Changes for page data-curation-copy

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edited by ingrreit
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edited by spieschnik
on 2023/05/08 14:18
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1 1  == Publishing neuroscience data, models and software via EBRAINS ==
2 2  
3 +The aim of this collab is to provide you with all the information you need to publish your experimental data, simulations, computational models, and software via EBRAINS. 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.
3 3  
4 -(% class="wikigeneratedid" %)
5 -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]].
6 -
7 7  {{box title="**Contents**"}}
8 8  {{toc depth="3" start="2"/}}
9 9  {{/box}}
10 10  
11 11  
12 -== **Information to get started** ==
10 +(% style="text-align: center;" %)
11 +**Get started! **
13 13  
14 -**Get started! [[REQUEST CURATION>>https://nettskjema.no/a/277393#/]] to share data, simulations, computational models, and software, - or a new version of an existing one. **
13 +(% style="text-align: center;" %)
14 +**[[REQUEST CURATION>>https://nettskjema.no/a/277393#/]] **
15 15  
16 -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.
16 +(% style="text-align: center;" %)
17 + Search existing data, models and software in [[the EBRAINS Knowledge Graph Search>>https://kg.ebrains.eu/search/?facet_type[0]=Dataset]]
17 17  
18 18  
19 -Search existing data, models and software in [[the EBRAINS Knowledge Graph Search>>https://kg.ebrains.eu/search/?facet_type[0]=Dataset]]
20 -
21 -
22 -EBRAINS accepts data from all modalities and from all species, as well as models, software, web services and metadata models (collectively referred to as research products) for sharing. You'll find detailed information about how to share each research product below. 
23 -
24 -
25 -(% class="box infomessage" %)
26 -(((
27 -We strongly recommend to **start preparing for data sharing as early as possible**. With a structured data repository and adequate notes on how the data was acquired, you greatly minimize the effort required to publish your data. The time it takes to share data on EBRAINS heavily depends on on the engagement from the researcher and how well the data and metadata is prepared before-hand. Contact us for personalised guidance on how to prepare for sharing.
28 -)))
29 -
30 -(% class="box successmessage" %)
31 -(((
32 -**Particular needs? Contact us! **The workflows for sharing can be modified for researchers or research groups aiming to frequently publish larger numbers of their research products through EBRAINS. Please contact the curation service team in such cases
33 -)))
34 -
35 35  ----
36 36  
37 37  == **The EBRAINS curation process** ==
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52 52  
53 53  (% class="box infomessage" %)
54 54  (((
55 -
40 +**We strongly recommend to start preparing for data sharing as early as possible.** With a structured data repository and adequate notes on how the data was acquired, you greatly minimize the effort required to publish your data. The time it takes to share data on EBRAINS heavily depends on on the engagement from the researcher and how well the data and metadata is prepared before-hand. **[[Contact us for personalised guidance on how to prepare for sharing>>mailto:curation-support@ebrains.eu]]. **
56 56  )))
57 57  
58 58  (% class="box successmessage" %)
59 59  (((
60 -
45 +**Particular needs? Contact us! **The workflows for sharing can be modified for researchers or research groups aiming to frequently publish larger numbers of their research products through EBRAINS. Please contact the curation service team in such cases.
61 61  )))
62 62  
63 63  ----
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114 114  
115 115  ==== **Sharing human data ** ====
116 116  
102 +We must ensure data shared on EBRAINS 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]].
103 +
117 117  (% class="box floatinginfobox" %)
118 118  (((
119 119  For **Human subject data**, the data must be //either//
120 120  
121 121  - Post-mortem data
109 +
122 122  - Aggregated data
111 +
123 123  - Pseudonymized subject data with a legal basis for sharing (e.g. Informed Consent)
124 124  
125 125  (% class="small" %)//If you have human data that do not classify as any of the above, please get in touch and we will clarify the available options. //
126 126  )))
127 127  
128 -We must ensure data shared on EBRAINS 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]].
117 +Pseudonymized data is shared via the Human Data Gateway (HDG) due to GDPR regulations. The HDG adds an authentication layer to the data.
129 129  
130 -Post-mortem and aggregated human data can be shared openly. Pseudonymized data is shared via the Human Data Gateway (HDG) due to GDPR regulations. The HDG adds an authentication layer to the data.
131 -
132 132  **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.
133 133  \\**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.
134 134  \\The Human Data Gateway (HDG) was introduced in February 2021 and developed across multiple teams in the HBP. The initiative to create the service and the initial design originated from EBRAINS Curation in close collaboration with the Data compliance team and the HBP Data Governance Working Group. HDG is a response to the needs of multiple data providers who are bringing data of human origin to EBRAINS. HDG covers the sharing of a limited range of data of human origin, i.e., data without direct identifiers and with very few indirect identifiers (strongly pseudonymized, de-identified). It 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.
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138 138  
139 139  === Step by Step - Models ===
140 140  
141 -(% style="color:#e74c3c" %){{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-1rb0hn"/}}
142 -
143 143  [place-holder-process-diagram]
144 144  
145 145  ==== **1. model step 1 ** ====
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156 156  
157 157  === Step by Step - Code ===
158 158  
159 -[[[[image:swc-flow-no-header.png||alt="swc-flow.png"]]>>https://www.ebrains.eu/tools/ebrains-curation-request-form||rel="noopener noreferrer" target="_blank"]]
144 +[place-holder-process-diagram]
160 160  
161 -1. Fill in the [[request form>>https://www.ebrains.eu/tools/ebrains-curation-request-form]].[[[[image:Thumb.png||alt="EBRAINS-Share-Software.pdf" height="377" style="float:right" width="257"]]>>attach:EBRAINS-Share-Software.pdf]]
162 -1. One of our creators will then open a ticket and contact you with futher instructions. In these instructions you will find the links to your software and software version entries in the Knowledge Graph.
163 -1. In the next step you need to enter the metadata of your software in the [[Knowledge Graph Editor>>url:https://editor.kg.ebrains.eu/]] by using the links provided in the ticket. The links will lead you to the space in the KG, which was created especially for you. You can start directly with the editing of your software. 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.
164 -1. 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.
165 -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.
146 +==== **1. code step 1 ** ====
166 166  
167 -If you want to add a new version to an already curated software, please write to [[curation-support@humanbrainproject.eu>>path:mailto:curation-support@humanbrainproject.eu]] or open a ticket at [[https:~~/~~/support.humanbrainproject.eu/.>>url:https://support.humanbrainproject.eu/]]
168 -For more information, visit our [[guide>>url:https://wiki.ebrains.eu/bin/view/Collabs/swc-guide]].
148 +Text
169 169  
150 +
151 +==== **2. code step 2** ====
152 +
153 +Text
154 +
170 170  ----
171 171  
172 172  === Webservices and metadata models ===
173 173  
174 174  (% class="wikigeneratedid" id="HContact...." %)
175 -(% style="color:#e74c3c; font-size:16px" %){{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-np253c"/}}(% style="color:#4a5568; font-size:16px" %)
160 +(% style="color:#e74c3c; font-size:16px" %)Contact....(% style="color:#4a5568; font-size:16px" %)
176 176  
177 177  ----
178 178  
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189 189  Neuroscience (PhD)(%%)
190 190  (% class="small" style="color:#4a5568" %)**Behavioral neuroscience and microscopy**
191 191  )))|(% style="width:303px" %)(((
192 -[[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
177 +[[image:My project.jpg||height="209" width="167"]]
193 193  
194 194  **Camilla H. Blixhavn**
195 195  
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216 216  (% class="small" style="color:#4a5568" %)**Neuroimaging **
217 217  )))
218 218  
219 -|(% style="width:303px" %)(((
220 -[[image:My project.jpg||height="209" width="167"]]
204 +
205 +
206 +**Located in Germany:**
221 221  
222 -**Heidi Kleven**
223 -
224 -(% class="small" %)Curation Scientist,
225 -Phd Student
226 -Neuroscience (M. Sc.)(%%)
227 -(% class="small" style="color:#4a5568" %)**Neuroanatomy and brain atlases**
228 -)))| | |
229 -
230 -
231 -\\**Located in Germany:**
232 -
233 -|(% style="width:303px" %)(((
234 234  [[image:My project (2).jpg||height="209" width="167"]]
235 235  
236 236  **Jan Gündling**
237 237  
238 -(% class="small" %)Curation Scientist,
239 -Phd Student
212 +(% class="small" %)Curation Scientist
240 240  Sensors and Cognitive Psychology (M. Sc.)(%%)
241 -(% class="small" style="color:#4a5568" %)**Human-Computer Interaction**
242 -)))|(% style="width:303px" %)(((
243 -
214 +(% class="small" style="color:#4a5568" %)**Human-Computer Interaction **
244 244  
245 -
246 -
247 -
248 -
249 -
250 -
251 -
252 -
253 -
254 -
255 -**Lyuba Zehl**
256 -
257 -(% class="small" %)Knowledge Systems Engineer
258 -Dr. rer. nat. (Systems Neuroscience)(%%)
259 -(% class="small" style="color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
260 -)))|(% style="width:303px" %) |
261 -
262 262  ----
263 263  
264 264  == **Information and resources for researchers looking to share data** ==
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269 269  
270 270  === **Improve your research product ** ===
271 271  
272 -(% class="wikigeneratedid" %)
273 -**{{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-fkdv6h"/}}**
274 -
275 275  ==== **Add a tutorial or learning resource to your research product ** ====
276 276  
277 277  ==== (% style="color:#e74c3c" %)- Learning resource [information](%%) ====
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289 289  
290 290  * 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]].
291 291  * 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]].
292 -* Add your data, models or software to a// Live paper//: (% style="color:#e74c3c" %)[description] {{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-62mbgl"/}}
243 +* Add your data, models or software to a// Live paper//: (% style="color:#e74c3c" %)[description]
293 293  * Integrate your data to //the Siibra//-explorer: The siibra-explorer is used for visualizing volumetric brain data in all the brain atlases provided by EBRAINS (Human, Monkey, Rat and Mouse). The siibra-explorer viewer uses siibra-api to enable navigation of brain region hierarchies, maps in different coordinate spaces, and linked regional data features. Furthermore, it is connected with the siibra toolsuite providing several analytical workflows. To learn more about how to integrate your data to atlases, check out the [[Atlas services>>https://ebrains.eu/services/atlases#Integratedatatoanatlas]] on ebrains.eu.
294 294  
295 295  ----
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