px" %)(((
457 457  [[image:My project1.jpg||height="209" width="167"]]
458 458  
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460 460  
461 461  (% class="small" %)Curation Scientist
462 462  Neurocognitive Psychology (M. Sc.)(%%)
463 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroimaging **
470 +(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroimaging **
464 464  )))
465 465  
466 466  |(% style="width:303px" %)(((
... ... @@ -471,7 +471,7 @@
471 471  (% class="small" %)Curation Scientist,
472 472  Phd Student
473 473  Neuroscience (M. Sc.)(%%)
474 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and brain atlases**
481 +(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and brain atlases**
475 475  )))| | |
476 476  
477 477  
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485 485  (% class="small" %)Curation Scientist,
486 486  Phd Student
487 487  Sensors and Cognitive Psychology (M. Sc.)(%%)
488 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Human-Computer Interaction**
495 +(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Human-Computer Interaction**
489 489  )))|(% style="width:303px" %)(((
490 490  [[image:Lyuba.jpg||height="209" width="167"]]
491 491  
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493 493  
494 494  (% class="small" %)Knowledge Systems Engineer
495 495  Dr. rer. nat. (Systems Neuroscience)(%%)
496 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
503 +(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
497 497  )))|(% style="width:303px" %) |(% style="width:303px" %)
498 498  
499 499  ----
Public

Data Curation