Changes for page data-curation-copy

Last modified by eapapp on 2023/07/04 16:46
From version 60.1
edited by ingrreit
on 2023/04/25 17:36
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To version 45.1
edited by ingrreit
on 2023/04/03 12:03
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1 -== Publishing neuroscience data, models and software via EBRAINS ==
1 +== Publishing data, models and software via EBRAINS ==
2 2  
3 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.
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21 21  
22 22  == **The EBRAINS curation process** ==
23 23  
24 -(% class="box successmessage" %)
25 -(((
26 -EBRAINS accepts **experimental data,** of all modalities and from all species, **models**, **software**, **web services **and **metadata models**. You'll find detailed information about each research product below.
27 -)))
28 -
29 29  In EBRAINS, multimodal and heterogenous neuroscience data, models and software are categorised and described in a standardised manner so that they can be effectively searched, compared, and analysed. This effort is referred to as curation. 
30 30  
31 31  >The EBRAINS curation process involves organising and annotating neuroscientific data to make the data discoverable and reusable.
32 32  
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33 33  Behind this process is the EBRAINS Curation team. Our mandate is to support you in sharing your data in line with the [[**FAIR principles**>>https://www.go-fair.org/fair-principles/]], whether you choose to describe only the key aspects of your data, or can invest in adding more detailed metadata.
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35 35  
36 -Curated data, models and software are made available in the [[the EBRAINS Knowledge Graph>>https://kg.ebrains.eu/]]. This makes the data and metadata discoverable in the [[Knowledge Graph Search>>url:https://search.kg.ebrains.eu/]] and programmatically via the [[Knowledge Graph API>>url:https://docs.kg.ebrains.eu/8387ccd27a186dea3dd0b949dc528842/api_endpoints.html]]. The data, models and software are integrated in the EBRAINS Knowledge Graph by interoperable metadata schemas as defined in [[openMINDS>>url:https://github.com/HumanBrainProject/openMINDS/wiki]].
37 -
38 -Data and models are linked to and discoverable via the species-specific [[EBRAINS siibra atlas viewer>>url:https://ebrains.eu/services/atlases/brain-atlases]] by using interoperable metadata schemas as defined in [[SANDS>>url:https://github.com/HumanBrainProject/SANDS/wiki]].
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40 40  (% class="box floatinginfobox" %)
41 41  (((
42 42  **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]]. **
43 43  )))
44 44  
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46 -(((
47 -**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.
48 -)))
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51 51  ----
52 52  
53 53  === Step by step - Experimental data ===
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157 157  
158 158  ----
159 159  
160 -=== Webservices and metadata models ===
152 +=== Output / result, when you've completed the curation process, what do you get ===
161 161  
162 -(% class="wikigeneratedid" id="HContact...." %)
163 -(% style="color:#e74c3c; font-size:16px" %)Contact....(% style="color:#4a5568; font-size:16px" %)
154 +Curated data, models and software are made available in the [[the EBRAINS Knowledge Graph>>https://kg.ebrains.eu/]]. This makes the data and metadata discoverable in the [[Knowledge Graph Search>>url:https://search.kg.ebrains.eu/]] and programmatically via the [[Knowledge Graph API>>url:https://docs.kg.ebrains.eu/8387ccd27a186dea3dd0b949dc528842/api_endpoints.html]]. The data, models and software are integrated in the EBRAINS Knowledge Graph by interoperable metadata schemas as defined in [[openMINDS>>url:https://github.com/HumanBrainProject/openMINDS/wiki]].
164 164  
165 -----
156 +Data and models are linked to and discoverable via the species-specific [[EBRAINS Interactive Atlas Viewer>>url:https://ebrains.eu/services/atlases/brain-atlases]] by using interoperable metadata schemas as defined in [[SANDS>>url:https://github.com/HumanBrainProject/SANDS/wiki]].
166 166  
167 -== **The curation team: meet the curators** ==
168 -
169 -[[image:fb6d6429-709e-4f4d-be3b-eab0a46695bd.JPG||height="184" width="137"]]
170 -
171 -**Sophia Pieschnik**
172 -(% class="small" %)Biology (B.Sc.)
173 -Neurocognitive Psychology (M.Sc.)
174 -
175 175  ----
176 176  
177 177  == **Information and resources for researchers looking to share data** ==
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180 180  
181 181  ----
182 182  
183 -=== **Improve your research product ** ===
166 +=== **The benefits of sharing data ** ===
184 184  
185 -==== **Add a tutorial or learning resource to your research product ** ====
168 +(% style="color:#000000" %)Sharing your data, models or code (research products) via EBRAINS makes it discoverable amongst other research products available in the (%%)[[(% style="color:#000000" %)EBRAINS Knowledge Graph>>https://kg.ebrains.eu/]](%%). This is made possible by the highly flexible metadata framework describing neuroscience data in detail.
186 186  
187 -==== (% style="color:#e74c3c" %)- Learning resource [information](%%) ====
170 +(% style="color:#000000" %)EBRAINS is gradually implementing interconnected tools and analysis workflows developed in the Human Brain Project (HBP) to further enhance the output from adding your dataset to the database.
188 188  
189 189  
190 -==== **Create a workflow for .... ? ** ====
173 +By sharing your data via EBRAINS, you gain access to the following benefits:
191 191  
192 -==== (% style="color:#e74c3c" %)- Workflows [information](%%) ====
175 +[[image:image-20230324170841-3.png]]
193 193  
194 -----
195 195  
196 -=== **Integrate your data on EBRAINS with other services** ===
197 197  
198 -EBRAINS supports further integration for a variety of data, and is continuously looking to increase the number of interoperable services.
179 +We support you to better follow the FAIR^^ ^^guiding principles 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.
199 199  
200 -* Integrate image data with //the Mio viewer//: (% style="color:#e74c3c" %)[description]
201 -* Integrate atlas-registered 2D image data with //the Localizoom viewer//: (% style="color:#e74c3c" %)[description](%%). See the [[LocaliZoom links available for this dataset>>https://doi.org/10.25493/T686-7BX]] as an example.
202 -* Add your data, models or software to a// Live paper//: (% style="color:#e74c3c" %)[description]
203 -* Integrate your data to //the atlas viewer Siibra//: (% style="color:#e74c3c" %)[description](%%). 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.
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205 205  ----
206 206  
207 -=== **The benefits of sharing data ** ===
184 +(% style="font-family:inherit" %) (% style="color:#1a202c; font-family:inherit; font-size:26px" %)**What can I share on EBRAINS? **
208 208  
209 -(% style="color:#000000" %)Sharing your data, models or code (research products) via EBRAINS makes it discoverable amongst other research products available in the (%%)[[(% style="color:#000000" %)EBRAINS Knowledge Graph>>https://kg.ebrains.eu/]](%%). This is made possible by the highly flexible metadata framework describing neuroscience data in detail.
186 +(% class="wikigeneratedid" id="H" %)
187 +[[image:image-20230324170829-2.png]]
210 210  
211 -(% style="color:#000000" %)EBRAINS is gradually implementing interconnected tools and analysis workflows developed in the Human Brain Project (HBP) to further enhance the output from adding your dataset to the database.
212 212  
190 +----
213 213  
214 -By sharing your data via EBRAINS, you gain access to the following benefits:
192 +=== **At a glance: "Sharing experimental data on EBRAINS" ** ===
215 215  
216 -[[image:image-20230324170841-3.png]]
217 217  
195 +|(% style="width:593px" %)(((
196 +[[[[image:image-20230324171114-2.png]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
197 +)))|(% style="width:1240px" %)(((
198 +[[[[image:image-20230324171109-1.png||height="358" width="254"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
199 +)))|(% style="width:1240px" %)[[[[image:image-20230330120354-1.png||height="355" width="252"]]>>https://drive.ebrains.eu/f/707147a883b94fae8e69/]]
200 +|(% style="width:593px" %)//Collection of useful information for researchers looking to share experimental data on EBRAINS.//|(% style="width:1240px" %)//The EBRAINS data descriptor//|(% style="width:1240px" %)Introduction to data organization: A [[collection of guidelines>>https://drive.ebrains.eu/smart-link/25299f04-c4e5-4028-8f5f-3b8208f9a532/]] on how to organise files and folders to ensure consistency and reproducibility in the future.
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219 219  
220 -We support you to better follow the FAIR^^ ^^guiding principles 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.
221 -
222 -
223 223  ----
224 224  
225 -=== **At a glance: "Sharing experimental data on EBRAINS" ** ===
205 +=== **Integrate your data in the EBRAINS atlas services** ===
226 226  
207 +EBRAINS supports viewers for a variety of data, and is continuously looking to improve the services for visualising data. For 2D histology image data that is registered to an EBRAINS supported brain atlas, the data and the overlying atlas plates can be uploaded to the LocaliZoom viewer. See for example the [[LocaliZoom links available for this dataset>>https://doi.org/10.25493/T686-7BX]] as an example.
227 227  
228 -|(% style="width:439px" %)(((
229 -[[[[image:image-20230324171114-2.png||height="354" width="250"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
230 -)))|(% style="width:461px" %)(((
231 -[[[[image:image-20230324171109-1.png||height="352" width="250"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
232 -)))|(% style="width:416px" %)[[[[image:image-20230330120354-1.png||height="352" width="250"]]>>https://drive.ebrains.eu/f/707147a883b94fae8e69/]]
233 -|(% style="width:439px" %)//Collection of useful information for researchers looking to share experimental data on EBRAINS.//|(% style="width:461px" %)//The EBRAINS data descriptor: a general overview //|(% style="width:416px" %)//Introduction to data organization: A [[collection of guidelines>>https://drive.ebrains.eu/smart-link/25299f04-c4e5-4028-8f5f-3b8208f9a532/]] on how to organise files and folders to ensure consistency and reproducibility in the future. //
209 +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.
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235 235  ----
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239 239  (((
240 240  ==== ====
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218 +>
219 +
242 242  (((
243 243  >The curation process is time consuming and difficult
244 244  )))
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