Changes for page data-curation-copy

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edited by ingrreit
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To version 128.1
edited by ingrreit
on 2023/05/23 17:57
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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 -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]].
37 37  
38 -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]].
39 -
40 -(% class="box floatinginfobox" %)
38 +(% class="box infomessage" %)
41 41  (((
42 42  **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]]. **
43 43  )))
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47 47  **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.
48 48  )))
49 49  
50 -
51 51  ----
52 52  
53 53  === Step by step - Experimental data ===
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80 80  
81 81  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.
82 82  
83 -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.
84 84  
85 85  
86 86  ==== **4. Write a Data Descriptor ** ====
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102 102  
103 103  ==== **Sharing human data ** ====
104 104  
105 -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]].
106 -
107 107  (% class="box floatinginfobox" %)
108 108  (((
109 109  For **Human subject data**, the data must be //either//
110 110  
111 111  - Post-mortem data
112 -
113 113  - Aggregated data
114 -
115 115  - Pseudonymized subject data with a legal basis for sharing (e.g. Informed Consent)
116 116  
117 117  (% 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. //
118 118  )))
119 119  
120 -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]].
121 121  
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 +
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.
124 124  \\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.
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128 128  
129 129  === Step by Step - Models ===
130 130  
126 +(% style="color:#e74c3c" %){{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-1rb0hn"/}}
127 +
131 131  [place-holder-process-diagram]
132 132  
133 133  ==== **1. model step 1 ** ====
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144 144  
145 145  === Step by Step - Code ===
146 146  
144 +(% style="color:#e74c3c" %)@Jan/Benni
145 +
147 147  [place-holder-process-diagram]
148 148  
149 149  ==== **1. code step 1 ** ====
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160 160  === Webservices and metadata models ===
161 161  
162 162  (% class="wikigeneratedid" id="HContact...." %)
163 -(% style="color:#e74c3c; font-size:16px" %)Contact....(% style="color:#4a5568; font-size:16px" %)
162 +(% style="color:#e74c3c; font-size:16px" %){{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-np253c"/}}(% style="color:#4a5568; font-size:16px" %)
164 164  
165 165  ----
166 166  
167 167  == **The curation team: meet the curators** ==
168 168  
169 -[[image:fb6d6429-709e-4f4d-be3b-eab0a46695bd.JPG||height="184" width="137"]]
168 +**Located in Norway:**
170 170  
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 +
171 171  **Sophia Pieschnik**
172 -(% class="small" %)Biology (B.Sc.)
173 -Neurocognitive Psychology (M.Sc.)
174 174  
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 +
175 175  ----
176 176  
177 177  == **Information and resources for researchers looking to share data** ==
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182 182  
183 183  === **Improve your research product ** ===
184 184  
227 +(% class="wikigeneratedid" %)
228 +**{{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-fkdv6h"/}}**
229 +
185 185  ==== **Add a tutorial or learning resource to your research product ** ====
186 186  
187 187  ==== (% style="color:#e74c3c" %)- Learning resource [information](%%) ====
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193 193  
194 194  ----
195 195  
196 -=== **Integrate your data on EBRAINS with other services** ===
241 +=== **Integrate your data, models or software with other services** ===
197 197  
198 198  EBRAINS supports further integration for a variety of data, and is continuously looking to increase the number of interoperable services.
199 199  
200 -* Integrate image data with //the Mio viewer//: (% style="color:#e74c3c" %)[description]
201 -* 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.
202 -* Add your data, models or software to a// Live paper//: (% style="color:#e74c3c" %)[description]
203 -* 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.
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.
204 204  
205 205  ----
206 206  
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286 286  
287 287  
288 288  {{putFootnotes/}}
334 +~)~)~)~)~)~)
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