Changes for page data-curation-copy

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From version 61.1
edited by ingrreit
on 2023/04/25 17:39
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To version 44.1
edited by ingrreit
on 2023/04/03 12:00
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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.
34 34  
35 -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]].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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38 -(% class="box infomessage" %)
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39 39  (((
40 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]]. **
41 41  )))
42 42  
43 -(% class="box successmessage" %)
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.
46 -)))
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42 +
48 48  ----
49 49  
50 50  === Step by step - Experimental data ===
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154 154  
155 155  ----
156 156  
157 -=== Webservices and metadata models ===
152 +=== Output / result, when you've completed the curation process, what do you get ===
158 158  
159 -(% class="wikigeneratedid" id="HContact...." %)
160 -(% 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]].
161 161  
162 -----
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]].
163 163  
164 -== **The curation team: meet the curators** ==
165 -
166 -[[image:fb6d6429-709e-4f4d-be3b-eab0a46695bd.JPG||height="184" width="137"]]
167 -
168 -**Sophia Pieschnik**
169 -(% class="small" %)Biology (B.Sc.)
170 -Neurocognitive Psychology (M.Sc.)
171 -
172 172  ----
173 173  
174 174  == **Information and resources for researchers looking to share data** ==
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177 177  
178 178  ----
179 179  
180 -=== **Improve your research product ** ===
166 +=== **The benefits of sharing data ** ===
181 181  
182 -==== **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.
183 183  
184 -==== (% 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.
185 185  
186 186  
187 -==== **Create a workflow for .... ? ** ====
173 +By sharing your data via EBRAINS, you gain access to the following benefits:
188 188  
189 -==== (% style="color:#e74c3c" %)- Workflows [information](%%) ====
175 +[[image:image-20230324170841-3.png]]
190 190  
191 -----
192 192  
193 -=== **Integrate your data on EBRAINS with other services** ===
194 194  
195 -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.
196 196  
197 -* Integrate image data with //the Mio viewer//: (% style="color:#e74c3c" %)[description]
198 -* 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.
199 -* Add your data, models or software to a// Live paper//: (% style="color:#e74c3c" %)[description]
200 -* 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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202 202  ----
203 203  
204 -=== **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? **
205 205  
206 -(% 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]]
207 207  
208 -(% 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.
209 209  
190 +----
210 210  
211 -By sharing your data via EBRAINS, you gain access to the following benefits:
192 +=== **At a glance: "Sharing experimental data on EBRAINS" ** ===
212 212  
213 -[[image:image-20230324170841-3.png]]
214 214  
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]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
199 +)))
200 +|(% style="width:593px" %)//Collection of useful information for researchers looking to share experimental data on EBRAINS.//|(% style="width:1240px" %)//The EBRAINS data descriptor//
215 215  
202 +=== **Introduction to data organisation ** ===
216 216  
217 -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.
204 +Have you ever experienced not being able to find a file that you were sure you had somewhere? We have prepared 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.
218 218  
206 +* Why is data organisation important?
207 +* How to organise my data repository?
219 219  
209 +[[[[image:image-20230330120354-1.png||height="344" width="244"]]>>https://drive.ebrains.eu/f/707147a883b94fae8e69/]]
210 +
220 220  ----
221 221  
222 -=== **At a glance: "Sharing experimental data on EBRAINS" ** ===
213 +=== **Integrate your data in the EBRAINS atlas services** ===
223 223  
215 +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.
224 224  
225 -|(% style="width:439px" %)(((
226 -[[[[image:image-20230324171114-2.png||height="354" width="250"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
227 -)))|(% style="width:461px" %)(((
228 -[[[[image:image-20230324171109-1.png||height="352" width="250"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
229 -)))|(% style="width:416px" %)[[[[image:image-20230330120354-1.png||height="352" width="250"]]>>https://drive.ebrains.eu/f/707147a883b94fae8e69/]]
230 -|(% 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. //
217 +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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232 232  ----
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236 236  (((
237 237  ==== ====
238 238  
226 +>
227 +
239 239  (((
240 240  >The curation process is time consuming and difficult
241 241  )))
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