Changes for page Data Curation

Last modified by abonard on 2025/06/03 10:55
From version 219.1
edited by eapapp
on 2024/06/20 12:30
Change comment: There is no comment for this version
To version 217.2
edited by eapapp
on 2024/01/17 17:03
Change comment: Updated link to minimally required metadata file

Summary

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Content
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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]]. **
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#/]]. **
96 96  
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.
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.
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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 +
102 102  ==== **2. Upload data ** ====
103 103  
104 104  (% class="box floatinginfobox" id="share-data-infographic" %)
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141 141  * [[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.
142 142  * [[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.
143 143  
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.
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/]] on EBRAINS.
145 145  
146 146  
147 147  ==== **4. Write a Data Descriptor** ====
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330 330  [[[[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]]
331 331  )))
332 332  
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"]].
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]].
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335 335  For feedback, requests, or contributions, please get in touch with the openMINDS development team via
336 336  
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]]
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]]
341 341  
342 342  ----
343 343  
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363 363  ==== **Add a tutorial or learning resource ** ====
364 364  
365 365  (% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
366 -(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
370 +(% style="--darkreader-inline-color:#e8e6e3; color:#000000" %)//More information will follow//
367 367  
368 368  
369 369  ==== **Create a workflow** ====
370 370  
371 371  (% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
372 -(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
376 +(% style="--darkreader-inline-color:#e8e6e3; color:#000000" %)//More information will follow//
373 373  
374 374  ----
375 375  
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379 379  
380 380  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]]. **
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]]. **
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384 384  
385 385  ----
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425 425  
426 426  ----
427 427  
428 -== (% style="--darkreader-inline-color:#f1ede6; color:#1a202c; font-family:inherit; font-size:29px" %)**The curation team: meet the curators**(%%) ==
432 +== (% style="--darkreader-inline-color:#d2cec8; color:#1a202c; font-family:inherit; font-size:29px" %)**The curation team: meet the curators**(%%) ==
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430 430  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.
431 431  
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441 441  
442 442  (% class="small" %)Curation Scientist
443 443  Neuroscience (PhD)(%%)
444 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Behavioral neuroscience and microscopy**
448 +(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Behavioral neuroscience and microscopy**
445 445  )))|(% style="width:303px" %)(((
446 446  [[image:Camilla.jpg||alt="My project.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:#cac2b7; color:#4a5568" %)**Neuroanatomy and data integration**
457 +(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Neuroanatomy and data integration**
454 454  )))|(% style="width:303px" %)(((
455 455  [[image:My project (1).jpg||height="209" width="167"]]
456 456  
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459 459  (% class="small" %)Curation Scientist,
460 460  Phd Student
461 461  Neuroscience (M. Sc.)(%%)
462 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and structural connectivity**
466 +(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Neuroanatomy and structural connectivity**
463 463  )))|(% style="width:303px" %)(((
464 464  [[image:My project1.jpg||height="209" width="167"]]
465 465  
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467 467  
468 468  (% class="small" %)Curation Scientist
469 469  Neurocognitive Psychology (M. Sc.)(%%)
470 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroimaging **
474 +(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Neuroimaging **
471 471  )))
472 472  
473 473  |(% style="width:303px" %)(((
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478 478  (% class="small" %)Curation Scientist,
479 479  Phd Student
480 480  Neuroscience (M. Sc.)(%%)
481 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and brain atlases**
485 +(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Neuroanatomy and brain atlases**
482 482  )))| | |
483 483  
484 484  
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492 492  (% class="small" %)Curation Scientist,
493 493  Phd Student
494 494  Sensors and Cognitive Psychology (M. Sc.)(%%)
495 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Human-Computer Interaction**
499 +(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Human-Computer Interaction**
496 496  )))|(% style="width:303px" %)(((
497 497  [[image:Lyuba.jpg||height="209" width="167"]]
498 498  
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500 500  
501 501  (% class="small" %)Knowledge Systems Engineer
502 502  Dr. rer. nat. (Systems Neuroscience)(%%)
503 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
507 +(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
504 504  )))|(% style="width:303px" %) |(% style="width:303px" %)
505 505  
506 506  ----
Public

Data Curation