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
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

Summary

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Content
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92 92  
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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]]**.
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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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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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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//
366 +(% 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//
372 +(% 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]]. **
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]]. **
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**(%%) ==
428 +== (% 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**
444 +(% 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  
... ... @@ -454,7 +454,7 @@
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**
453 +(% 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  
... ... @@ -463,7 +463,7 @@
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**
462 +(% 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 **
470 +(% 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**
481 +(% 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**
495 +(% 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  
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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**
503 +(% 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