Changes for page data-curation-copy

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From version 44.1
edited by ingrreit
on 2023/04/03 12:00
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To version 62.1
edited by ingrreit
on 2023/04/25 17:41
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1 -== Publishing data, models and software via EBRAINS ==
1 +== Publishing neuroscience 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.
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28 +
24 24  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. 
25 25  
26 26  >The EBRAINS curation process involves organising and annotating neuroscientific data to make the data discoverable and reusable.
27 27  
28 -
29 29  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.
30 30  
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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33 33  (((
34 34  **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]]. **
35 35  )))
36 36  
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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 -
43 43  ----
44 44  
45 45  === Step by step - Experimental data ===
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149 149  
150 150  ----
151 151  
152 -=== Output / result, when you've completed the curation process, what do you get ===
157 +=== Webservices and metadata models ===
153 153  
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]].
159 +(% class="wikigeneratedid" id="HContact...." %)
160 +(% style="color:#e74c3c; font-size:16px" %)Contact....(% style="color:#4a5568; font-size:16px" %)
155 155  
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]].
162 +----
157 157  
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 +
158 158  ----
159 159  
160 160  == **Information and resources for researchers looking to share data** ==
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163 163  
164 164  ----
165 165  
166 -=== **The benefits of sharing data ** ===
180 +=== **Improve your research product ** ===
167 167  
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.
182 +==== **Add a tutorial or learning resource to your research product ** ====
169 169  
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.
184 +==== (% style="color:#e74c3c" %)- Learning resource [information](%%) ====
171 171  
172 172  
173 -By sharing your data via EBRAINS, you gain access to the following benefits:
187 +==== **Create a workflow for .... ? ** ====
174 174  
175 -[[image:image-20230324170841-3.png]]
189 +==== (% style="color:#e74c3c" %)- Workflows [information](%%) ====
176 176  
191 +----
177 177  
193 +=== **Integrate your data, models or software with other services** ===
178 178  
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.
195 +EBRAINS supports further integration for a variety of data, and is continuously looking to increase the number of interoperable services.
180 180  
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.
181 181  
182 182  ----
183 183  
184 -(% style="font-family:inherit" %) (% style="color:#1a202c; font-family:inherit; font-size:26px" %)**What can I share on EBRAINS? **
204 +=== **The benefits of sharing data ** ===
185 185  
186 -(% class="wikigeneratedid" id="H" %)
187 -[[image:image-20230324170829-2.png]]
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.
188 188  
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.
189 189  
190 -----
191 191  
192 -=== **At a glance: "Sharing experimental data on EBRAINS" ** ===
211 +By sharing your data via EBRAINS, you gain access to the following benefits:
193 193  
213 +[[image:image-20230324170841-3.png]]
194 194  
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//
201 201  
202 -=== **Introduction to data organisation ** ===
203 203  
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.
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.
205 205  
206 -* Why is data organisation important?
207 -* How to organise my data repository?
208 208  
209 -[[[[image:image-20230330120354-1.png||height="344" width="244"]]>>https://drive.ebrains.eu/f/707147a883b94fae8e69/]]
210 -
211 211  ----
212 212  
213 -=== **Integrate your data in the EBRAINS atlas services** ===
222 +=== **At a glance: "Sharing experimental data on EBRAINS" ** ===
214 214  
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.
216 216  
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.
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. //
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223 223  (((
224 224  ==== ====
225 225  
226 ->
227 -
228 228  (((
229 229  >The curation process is time consuming and difficult
230 230  )))
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