Changes for page Data Curation

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edited by eapapp
on 2023/06/13 10:26
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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 ===
... ... @@ -85,6 +85,8 @@
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  
... ... @@ -141,7 +141,7 @@
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** ====
... ... @@ -162,11 +162,12 @@
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** ====
... ... @@ -177,167 +177,171 @@
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  
176 +----
180 180  
178 +==== ====
181 181  
182 -----
180 +==== **Sharing human subject data** ====
183 183  
184 -=== Step by Step - Models ===
182 +(% class="box floatinginfobox" %)
183 +(((
184 +**Human subject data that can be shared on EBRAINS:**
185 +// //
186 +// - Post-mortem data//
187 +// - Aggregated data//
188 +// - Strongly pseudonymized or de-identified subject data//
189 +// with a legal basis for sharing (e.g. Informed Consent)//
190 +// //
185 185  
192 +(% class="small" %)
193 +//If you have human data that does not qualify as any of the above,//
194 +//please [[get in touch>>https://www.ebrains.eu/contact/]] and we will clarify the available options.//
195 +)))
186 186  
187 -==== 1. Start early ====
188 188  
189 -It is not necessary to wait until you are ready to publish to register your model with EBRAINS.
198 +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]].
190 190  
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.
200 +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).
193 193  
194 -==== 2. Create/choose a Collab workspace ====
202 +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.
195 195  
196 -We use EBRAINS Collaboratory "collab" workspaces to help manage the model curation process.
204 +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.
197 197  
198 -In particular, we use collab membership (the "Team") to control who can view or edit your model metadata prior to publication.
206 +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.
199 199  
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).
202 202  
203 -Collabs are also useful for storing simulation results, adding documentation for your model,
204 -and/or providing tutorials in Jupyter notebooks.
209 +----
205 205  
206 -==== 3. Upload code ====
211 +=== Step by Step - Models ===
207 207  
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.
210 210  
211 -Alternatively, you can upload code to the Collab Drive or Bucket storage.
214 +~1. Request curation using the [[Curation request form>>https://nettskjema.no/a/277393#/]]. You will be contacted by a curator with more information.
212 212  
213 -==== 4. Submit metadata ====
214 214  
215 -We recommend submitting metadata using the Model Catalog app, installed in your collab.
217 +//Additional information will be added soon.//
216 216  
217 -To install it:
219 +----
218 218  
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"
221 +=== Step by Step - Software ===
222 222  
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".
226 226  
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".
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 +)))
229 229  
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 +(% 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"]]
232 232  
233 -==== 5. Provide a reference dataset ====
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.
234 234  
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 +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]].
238 238  
239 -These reference data will be linked to the model, and will be helpful to anyone trying to
240 -reuse your model.
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.
241 241  
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.
244 244  
245 -==== 6. Request publication, preview and publish ====
243 +----
246 246  
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.
245 +== **The openMINDS metadata framework** ==
250 250  
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.
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]].
252 252  
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.
249 +For feedback, requests, or contributions, please get in touch with the openMINDS development team via
254 254  
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]]
255 255  
256 -Curators will then perform a number of checks:
255 +----
257 257  
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.
257 +== **The curation team: meet the curators** ==
261 261  
262 -The curators will also take a snapshot of your model code.
259 +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.
263 263  
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.
261 +The curators in EBRAINS are located in Oslo, Jülich, Trier and Paris. 
262 +
266 266  
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.
264 +**Located in Norway:**
269 269  
270 -----
266 +|(% style="width:303px" %)(((
267 +[[image:My project2.jpg||height="209" width="167"]]
271 271  
272 -=== Step by Step - Software ===
269 +**Archana Golla**
273 273  
271 +(% class="small" %)Curation Scientist
272 +Neuroscience (PhD)(%%)
273 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Behavioral neuroscience and microscopy**
274 +)))|(% style="width:303px" %)(((
275 +[[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
274 274  
275 -(% class="box floatinginfobox" id="software-curation-infographic" %)
276 -(((
277 -(% style="text-align:center" %)
278 -//Software curation at a glance//
279 -// //
280 -[[[[image:Thumb2.png||alt="EBRAINS-Share-Software.pdf" height="287" width="197"]]>>attach:EBRAINS-Share-Software-4.pdf]]
281 -)))
277 +**Camilla H. Blixhavn**
282 282  
283 -(% 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"]]
279 +(% class="small" %)Curation Scientist,
280 +Phd Student
281 +Neuroscience (M. Sc.)(%%)
282 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and data integration**
283 +)))|(% style="width:303px" %)(((
284 +[[image:My project (1).jpg||height="209" width="167"]]
284 284  
285 -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.
286 -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.
287 -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.
286 +**Ingrid Reiten**
288 288  
289 -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]].
288 +(% class="small" %)Curation Scientist,
289 +Phd Student
290 +Neuroscience (M. Sc.)(%%)
291 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and structural connectivity**
292 +)))|(% style="width:303px" %)(((
293 +[[image:My project1.jpg||height="209" width="167"]]
290 290  
291 -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.
295 +**Sophia Pieschnik**
292 292  
297 +(% class="small" %)Curation Scientist
298 +Neurocognitive Psychology (M. Sc.)(%%)
299 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroimaging **
300 +)))
293 293  
294 -----
302 +|(% style="width:303px" %)(((
303 +[[image:My project.jpg||height="209" width="167"]]
295 295  
296 -=== Sharing human subject data ===
305 +**Heidi Kleven**
297 297  
298 -(% class="box floatinginfobox" %)
299 -(((
300 -**Human subject data that can be shared on EBRAINS:**
301 -// //
302 -// - Post-mortem data//
303 -// - Aggregated data//
304 -// - Strongly pseudonymized or de-identified subject data//
305 -// with a legal basis for sharing (e.g. Informed Consent)//
306 -// //
307 +(% class="small" %)Curation Scientist,
308 +Phd Student
309 +Neuroscience (M. Sc.)(%%)
310 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and brain atlases**
311 +)))| | |
307 307  
308 -(% class="small" %)
309 -//If you have human data that does not qualify as any of the above,//
310 -//please [[get in touch>>https://www.ebrains.eu/contact/]] and we will clarify the available options.//
311 -)))
313 +
314 +\\**Located in Germany:**
312 312  
316 +|(% style="width:303px" %)(((
317 +[[image:My project (2).jpg||height="209" width="167"]]
313 313  
314 -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]].
319 +**Jan Gündling**
315 315  
316 -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).
321 +(% class="small" %)Curation Scientist,
322 +Phd Student
323 +Sensors and Cognitive Psychology (M. Sc.)(%%)
324 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Human-Computer Interaction**
325 +)))|(% style="width:328px" %)(((
326 +
317 317  
318 -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.
319 319  
320 -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.
321 321  
322 -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.
323 323  
324 -----
325 325  
326 -== **The openMINDS metadata framework** ==
327 327  
328 -(% class="box floatinginfobox" %)
329 -(((
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 -)))
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"]].
334 334  
335 -For feedback, requests, or contributions, please get in touch with the openMINDS development team via
335 +**Lyuba Zehl**
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]]
337 +(% class="small" %)Knowledge Systems Engineer
338 +Dr. rer. nat. (Systems Neuroscience)(%%)
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" %)
341 341  
342 342  ----
343 343  
... ... @@ -344,6 +344,8 @@
344 344  == **Add practical value to your shared data, model or software** ==
345 345  
346 346  
347 +----
348 +
347 347  === **Showcase shared data, models or software in other services** ===
348 348  
349 349  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.
... ... @@ -358,6 +358,7 @@
358 358  |(% colspan="2" %)**Use your research product in an interactive publication**
359 359  |[[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]].
360 360  
363 +
361 361  ----
362 362  
363 363  ==== **Add a tutorial or learning resource ** ====
... ... @@ -373,19 +373,8 @@
373 373  
374 374  ----
375 375  
376 -== **EBRAINS commits to the FAIR principles** ==
379 +=== **The benefits of sharing data ** ===
377 377  
378 -In 2016, the 'FAIR Guiding Principles for the management and guardianship of scientific data'{{footnote}}Wilkinson, M., Dumontier, M., Aalbersberg, I. et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data 3, 160018 (2016). https://doi.org/10.1038/sdata.2016.18 {{/footnote}} were introduced to the scientific community. The objective of the authors was to provide a set of general recommendations aimed at enhancing the Findability, Accessibility, Interoperability, and Reusability of digital resources (data). They emphasize the importance of making data more open, discoverable, and usable, ultimately facilitating collaboration and knowledge sharing within the scientific community. Today, the FAIR principles are widely recognized and adopted as best practices in data management and stewardship across scientific fields.
379 -
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.
381 -
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]]. **
383 -
384 -
385 -----
386 -
387 -== **General benefits of sharing data ** ==
388 -
389 389  By sharing your data via EBRAINS, you gain access to the following benefits:
390 390  
391 391  [[image:image-20230324170841-3.png]]
... ... @@ -392,13 +392,19 @@
392 392  
393 393  
394 394  
395 -We support you to better follow the [[FAIR^^ ^^guiding principles>>https://www.nature.com/articles/sdata201618]] for data management and stewardship. Publishing data, models or code via EBRAINS will provide you with a citeable [[DataCite DOI>>https://www.doi.org/the-identifier/resources/handbook/]] for your research product.
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.
396 396  
397 397  ----
398 398  
399 -== **Frequently asked questions ** ==
391 +=== **Frequently asked questions ** ===
400 400  
393 +(((
394 +==== ====
395 +
396 +(((
401 401  >Is the curation process time consuming and difficult?
398 +)))
399 +)))
402 402  
403 403  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.
404 404  
... ... @@ -425,104 +425,11 @@
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**(%%) ==
429 -
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 -
432 -The curators in EBRAINS are located in Oslo, Jülich, Trier and Paris. 
433 -
434 -
435 -**Located in Norway**
436 -
437 -|(% style="width:303px" %)(((
438 -[[image:My project2.jpg||height="209" width="167"]]
439 -
440 -**Archana Golla**
441 -
442 -(% class="small" %)Curation Scientist
443 -Neuroscience (PhD)(%%)
444 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Behavioral neuroscience and microscopy**
445 -)))|(% style="width:303px" %)(((
446 -[[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
447 -
448 -**Camilla H. Blixhavn**
449 -
450 -(% class="small" %)Curation Scientist,
451 -Phd Student
452 -Neuroscience (M. Sc.)(%%)
453 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and data integration**
454 -)))|(% style="width:303px" %)(((
455 -[[image:My project (1).jpg||height="209" width="167"]]
456 -
457 -**Ingrid Reiten**
458 -
459 -(% class="small" %)Curation Scientist,
460 -Phd Student
461 -Neuroscience (M. Sc.)(%%)
462 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and structural connectivity**
463 -)))|(% style="width:303px" %)(((
464 -[[image:My project1.jpg||height="209" width="167"]]
465 -
466 -**Sophia Pieschnik**
467 -
468 -(% class="small" %)Curation Scientist
469 -Neurocognitive Psychology (M. Sc.)(%%)
470 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroimaging **
471 -)))
472 -
473 -|(% style="width:303px" %)(((
474 -[[image:My project.jpg||height="209" width="167"]]
475 -
476 -**Heidi Kleven**
477 -
478 -(% class="small" %)Curation Scientist,
479 -Phd Student
480 -Neuroscience (M. Sc.)(%%)
481 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and brain atlases**
482 -)))| | |
483 -
484 -
485 -\\**Located in Germany**
486 -
487 -|(% style="width:303px" %)(((
488 -[[image:My project (2).jpg||height="209" width="167"]]
489 -
490 -**Jan Gündling**
491 -
492 -(% class="small" %)Curation Scientist,
493 -Phd Student
494 -Sensors and Cognitive Psychology (M. Sc.)(%%)
495 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Human-Computer Interaction**
496 -)))|(% style="width:303px" %)(((
497 -[[image:Lyuba.jpg||height="209" width="167"]]
498 -
499 -**Lyuba Zehl**
500 -
501 -(% class="small" %)Knowledge Systems Engineer
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**
504 -)))|(% style="width:303px" %) |(% style="width:303px" %)
505 -
506 -----
507 -
508 -
509 -
510 -----
511 -
512 512  == Contact ==
513 513  
514 514  [[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
515 515  
516 -----
517 517  
518 -== Affiliated laboratories ==
519 -
520 -//Institute of Basic Medical Sciences,** **University of Oslo, Norway (PI: Jan G. Bjaalie, Trygve B. Leergaard)//
521 -
522 -//Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Germany (PI: Timo Dicksheid)//
523 -
524 -----
525 -
526 526  == References ==
527 527  
528 528  {{putFootnotes/}}
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Data Curation