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 194.1
edited by ingrreit
on 2023/06/14 09:01
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To version 228.1
edited by puchades
on 2025/05/07 15:03
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17 17  {{/html}}
18 18  
19 19  
20 -== Publishing neuroscience data, models and software via EBRAINS ==
20 +(% class="wikigeneratedid" id="HPublishingneurosciencedata2CmodelsandsoftwareviaEBRAINS" %)
21 +(% style="font-size:2em" %)**Publishing neuroscience data, models and software via EBRAINS**
21 21  
22 -
23 23  (% class="wikigeneratedid" %)
24 24  The aim of this collab is to provide you with detailed information about publishing data, simulations, computational models, and software via EBRAINS. If you want a quick overview of the sharing process, see [[https:~~/~~/ebrains.eu/service/share-data>>https://ebrains.eu/service/share-data]].
25 25  
... ... @@ -29,7 +29,7 @@
29 29  
30 30  == **Information to get started** ==
31 31  
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. **
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. **
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  
... ... @@ -67,7 +67,9 @@
67 67  
68 68  The curation of data, models and software is different. Thus, below we explain the process for sharing for each research product separately.
69 69  
70 +**Before you get started, make sure you[[ sign up for a free EBRAINS account>>https://www.ebrains.eu/page/sign-up]]. This is needed to complete the data sharing process. **
70 70  
72 +
71 71  ----
72 72  
73 73  === Step by step - Data ===
... ... @@ -82,9 +82,7 @@
82 82  //with all you need to know//
83 83  //to share data on EBRAINS: //
84 84  // //
85 -[[[[image:image-20230324171114-2.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
86 -
87 -
87 +[[~[~[image:image-20230324171114-2.png~|~|height="150" width="106"~]~]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
88 88  )))
89 89  
90 90  
... ... @@ -92,24 +92,28 @@
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 [[Curation request form>>https://nettskjema.no/a/277393#/]]. **
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]]. **
96 96  
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.
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.
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.
99 99  
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 -This form collects the necessary information needed for us to evaluate whether we can ethically and legally share the data via EBRAINS.
103 -
104 -See below for information about the ethical and legal aspects concerning sharing of human subject data.
105 -
106 -
107 107  ==== **2. Upload data ** ====
108 108  
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: //
109 109  
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 +
110 110  (% 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. **
111 111  
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.
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.
113 113  
114 114  (% 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).**
115 115  
... ... @@ -118,7 +118,7 @@
118 118  **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.
119 119  
120 120  
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. 
125 +EBRAINS offers secure, long-term storage at FENIX Supercomputing Centres in Europe.
122 122  
123 123  If a data collection is already uploaded elsewhere, we may link to the already existing repository.
124 124  
... ... @@ -136,7 +136,7 @@
136 136  * [[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.
137 137  * [[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.
138 138  
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.
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.
140 140  
141 141  
142 142  ==== **4. Write a Data Descriptor** ====
... ... @@ -157,12 +157,11 @@
157 157  (% class="box floatinginfobox" id="data-descriptor-infographic" %)
158 158  (((
159 159  (% style="text-align:center" %)
160 -//Download our infographic: //
161 -//The EBRAINS Data//
162 -//Descriptor at a glance//
164 +//Download our infographic
165 +about the EBRAINS Data//
166 +//Descriptor//
163 163  // //
164 -[[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
165 -
168 +[[~[~[image:image-20230324171109-1.png~|~|height="150" width="106"~]~]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
166 166  )))
167 167  
168 168  ==== **5. Preview and publish** ====
... ... @@ -173,184 +173,162 @@
173 173  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.
174 174  
175 175  
176 -----
177 177  
178 -==== ====
179 179  
180 -==== **Sharing human subject data** ====
181 +----
181 181  
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 -// //
183 +=== Step by Step - Models ===
191 191  
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 -)))
196 196  
186 +==== 1. Start early ====
197 197  
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]].
188 +It is not necessary to wait until you are ready to publish to register your model with EBRAINS.
199 199  
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).
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.
201 201  
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.
193 +==== 2. Create/choose a Collab workspace ====
203 203  
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.
195 +We use EBRAINS Collaboratory "collab" workspaces to help manage the model curation process.
205 205  
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.
197 +In particular, we use collab membership (the "Team") to control who can view or edit your model metadata prior to publication.
207 207  
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).
208 208  
209 -----
202 +Collabs are also useful for storing simulation results, adding documentation for your model,
203 +and/or providing tutorials in Jupyter notebooks.
210 210  
211 -=== Step by Step - Models ===
205 +==== 3. Upload code ====
212 212  
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.
213 213  
214 -~1. Request curation using the [[Curation request form>>https://nettskjema.no/a/277393#/]]. You will be contacted by a curator with more information.
210 +Alternatively, you can upload code to the Collab Drive or Bucket storage.
215 215  
212 +==== 4. Submit metadata ====
216 216  
217 -//Additional information will be added soon.//
214 +We recommend submitting metadata using the Model Catalog app, installed in your collab.
218 218  
219 -----
216 +To install it:
220 220  
221 -=== Step by Step - Software ===
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"
222 222  
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".
223 223  
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 -)))
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".
231 231  
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"]]
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.
233 233  
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.
232 +==== 5. Provide a reference dataset ====
237 237  
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]].
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.
239 239  
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.
238 +These reference data will be linked to the model, and will be helpful to anyone trying to
239 +reuse your model.
241 241  
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.
242 242  
243 -----
244 +==== 6. Request publication, preview and publish ====
244 244  
245 -== **The openMINDS metadata framework** ==
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.
246 246  
247 -(% class="box floatinginfobox" %)
248 -(((
249 -[[[[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]]
250 -)))
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.
251 251  
252 -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 +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.
253 253  
254 -For feedback, requests, or contributions, please get in touch with the openMINDS development team via
255 255  
256 -* the support-email: [[openminds@ebrains.eu>>path:mailto:openminds@ebrains.eu]]
257 -* the [[GitHub issue tracker>>url:https://github.com/HumanBrainProject/openMINDS/issues]]
258 -* the INCF NeuroStars [[openMINDS Community Forum>>url:https://neurostars.org/t/openminds-community-forum-virtual/20156]]
255 +Curators will then perform a number of checks:
259 259  
260 -----
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.
261 261  
262 -== **The curation team: meet the curators** ==
261 +The curators will also take a snapshot of your model code.
263 263  
264 -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 +* 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.
265 265  
266 -The curators in EBRAINS are located in Oslo, Jülich, Trier and Paris. 
267 -
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.
268 268  
269 -**Located in Norway:**
269 +----
270 270  
271 -|(% style="width:303px" %)(((
272 -[[image:My project2.jpg||height="209" width="167"]]
271 +=== Step by Step - Software ===
273 273  
274 -**Archana Golla**
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.
275 275  
276 -(% class="small" %)Curation Scientist
277 -Neuroscience (PhD)(%%)
278 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Behavioral neuroscience and microscopy**
279 -)))|(% style="width:303px" %)(((
280 -[[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
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.
281 281  
282 -**Camilla H. Blixhavn**
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.
283 283  
284 -(% class="small" %)Curation Scientist,
285 -Phd Student
286 -Neuroscience (M. Sc.)(%%)
287 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and data integration**
288 -)))|(% style="width:303px" %)(((
289 -[[image:My project (1).jpg||height="209" width="167"]]
282 +----
290 290  
291 -**Ingrid Reiten**
284 +=== Sharing human subject data ===
292 292  
293 -(% class="small" %)Curation Scientist,
294 -Phd Student
295 -Neuroscience (M. Sc.)(%%)
296 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and structural connectivity**
297 -)))|(% style="width:303px" %)(((
298 -[[image:My project1.jpg||height="209" width="167"]]
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 +// //
299 299  
300 -**Sophia Pieschnik**
301 -
302 -(% class="small" %)Curation Scientist
303 -Neurocognitive Psychology (M. Sc.)(%%)
304 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroimaging **
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.//
305 305  )))
306 306  
307 -|(% style="width:303px" %)(((
308 -[[image:My project.jpg||height="209" width="167"]]
309 309  
310 -**Heidi Kleven**
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]].
311 311  
312 -(% class="small" %)Curation Scientist,
313 -Phd Student
314 -Neuroscience (M. Sc.)(%%)
315 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and brain atlases**
316 -)))| | |
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).
317 317  
318 -
319 -\\**Located in Germany:**
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.
320 320  
321 -|(% style="width:303px" %)(((
322 -[[image:My project (2).jpg||height="209" width="167"]]
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.
323 323  
324 -**Jan Gündling**
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.
325 325  
326 -(% class="small" %)Curation Scientist,
327 -Phd Student
328 -Sensors and Cognitive Psychology (M. Sc.)(%%)
329 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Human-Computer Interaction**
330 -)))|(% style="width:328px" %)(((
331 -
312 +----
332 332  
314 +== **The openMINDS metadata framework** ==
333 333  
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 +)))
334 334  
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"]].
335 335  
323 +For feedback, requests, or contributions, please get in touch with the openMINDS development team via
336 336  
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]]
337 337  
338 -
339 -
340 -**Lyuba Zehl**
341 -
342 -(% class="small" %)Knowledge Systems Engineer
343 -Dr. rer. nat. (Systems Neuroscience)(%%)
344 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
345 -)))|(% style="width:321px" %) |(% style="width:324px" %)
346 -
347 347  ----
348 348  
349 349  == **Add practical value to your shared data, model or software** ==
350 350  
351 351  
352 -----
353 -
354 354  === **Showcase shared data, models or software in other services** ===
355 355  
356 356  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.
... ... @@ -357,7 +357,7 @@
357 357  
358 358  
359 359  |(% colspan="2" %)**Viewer for 2D images**
360 -|[[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]].
341 +|[[image:MIO_screenshot.PNG]]|Integrate image data with //SeriesZoom viewer//: EBRAINS 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 [[viewer links available for this dataset>>https://search.kg.ebrains.eu/?category=Dataset&q=nr2f1#9677359c-73fa-4425-b8fa-3de794e9017a]] as an example.
361 361  |(% colspan="2" %)**Viewer for sequential atlas-registered 2D images with annotation options**
362 362  |[[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]].
363 363  |(% colspan="2" %)**Interactive 3D atlas viewer with options for data visualization**
... ... @@ -380,8 +380,19 @@
380 380  
381 381  ----
382 382  
383 -=== **The benefits of sharing data ** ===
364 +== **EBRAINS commits to the FAIR principles** ==
384 384  
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 +
385 385  By sharing your data via EBRAINS, you gain access to the following benefits:
386 386  
387 387  [[image:image-20230324170841-3.png]]
... ... @@ -388,19 +388,13 @@
388 388  
389 389  
390 390  
391 -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.
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.
392 392  
393 393  ----
394 394  
395 -=== **Frequently asked questions ** ===
387 +== **Frequently asked questions ** ==
396 396  
397 -(((
398 -==== ====
399 -
400 -(((
401 401  >Is the curation process time consuming and difficult?
402 -)))
403 -)))
404 404  
405 405  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.
406 406  
... ... @@ -425,13 +425,22 @@
425 425  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.
426 426  
427 427  
428 -----
429 -
430 430  == Contact ==
431 431  
432 432  [[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
433 433  
418 +----
434 434  
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 +
435 435  == References ==
436 436  
437 437  {{putFootnotes/}}
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Data Curation