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Changes for page data-curation-copy

Last modified by eapapp on 2023/07/04 16:46
From version 46.1
edited by ingrreit
on 2023/04/03 12:05
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To version 128.1
edited by ingrreit
on 2023/05/23 17:57
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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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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.
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]].
31 31  
32 -(% class="box floatinginfobox" %)
37 +
38 +(% class="box infomessage" %)
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  
43 +(% class="box successmessage" %)
44 +(((
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 +)))
37 37  
38 -
39 -
40 -
41 -
42 -
43 43  ----
44 44  
45 45  === Step by step - Experimental data ===
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72 72  
73 73  Easily submit openMINDS-compatible metadata via our [[metadata wizard>>https://ebrains-metadata-wizard.apps.hbp.eu/]]. This form covers all the required metadata for sharing data via EBRAINS. When you're ready to 'Submit', the metadata and all uploaded files will be sent to the Curation team.
74 74  
75 -For power-users interested in exploring the full span of the openMINDS framework, please check out the [[openMINDS GitHub>>https://github.com/HumanBrainProject/openMINDS]] to learn more about how to programmatically gather your metadata. A stable version of the openMINDS package can be found on [[PyPi>>https://pypi.org/project/openMINDS/]]. We accept openMINDS metadata as JSON-LD (share these with us via curation-support@ebrains.eu). Additional documentation of openMINDS metadata submodules and schemas can be found on [[the openMINDS GitHub Wiki>>https://humanbrainproject.github.io/openMINDS/]].
80 +For power-users interested in exploring the full span of the openMINDS framework, please check out the [[openMINDS GitHub>>https://github.com/HumanBrainProject/openMINDS]] to learn more about how to programmatically gather your metadata. A stable version of the openMINDS package can be found on [[PyPi>>https://pypi.org/project/openMINDS/]]. We accept openMINDS metadata as JSON-LD (share these with us via curation-support@ebrains.eu). Additional documentation of openMINDS metadata submodules and schemas can be found on [[the openMINDS GitHub Wiki>>https://humanbrainproject.github.io/openMINDS/]]. We have prepared [[a list of the metadata properties that are required>>https://drive.ebrains.eu/lib/47995dbc-f576-4008-a76c-eefbfd818529/file/ebrains-minimum-required-metadata.xlsx]] for publishing data on EBRAINS.
76 76  
77 77  
78 78  ==== **4. Write a Data Descriptor ** ====
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94 94  
95 95  ==== **Sharing human data ** ====
96 96  
97 -We must ensure data shared on EBRAINS comply with [[GDPR >>https://gdpr-info.eu/]]and [[EU directives>>https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=celex%3A32010L0063]]. The information we need to assess this is collected via our [[Ethics and Regulatory Compliance Survey>>https://nettskjema.no/a/224765]].
98 -
99 99  (% class="box floatinginfobox" %)
100 100  (((
101 101  For **Human subject data**, the data must be //either//
102 102  
103 103  - Post-mortem data
104 -
105 105  - Aggregated data
106 -
107 107  - Pseudonymized subject data with a legal basis for sharing (e.g. Informed Consent)
108 108  
109 109  (% class="small" %)//If you have human data that do not classify as any of the above, please get in touch and we will clarify the available options. //
110 110  )))
111 111  
112 -Pseudonymized data is shared via the Human Data Gateway (HDG) due to GDPR regulations. The HDG adds an authentication layer to the data.
113 +We must ensure data shared on EBRAINS comply with [[GDPR >>https://gdpr-info.eu/]]and [[EU directives>>https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=celex%3A32010L0063]]. The information we need to assess this is collected via our [[Ethics and Regulatory Compliance Survey>>https://nettskjema.no/a/224765]].
113 113  
115 +Post-mortem and aggregated human data can be shared openly. Pseudonymized data is shared via the Human Data Gateway (HDG) due to GDPR regulations. The HDG adds an authentication layer to the data.
116 +
114 114  **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.
115 115  \\**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.
116 116  \\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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120 120  
121 121  === Step by Step - Models ===
122 122  
126 +(% style="color:#e74c3c" %){{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-1rb0hn"/}}
127 +
123 123  [place-holder-process-diagram]
124 124  
125 125  ==== **1. model step 1 ** ====
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136 136  
137 137  === Step by Step - Code ===
138 138  
144 +(% style="color:#e74c3c" %)@Jan/Benni
145 +
139 139  [place-holder-process-diagram]
140 140  
141 141  ==== **1. code step 1 ** ====
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149 149  
150 150  ----
151 151  
152 -=== Output / result, when you've completed the curation process, what do you get ===
159 +=== 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]].
161 +(% class="wikigeneratedid" id="HContact...." %)
162 +(% style="color:#e74c3c; font-size:16px" %){{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-np253c"/}}(% 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]].
164 +----
157 157  
166 +== **The curation team: meet the curators** ==
167 +
168 +**Located in Norway:**
169 +
170 +|(% style="width:303px" %)(((
171 +[[image:My project2.jpg||height="209" width="167"]]
172 +
173 +**Archana Golla**
174 +
175 +(% class="small" %)Curation Scientist
176 +Neuroscience (PhD)(%%)
177 +(% class="small" style="color:#4a5568" %)**Behavioral neuroscience and microscopy**
178 +)))|(% style="width:303px" %)(((
179 +[[image:My project.jpg||height="209" width="167"]]
180 +
181 +**Camilla H. Blixhavn**
182 +
183 +(% class="small" %)Curation Scientist,
184 +Phd Student
185 +Neuroscience (M. Sc.)(%%)
186 +(% class="small" style="color:#4a5568" %)**Neuroanatomy and data integration**
187 +)))|(% style="width:303px" %)(((
188 +[[image:My project (1).jpg||height="209" width="167"]]
189 +
190 +**Ingrid Reiten**
191 +
192 +(% class="small" %)Curation Scientist,
193 +Phd Student
194 +Neuroscience (M. Sc.)(%%)
195 +(% class="small" style="color:#4a5568" %)**Neuroanatomy and structural connectivity**
196 +)))|(% style="width:303px" %)(((
197 +[[image:My project1.jpg||height="209" width="167"]]
198 +
199 +**Sophia Pieschnik**
200 +
201 +(% class="small" %)Curation Scientist
202 +Neurocognitive Psychology (M. Sc.)(%%)
203 +(% class="small" style="color:#4a5568" %)**Neuroimaging **
204 +)))
205 +
206 +
207 +\\**Located in Germany:**
208 +
209 +[[image:My project (2).jpg||height="209" width="167"]]
210 +
211 +**Jan Gündling**
212 +
213 +(% class="small" %)Curation Scientist
214 +Sensors and Cognitive Psychology (M. Sc.)(%%)
215 +(% class="small" style="color:#4a5568" %)**Human-Computer Interaction **
216 +
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  
225 +=== **Improve your research product ** ===
226 +
227 +(% class="wikigeneratedid" %)
228 +**{{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-fkdv6h"/}}**
229 +
230 +==== **Add a tutorial or learning resource to your research product ** ====
231 +
232 +==== (% style="color:#e74c3c" %)- Learning resource [information](%%) ====
233 +
234 +
235 +==== **Create a workflow for .... ? ** ====
236 +
237 +==== (% style="color:#e74c3c" %)- Workflows [information](%%) ====
238 +
239 +----
240 +
241 +=== **Integrate your data, models or software with other services** ===
242 +
243 +EBRAINS supports further integration for a variety of data, and is continuously looking to increase the number of interoperable services.
244 +
245 +* Integrate image data with //the Mio viewer//: EBRAINS Multi-Image OpenSeadragon viewer provides an intuitive way of navigating high-resolution 2D image series. It has browser-based classic pan and zoom capabilities. A collection can be displayed as a filmstrip (Filmstrip Mode) or as a table (Collection Mode) with adjustable number of row and columns. See [[Mio viewer links available for this dataset>>https://search.kg.ebrains.eu/?category=Dataset&q=nr2f1#9677359c-73fa-4425-b8fa-3de794e9017a]] as an example. MioViewer user manual is found [[here>>https://multi-image-osd.readthedocs.io/en/latest/index.html]].
246 +* Integrate atlas-registered 2D image data with //the LocaliZoom viewer//: The EBRAINS LocaliZoom serial section viewer displays series of registered 2D section images with atlas overlay, allowing the users to zoom into high-resolution images and have information about the brain regions. See the [[LocaliZoom links available for this dataset>>https://doi.org/10.25493/T686-7BX]] as an example. LocaliZoom user manual is found [[here>>https://localizoom.readthedocs.io/en/latest/index.html]].
247 +* Add your data, models or software to a// Live paper//: (% style="color:#e74c3c" %)[description] {{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-62mbgl"/}}
248 +* Integrate your data to //the Siibra//-explorer: The siibra-explorer is used for visualizing volumetric brain data in all the brain atlases provided by EBRAINS (Human, Monkey, Rat and Mouse). The siibra-explorer viewer uses siibra-api to enable navigation of brain region hierarchies, maps in different coordinate spaces, and linked regional data features. Furthermore, it is connected with the siibra toolsuite providing several analytical workflows. 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.
249 +
250 +----
251 +
166 166  === **The benefits of sharing data ** ===
167 167  
168 168  (% 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.
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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? **
185 -
186 -(% class="wikigeneratedid" id="H" %)
187 -[[image:image-20230324170829-2.png]]
188 -
189 -
190 -----
191 -
192 192  === **At a glance: "Sharing experimental data on EBRAINS" ** ===
193 193  
194 194  
195 195  |(% style="width:439px" %)(((
196 -[[[[image:image-20230324171114-2.png]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
274 +[[[[image:image-20230324171114-2.png||height="354" width="250"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
197 197  )))|(% style="width:461px" %)(((
198 -[[[[image:image-20230324171109-1.png||height="358" width="254"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
199 -)))|(% style="width:416px" %)[[[[image:image-20230330120354-1.png||height="355" width="252"]]>>https://drive.ebrains.eu/f/707147a883b94fae8e69/]]
276 +[[[[image:image-20230324171109-1.png||height="352" width="250"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
277 +)))|(% style="width:416px" %)[[[[image:image-20230330120354-1.png||height="352" width="250"]]>>https://drive.ebrains.eu/f/707147a883b94fae8e69/]]
200 200  |(% 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. //
201 201  
202 202  ----
203 203  
204 -=== **Integrate your data in the EBRAINS atlas services** ===
205 -
206 -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.
207 -
208 -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.
209 -
210 -----
211 -
212 212  === **Common concerns - and answers ** ===
213 213  
214 214  (((
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261 261  
262 262  
263 263  {{putFootnotes/}}
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