Changes for page Data Curation

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1 -data-curation
1 +Data Curation
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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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67 67  
68 68  The curation of data, models and software is different. Thus, below we explain the process for sharing for each research product separately.
69 69  
70 +**Before you get started, make sure you[[ sign up for a free EBRAINS account>>https://www.ebrains.eu/page/sign-up]]. This is needed to complete the data sharing process. **
70 70  
72 +
71 71  ----
72 72  
73 73  === Step by step - Data ===
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90 90  
91 91  
92 92  
93 -(% 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]]. **
94 94  
95 -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.
96 96  
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.
97 97  
98 -(% 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]]**.
99 99  
100 -This form collects the necessary information needed for us to evaluate whether we can ethically and legally share the data via EBRAINS.
101 -
102 -See below for information about the ethical and legal aspects concerning sharing of human subject data.
103 -
104 -
105 105  ==== **2. Upload data ** ====
106 106  
107 107  (% class="box floatinginfobox" id="share-data-infographic" %)
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144 144  * [[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.
145 145  * [[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.
146 146  
147 -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.
148 148  
149 149  
150 150  ==== **4. Write a Data Descriptor** ====
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213 213  
214 214  Alternatively, you can upload code to the Collab Drive or Bucket storage.
215 215  
216 -==== 4.Submit metadata ====
213 +==== 4. Submit metadata ====
217 217  
218 218  We recommend submitting metadata using the Model Catalog app, installed in your collab.
219 219  
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230 230  As development of your model proceeds, you can easily register new versions of the code,
231 231  and new parameterizations, by clicking "Add new version".
232 232  
233 -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]].,
234 234  and you will be contacted by e-mail with further instructions.
235 235  
236 236  ==== 5. Provide a reference dataset ====
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285 285  
286 286  (% 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"]]
287 287  
288 -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.
289 289  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.
290 290  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.
291 291  
292 -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]].
293 293  
294 294  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.
295 295  
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333 333  [[[[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]]
334 334  )))
335 335  
336 -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"]].
337 337  
338 338  For feedback, requests, or contributions, please get in touch with the openMINDS development team via
339 339  
340 -* the support-email: [[openminds@ebrains.eu>>path:mailto:openminds@ebrains.eu]]
341 -* the [[GitHub issue tracker>>url:https://github.com/HumanBrainProject/openMINDS/issues]]
342 -* 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]]
343 343  
344 344  ----
345 345  
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375 375  
376 376  ----
377 377  
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 +
378 378  == **General benefits of sharing data ** ==
379 379  
380 380  By sharing your data via EBRAINS, you gain access to the following benefits:
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383 383  
384 384  
385 385  
386 -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.
387 387  
388 388  ----
389 389  
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416 416  
417 417  ----
418 418  
419 -== (% 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**(%%) ==
420 420  
421 421  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.
422 422  
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432 432  
433 433  (% class="small" %)Curation Scientist
434 434  Neuroscience (PhD)(%%)
435 -(% 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**
436 436  )))|(% style="width:303px" %)(((
437 437  [[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
438 438  
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441 441  (% class="small" %)Curation Scientist,
442 442  Phd Student
443 443  Neuroscience (M. Sc.)(%%)
444 -(% 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**
445 445  )))|(% style="width:303px" %)(((
446 446  [[image:My project (1).jpg||height="209" width="167"]]
447 447  
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450 450  (% class="small" %)Curation Scientist,
451 451  Phd Student
452 452  Neuroscience (M. Sc.)(%%)
453 -(% 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**
454 454  )))|(% style="width:303px" %)(((
455 455  [[image:My project1.jpg||height="209" width="167"]]
456 456  
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458 458  
459 459  (% class="small" %)Curation Scientist
460 460  Neurocognitive Psychology (M. Sc.)(%%)
461 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroimaging **
470 +(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroimaging **
462 462  )))
463 463  
464 464  |(% style="width:303px" %)(((
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469 469  (% class="small" %)Curation Scientist,
470 470  Phd Student
471 471  Neuroscience (M. Sc.)(%%)
472 -(% 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**
473 473  )))| | |
474 474  
475 475  
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483 483  (% class="small" %)Curation Scientist,
484 484  Phd Student
485 485  Sensors and Cognitive Psychology (M. Sc.)(%%)
486 -(% 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**
487 487  )))|(% style="width:303px" %)(((
488 488  [[image:Lyuba.jpg||height="209" width="167"]]
489 489  
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491 491  
492 492  (% class="small" %)Knowledge Systems Engineer
493 493  Dr. rer. nat. (Systems Neuroscience)(%%)
494 -(% 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**
495 495  )))|(% style="width:303px" %) |(% style="width:303px" %)
496 496  
497 497  ----
Public

Data Curation