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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.
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 -
29 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. 
30 30  
31 31  >The EBRAINS curation process involves organising and annotating neuroscientific data to make the data discoverable and reusable.
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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]].
36 -
37 -
38 -(% class="box infomessage" %)
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39 39  (((
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]]. **
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]]. **
41 41  )))
42 42  
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 -)))
35 +=== ===
47 47  
48 -----
37 +=== ===
49 49  
50 50  === Step by step - Experimental data ===
51 51  
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52 52  
53 53  [[image:image-20230326054341-1.png]]
54 54  
55 -==== ====
56 -
57 57  ==== **1. Provide some general information about your dataset** ====
58 58  
59 59  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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65 65  
66 66  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. 
67 67  
68 -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.
69 69  
70 -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.
71 71  
72 72  
73 73  If a data collection is already uploaded elsewhere, we may link to the already existing repository.
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77 77  
78 78  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.
79 79  
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.
67 +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/]].
81 81  
82 82  
83 83  ==== **4. Write a Data Descriptor ** ====
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118 118  
119 119  **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.
120 120  \\**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.
121 -\\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.
122 122  
123 123  
124 124  ----
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154 154  
155 155  ----
156 156  
157 -=== Webservices and metadata models ===
145 +=== Output / result, when you've completed the curation process, what do you get ===
158 158  
159 -(% class="wikigeneratedid" id="HContact...." %)
160 -(% style="color:#e74c3c; font-size:16px" %)Contact....(% style="color:#4a5568; font-size:16px" %)
147 +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]].
161 161  
162 -----
149 +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]].
163 163  
164 -== **The curation team: meet the curators** ==
165 -
166 -**Located in Norway:**
167 -
168 -[[image:fb6d6429-709e-4f4d-be3b-eab0a46695bd.JPG||height="184" width="137"]] [[image:ansattfoto2.jpg||height="184" width="137"]]
169 -
170 -**Sophia Pieschnik  Ingrid Reiten**
171 -
172 -Curation scientist  Curation Scientist, Phd Student
173 -(% class="small" %)Neurocognitive Psychology (M.Sc.) 
174 -Neuroimaging  Neuroanatomy and structural connectivity
175 -
176 -
177 -**Located in Germany:**
178 -
179 -[[image:csm_Jan_Gruendling_3_bf9567ebb1.jpg||height="180" width="180"]]
180 -
181 -**Jan Gündling**
182 -
183 -Curation Scientist
184 -(% class="small" %)Sensors and Cognitive Psychology (M.Sc.)
185 -Human-Computer Interaction
186 -
187 187  ----
188 188  
189 -== **Information and resources for researchers looking to share data** ==
153 +== **Resources for researchers looking to share data** ==
190 190  
191 191  Below you can find some resources that can come in handy if you are looking to share data via EBRAINS, or in general.
192 192  
193 193  ----
194 194  
195 -=== **Improve your research product ** ===
159 +=== **Why should I share data?** ===
196 196  
197 -==== **Add a tutorial or learning resource to your research product ** ====
161 +(% style="color:#e74c3c" %)[EDIT required]
198 198  
199 -==== (% style="color:#e74c3c" %)- Learning resource [information](%%) ====
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.
200 200  
201 201  
202 -==== **Create a workflow for .... ? ** ====
166 +By sharing your data via EBRAINS, you gain access to the following benefits:
203 203  
204 -==== (% style="color:#e74c3c" %)- Workflows [information](%%) ====
168 +[[image:image-20230324170841-3.png]]
205 205  
206 -----
207 207  
208 -=== **Integrate your data, models or software with other services** ===
209 209  
210 -EBRAINS supports further integration for a variety of data, and is continuously looking to increase the number of interoperable services.
172 +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.
211 211  
212 -* 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]].
213 -* 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]].
214 -* Add your data, models or software to a// Live paper//: (% style="color:#e74c3c" %)[description]
215 -* 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.
216 216  
217 217  ----
218 218  
219 -=== **The benefits of sharing data ** ===
177 +(% style="font-family:inherit" %) (% style="color:#1a202c; font-family:inherit; font-size:26px" %)**What can I share on EBRAINS? **
220 220  
221 -(% 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.
179 +(% class="wikigeneratedid" id="H" %)
180 +[[image:image-20230324170829-2.png]]
222 222  
223 -(% 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.
224 224  
183 +----
225 225  
226 -By sharing your data via EBRAINS, you gain access to the following benefits:
185 +=== **Useful information about sharing of experimental data on EBRAINS ** ===
227 227  
228 -[[image:image-20230324170841-3.png]]
229 229  
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//
230 230  
195 +----
231 231  
232 -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.
197 +=== **Introduction to data organisation ** ===
233 233  
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.
234 234  
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 +
235 235  ----
236 236  
237 -=== **At a glance: "Sharing experimental data on EBRAINS" ** ===
207 +=== **Integrate your data in the EBRAINS atlas services** ===
238 238  
209 +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.
239 239  
240 -|(% style="width:439px" %)(((
241 -[[[[image:image-20230324171114-2.png||height="354" width="250"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
242 -)))|(% style="width:461px" %)(((
243 -[[[[image:image-20230324171109-1.png||height="352" width="250"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
244 -)))|(% style="width:416px" %)[[[[image:image-20230330120354-1.png||height="352" width="250"]]>>https://drive.ebrains.eu/f/707147a883b94fae8e69/]]
245 -|(% 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. //
211 +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.
246 246  
247 247  ----
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251 251  (((
252 252  ==== ====
253 253  
220 +>
221 +
254 254  (((
255 255  >The curation process is time consuming and difficult
256 256  )))
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