Changes for page Data Curation

Last modified by abonard on 2025/06/03 10:55
From version 213.1
edited by ingrreit
on 2023/09/27 16:10
Change comment: There is no comment for this version
To version 219.1
edited by eapapp
on 2024/06/20 12:30
Change comment: There is no comment for this version

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1 -XWiki.ingrreit
1 +XWiki.eapapp
Content
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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.
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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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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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379 379  
380 380  == **EBRAINS commits to the FAIR principles** ==
381 381  
382 -Datasets, models and software shared via EBRAINS 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.
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.
383 383  
384 -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]]: Go to the [[FAIR Assessment of EBRAINS datasets>>doc:.FAIR assessment of EBRAINS datasets.WebHome]].
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.
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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]]. **
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384 +
387 387  ----
388 388  
389 389  == **General benefits of sharing data ** ==
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396 396  
397 -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.
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399 399  ----
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427 427  
428 428  ----
429 429  
430 -== (% 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**(%%) ==
431 431  
432 432  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.
433 433  
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443 443  
444 444  (% class="small" %)Curation Scientist
445 445  Neuroscience (PhD)(%%)
446 -(% 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**
447 447  )))|(% style="width:303px" %)(((
448 448  [[image:Camilla.jpg||alt="My project.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 data integration**
453 +(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and data integration**
456 456  )))|(% style="width:303px" %)(((
457 457  [[image:My project (1).jpg||height="209" width="167"]]
458 458  
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461 461  (% class="small" %)Curation Scientist,
462 462  Phd Student
463 463  Neuroscience (M. Sc.)(%%)
464 -(% 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**
465 465  )))|(% style="width:303px" %)(((
466 466  [[image:My project1.jpg||height="209" width="167"]]
467 467  
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469 469  
470 470  (% class="small" %)Curation Scientist
471 471  Neurocognitive Psychology (M. Sc.)(%%)
472 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroimaging **
470 +(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroimaging **
473 473  )))
474 474  
475 475  |(% style="width:303px" %)(((
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480 480  (% class="small" %)Curation Scientist,
481 481  Phd Student
482 482  Neuroscience (M. Sc.)(%%)
483 -(% 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**
484 484  )))| | |
485 485  
486 486  
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494 494  (% class="small" %)Curation Scientist,
495 495  Phd Student
496 496  Sensors and Cognitive Psychology (M. Sc.)(%%)
497 -(% 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**
498 498  )))|(% style="width:303px" %)(((
499 499  [[image:Lyuba.jpg||height="209" width="167"]]
500 500  
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502 502  
503 503  (% class="small" %)Knowledge Systems Engineer
504 504  Dr. rer. nat. (Systems Neuroscience)(%%)
505 -(% 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**
506 506  )))|(% style="width:303px" %) |(% style="width:303px" %)
507 507  
508 508  ----
Public

Data Curation