Changes for page Data Curation

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1 -Data Curation
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1 -Collabs.WebHome
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17 17  {{/html}}
18 18  
19 19  
20 -(% class="wikigeneratedid" id="HPublishingneurosciencedata2CmodelsandsoftwareviaEBRAINS" %)
21 -(% style="font-size:2em" %)**Publishing neuroscience data, models and software via EBRAINS**
20 +== Publishing neuroscience data, models and software via EBRAINS ==
22 22  
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  
... ... @@ -29,7 +29,7 @@
29 29  
30 30  == **Information to get started** ==
31 31  
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. **
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. **
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  
... ... @@ -67,9 +67,7 @@
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. **
71 71  
72 -
73 73  ----
74 74  
75 75  === Step by step - Data ===
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85 85  //to share data on EBRAINS: //
86 86  // //
87 87  [[[[image:image-20230324171114-2.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
86 +
87 +
88 88  )))
89 89  
90 90  
... ... @@ -92,29 +92,24 @@
92 92  
93 93  
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 [[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.
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.
100 100  
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 -==== **2. Upload data ** ====
102 +This form collects the necessary information needed for us to evaluate whether we can ethically and legally share the data via EBRAINS.
103 103  
104 -(% class="box floatinginfobox" id="share-data-infographic" %)
105 -(((
106 -(% style="text-align:center" %)
107 -//Download our infographic//
108 -//with guidelines
109 -on data organization: //
104 +See below for information about the ethical and legal aspects concerning sharing of human subject data.
110 110  
111 -(% style="text-align:center" %)
112 -[[[[image:image-20230621121014-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/lib/f5cf4964-f095-49bd-8c34-e4ffda05a497/file/ebrains-infographic-data-organisation.pdf/]]
113 -)))
114 114  
107 +==== **2. Upload data ** ====
108 +
109 +
115 115  (% style="margin-right:10px" %)[[image:https://lh5.googleusercontent.com/sieKO-kW8O18iPaUyonwyo4UfHBmtc2E9BDnjbx52j6J_uGmm-OzGAo7sloMk3sYwKa6QW3hYQsOA9N4H7uGQpca088Wrk0Nurpt_J3B0-NSbcaPNdZIh21otQcG6jnAxLGiKoEvkTyaDGTMk3fu7me8mQ=s2048||height="94px;" width="94px;"]](%%)**Ensure data is structured consistently prior to upload. **
116 116  
117 -We look for organized data, not organized according to our standard. This is to support the broadest degree of sharing possible. We do however require that the data is organized in a consistent and precise manner. Please see our// //[[guidelines on data organization>>https://drive.ebrains.eu/smart-link/25299f04-c4e5-4028-8f5f-3b8208f9a532/]] for further guidance.
112 +We look for organized data, not organized according to our standard. This is to support the broadest degree of sharing possible. We do however require that the data is organized in a consistent and precise manner. Please see our// //[[collection of guidelines on data organization>>https://drive.ebrains.eu/smart-link/25299f04-c4e5-4028-8f5f-3b8208f9a532/]] for further guidance.
118 118  
119 119  (% style="margin-right:10px" %)[[image:https://lh5.googleusercontent.com/EWtYwfVlbeC-jqPasgmzidqc50GrkKIEgwXeUeql8aaMHIukmFdWEy0nufVWWATbxDDK3XwwZEDmASrbpCsBk1u0HpAd8x4ZgAMsMPRcWyrb9etlV6FgKE_QN2e6SqKxHE0rzkR8uI1rRW_5z21TFGYVnw=s2048||height="91px;" width="91px;"]](%%)**Upload data to EBRAINS Storage, either using a drag-and-drop solution (opt. 1) or an interactive python script (opt. 2).**
120 120  
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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.
139 +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.
145 145  
146 146  
147 147  ==== **4. Write a Data Descriptor** ====
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162 162  (% class="box floatinginfobox" id="data-descriptor-infographic" %)
163 163  (((
164 164  (% style="text-align:center" %)
165 -//Download our infographic
166 -about the EBRAINS Data//
167 -//Descriptor//
160 +//Download our infographic: //
161 +//The EBRAINS Data//
162 +//Descriptor at a glance//
168 168  // //
169 169  [[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
165 +
170 170  )))
171 171  
172 172  ==== **5. Preview and publish** ====
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177 177  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.
178 178  
179 179  
180 -
181 -
182 182  ----
183 183  
184 -=== Step by Step - Models ===
178 +==== ====
185 185  
180 +==== **Sharing human subject data** ====
186 186  
187 -==== 1. Start early ====
188 -
189 -It is not necessary to wait until you are ready to publish to register your model with EBRAINS.
190 -
191 -By registering a model early in your project, you can take advantage of EBRAINS tools
192 -to keep track of simulations and to share them with your collaborators.
193 -
194 -==== 2. Create/choose a Collab workspace ====
195 -
196 -We use EBRAINS Collaboratory "collab" workspaces to help manage the model curation process.
197 -
198 -In particular, we use collab membership (the "Team") to control who can view or edit your model metadata prior to publication.
199 -
200 -It is up to you whether you create a new collab for each model, or reuse an existing collab
201 -(it is no problem to have multiple models associated with a single collab).
202 -
203 -Collabs are also useful for storing simulation results, adding documentation for your model,
204 -and/or providing tutorials in Jupyter notebooks.
205 -
206 -==== 3. Upload code ====
207 -
208 -We recommend storing model code and/or configuration files in an online Git repository, for example on GitHub.
209 -This repository should be public when you publish the model, but a private repository can be used for model development.
210 -
211 -Alternatively, you can upload code to the Collab Drive or Bucket storage.
212 -
213 -==== 4. Submit metadata ====
214 -
215 -We recommend submitting metadata using the Model Catalog app, installed in your collab.
216 -
217 -To install it:
218 -
219 -1. click the "+ Create" button
220 -1. in the "Create Page" form, add a title, such as "Model Catalog", and select "Community App", then click "Create"
221 -1. scroll down until you find the "Model Catalog" app, click "Select", then "Save & View"
222 -
223 -You will then see a table of all the models and validation tests associated with this collab.
224 -If this is your first time using the app, the table will probably be empty.
225 -To add your model, click "+", fill in the form, then click "Add model".
226 -
227 -As development of your model proceeds, you can easily register new versions of the code,
228 -and new parameterizations, by clicking "Add new version".
229 -
230 -If you prefer not to use the app, you can instead fill in the [[EBRAINS Curation Request Form>>https://nettskjema.no/a/386195]].,
231 -and you will be contacted by e-mail with further instructions.
232 -
233 -==== 5. Provide a reference dataset ====
234 -
235 -Once you're ready to publish your model entry in the EBRAINS Knowledge Graph,
236 -we encourage you to provide a dataset containing the simulation results produced by your model,
237 -following the process under "Step by step - Data" above.
238 -
239 -These reference data will be linked to the model, and will be helpful to anyone trying to
240 -reuse your model.
241 -
242 -We will soon introduce a "Reproducible" badge for all models that include a reference dataset,
243 -and whose simulation results can be reproduced by an EBRAINS curator.
244 -
245 -==== 6. Request publication, preview and publish ====
246 -
247 -Until you request your model entry to be published in the EBRAINS Knowledge Graph,
248 -only members of the collab will be able to view the model entry, in the Model Catalog app
249 -or using the Model Validation Python client.
250 -
251 -After publication, the model will appear in the [[EBRAINS public search results>>https://search.kg.ebrains.eu/?category=Model||rel="noopener noreferrer" target="_blank"]], and will receive a DOI.
252 -
253 -To request publication, [[contact EBRAINS support>>https://ebrains.eu/support||rel="noopener noreferrer" target="_blank"]], providing the collab name and the model name or ID.
254 -
255 -
256 -Curators will then perform a number of checks:
257 -
258 -1. Does the model description provide sufficient context to understand the purpose and use of the model?
259 -1. Does the code repository contain a licence file, explaining the conditions for reusing the code?
260 -1. Does the model have a clearly defined version identifier (e.g. v1.0)? For models in a Git repository, the version identifier should match the name of a tag or release.
261 -
262 -The curators will also take a snapshot of your model code.
263 -
264 -* For models in public Git repositories, we archive a copy of the repository in [[Software Heritage>>https://www.softwareheritage.org/||rel="noopener noreferrer" target="_blank"]].
265 -* For models in a collab Bucket or Drive, we make a read-only copy of the code in a public container in the EBRAINS repository.
266 -
267 -Once this is done, you will be invited to review a preview of how the model entry will appear in the KG Search,
268 -and will have the opportunity to request modifications prior to approval and publication.
269 -
270 -----
271 -
272 -=== Step by Step - Software ===
273 -
274 -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.
275 -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.
276 -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.
277 -
278 -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]].
279 -
280 -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.
281 -
282 -
283 -----
284 -
285 -=== Sharing human subject data ===
286 -
287 287  (% class="box floatinginfobox" %)
288 288  (((
289 289  **Human subject data that can be shared on EBRAINS:**
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310 310  
311 311  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.
312 312  
313 -----
314 314  
315 -== **The openMINDS metadata framework** ==
316 -
317 -(% class="box floatinginfobox" %)
318 -(((
319 -[[[[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]]
320 -)))
321 -
322 -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"]].
323 -
324 -For feedback, requests, or contributions, please get in touch with the openMINDS development team via
325 -
326 -* [[support@openmetadatainitiative.org>>mailto:mailto:support@openmetadatainitiative.org]]
327 -* [[GitHub Issues>>https://github.com/openMetadataInitiative/openMINDS/issues]] (for metadata schemas)
328 -* [[GitHub Issues>>https://github.com/openMetadataInitiative/openMINDS_instances/issues]] (for metadata instances)
329 -* [[openMINDS Community Forum>>https://neurostars.org/t/openminds-community-forum-virtual]]
330 -
331 331  ----
332 332  
333 -== **Add practical value to your shared data, model or software** ==
211 +=== Step by Step - Models ===
334 334  
335 335  
336 -=== **Showcase shared data, models or software in other services** ===
214 +~1. Request curation using the [[Curation request form>>https://nettskjema.no/a/277393#/]]. You will be contacted by a curator with more information.
337 337  
338 -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.
339 339  
217 +//Additional information will be added soon.//
340 340  
341 -|(% colspan="2" %)**Viewer for 2D images**
342 -|[[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]].
343 -|(% colspan="2" %)**Viewer for sequential atlas-registered 2D images with annotation options**
344 -|[[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]].
345 -|(% colspan="2" %)**Interactive 3D atlas viewer with options for data visualization**
346 -|[[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]].
347 -|(% colspan="2" %)**Use your research product in an interactive publication**
348 -|[[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]].
349 -
350 350  ----
351 351  
352 -==== **Add a tutorial or learning resource ** ====
221 +=== Step by Step - Software ===
353 353  
354 -(% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
355 -(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
356 356  
224 +(% class="box floatinginfobox" id="software-curation-infographic" %)
225 +(((
226 +(% style="text-align:center" %)
227 +//Software curation at a glance//
228 +// //
229 +[[[[image:Thumb2.png||alt="EBRAINS-Share-Software.pdf" height="287" width="197"]]>>attach:EBRAINS-Share-Software-4.pdf]]
230 +)))
357 357  
358 -==== **Create a workflow** ====
232 +(% 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"]]
359 359  
360 -(% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
361 -(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
234 +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.
235 +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.
236 +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.
362 362  
363 -----
238 +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]].
364 364  
365 -== **EBRAINS commits to the FAIR principles** ==
240 +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.
366 366  
367 -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.
368 368  
369 -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.
370 -
371 -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]]. **
372 -
373 -
374 374  ----
375 375  
376 -== **General benefits of sharing data ** ==
245 +== **The openMINDS metadata framework** ==
377 377  
378 -By sharing your data via EBRAINS, you gain access to the following benefits:
247 +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]].
379 379  
380 -[[image:image-20230324170841-3.png]]
249 +For feedback, requests, or contributions, please get in touch with the openMINDS development team via
381 381  
251 +* the support-email: [[openminds@ebrains.eu>>path:mailto:openminds@ebrains.eu]]
252 +* the [[GitHub issue tracker>>url:https://github.com/HumanBrainProject/openMINDS/issues]]
253 +* the INCF NeuroStars [[openMINDS Community Forum>>url:https://neurostars.org/t/openminds-community-forum-virtual/20156]]
382 382  
383 -
384 -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.
385 -
386 386  ----
387 387  
388 -== **Frequently asked questions ** ==
257 +== **The curation team: meet the curators** ==
389 389  
390 ->Is the curation process time consuming and difficult?
391 -
392 -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.
393 -
394 ->Is sharing my data also beneficial for me or only for others?
395 -
396 -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.
397 -
398 ->Can my data be too insignificant to share?
399 -
400 -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.
401 -
402 ->Can my data be easily misused if I share it?
403 -
404 -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.
405 -
406 ->Can I share my data before my paper is published?
407 -
408 -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.
409 -
410 ->Can I lose my competitive edge if I share my data before I publish the associated paper?
411 -
412 -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.
413 -
414 -
415 -----
416 -
417 -== (% style="--darkreader-inline-color:#f1ede6; color:#1a202c; font-family:inherit; font-size:29px" %)**The curation team: meet the curators**(%%) ==
418 -
419 419  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.
420 420  
421 421  The curators in EBRAINS are located in Oslo, Jülich, Trier and Paris. 
422 422  
423 423  
424 -**Located in Norway**
264 +**Located in Norway:**
425 425  
426 426  |(% style="width:303px" %)(((
427 427  [[image:My project2.jpg||height="209" width="167"]]
... ... @@ -430,7 +430,7 @@
430 430  
431 431  (% class="small" %)Curation Scientist
432 432  Neuroscience (PhD)(%%)
433 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Behavioral neuroscience and microscopy**
273 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Behavioral neuroscience and microscopy**
434 434  )))|(% style="width:303px" %)(((
435 435  [[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
436 436  
... ... @@ -439,7 +439,7 @@
439 439  (% class="small" %)Curation Scientist,
440 440  Phd Student
441 441  Neuroscience (M. Sc.)(%%)
442 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and data integration**
282 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and data integration**
443 443  )))|(% style="width:303px" %)(((
444 444  [[image:My project (1).jpg||height="209" width="167"]]
445 445  
... ... @@ -448,7 +448,7 @@
448 448  (% class="small" %)Curation Scientist,
449 449  Phd Student
450 450  Neuroscience (M. Sc.)(%%)
451 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and structural connectivity**
291 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and structural connectivity**
452 452  )))|(% style="width:303px" %)(((
453 453  [[image:My project1.jpg||height="209" width="167"]]
454 454  
... ... @@ -456,7 +456,7 @@
456 456  
457 457  (% class="small" %)Curation Scientist
458 458  Neurocognitive Psychology (M. Sc.)(%%)
459 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroimaging **
299 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroimaging **
460 460  )))
461 461  
462 462  |(% style="width:303px" %)(((
... ... @@ -467,11 +467,11 @@
467 467  (% class="small" %)Curation Scientist,
468 468  Phd Student
469 469  Neuroscience (M. Sc.)(%%)
470 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and brain atlases**
310 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and brain atlases**
471 471  )))| | |
472 472  
473 473  
474 -\\**Located in Germany**
314 +\\**Located in Germany:**
475 475  
476 476  |(% style="width:303px" %)(((
477 477  [[image:My project (2).jpg||height="209" width="167"]]
... ... @@ -481,37 +481,113 @@
481 481  (% class="small" %)Curation Scientist,
482 482  Phd Student
483 483  Sensors and Cognitive Psychology (M. Sc.)(%%)
484 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Human-Computer Interaction**
485 -)))|(% style="width:303px" %)(((
486 -[[image:Lyuba.jpg||height="209" width="167"]]
324 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Human-Computer Interaction**
325 +)))|(% style="width:328px" %)(((
326 +
487 487  
328 +
329 +
330 +
331 +
332 +
333 +
334 +
488 488  **Lyuba Zehl**
489 489  
490 490  (% class="small" %)Knowledge Systems Engineer
491 491  Dr. rer. nat. (Systems Neuroscience)(%%)
492 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
493 -)))|(% style="width:303px" %) |(% style="width:303px" %)
339 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
340 +)))|(% style="width:321px" %) |(% style="width:324px" %)
494 494  
495 495  ----
496 496  
344 +== **Add practical value to your shared data, model or software** ==
497 497  
498 498  
499 499  ----
500 500  
501 -== Contact ==
349 +=== **Showcase shared data, models or software in other services** ===
502 502  
503 -[[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
351 +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.
504 504  
353 +
354 +|(% colspan="2" %)**Viewer for 2D images**
355 +|[[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]].
356 +|(% colspan="2" %)**Viewer for sequential atlas-registered 2D images with annotation options**
357 +|[[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]].
358 +|(% colspan="2" %)**Interactive 3D atlas viewer with options for data visualization**
359 +|[[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]].
360 +|(% colspan="2" %)**Use your research product in an interactive publication**
361 +|[[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]].
362 +
363 +
505 505  ----
506 506  
507 -== Affiliated laboratories ==
366 +==== **Add a tutorial or learning resource ** ====
508 508  
509 -//Institute of Basic Medical Sciences,** **University of Oslo, Norway (PI: Jan G. Bjaalie, Trygve B. Leergaard)//
368 +(% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
369 +(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
510 510  
511 -//Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Germany (PI: Timo Dicksheid)//
512 512  
372 +==== **Create a workflow** ====
373 +
374 +(% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
375 +(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
376 +
513 513  ----
514 514  
379 +=== **The benefits of sharing data ** ===
380 +
381 +By sharing your data via EBRAINS, you gain access to the following benefits:
382 +
383 +[[image:image-20230324170841-3.png]]
384 +
385 +
386 +
387 +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.
388 +
389 +----
390 +
391 +=== **Frequently asked questions ** ===
392 +
393 +(((
394 +==== ====
395 +
396 +(((
397 +>Is the curation process time consuming and difficult?
398 +)))
399 +)))
400 +
401 +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.
402 +
403 +>Is sharing my data also beneficial for me or only for others?
404 +
405 +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.
406 +
407 +>Can my data be too insignificant to share?
408 +
409 +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.
410 +
411 +>Can my data be easily misused if I share it?
412 +
413 +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.
414 +
415 +>Can I share my data before my paper is published?
416 +
417 +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.
418 +
419 +>Can I lose my competitive edge if I share my data before I publish the associated paper?
420 +
421 +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.
422 +
423 +
424 +----
425 +
426 +== Contact ==
427 +
428 +[[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
429 +
430 +
515 515  == References ==
516 516  
517 517  {{putFootnotes/}}
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Data Curation