Changes for page data-curation-copy

Last modified by eapapp on 2023/07/04 16:46
From version 56.1
edited by ingrreit
on 2023/04/25 17:28
Change comment: There is no comment for this version
To version 128.1
edited by ingrreit
on 2023/05/23 17:57
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -32,26 +32,19 @@
32 32  
33 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.
34 34  
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]].
35 35  
36 -(% class="box successmessage" %)
37 +
38 +(% class="box infomessage" %)
37 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.
40 +**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]]. **
39 39  )))
40 40  
41 -(% class="box floatinginfobox" %)
43 +(% class="box successmessage" %)
42 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]]. **
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.
44 44  )))
45 45  
46 -
47 -
48 -
49 -
50 -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]].
51 -
52 -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]].
53 -
54 -
55 55  ----
56 56  
57 57  === Step by step - Experimental data ===
... ... @@ -84,7 +84,7 @@
84 84  
85 85  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.
86 86  
87 -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.
88 88  
89 89  
90 90  ==== **4. Write a Data Descriptor ** ====
... ... @@ -106,23 +106,21 @@
106 106  
107 107  ==== **Sharing human data ** ====
108 108  
109 -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]].
110 -
111 111  (% class="box floatinginfobox" %)
112 112  (((
113 113  For **Human subject data**, the data must be //either//
114 114  
115 115  - Post-mortem data
116 -
117 117  - Aggregated data
118 -
119 119  - Pseudonymized subject data with a legal basis for sharing (e.g. Informed Consent)
120 120  
121 121  (% 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. //
122 122  )))
123 123  
124 -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]].
125 125  
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 +
126 126  **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.
127 127  \\**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.
128 128  \\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.
... ... @@ -132,6 +132,8 @@
132 132  
133 133  === Step by Step - Models ===
134 134  
126 +(% style="color:#e74c3c" %){{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-1rb0hn"/}}
127 +
135 135  [place-holder-process-diagram]
136 136  
137 137  ==== **1. model step 1 ** ====
... ... @@ -148,6 +148,8 @@
148 148  
149 149  === Step by Step - Code ===
150 150  
144 +(% style="color:#e74c3c" %)@Jan/Benni
145 +
151 151  [place-holder-process-diagram]
152 152  
153 153  ==== **1. code step 1 ** ====
... ... @@ -163,18 +163,62 @@
163 163  
164 164  === Webservices and metadata models ===
165 165  
166 -=== (% style="color:#e74c3c; font-size:16px" %)Contact....(% style="color:#4a5568; font-size:16px" %) (%%) ===
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" %)
167 167  
168 168  ----
169 169  
170 -=== **The curation team: meet the curators** ===
166 +== **The curation team: meet the curators** ==
171 171  
172 -[[image:fb6d6429-709e-4f4d-be3b-eab0a46695bd.JPG||height="184" width="137"]]
168 +**Located in Norway:**
173 173  
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 +
174 174  **Sophia Pieschnik**
175 -(% class="small" %)Biology (B.Sc.)
176 -Neurocognitive Psychology (M.Sc.)
177 177  
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 +
178 178  ----
179 179  
180 180  == **Information and resources for researchers looking to share data** ==
... ... @@ -183,14 +183,33 @@
183 183  
184 184  ----
185 185  
186 -=== **Enrich your dataset, model or software** ===
225 +=== **Improve your research product ** ===
187 187  
188 -(% style="color:#e74c3c" %)- Workflows [information]
227 +(% class="wikigeneratedid" %)
228 +**{{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-fkdv6h"/}}**
189 189  
190 -(% style="color:#e74c3c" %)- Learning resource [information]
230 +==== **Add a tutorial or learning resource to your research product ** ====
191 191  
232 +==== (% style="color:#e74c3c" %)- Learning resource [information](%%) ====
233 +
234 +
235 +==== **Create a workflow for .... ? ** ====
236 +
237 +==== (% style="color:#e74c3c" %)- Workflows [information](%%) ====
238 +
192 192  ----
193 193  
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 +
194 194  === **The benefits of sharing data ** ===
195 195  
196 196  (% 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.
... ... @@ -221,17 +221,6 @@
221 221  
222 222  ----
223 223  
224 -=== **Integrate your data on EBRAINS with other services** ===
225 -
226 -EBRAINS supports further integration for a variety of data, and is continuously looking to increase the number of interoperable services.
227 -
228 -* Integrate image data with //the Mio viewer//: (% style="color:#e74c3c" %)[description]
229 -* 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.
230 -* Add your data, models or software to a// Live paper//: (% style="color:#e74c3c" %)[description]
231 -* 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.
232 -
233 -----
234 -
235 235  === **Common concerns - and answers ** ===
236 236  
237 237  (((
... ... @@ -284,3 +284,7 @@
284 284  
285 285  
286 286  {{putFootnotes/}}
334 +~)~)~)~)~)~)
335 +~)~)~)
336 +~)~)~)~)~)~)~)~)~)
337 +~)~)~)~)~)~)
69399800_399857187337623_8446982631391756288_n.jpg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.spieschnik
Size
... ... @@ -1,0 +1,1 @@
1 +198.8 KB
Content
Image-1.jpg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.spieschnik
Size
... ... @@ -1,0 +1,1 @@
1 +154.3 KB
Content
My project (1).jpg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.spieschnik
Size
... ... @@ -1,0 +1,1 @@
1 +772.0 KB
Content
My project (2).jpg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.spieschnik
Size
... ... @@ -1,0 +1,1 @@
1 +564.9 KB
Content
My project.jpg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.spieschnik
Size
... ... @@ -1,0 +1,1 @@
1 +607.5 KB
Content
My project1.jpg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.spieschnik
Size
... ... @@ -1,0 +1,1 @@
1 +718.0 KB
Content
My project2.jpg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.spieschnik
Size
... ... @@ -1,0 +1,1 @@
1 +701.2 KB
Content
ansattfoto2.jpg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.spieschnik
Size
... ... @@ -1,0 +1,1 @@
1 +1.8 MB
Content
csm_Jan_Gruendling_3_bf9567ebb1.jpg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.spieschnik
Size
... ... @@ -1,0 +1,1 @@
1 +108.6 KB
Content