Changes for page data-curation-copy

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edited by ingrreit
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To version 36.1
edited by ingrreit
on 2023/03/26 07:26
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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  
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37 -(((
38 -**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.
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40 -
41 41  (% class="box floatinginfobox" %)
42 42  (((
43 43  **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]]. **
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47 47  
48 48  
49 49  
50 -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]].
51 51  
52 -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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54 -
55 55  ----
56 56  
57 57  === Step by step - Experimental data ===
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59 59  
60 60  [[image:image-20230326054341-1.png]]
61 61  
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62 62  ==== ====
63 63  
64 64  ==== **1. Provide some general information about your dataset** ====
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161 161  
162 162  ----
163 163  
164 -=== Webservices and metadata models ===
153 +=== Output / result, when you've completed the curation process, what do you get ===
165 165  
166 -=== (% style="color:#e74c3c; font-size:16px" %)Contact....(% style="color:#4a5568; font-size:16px" %) (%%) ===
155 +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]].
167 167  
157 +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]].
158 +
168 168  ----
169 169  
170 -=== **The curation team: meet the curators** ===
161 +== **Resources for researchers looking to share data** ==
171 171  
172 -[[image:fb6d6429-709e-4f4d-be3b-eab0a46695bd.JPG||height="184" width="137"]]
163 +Below you can find some resources that can come in handy if you are looking to share data via EBRAINS, or in general.
173 173  
174 -**Sophia Pieschnik**
175 -(% class="small" %)Biology (B.Sc.)
176 -Neurocognitive Psychology (M.Sc.)
177 -
178 178  ----
179 179  
180 -== **Information and resources for researchers looking to share data** ==
167 +=== **Why should I share data?** ===
181 181  
182 -Below you can find some resources that can come in handy if you are looking to share data via EBRAINS, or in general.
169 +(% style="color:#e74c3c" %)[EDIT required]
183 183  
184 -----
171 +(% style="color:#e74c3c" %)Sharing your data, models or code (research products) via EBRAINS makes it discoverable amongst other research products available in the [[EBRAINS Knowledge Graph>>https://kg.ebrains.eu/]]. This is made possible by the highly flexible metadata framework describing neuroscience data in detail. 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 -=== **Enrich your dataset, model or software** ===
187 187  
188 -(% style="color:#e74c3c" %)- Workflows [information]
174 +By sharing your data via EBRAINS, you gain access to the following benefits:
189 189  
190 -(% style="color:#e74c3c" %)- Learning resource [information]
176 +[[image:image-20230324170841-3.png]]
191 191  
192 -----
193 193  
194 -=== **The benefits of sharing data ** ===
195 195  
196 -(% 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.
180 +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.
197 197  
198 -(% 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.
199 199  
183 +----
200 200  
201 -By sharing your data via EBRAINS, you gain access to the following benefits:
185 +(% style="font-family:inherit" %) (% style="color:#1a202c; font-family:inherit; font-size:26px" %)**What can I share on EBRAINS? **
202 202  
203 -[[image:image-20230324170841-3.png]]
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188 +[[image:image-20230324170829-2.png]]
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191 +----
206 206  
207 -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.
193 +=== **Useful information about sharing of experimental data on EBRAINS ** ===
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209 209  
196 +|(% style="width:593px" %)(((
197 +[[[[image:image-20230324171114-2.png]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
198 +)))|(% style="width:1240px" %)(((
199 +[[[[image:image-20230324171109-1.png]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
200 +)))
201 +|(% style="width:593px" %)//Collection of useful information for researchers looking to share experimental data on EBRAINS.//|(% style="width:1240px" %)//The EBRAINS data descriptor//
202 +
210 210  ----
211 211  
212 -=== **At a glance: "Sharing experimental data on EBRAINS" ** ===
205 +=== **Introduction to data organisation ** ===
213 213  
207 +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/]] and [[advice>>https://drive.ebrains.eu/lib/f5cf4964-f095-49bd-8c34-e4ffda05a497/file/DataOrganisation.zip]] on how to organise files and folders to ensure consistency and reproducibility in the future.
214 214  
215 -|(% style="width:439px" %)(((
216 -[[[[image:image-20230324171114-2.png||height="354" width="250"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
217 -)))|(% style="width:461px" %)(((
218 -[[[[image:image-20230324171109-1.png||height="352" width="250"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
219 -)))|(% style="width:416px" %)[[[[image:image-20230330120354-1.png||height="352" width="250"]]>>https://drive.ebrains.eu/f/707147a883b94fae8e69/]]
220 -|(% 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 +* Why is data organisation important?
210 +* How to organise my data repository?
211 +* What is a Data Descriptor and why do I need one?
221 221  
222 222  ----
223 223  
224 -=== **Integrate your data on EBRAINS with other services** ===
215 +=== **Integrate your data in the EBRAINS atlas services** ===
225 225  
226 -EBRAINS supports further integration for a variety of data, and is continuously looking to increase the number of interoperable services.
217 +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 -* Integrate image data with //the Mio viewer//: (% style="color:#e74c3c" %)[description]
229 -* 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.
230 -* Add your data, models or software to a// Live paper//: (% style="color:#e74c3c" %)[description]
231 -* 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.
219 +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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237 237  (((
238 238  ==== ====
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228 +>
229 +
240 240  (((
241 241  >The curation process is time consuming and difficult
242 242  )))
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