Attention: The Collaboratory IAM will down for up to 1 hour on Monday, the 7th of July 2025 starting from 5pm CEST (my timezone) for up to 1 hour. Any and all services, which require a user login with an EBRAINS account, will be un-available during that time


Changes for page Data Curation

Last modified by abonard on 2025/06/03 10:55
From version 227.1
edited by spieschnik
on 2025/03/06 10:52
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To version 192.1
edited by eapapp
on 2023/06/13 10:26
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1 -Data Curation
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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 ===
... ... @@ -84,7 +84,9 @@
84 84  //with all you need to know//
85 85  //to share data on EBRAINS: //
86 86  // //
87 -[[~[~[image:image-20230324171114-2.png~|~|height="150" width="106"~]~]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
85 +[[[[image:image-20230324171114-2.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
86 +
87 +
88 88  )))
89 89  
90 90  
... ... @@ -92,28 +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 -[[~[~[image:image-20230621121014-1.png~|~|data-xwiki-image-style-alignment="center" height="150" width="106"~]~]>>https://drive.ebrains.eu/lib/f5cf4964-f095-49bd-8c34-e4ffda05a497/file/ebrains-infographic-data-organisation.pdf/]]
112 -)))
113 113  
107 +==== **2. Upload data ** ====
108 +
109 +
114 114  (% 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. **
115 115  
116 -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.
117 117  
118 118  (% 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).**
119 119  
... ... @@ -122,7 +122,7 @@
122 122  **Opt. 2. **For larger datasets or datasets with a large amount of files, we recommend using a programmatic approach. The [[python script>>https://github.com/eapapp/ebrains-data-storage/tree/main/data-proxy]] is interactive and does not require any additional programming.
123 123  
124 124  
125 -EBRAINS offers secure, long-term storage at FENIX Supercomputing Centres in Europe.
121 +EBRAINS offers secure, long-term storage at [[CSCS Swiss National Supercomputing Centre>>url:https://www.cscs.ch/]], with currently no upper limit of storage capacity. 
126 126  
127 127  If a data collection is already uploaded elsewhere, we may link to the already existing repository.
128 128  
... ... @@ -140,7 +140,7 @@
140 140  * [[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.
141 141  * [[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.
142 142  
143 -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.
144 144  
145 145  
146 146  ==== **4. Write a Data Descriptor** ====
... ... @@ -161,11 +161,12 @@
161 161  (% class="box floatinginfobox" id="data-descriptor-infographic" %)
162 162  (((
163 163  (% style="text-align:center" %)
164 -//Download our infographic
165 -about the EBRAINS Data//
166 -//Descriptor//
160 +//Download our infographic: //
161 +//The EBRAINS Data//
162 +//Descriptor at a glance//
167 167  // //
168 -[[~[~[image:image-20230324171109-1.png~|~|height="150" width="106"~]~]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
164 +[[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
165 +
169 169  )))
170 170  
171 171  ==== **5. Preview and publish** ====
... ... @@ -176,162 +176,179 @@
176 176  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.
177 177  
178 178  
176 +----
179 179  
178 +==== ====
180 180  
181 -----
180 +==== **Sharing human subject data** ====
182 182  
183 -=== 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 +// //
184 184  
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 +)))
185 185  
186 -==== 1. Start early ====
187 187  
188 -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]].
189 189  
190 -By registering a model early in your project, you can take advantage of EBRAINS tools
191 -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).
192 192  
193 -==== 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.
194 194  
195 -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.
196 196  
197 -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.
198 198  
199 -It is up to you whether you create a new collab for each model, or reuse an existing collab
200 -(it is no problem to have multiple models associated with a single collab).
201 201  
202 -Collabs are also useful for storing simulation results, adding documentation for your model,
203 -and/or providing tutorials in Jupyter notebooks.
209 +----
204 204  
205 -==== 3. Upload code ====
211 +=== Step by Step - Models ===
206 206  
207 -We recommend storing model code and/or configuration files in an online Git repository, for example on GitHub.
208 -This repository should be public when you publish the model, but a private repository can be used for model development.
209 209  
210 -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.
211 211  
212 -==== 4. Submit metadata ====
213 213  
214 -We recommend submitting metadata using the Model Catalog app, installed in your collab.
217 +//Additional information will be added soon.//
215 215  
216 -To install it:
219 +----
217 217  
218 -1. click the "+ Create" button
219 -1. in the "Create Page" form, add a title, such as "Model Catalog", and select "Community App", then click "Create"
220 -1. scroll down until you find the "Model Catalog" app, click "Select", then "Save & View"
221 +=== Step by Step - Software ===
221 221  
222 -You will then see a table of all the models and validation tests associated with this collab.
223 -If this is your first time using the app, the table will probably be empty.
224 -To add your model, click "+", fill in the form, then click "Add model".
225 225  
226 -As development of your model proceeds, you can easily register new versions of the code,
227 -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 +)))
228 228  
229 -If you prefer not to use the app, you can instead fill in the [[EBRAINS Curation Request Form>>https://nettskjema.no/a/386195]].,
230 -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"]]
231 231  
232 -==== 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.
233 233  
234 -Once you're ready to publish your model entry in the EBRAINS Knowledge Graph,
235 -we encourage you to provide a dataset containing the simulation results produced by your model,
236 -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]].
237 237  
238 -These reference data will be linked to the model, and will be helpful to anyone trying to
239 -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.
240 240  
241 -We will soon introduce a "Reproducible" badge for all models that include a reference dataset,
242 -and whose simulation results can be reproduced by an EBRAINS curator.
243 243  
244 -==== 6. Request publication, preview and publish ====
243 +----
245 245  
246 -Until you request your model entry to be published in the EBRAINS Knowledge Graph,
247 -only members of the collab will be able to view the model entry, in the Model Catalog app
248 -or using the Model Validation Python client.
245 +== **The openMINDS metadata framework** ==
249 249  
250 -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]].
251 251  
252 -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
253 253  
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]]
254 254  
255 -Curators will then perform a number of checks:
255 +----
256 256  
257 -1. Does the model description provide sufficient context to understand the purpose and use of the model?
258 -1. Does the code repository contain a licence file, explaining the conditions for reusing the code?
259 -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** ==
260 260  
261 -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.
262 262  
263 -* 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"]].
264 -* 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 +
265 265  
266 -Once this is done, you will be invited to review a preview of how the model entry will appear in the KG Search,
267 -and will have the opportunity to request modifications prior to approval and publication.
264 +**Located in Norway:**
268 268  
269 -----
266 +|(% style="width:303px" %)(((
267 +[[image:My project2.jpg||height="209" width="167"]]
270 270  
271 -=== Step by Step - Software ===
269 +**Archana Golla**
272 272  
273 -We ask software developers to provide their metadata in the "CodeMeta" format. [[CodeMeta>>https://codemeta.github.io/]] is a common format for software metadata, supported by GitHub, Zenodo, FigShare, DataCite, and the US National Science Foundation.
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 -1. Create a codemeta.json file for your software. There are several [[tools>>https://codemeta.github.io/tools/]] to help you do this, for example the [[CodeMeta generator>>https://codemeta.github.io/codemeta-generator]] app. Please fill in as many of the fields as possible.
276 -1. Place this file in the root folder of your code repository.
277 -1. Contact [[EBRAINS support>>https://www.ebrains.eu/contact/]] to request curation of your software, letting us know the URL of your code repository. If you need help hosting your code online, please also let us know.
278 -1. After a quality check, we integrate and publish the information contained in your codemeta.json file to the Knowledge Graph. Your software is then searchable and usable for the neuroscience community.
277 +**Camilla H. Blixhavn**
279 279  
280 -When you release a new version of your software, just update the codemeta.json file in your repository. We will check the repository on a regular basis, and if the version identifier has changed the Knowledge Graph will be updated accordingly.
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"]]
281 281  
282 -----
286 +**Ingrid Reiten**
283 283  
284 -=== Sharing human subject data ===
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"]]
285 285  
286 -(% class="box floatinginfobox" %)
287 -(((
288 -**Human subject data that can be shared on EBRAINS:**
289 -// //
290 -// - Post-mortem data//
291 -// - Aggregated data//
292 -// - Strongly pseudonymized or de-identified subject data//
293 -// with a legal basis for sharing (e.g. Informed Consent)//
294 -// //
295 +**Sophia Pieschnik**
295 295  
296 -(% class="small" %)
297 -//If you have human data that does not qualify as any of the above,//
298 -//please [[get in touch>>https://www.ebrains.eu/contact/]] and we will clarify the available options.//
297 +(% class="small" %)Curation Scientist
298 +Neurocognitive Psychology (M. Sc.)(%%)
299 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroimaging **
299 299  )))
300 300  
302 +|(% style="width:303px" %)(((
303 +[[image:My project.jpg||height="209" width="167"]]
301 301  
302 -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]].
305 +**Heidi Kleven**
303 303  
304 -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).
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 +)))| | |
305 305  
306 -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.
313 +
314 +\\**Located in Germany:**
307 307  
308 -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.
316 +|(% style="width:303px" %)(((
317 +[[image:My project (2).jpg||height="209" width="167"]]
309 309  
310 -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.
319 +**Jan Gündling**
311 311  
312 -----
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 +
313 313  
314 -== **The openMINDS metadata framework** ==
315 315  
316 -(% class="box floatinginfobox" %)
317 -(((
318 -[[~[~[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]]
319 -)))
320 320  
321 -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"]].
322 322  
323 -For feedback, requests, or contributions, please get in touch with the openMINDS development team via
324 324  
325 -* [[support@openmetadatainitiative.org>>mailto:mailto:support@openmetadatainitiative.org]]
326 -* [[GitHub Issues>>https://github.com/openMetadataInitiative/openMINDS/issues]] (for metadata schemas)
327 -* [[GitHub Issues>>https://github.com/openMetadataInitiative/openMINDS_instances/issues]] (for metadata instances)
328 -* [[openMINDS Community Forum>>https://neurostars.org/t/openminds-community-forum-virtual]]
329 329  
333 +
334 +
335 +**Lyuba Zehl**
336 +
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 +
330 330  ----
331 331  
332 332  == **Add practical value to your shared data, model or software** ==
333 333  
334 334  
347 +----
348 +
335 335  === **Showcase shared data, models or software in other services** ===
336 336  
337 337  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.
... ... @@ -346,6 +346,7 @@
346 346  |(% colspan="2" %)**Use your research product in an interactive publication**
347 347  |[[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]].
348 348  
363 +
349 349  ----
350 350  
351 351  ==== **Add a tutorial or learning resource ** ====
... ... @@ -361,19 +361,8 @@
361 361  
362 362  ----
363 363  
364 -== **EBRAINS commits to the FAIR principles** ==
379 +=== **The benefits of sharing data ** ===
365 365  
366 -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.
367 -
368 -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.
369 -
370 -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]]. **
371 -
372 -
373 -----
374 -
375 -== **General benefits of sharing data ** ==
376 -
377 377  By sharing your data via EBRAINS, you gain access to the following benefits:
378 378  
379 379  [[image:image-20230324170841-3.png]]
... ... @@ -380,13 +380,19 @@
380 380  
381 381  
382 382  
383 -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.
384 384  
385 385  ----
386 386  
387 -== **Frequently asked questions ** ==
391 +=== **Frequently asked questions ** ===
388 388  
393 +(((
394 +==== ====
395 +
396 +(((
389 389  >Is the curation process time consuming and difficult?
398 +)))
399 +)))
390 390  
391 391  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.
392 392  
... ... @@ -411,22 +411,13 @@
411 411  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.
412 412  
413 413  
424 +----
425 +
414 414  == Contact ==
415 415  
416 416  [[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
417 417  
418 -----
419 419  
420 -== Affiliated laboratories ==
421 -
422 -//Institute of Basic Medical Sciences,** **University of Oslo, Norway (PI: Jan G. Bjaalie, Trygve B. Leergaard)//
423 -
424 -//Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Germany (PI: Timo Dicksheid)//
425 -
426 -//Paris-Saclay Institute of Neuroscience, CNRS, Université Paris-Saclay, France (PI: Andrew P. Davison)//
427 -
428 -----
429 -
430 430  == References ==
431 431  
432 432  {{putFootnotes/}}
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Data Curation