Changes for page Data Curation

Last modified by abonard on 2025/06/03 10:55
From version 200.1
edited by ingrreit
on 2023/06/21 12:15
Change comment: There is no comment for this version
To version 218.1
edited by lzehl
on 2024/05/06 09:51
Change comment: There is no comment for this version

Summary

Details

Page properties
Title
... ... @@ -1,1 +1,1 @@
1 -test-ir2
1 +Data Curation
Parent
... ... @@ -1,1 +1,1 @@
1 -CollabClass
1 +Collabs.WebHome
Author
... ... @@ -1,1 +1,1 @@
1 -XWiki.ingrreit
1 +XWiki.lzehl
Content
... ... @@ -17,9 +17,9 @@
17 17  {{/html}}
18 18  
19 19  
20 -== Publishing neuroscience data, models and software via EBRAINS ==
20 +(% class="wikigeneratedid" id="HPublishingneurosciencedata2CmodelsandsoftwareviaEBRAINS" %)
21 +(% style="font-size:2em" %)**Publishing neuroscience data, models and software via EBRAINS**
21 21  
22 -
23 23  (% class="wikigeneratedid" %)
24 24  The aim of this collab is to provide you with detailed information about publishing data, simulations, computational models, and software via EBRAINS. If you want a quick overview of the sharing process, see [[https:~~/~~/ebrains.eu/service/share-data>>https://ebrains.eu/service/share-data]].
25 25  
... ... @@ -67,7 +67,9 @@
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 ===
... ... @@ -144,7 +144,7 @@
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.
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.
148 148  
149 149  
150 150  ==== **4. Write a Data Descriptor** ====
... ... @@ -180,39 +180,8 @@
180 180  Once a Curator has assembled the dataset in the EBRAINS Knowledge Graph, combining the data, metadata and data descriptor, the data provider will receive a private URL for previewing the dataset prior to release. We need an official approval from the data custodian{{footnote}}The Data Custodian is responsible for the content and quality of the Data and metadata, and is the person to be contacted by EBRAINS CS in case of any misconduct related to the Data. It is the obligation of a Data Custodian to keep EBRAINS informed about changes in the contact information of the authors of the Datasets provided by them ([[EBRAINS Data Provision Protocol - version 1.1>>https://strapi-prod.sos-ch-dk-2.exo.io/EBRAINS_Data_Provision_Protocol_dfe0dcb104.pdf]]).{{/footnote}} to release the dataset. Once released, a [[DataCite DOI>>https://datacite.org/]] will be generated for the dataset. If the identical data collection has received a DOI elsewhere, we recommend re-using the already issued DOI.
181 181  
182 182  
183 -----
184 184  
185 -==== ====
186 186  
187 -==== **Sharing human subject data** ====
188 -
189 -(% class="box floatinginfobox" %)
190 -(((
191 -**Human subject data that can be shared on EBRAINS:**
192 -// //
193 -// - Post-mortem data//
194 -// - Aggregated data//
195 -// - Strongly pseudonymized or de-identified subject data//
196 -// with a legal basis for sharing (e.g. Informed Consent)//
197 -// //
198 -
199 -(% class="small" %)
200 -//If you have human data that does not qualify as any of the above,//
201 -//please [[get in touch>>https://www.ebrains.eu/contact/]] and we will clarify the available options.//
202 -)))
203 -
204 -
205 -Human subject data shared on EBRAINS must comply with [[GDPR >>https://gdpr-info.eu/]]and [[EU directives>>https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=celex%3A32010L0063]]. The information we need to assess this is collected via our [[Ethics and Regulatory Compliance Survey>>https://nettskjema.no/a/224765]].
206 -
207 -Post-mortem and aggregated human data can be shared openly, given direct identifiers in the metadata are removed. Strongly pseudonymized and de-identified data can be shared via the Human Data Gateway (HDG).
208 -
209 -The Human Data Gateway (HDG) was introduced in February 2021 as a response to the needs of multiple data providers who are bringing human subject data to EBRAINS. HDG covers the sharing of strongly pseudonymized or de-identified data, a limited range human subject data without direct identifiers and with very few indirect identifiers.
210 -
211 -The HDG adds an an authentication layer on top of the data. This means that **data users **must request access to the data (via their EBRAINS account) and will receive access provided they actively accept the [[EBRAINS Access Policy>>https://ebrains.eu/terms#access-policy]], the [[EBRAINS General Terms of Use>>https://ebrains.eu/terms#general-terms-of-use]], and the [[EBRAINS Data Use Agreement>>https://ebrains.eu/terms#data-use-agreement]]. The account holder also have to accept that information about their request and access to specific data under HDG is being tracked and stored. **Data owners** must be aware that sharing under the HDG affects the legal responsibilities for the data. They must agree to joint control of the data (see the [[Data Provision Protocol v1>>url:https://strapi-prod.sos-ch-dk-2.exo.io/EBRAINS_Data_Provision_Protocol_dfe0dcb104.pdf]], section 1.4 - 1.5) and the Data Protection Officers of the responsible institutions must have accepted that the data can be shared under HDG.
212 -
213 -The HDG is an extension of the existing services and does not replace the future EBRAINS Service for sensitive data (planned for 2024) which is outside the domain of the current EBRAINS Data and Knowledge services.
214 -
215 -
216 216  ----
217 217  
218 218  === Step by Step - Models ===
... ... @@ -327,6 +327,36 @@
327 327  
328 328  ----
329 329  
301 +=== Sharing human subject data ===
302 +
303 +(% class="box floatinginfobox" %)
304 +(((
305 +**Human subject data that can be shared on EBRAINS:**
306 +// //
307 +// - Post-mortem data//
308 +// - Aggregated data//
309 +// - Strongly pseudonymized or de-identified subject data//
310 +// with a legal basis for sharing (e.g. Informed Consent)//
311 +// //
312 +
313 +(% class="small" %)
314 +//If you have human data that does not qualify as any of the above,//
315 +//please [[get in touch>>https://www.ebrains.eu/contact/]] and we will clarify the available options.//
316 +)))
317 +
318 +
319 +Human subject data shared on EBRAINS must comply with [[GDPR >>https://gdpr-info.eu/]]and [[EU directives>>https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=celex%3A32010L0063]]. The information we need to assess this is collected via our [[Ethics and Regulatory Compliance Survey>>https://nettskjema.no/a/224765]].
320 +
321 +Post-mortem and aggregated human data can be shared openly, given direct identifiers in the metadata are removed. Strongly pseudonymized and de-identified data can be shared via the Human Data Gateway (HDG).
322 +
323 +The Human Data Gateway (HDG) was introduced in February 2021 as a response to the needs of multiple data providers who are bringing human subject data to EBRAINS. HDG covers the sharing of strongly pseudonymized or de-identified data, a limited range human subject data without direct identifiers and with very few indirect identifiers.
324 +
325 +The HDG adds an an authentication layer on top of the data. This means that **data users **must request access to the data (via their EBRAINS account) and will receive access provided they actively accept the [[EBRAINS Access Policy>>https://ebrains.eu/terms#access-policy]], the [[EBRAINS General Terms of Use>>https://ebrains.eu/terms#general-terms-of-use]], and the [[EBRAINS Data Use Agreement>>https://ebrains.eu/terms#data-use-agreement]]. The account holder also have to accept that information about their request and access to specific data under HDG is being tracked and stored. **Data owners** must be aware that sharing under the HDG affects the legal responsibilities for the data. They must agree to joint control of the data (see the [[Data Provision Protocol v1>>url:https://strapi-prod.sos-ch-dk-2.exo.io/EBRAINS_Data_Provision_Protocol_dfe0dcb104.pdf]], section 1.4 - 1.5) and the Data Protection Officers of the responsible institutions must have accepted that the data can be shared under HDG.
326 +
327 +The HDG is an extension of the existing services and does not replace the future EBRAINS Service for sensitive data (planned for 2024) which is outside the domain of the current EBRAINS Data and Knowledge services.
328 +
329 +----
330 +
330 330  == **The openMINDS metadata framework** ==
331 331  
332 332  (% class="box floatinginfobox" %)
... ... @@ -334,24 +334,109 @@
334 334  [[[[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]]
335 335  )))
336 336  
337 -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]].
338 +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||target="_blank"]].
338 338  
339 339  For feedback, requests, or contributions, please get in touch with the openMINDS development team via
340 340  
341 -* the support-email: [[openminds@ebrains.eu>>path:mailto:openminds@ebrains.eu]]
342 -* the [[GitHub issue tracker>>url:https://github.com/HumanBrainProject/openMINDS/issues]]
343 -* the INCF NeuroStars [[openMINDS Community Forum>>url:https://neurostars.org/t/openminds-community-forum-virtual/20156]]
342 +* [[support@openmetadatainitiative.org>>mailto:mailto:support@openmetadatainitiative.org]]
343 +* [[GitHub Issues>>https://github.com/openMetadataInitiative/openMINDS/issues]] (for metadata schemas)
344 +* [[GitHub Issues>>https://github.com/openMetadataInitiative/openMINDS_instances/issues]] (for metadata instances)
345 +* [[openMINDS Community Forum>>https://neurostars.org/t/openminds-community-forum-virtual]]
344 344  
345 345  ----
346 346  
347 -== **The curation team: meet the curators** ==
349 +== **Add practical value to your shared data, model or software** ==
348 348  
351 +
352 +=== **Showcase shared data, models or software in other services** ===
353 +
354 +Below is a list of additional services that data, models or software shared via EBRAINS can benefit from. EBRAINS is continuously looking to increase the number of interoperable services.
355 +
356 +
357 +|(% colspan="2" %)**Viewer for 2D images**
358 +|[[image:MIO_screenshot.PNG]]|Integrate image data with //the Mio viewer//: EBRAINS Multi-Image OpenSeadragon viewer provides an intuitive way of navigating high-resolution 2D image series. It has browser-based classic pan and zoom capabilities. A collection can be displayed as a filmstrip (Filmstrip Mode) or as a table (Collection Mode) with adjustable number of row and columns. See [[Mio viewer links available for this dataset>>https://search.kg.ebrains.eu/?category=Dataset&q=nr2f1#9677359c-73fa-4425-b8fa-3de794e9017a]] as an example. MioViewer user manual is found [[here>>https://multi-image-osd.readthedocs.io/en/latest/index.html]].
359 +|(% colspan="2" %)**Viewer for sequential atlas-registered 2D images with annotation options**
360 +|[[image:LZ_screenshot.PNG]]|Integrate atlas-registered 2D image data with //the LocaliZoom viewer//: The EBRAINS LocaliZoom serial section viewer displays series of registered 2D section images with atlas overlay, allowing the users to zoom into high-resolution images and have information about the brain regions. See the [[LocaliZoom links available for this dataset>>https://doi.org/10.25493/T686-7BX]] as an example. LocaliZoom user manual is found [[here>>https://localizoom.readthedocs.io/en/latest/index.html]].
361 +|(% colspan="2" %)**Interactive 3D atlas viewer with options for data visualization**
362 +|[[image:3Datlas_screenshot.PNG]]|Upload your data to the //Siibra-explorer//: The siibra-explorer is used for visualizing volumetric brain data in all the brain atlases provided by EBRAINS (Human, Monkey, Rat and Mouse). The siibra-explorer viewer uses siibra-api to enable navigation of brain region hierarchies, maps in different coordinate spaces, and linked regional data features. Furthermore, it is connected with the siibra toolsuite providing several analytical workflows. To learn more about how to register your data to atlases, read about the [[Atlas services on ebrains.eu>>https://ebrains.eu/services/atlases#Integratedatatoanatlas]].
363 +|(% colspan="2" %)**Use your research product in an interactive publication**
364 +|[[image:LivePaper_screenshot.PNG]]|Add your data, models or software to a// Live paper. //Read more about [[Live papers on ebrains.eu>>https://www.ebrains.eu/data/live-papers/live-papers]].
365 +
366 +----
367 +
368 +==== **Add a tutorial or learning resource ** ====
369 +
370 +(% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
371 +(% style="--darkreader-inline-color:#e8e6e3; color:#000000" %)//More information will follow//
372 +
373 +
374 +==== **Create a workflow** ====
375 +
376 +(% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
377 +(% style="--darkreader-inline-color:#e8e6e3; color:#000000" %)//More information will follow//
378 +
379 +----
380 +
381 +== **EBRAINS commits to the FAIR principles** ==
382 +
383 +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.
384 +
385 +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.
386 +
387 +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]]. **
388 +
389 +
390 +----
391 +
392 +== **General benefits of sharing data ** ==
393 +
394 +By sharing your data via EBRAINS, you gain access to the following benefits:
395 +
396 +[[image:image-20230324170841-3.png]]
397 +
398 +
399 +
400 +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.
401 +
402 +----
403 +
404 +== **Frequently asked questions ** ==
405 +
406 +>Is the curation process time consuming and difficult?
407 +
408 +No, if communication is on a regular basis, we are able to finish curation within two weeks. Publishing your data naturally takes some effort but we will support you as much as possible.
409 +
410 +>Is sharing my data also beneficial for me or only for others?
411 +
412 +When you publish your data via EBRAINS, we provide comprehensive data management support and safe long term storage - all free of charge. Additionally, your data can be cited, just like a scientific journal article. Sharing your data may even lead to new funding opportunities. Many funders specifically support projects that are part of the “Open Science” initiative.
413 +
414 +>Can my data be too insignificant to share?
415 +
416 +No, there is no such thing as insignificant data. Data that is considered insignificant for a given topic, may have great significance for another. By making “insignificant” data publicly available, other researchers may find something interesting that was off-topic for your own purposes.
417 +
418 +>Can my data be easily misused if I share it?
419 +
420 +No, your data will be covered by a Creative Commons license of your choice. There are a variety of licenses available, enabling you to prevent use for specific purposes, e.g. commercial use.
421 +
422 +>Can I share my data before my paper is published?
423 +
424 +Yes, if you do not want to share your data before publishing the results in an article, you can publish your dataset with an embargo status. This will make it possible to find information about the data without making the data itself available, and give you a citeable DOI.
425 +
426 +>Can I lose my competitive edge if I share my data before I publish the associated paper?
427 +
428 +No, publishing your data does not mean that others can use it however they want. Use of your data will require citation, and by choosing an appropriate Creative Commons licence you decide what others are allowed to do with it. If you still feel worried, you can publish your data under embargo, and in this way delay the date of data release, but still make it possible for others to find the information about the data.
429 +
430 +
431 +----
432 +
433 +== (% style="--darkreader-inline-color:#d2cec8; color:#1a202c; font-family:inherit; font-size:29px" %)**The curation team: meet the curators**(%%) ==
434 +
349 349  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.
350 350  
351 351  The curators in EBRAINS are located in Oslo, Jülich, Trier and Paris. 
352 352  
353 353  
354 -**Located in Norway:**
440 +**Located in Norway**
355 355  
356 356  |(% style="width:303px" %)(((
357 357  [[image:My project2.jpg||height="209" width="167"]]
... ... @@ -360,7 +360,7 @@
360 360  
361 361  (% class="small" %)Curation Scientist
362 362  Neuroscience (PhD)(%%)
363 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Behavioral neuroscience and microscopy**
449 +(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Behavioral neuroscience and microscopy**
364 364  )))|(% style="width:303px" %)(((
365 365  [[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
366 366  
... ... @@ -369,7 +369,7 @@
369 369  (% class="small" %)Curation Scientist,
370 370  Phd Student
371 371  Neuroscience (M. Sc.)(%%)
372 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and data integration**
458 +(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Neuroanatomy and data integration**
373 373  )))|(% style="width:303px" %)(((
374 374  [[image:My project (1).jpg||height="209" width="167"]]
375 375  
... ... @@ -378,7 +378,7 @@
378 378  (% class="small" %)Curation Scientist,
379 379  Phd Student
380 380  Neuroscience (M. Sc.)(%%)
381 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and structural connectivity**
467 +(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Neuroanatomy and structural connectivity**
382 382  )))|(% style="width:303px" %)(((
383 383  [[image:My project1.jpg||height="209" width="167"]]
384 384  
... ... @@ -386,7 +386,7 @@
386 386  
387 387  (% class="small" %)Curation Scientist
388 388  Neurocognitive Psychology (M. Sc.)(%%)
389 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroimaging **
475 +(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Neuroimaging **
390 390  )))
391 391  
392 392  |(% style="width:303px" %)(((
... ... @@ -397,11 +397,11 @@
397 397  (% class="small" %)Curation Scientist,
398 398  Phd Student
399 399  Neuroscience (M. Sc.)(%%)
400 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and brain atlases**
486 +(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Neuroanatomy and brain atlases**
401 401  )))| | |
402 402  
403 403  
404 -\\**Located in Germany:**
490 +\\**Located in Germany**
405 405  
406 406  |(% style="width:303px" %)(((
407 407  [[image:My project (2).jpg||height="209" width="167"]]
... ... @@ -411,7 +411,7 @@
411 411  (% class="small" %)Curation Scientist,
412 412  Phd Student
413 413  Sensors and Cognitive Psychology (M. Sc.)(%%)
414 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Human-Computer Interaction**
500 +(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Human-Computer Interaction**
415 415  )))|(% style="width:303px" %)(((
416 416  [[image:Lyuba.jpg||height="209" width="167"]]
417 417  
... ... @@ -419,97 +419,29 @@
419 419  
420 420  (% class="small" %)Knowledge Systems Engineer
421 421  Dr. rer. nat. (Systems Neuroscience)(%%)
422 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
508 +(% class="small" style="--darkreader-inline-color:#b0a99f; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
423 423  )))|(% style="width:303px" %) |(% style="width:303px" %)
424 424  
425 425  ----
426 426  
427 -== **Add practical value to your shared data, model or software** ==
428 428  
429 429  
430 430  ----
431 431  
432 -=== **Showcase shared data, models or software in other services** ===
517 +== Contact ==
433 433  
434 -Below is a list of additional services that data, models or software shared via EBRAINS can benefit from. EBRAINS is continuously looking to increase the number of interoperable services.
519 +[[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
435 435  
436 -
437 -|(% colspan="2" %)**Viewer for 2D images**
438 -|[[image:MIO_screenshot.PNG]]|Integrate image data with //the Mio viewer//: EBRAINS Multi-Image OpenSeadragon viewer provides an intuitive way of navigating high-resolution 2D image series. It has browser-based classic pan and zoom capabilities. A collection can be displayed as a filmstrip (Filmstrip Mode) or as a table (Collection Mode) with adjustable number of row and columns. See [[Mio viewer links available for this dataset>>https://search.kg.ebrains.eu/?category=Dataset&q=nr2f1#9677359c-73fa-4425-b8fa-3de794e9017a]] as an example. MioViewer user manual is found [[here>>https://multi-image-osd.readthedocs.io/en/latest/index.html]].
439 -|(% colspan="2" %)**Viewer for sequential atlas-registered 2D images with annotation options**
440 -|[[image:LZ_screenshot.PNG]]|Integrate atlas-registered 2D image data with //the LocaliZoom viewer//: The EBRAINS LocaliZoom serial section viewer displays series of registered 2D section images with atlas overlay, allowing the users to zoom into high-resolution images and have information about the brain regions. See the [[LocaliZoom links available for this dataset>>https://doi.org/10.25493/T686-7BX]] as an example. LocaliZoom user manual is found [[here>>https://localizoom.readthedocs.io/en/latest/index.html]].
441 -|(% colspan="2" %)**Interactive 3D atlas viewer with options for data visualization**
442 -|[[image:3Datlas_screenshot.PNG]]|Upload your data to the //Siibra-explorer//: The siibra-explorer is used for visualizing volumetric brain data in all the brain atlases provided by EBRAINS (Human, Monkey, Rat and Mouse). The siibra-explorer viewer uses siibra-api to enable navigation of brain region hierarchies, maps in different coordinate spaces, and linked regional data features. Furthermore, it is connected with the siibra toolsuite providing several analytical workflows. To learn more about how to register your data to atlases, read about the [[Atlas services on ebrains.eu>>https://ebrains.eu/services/atlases#Integratedatatoanatlas]].
443 -|(% colspan="2" %)**Use your research product in an interactive publication**
444 -|[[image:LivePaper_screenshot.PNG]]|Add your data, models or software to a// Live paper. //Read more about [[Live papers on ebrains.eu>>https://www.ebrains.eu/data/live-papers/live-papers]].
445 -
446 446  ----
447 447  
448 -==== **Add a tutorial or learning resource ** ====
523 +== Affiliated laboratories ==
449 449  
450 -(% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
451 -(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
525 +//Institute of Basic Medical Sciences,** **University of Oslo, Norway (PI: Jan G. Bjaalie, Trygve B. Leergaard)//
452 452  
527 +//Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Germany (PI: Timo Dicksheid)//
453 453  
454 -==== **Create a workflow** ====
455 -
456 -(% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
457 -(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
458 -
459 459  ----
460 460  
461 -=== **The benefits of sharing data ** ===
462 -
463 -By sharing your data via EBRAINS, you gain access to the following benefits:
464 -
465 -[[image:image-20230324170841-3.png]]
466 -
467 -
468 -
469 -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.
470 -
471 -----
472 -
473 -=== **Frequently asked questions ** ===
474 -
475 -(((
476 -==== ====
477 -
478 -(((
479 ->Is the curation process time consuming and difficult?
480 -)))
481 -)))
482 -
483 -No, if communication is on a regular basis, we are able to finish curation within two weeks. Publishing your data naturally takes some effort but we will support you as much as possible.
484 -
485 ->Is sharing my data also beneficial for me or only for others?
486 -
487 -When you publish your data via EBRAINS, we provide comprehensive data management support and safe long term storage - all free of charge. Additionally, your data can be cited, just like a scientific journal article. Sharing your data may even lead to new funding opportunities. Many funders specifically support projects that are part of the “Open Science” initiative.
488 -
489 ->Can my data be too insignificant to share?
490 -
491 -No, there is no such thing as insignificant data. Data that is considered insignificant for a given topic, may have great significance for another. By making “insignificant” data publicly available, other researchers may find something interesting that was off-topic for your own purposes.
492 -
493 ->Can my data be easily misused if I share it?
494 -
495 -No, your data will be covered by a Creative Commons license of your choice. There are a variety of licenses available, enabling you to prevent use for specific purposes, e.g. commercial use.
496 -
497 ->Can I share my data before my paper is published?
498 -
499 -Yes, if you do not want to share your data before publishing the results in an article, you can publish your dataset with an embargo status. This will make it possible to find information about the data without making the data itself available, and give you a citeable DOI.
500 -
501 ->Can I lose my competitive edge if I share my data before I publish the associated paper?
502 -
503 -No, publishing your data does not mean that others can use it however they want. Use of your data will require citation, and by choosing an appropriate Creative Commons licence you decide what others are allowed to do with it. If you still feel worried, you can publish your data under embargo, and in this way delay the date of data release, but still make it possible for others to find the information about the data.
504 -
505 -
506 -----
507 -
508 -== Contact ==
509 -
510 -[[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
511 -
512 -
513 513  == References ==
514 514  
515 515  {{putFootnotes/}}
Collaboratory.Apps.Collab.Code.CollabClass[0]
Public
... ... @@ -1,1 +1,1 @@
1 -No
1 +Yes
XWiki.XWikiRights[3]
Allow/Deny
... ... @@ -1,0 +1,1 @@
1 +Allow
Levels
... ... @@ -1,0 +1,1 @@
1 +view
Users
... ... @@ -1,0 +1,1 @@
1 +XWiki.XWikiGuest
XWiki.XWikiRights[4]
Allow/Deny
... ... @@ -1,0 +1,1 @@
1 +Allow
Groups
... ... @@ -1,0 +1,1 @@
1 +XWiki.XWikiAllGroup
Levels
... ... @@ -1,0 +1,1 @@
1 +view
Public

Data Curation