Changes for page data-curation-copy

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From version 35.1
edited by ingrreit
on 2023/03/26 07:25
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To version 55.1
edited by ingrreit
on 2023/04/25 17:28
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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.
27 +)))
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.
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28 28  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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30 30  
36 +(% class="box successmessage" %)
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.
39 +)))
40 +
31 31  (% class="box floatinginfobox" %)
32 32  (((
33 33  **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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37 37  
38 38  
39 39  
50 +=== When you've completed the curation process ===
40 40  
52 +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]].
41 41  
54 +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]].
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56 +
42 42  ----
43 43  
44 44  === Step by step - Experimental data ===
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46 46  
47 47  [[image:image-20230326054341-1.png]]
48 48  
64 +==== ====
65 +
49 49  ==== **1. Provide some general information about your dataset** ====
50 50  
51 51  The [[Curation request form>>https://nettskjema.no/a/277393#/]] collects preliminary information about your data, allowing us to assess whether the dataset fits within the scope of EBRAINS. The submission generates a curation ID allowing us to track the case.
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146 146  
147 147  ----
148 148  
149 -=== Output / result, when you've completed the curation process, what do you get ===
166 +=== Webservices and metadata models ===
150 150  
151 -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]].
168 +=== (% style="color: rgb(231, 76, 60); font-size: 16px" %)Contact....(% style="color:#4a5568; font-size:16px" %) (%%) ===
152 152  
153 -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]].
154 -
155 155  ----
156 156  
157 -== **Resources for researchers looking to share data** ==
172 +=== **The curation team: meet the curators** ===
158 158  
159 -Below you can find some resources that can come in handy if you are looking to share data via EBRAINS, or in general.
174 +[[image:fb6d6429-709e-4f4d-be3b-eab0a46695bd.JPG||height="184" width="137"]]
160 160  
176 +**Sophia Pieschnik**
177 +(% class="small" %)Biology (B.Sc.)
178 +Neurocognitive Psychology (M.Sc.)
179 +
161 161  ----
162 162  
163 -=== **Why should I share data?** ===
182 +== **Information and resources for researchers looking to share data** ==
164 164  
165 -(% style="color:#e74c3c" %)[EDIT required]
184 +Below you can find some resources that can come in handy if you are looking to share data via EBRAINS, or in general.
166 166  
167 -(% 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.
186 +----
168 168  
188 +=== **Enrich your dataset, model or software** ===
169 169  
170 -By sharing your data via EBRAINS, you gain access to the following benefits:
190 +(% style="color:#e74c3c" %)- Workflows [information]
171 171  
172 -[[image:image-20230324170841-3.png]]
192 +(% style="color:#e74c3c" %)- Learning resource [information]
173 173  
194 +----
174 174  
196 +=== **The benefits of sharing data ** ===
175 175  
176 -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.
198 +(% 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.
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200 +(% 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.
178 178  
179 -----
180 180  
181 -(% style="font-family:inherit" %) (% style="color:#1a202c; font-family:inherit; font-size:26px" %)**What can I share on EBRAINS? **
203 +By sharing your data via EBRAINS, you gain access to the following benefits:
182 182  
183 -(% class="wikigeneratedid" id="H" %)
184 -[[image:image-20230324170829-2.png]]
205 +[[image:image-20230324170841-3.png]]
185 185  
186 186  
187 -----
188 188  
189 -=== **Useful information about sharing of experimental data on EBRAINS ** ===
209 +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.
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191 191  
192 -|(% style="width:593px" %)(((
193 -[[[[image:image-20230324171114-2.png]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
194 -)))|(% style="width:1240px" %)(((
195 -[[[[image:image-20230324171109-1.png]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
196 -)))
197 -|(% style="width:593px" %)//Collection of useful information for researchers looking to share experimental data on EBRAINS.//|(% style="width:1240px" %)//The EBRAINS data descriptor//
198 -
199 199  ----
200 200  
201 -=== **Introduction to data organisation ** ===
214 +=== **At a glance: "Sharing experimental data on EBRAINS" ** ===
202 202  
203 -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.
204 204  
205 -* Why is data organisation important?
206 -* How to organise my data repository?
207 -* What is a Data Descriptor and why do I need one?
217 +|(% style="width:439px" %)(((
218 +[[[[image:image-20230324171114-2.png||height="354" width="250"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
219 +)))|(% style="width:461px" %)(((
220 +[[[[image:image-20230324171109-1.png||height="352" width="250"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
221 +)))|(% style="width:416px" %)[[[[image:image-20230330120354-1.png||height="352" width="250"]]>>https://drive.ebrains.eu/f/707147a883b94fae8e69/]]
222 +|(% 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. //
208 208  
209 209  ----
210 210  
211 -=== **Integrate your data in the EBRAINS atlas services** ===
226 +=== **Integrate your data on EBRAINS with other services** ===
212 212  
213 -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.
228 +EBRAINS supports further integration for a variety of data, and is continuously looking to increase the number of interoperable services.
214 214  
215 -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.
230 +* Integrate image data with //the Mio viewer//: (% style="color:#e74c3c" %)[description]
231 +* 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.
232 +* Add your data, models or software to a// Live paper//: (% style="color:#e74c3c" %)[description]
233 +* 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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235 +
217 217  ----
218 218  
219 219  === **Common concerns - and answers ** ===
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221 221  (((
222 222  ==== ====
223 223  
224 ->
225 -
226 226  (((
227 227  >The curation process is time consuming and difficult
228 228  )))
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