Changes for page data-curation-copy

Last modified by eapapp on 2023/07/04 16:46
From version 109.1
edited by spieschnik
on 2023/05/08 09:55
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To version 146.2
edited by ingrreit
on 2023/06/05 09:23
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1 +XWiki.ingrreit
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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.
4 4  
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 +
5 5  {{box title="**Contents**"}}
6 6  {{toc depth="3" start="2"/}}
7 7  {{/box}}
8 8  
9 9  
10 -(% style="text-align: center;" %)
11 -**Get started! **
12 +== **Information to get started** ==
12 12  
13 -(% style="text-align: center;" %)
14 -**[[REQUEST CURATION>>https://nettskjema.no/a/277393#/]] **
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. **
15 15  
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]]
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.
18 18  
19 19  
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 +
20 20  ----
21 21  
22 22  == **The EBRAINS curation process** ==
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37 37  
38 38  (% class="box infomessage" %)
39 39  (((
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]]. **
55 +
41 41  )))
42 42  
43 43  (% class="box successmessage" %)
44 44  (((
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.
60 +
46 46  )))
47 47  
48 48  ----
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99 99  
100 100  ==== **Sharing human data ** ====
101 101  
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 -
104 104  (% class="box floatinginfobox" %)
105 105  (((
106 106  For **Human subject data**, the data must be //either//
107 107  
108 108  - Post-mortem data
109 -
110 110  - Aggregated data
111 -
112 112  - Pseudonymized subject data with a legal basis for sharing (e.g. Informed Consent)
113 113  
114 114  (% 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. //
115 115  )))
116 116  
117 -Pseudonymized data is shared via the Human Data Gateway (HDG) due to GDPR regulations. The HDG adds an authentication layer to the data.
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]].
118 118  
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 +
119 119  **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.
120 120  \\**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.
121 121  \\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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125 125  
126 126  === Step by Step - Models ===
127 127  
141 +(% style="color:#e74c3c" %){{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-1rb0hn"/}}
142 +
128 128  [place-holder-process-diagram]
129 129  
130 130  ==== **1. model step 1 ** ====
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141 141  
142 142  === Step by Step - Code ===
143 143  
144 -[place-holder-process-diagram]
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"]]
145 145  
146 -==== **1. code step 1 ** ====
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.
147 147  
148 -Text
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]].
149 149  
150 -
151 -==== **2. code step 2** ====
152 -
153 -Text
154 -
155 155  ----
156 156  
157 157  === Webservices and metadata models ===
158 158  
159 159  (% class="wikigeneratedid" id="HContact...." %)
160 -(% style="color:#e74c3c; font-size:16px" %)Contact....(% style="color:#4a5568; font-size:16px" %)
175 +(% style="color:#e74c3c; font-size:16px" %){{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-np253c"/}}(% style="color:#4a5568; font-size:16px" %)
161 161  
162 162  ----
163 163  
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165 165  
166 166  **Located in Norway:**
167 167  
168 -
169 169  |(% style="width:303px" %)(((
170 -[[image:My project2.jpg]]
184 +[[image:My project2.jpg||height="209" width="167"]]
171 171  
172 172  **Archana Golla**
173 173  
174 -Curation Scientist
188 +(% class="small" %)Curation Scientist
189 +Neuroscience (PhD)(%%)
190 +(% class="small" style="color:#4a5568" %)**Behavioral neuroscience and microscopy**
191 +)))|(% style="width:303px" %)(((
192 +[[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
175 175  
176 -(% class="small" %)Neuroscience (PhD)
194 +**Camilla H. Blixhavn**
177 177  
178 -(% class="small" %)Behavioral neuroscience and microscopy
196 +(% class="small" %)Curation Scientist,
197 +Phd Student
198 +Neuroscience (M. Sc.)(%%)
199 +(% class="small" style="color:#4a5568" %)**Neuroanatomy and data integration**
179 179  )))|(% style="width:303px" %)(((
180 -[[image:My project1.jpg]]
201 +[[image:My project (1).jpg||height="209" width="167"]]
181 181  
182 -**Sophia Pieschnik**
203 +**Ingrid Reiten**
183 183  
184 -Curation Scientist
205 +(% class="small" %)Curation Scientist,
206 +Phd Student
207 +Neuroscience (M. Sc.)(%%)
208 +(% class="small" style="color:#4a5568" %)**Neuroanatomy and structural connectivity**
209 +)))|(% style="width:303px" %)(((
210 +[[image:My project1.jpg||height="209" width="167"]]
185 185  
186 -(% class="small" %)Neurocognitive Psychology (M. Sc.)
212 +**Sophia Pieschnik**
187 187  
188 -(% class="small" %)Neuroimaging
189 -)))|(% style="width:303px" %)(((
190 -[[image:My project (1).jpg]]
214 +(% class="small" %)Curation Scientist
215 +Neurocognitive Psychology (M. Sc.)(%%)
216 +(% class="small" style="color:#4a5568" %)**Neuroimaging **
217 +)))
191 191  
192 -**Ingrid Reiten**
219 +|(% style="width:303px" %)(((
220 +[[image:My project.jpg||height="209" width="167"]]
193 193  
194 -Curation Scientist,
222 +**Heidi Kleven**
223 +
224 +(% class="small" %)Curation Scientist,
195 195  Phd Student
196 -(% class="small" %)Neuroscience (M. Sc.)
226 +Neuroscience (M. Sc.)(%%)
227 +(% class="small" style="color:#4a5568" %)**Neuroanatomy and brain atlases**
228 +)))| | |
197 197  
198 -(% class="small" %)Neuroanatomy and structural connectivity
199 -)))|(% style="width:303px" %)(((
200 -[[image:My project.jpg]]
230 +
231 +\\**Located in Germany:**
201 201  
202 -**Camilla H. Blixhavn**
233 +|(% style="width:303px" %)(((
234 +[[image:My project (2).jpg||height="209" width="167"]]
203 203  
204 -Curation Scientist,
236 +**Jan Gündling**
237 +
238 +(% class="small" %)Curation Scientist,
205 205  Phd Student
206 -(% class="small" %)Neuroscience (M. Sc.)
240 +Sensors and Cognitive Psychology (M. Sc.)(%%)
241 +(% class="small" style="color:#4a5568" %)**Human-Computer Interaction**
242 +)))|(% style="width:303px" %)(((
243 +
207 207  
208 -(% class="small" %)Neuroanatomy and data integration
209 -)))
210 -|(% style="width:303px" %) |(% style="width:303px" %) |(% style="width:303px" %) |(% style="width:303px" %)
211 -|(% style="width:303px" %) |(% style="width:303px" %) |(% style="width:303px" %) |(% style="width:303px" %)
212 -|(% class="small" style="width:303px" %) |(% class="small" style="width:303px" %) |(% class="small" style="width:303px" %) |(% class="small" style="width:303px" %)
213 -|(% class="small" style="width:303px" %) |(% class="small" style="width:303px" %) |(% class="small" style="width:303px" %) |(% class="small" style="width:303px" %)
214 214  
215 -
216 -
217 -
218 -**Located in Germany:**
219 219  
220 -[[image:My project (2).jpg||height="289" width="231"]]
221 221  
222 -**Jan Gündling**
223 223  
224 -Curation Scientist
225 -(% class="small" %)Sensors and Cognitive Psychology (M. Sc.)
226 -Human-Computer Interaction
227 227  
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 +
228 228  ----
229 229  
230 230  == **Information and resources for researchers looking to share data** ==
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235 235  
236 236  === **Improve your research product ** ===
237 237  
272 +(% class="wikigeneratedid" %)
273 +**{{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-fkdv6h"/}}**
274 +
238 238  ==== **Add a tutorial or learning resource to your research product ** ====
239 239  
240 240  ==== (% style="color:#e74c3c" %)- Learning resource [information](%%) ====
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252 252  
253 253  * 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]].
254 254  * 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]].
255 -* Add your data, models or software to a// Live paper//: (% style="color:#e74c3c" %)[description]
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"/}}
256 256  * 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.
257 257  
258 258  ----
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340 340  
341 341  {{putFootnotes/}}
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