Changes for page data-curation-copy

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edited by ingrreit
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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.
4 4  
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19 19  
20 20  ----
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 +)))
24 24  
25 -(% style="color:#e74c3c" %)Their comparability and
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. 
26 26  
27 -(% style="color:#e74c3c" %)Sharing your data, models or code (research products) via EBRAINS makes it discoverable amongst other research products available in (%%)[[(% style="color:#e74c3c" %)the EBRAINS Knowledge Graph>>https://kg.ebrains.eu/]](%%). This is made possible by the highly flexible metadata framework describing neuroscience data in detail, [[(% style="color:#e74c3c" %)openMINDS>>https://github.com/HumanBrainProject/openMINDS]](%%). 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.
31 +>The EBRAINS curation process involves organising and annotating neuroscientific data to make the data discoverable and reusable.
28 28  
29 -----
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.
30 30  
31 -== **The EBRAINS data curation process** ==
32 32  
33 -Neuroscience data are multimodal, heterogenous, and organised in different ways. All these diverse data need to be categorised and described in a standardised manner so that they can be effectively searched, compared, and analysed by using the tools and workflows on the EBRAINS platform. This effort is referred to as curation.
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 +)))
34 34  
35 ->The EBRAINS data curation process involves organising and annotating neuroscientific data to make the data discoverable and reusable.
41 +(% class="box floatinginfobox" %)
42 +(((
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]]. **
44 +)))
36 36  
37 37  
38 -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. 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.
39 39  
40 40  
41 -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. 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. **Want to learn more about how to Prepare to Share? **Contact us!
42 42  
50 +=== When you've completed the curation process ===
51 +
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]].
53 +
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]].
55 +
56 +
57 +----
58 +
43 43  === Step by step - Experimental data ===
44 44  
45 45  
46 46  [[image:image-20230326054341-1.png]]
47 47  
64 +==== ====
65 +
48 48  ==== **1. Provide some general information about your dataset** ====
49 49  
50 50  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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56 56  
57 57  EBRAINS offers secure, long-term storage at [[CSCS Swiss National Supercomputing Centre>>url:https://www.cscs.ch/]], with currently no upper limit of storage capacity. The data must be consistently structured prior to upload. 
58 58  
59 -For smaller datasets with a reasonable amount of files, we recommend using the **Collab-Bucket solution (drag-and-drop)**. A Collab Bucket must first be assigned to a dataset, which happens when a datasets is accepted for sharing.
77 +For smaller datasets with a reasonable amount of files, we recommend using the Collab-Bucket solution (drag-and-drop). A Collab Bucket must first be assigned to a dataset, which happens when a datasets is accepted for sharing.
60 60  
61 -For larger datasets or datasets with a large amount of files, we recommend using a **programmatic approach**. The [[python script>>https://github.com/eapapp/ebrains-data-storage/tree/main/data-proxy]] is interactive and does not require any additional programming.
79 +For larger datasets or datasets with a large amount of files, we recommend using a programmatic approach. The [[python script>>https://github.com/eapapp/ebrains-data-storage/tree/main/data-proxy]] is interactive and does not require any additional programming.
62 62  
63 63  
64 64  If a data collection is already uploaded elsewhere, we may link to the already existing repository.
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109 109  
110 110  **Data users** must request access to the data (via their EBRAINS account) and will receive access provided they actively accept the [[EBRAINS Access Policy>>https://ebrains.eu/terms#access-policy]], the [[EBRAINS General Terms of Use>>https://ebrains.eu/terms#general-terms-of-use]], and the [[EBRAINS Data Use Agreement>>https://ebrains.eu/terms#data-use-agreement]]. The account holder also have to accept that information about their request and access to specific data under HDG is being tracked and stored.
111 111  \\**Data owners** must be aware that sharing under the HDG affects the legal responsibilities for the data. They must agree to joint control of the data (see the [[Data Provision Protocol v1>>url:https://strapi-prod.sos-ch-dk-2.exo.io/EBRAINS_Data_Provision_Protocol_dfe0dcb104.pdf]], section 1.4 - 1.5) and the Data Protection Officers of the responsible institutions must have accepted that the data can be shared under HDG.
112 -\\**Human Data Gateway, Background**
113 -HDG was introduced in February 2021 and developed across multiple teams in the HBP. The initiative to create the service and the initial design originated from EBRAINS Curation in close collaboration with the Data compliance team and the HBP Data Governance Working Group. HDG is a response to the needs of multiple data providers who are bringing data of human origin to EBRAINS. HDG covers the sharing of a limited range of data of human origin, i.e., data without direct identifiers and with very few indirect identifiers (strongly pseudonymized, de-identified). It is an extension of the existing services and does not replace the future EBRAINS Service for sensitive data (planned for 2024) which is outside the domain of the current EBRAINS Data and Knowledge services.
130 +\\The Human Data Gateway (HDG) was introduced in February 2021 and developed across multiple teams in the HBP. The initiative to create the service and the initial design originated from EBRAINS Curation in close collaboration with the Data compliance team and the HBP Data Governance Working Group. HDG is a response to the needs of multiple data providers who are bringing data of human origin to EBRAINS. HDG covers the sharing of a limited range of data of human origin, i.e., data without direct identifiers and with very few indirect identifiers (strongly pseudonymized, de-identified). It is an extension of the existing services and does not replace the future EBRAINS Service for sensitive data (planned for 2024) which is outside the domain of the current EBRAINS Data and Knowledge services.
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115 115  
116 116  ----
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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]].
170 +----
154 154  
172 +=== **The curation team: meet the curators** ===
173 +
174 +[[image:fb6d6429-709e-4f4d-be3b-eab0a46695bd.JPG||height="184" width="137"]]
175 +
176 +**Sophia Pieschnik**
177 +(% class="small" %)Biology (B.Sc.)
178 +Neurocognitive Psychology (M.Sc.)
179 +
155 155  ----
156 156  
157 -== **Resources for researchers looking to share data** ==
182 +== **Information and resources for researchers looking to share data** ==
158 158  
159 159  Below you can find some resources that can come in handy if you are looking to share data via EBRAINS, or in general.
160 160  
161 161  ----
162 162  
163 -=== **Why should I share data?** ===
188 +=== **Enrich your dataset, model or software** ===
164 164  
165 -By sharing your data via EBRAINS, you gain access to the following benefits:
190 +(% style="color:#e74c3c" %)- Workflows [information]
166 166  
167 -[[image:image-20230324170841-3.png]]
192 +(% style="color:#e74c3c" %)- Learning resource [information]
168 168  
194 +----
169 169  
170 -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}}.
196 +=== **The benefits of sharing data ** ===
171 171  
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.
172 172  
173 -----
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.
174 174  
175 -(% style="font-family:inherit" %) (% style="color:#1a202c; font-family:inherit; font-size:26px" %)**What can I share on EBRAINS? **
176 176  
177 -(% class="wikigeneratedid" id="H" %)
178 -[[image:image-20230324170829-2.png]]
203 +By sharing your data via EBRAINS, you gain access to the following benefits:
179 179  
205 +[[image:image-20230324170841-3.png]]
180 180  
181 -----
182 182  
183 -=== **Useful information about sharing of experimental data on EBRAINS ** ===
184 184  
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.
185 185  
186 -|(% style="width:593px" %)(((
187 -[[[[image:image-20230324171114-2.png]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
188 -)))|(% style="width:1240px" %)(((
189 -[[[[image:image-20230324171109-1.png]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
190 -)))
191 -|(% style="width:593px" %)//Collection of useful information for researchers looking to share experimental data on EBRAINS.//|(% style="width:1240px" %)//The EBRAINS data descriptor//
192 192  
193 193  ----
194 194  
195 -=== **Introduction to data organisation ** ===
214 +=== **At a glance: "Sharing experimental data on EBRAINS" ** ===
196 196  
197 -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.
198 198  
199 -* Why is data organisation important?
200 -* How to organise my data repository?
201 -* 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. //
202 202  
203 203  ----
204 204  
205 -=== **Integrate your data in the EBRAINS atlas services** ===
226 +=== **Integrate your data on EBRAINS with other services** ===
206 206  
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.
228 +EBRAINS supports further integration for a variety of data, and is continuously looking to increase the number of interoperable services.
208 208  
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.
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.
210 210  
235 +
211 211  ----
212 212  
213 213  === **Common concerns - and answers ** ===
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215 215  (((
216 216  ==== ====
217 217  
218 ->
219 -
220 220  (((
221 221  >The curation process is time consuming and difficult
222 222  )))
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