Changes for page data-curation-copy

Last modified by eapapp on 2023/07/04 16:46
From version 49.1
edited by ingrreit
on 2023/04/25 15:11
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To version 33.1
edited by ingrreit
on 2023/03/26 07:17
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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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27 27  
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.
29 29  
30 -(% style="text-align: center;" %)
31 -(% style="color:#e74c3c" %)[PLACEHOLDER: ABOUT THE CURATION TEAM]
32 -
33 -
34 -(% class="box successmessage" %)
35 -(((
36 -**Particular needs? Contact us! **The process of sharing data can be modified to fit the needs of researchers and large-scale projects. Contact us if you have such requests and we'll be happy to work with you to find a solution that suits us both.
37 -)))
38 -
39 39  (% class="box floatinginfobox" %)
40 40  (((
41 -**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]]. **
32 +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 to prepare for sharing>>mailto:curation-support@ebrains.eu]]. **
42 42  )))
43 43  
35 +=== ===
44 44  
37 +=== ===
45 45  
46 -
47 -
48 -We promote sharing of experimental data, models, software, web services, metadata models,
49 -
50 -
51 -----
52 -
53 53  === Step by step - Experimental data ===
54 54  
55 55  
56 56  [[image:image-20230326054341-1.png]]
57 57  
58 -==== ====
59 -
60 60  ==== **1. Provide some general information about your dataset** ====
61 61  
62 62  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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68 68  
69 69  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. 
70 70  
71 -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.
55 +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.
72 72  
73 -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.
57 +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.
74 74  
75 75  
76 76  If a data collection is already uploaded elsewhere, we may link to the already existing repository.
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121 121  
122 122  **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.
123 123  \\**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.
124 -\\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.
108 +\\**Human Data Gateway, Background**
109 +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.
125 125  
126 126  
127 127  ----
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157 157  
158 158  ----
159 159  
160 -=== When you've completed the curation process ===
145 +=== Output / result, when you've completed the curation process, what do you get ===
161 161  
162 162  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]].
163 163  
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165 165  
166 166  ----
167 167  
168 -== **Information and resources for researchers looking to share data** ==
153 +== **Resources for researchers looking to share data** ==
169 169  
170 170  Below you can find some resources that can come in handy if you are looking to share data via EBRAINS, or in general.
171 171  
172 172  ----
173 173  
174 -=== **The benefits of sharing data ** ===
159 +=== **Why should I share data?** ===
175 175  
176 -(% 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.
161 +(% style="color:#e74c3c" %)[EDIT required]
177 177  
178 -(% 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.
163 +(% 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.
179 179  
180 180  
181 181  By sharing your data via EBRAINS, you gain access to the following benefits:
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197 197  
198 198  ----
199 199  
200 -=== **At a glance: "Sharing experimental data on EBRAINS" ** ===
185 +=== **Useful information about sharing of experimental data on EBRAINS ** ===
201 201  
202 202  
203 -|(% style="width:439px" %)(((
204 -[[[[image:image-20230324171114-2.png||height="354" width="250"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
205 -)))|(% style="width:461px" %)(((
206 -[[[[image:image-20230324171109-1.png||height="352" width="250"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
207 -)))|(% style="width:416px" %)[[[[image:image-20230330120354-1.png||height="352" width="250"]]>>https://drive.ebrains.eu/f/707147a883b94fae8e69/]]
208 -|(% 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. //
188 +|(% style="width:593px" %)(((
189 +[[[[image:image-20230324171114-2.png]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
190 +)))|(% style="width:1240px" %)(((
191 +[[[[image:image-20230324171109-1.png]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
192 +)))
193 +|(% style="width:593px" %)//Collection of useful information for researchers looking to share experimental data on EBRAINS.//|(% style="width:1240px" %)//The EBRAINS data descriptor//
209 209  
210 210  ----
211 211  
197 +=== **Introduction to data organisation ** ===
198 +
199 +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.
200 +
201 +* Why is data organisation important?
202 +* How to organise my data repository?
203 +* What is a Data Descriptor and why do I need one?
204 +
205 +----
206 +
212 212  === **Integrate your data in the EBRAINS atlas services** ===
213 213  
214 214  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.
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222 222  (((
223 223  ==== ====
224 224  
220 +>
221 +
225 225  (((
226 226  >The curation process is time consuming and difficult
227 227  )))
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