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18
19
20 == Publishing neuroscience data, models and software via EBRAINS ==
21
22
23 (% class="wikigeneratedid" %)
24 The aim of this collab is to provide you with detailed information about publishing data, simulations, computational models, and software via EBRAINS. If you want a quick overview of the sharing process, see [[https:~~/~~/ebrains.eu/service/share-data>>https://ebrains.eu/service/share-data]].
25
26 {{box title="**Contents**"}}
27 {{toc depth="3" start="2"/}}
28 {{/box}}
29
30 == **Information to get started** ==
31
32 **[[REQUEST CURATION>>https://nettskjema.no/a/277393#/]] to share data, simulations, computational models, and software, - or to add a new version of an existing one. **
33
34 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.
35
36
37 (% class="box" style="text-align: center; font-size: 1.2em" %)
38 (((
39 Search existing data, models and software in the [[EBRAINS Knowledge Graph>>https://kg.ebrains.eu/search/?facet_type[0]=Dataset]]
40 )))
41
42
43 EBRAINS accepts data from all modalities and from all species, as well as models, software, web services and metadata models (collectively referred to as research products) for sharing. You'll find detailed information about how to share each research product below. 
44
45
46 (% class="box infomessage" %)
47 (((
48 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.
49 )))
50
51 (% class="box successmessage" %)
52 (((
53 **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. Reach us at [[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
54 )))
55
56 ----
57
58 == **The EBRAINS curation process** ==
59
60 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. 
61
62 >The EBRAINS curation process involves organising and annotating neuroscientific data to make the data discoverable and reusable.
63
64 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.
65
66 Curated data, models and software are made available in [[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 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 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]].
67
68 The curation of data, models and software is different. Thus, below we explain the process for sharing for each research product separately.
69
70
71 ----
72
73 === Step by step - Data ===
74
75
76 [[image:image-20230326054341-1.png]]
77
78 (% class="box floatinginfobox" id="share-data-infographic" %)
79 (((
80 (% style="text-align:center" %)
81 //Download our infographic//
82 //with all you need to know//
83 //to share data on EBRAINS: //
84 // //
85 [[[[image:image-20230324171114-2.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
86
87
88 )))
89
90
91 ==== **1. Provide some general information about your dataset** ====
92
93
94
95 (% style="margin-right:10px" %)[[image:https://lh3.googleusercontent.com/zh7TvO6w04YGW9jIhfhmdT6CexdGs-AWOLfJXKRq7-tdHOu6ar1rOQx8o4rZevrjXqgPZ7-Ejv4b6X9XpgXuHpdUXi-mBTHIUnv5Vz-DktHt0sP-PZ3gE8XgZid3TV3swV1uTCBhHx11ge0pjP7RVxswGQ=s2048||height="85px;" width="91px;"]](%%)** Fill in the [[Curation request form>>https://nettskjema.no/a/277393#/]]. **
96
97 This form 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.
98
99
100 (% style="margin-right:10px" %)[[image:https://lh6.googleusercontent.com/yw442oS6BwZOlY-_0BoVxyCW3DrdcJ5ogCes92iOD16_rgNEVk56aNMDaVWXFfBLYv24bHzmGgBF9wg0szjH70xzuRTqxoQAeuy3knNO7axCHoyZDXwtyTcMgFnYwbOYxOT29LK-zchrUKLW6Mle93kOkQ=s2048||height="94px;" width="94px;"]](%%)**Fill in the [[Ethics and Regulatory compliance form>>https://nettskjema.no/a/224765]]**.
101
102 This form collects the necessary information needed for us to evaluate whether we can ethically and legally share the data via EBRAINS.
103
104 See below for information about the ethical and legal aspects concerning sharing of human subject data.
105
106
107 ==== **2. Upload data ** ====
108
109
110 (% style="margin-right:10px" %)[[image:https://lh5.googleusercontent.com/sieKO-kW8O18iPaUyonwyo4UfHBmtc2E9BDnjbx52j6J_uGmm-OzGAo7sloMk3sYwKa6QW3hYQsOA9N4H7uGQpca088Wrk0Nurpt_J3B0-NSbcaPNdZIh21otQcG6jnAxLGiKoEvkTyaDGTMk3fu7me8mQ=s2048||height="94px;" width="94px;"]](%%)**Ensure data is structured consistently prior to upload. **
111
112 We look for organized data, not organized according to our standard. This is to support the broadest degree of sharing possible. We do however require that the data is organized in a consistent and precise manner. Please see our// //[[collection of guidelines on data organization>>https://drive.ebrains.eu/smart-link/25299f04-c4e5-4028-8f5f-3b8208f9a532/]] for further guidance.
113
114 (% style="margin-right:10px" %)[[image:https://lh5.googleusercontent.com/EWtYwfVlbeC-jqPasgmzidqc50GrkKIEgwXeUeql8aaMHIukmFdWEy0nufVWWATbxDDK3XwwZEDmASrbpCsBk1u0HpAd8x4ZgAMsMPRcWyrb9etlV6FgKE_QN2e6SqKxHE0rzkR8uI1rRW_5z21TFGYVnw=s2048||height="91px;" width="91px;"]](%%)**Upload data to EBRAINS Storage, either using a drag-and-drop solution (opt. 1) or an interactive python script (opt. 2).**
115
116 **Opt. 1. **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.
117
118 **Opt. 2. **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.
119
120
121 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. 
122
123 If a data collection is already uploaded elsewhere, we may link to the already existing repository.
124
125
126 ==== **3. Submit metadata** ====
127
128
129 (% style="margin-right:10px" %)[[image:https://lh5.googleusercontent.com/WS4T2LhF9znWWChn3Z550agLrrb-KTWdYVsJSv0lh4cGjKbjuN1WV68WER9xkYqi1UqN7KYZz7bImYz3_TpOuTuvma7T192QUiUZoyJVPk1fj5NSDSQh_kpIeBufAOdDtsDRpPKK_P5EDPqRCTAaOTNyCw=s2048||height="91px;" width="91px;"]](%%)**Submit metadata using the **[[EBRAINS Metadata Wizard>>https://ebrains-metadata-wizard.apps.hbp.eu/]]** (opt. 1), or directly via the Knowledge Graph (opt. 2) **
130
131 **Opt. 1.** Manually submit the minimal required metadata via the [[EBRAINS Metadata Wizard>>https://ebrains-metadata-wizard.apps.hbp.eu/]]. The minimal required metadata covers extended bibliographic information necessary to publish your dataset on EBRAINS. The submitted information, including uploaded files, will be sent to the Curation team automatically
132
133 **Opt. 2.** To go beyond the minimal required metadata, you can directly interact with the Knowledge Graph (KG) in your private space. Within the private space, you can upload metadata and interact with them, moreover you can connect your metadata to existing publicly accessible entries. Access to your private space is granted upon the initiation of the curation process. You can access your private space via:
134
135 * Knowledge Graph Editor: This User Interface allows you to manually enter metadata into your KG space and validate metadata that are programmatically uploaded. The Editor contains a basic set of openMINDS metadata templates, but can be extended to the full openMINDS metadata model on request. Access is granted once the request is accepted.
136 * [[Fairgraph>>https://fairgraph.readthedocs.io/en/stable/]]: This is the recommended software tool for programmatic interaction with the KG. It allows you to programmatically upload openMINDS compliant metadata into your KG space and interact with existing metadata.
137 * [[KG Core Python SDK>>https://github.com/HumanBrainProject/kg-core-sdks]]: This python package gives you full freedom in interacting with he KG. It allows you to upload any JSON-LD with metadata into your private space. Note, for dataset publications in EBRAINS, the JSON-LD metadata files have to comply to openMINDS.
138
139 Datasets published through the EBRAINS Knowledge Graph have to be registered using **openMINDS compliant metadata** delivered as JSON-LD files. See this summary table for an overview of [[the minimally required openMINDS properties for publishing>>https://drive.ebrains.eu/lib/47995dbc-f576-4008-a76c-eefbfd818529/file/ebrains-minimum-required-metadata.xlsx]] on EBRAINS.
140
141
142 ==== **4. Write a Data Descriptor** ====
143
144
145
146 (% style="margin-right:10px" %)[[image:https://lh4.googleusercontent.com/lMYEKOXzejbBydOdotWWteXQo7j363xRyntBGjcPZVEdtIU1CJYX7q1STpdr2JPZK4hpWWXk20UlkUOqDGL5kX6vnQVBSdrfUo6EGfXOwpuGq1Uygv0tTZJ0lRO6voJvg56QC2mufvjAcRXGfAKFOjtc6w=s2048||height="94px;" width="94px;"]](%%)**Write a data descriptor by filling in **[[this template>>https://drive.ebrains.eu/f/a2e07c95b1a54090bbbc/?dl=1]]**.**
147
148 The Data Descriptor is a document helping others interpret and reuse (and prevent misuse) of your data, and is critical to achieve a basic level of FAIR. The document will be uploaded in the repository of the data, shared as a PDF. 
149
150 See our infographic about the data descriptor for inspiration or guidance.
151
152 Check out previous examples in the KG Search. See e.g., the data descriptor for the dataset "[[Anterogradely labeled axonal projections from the orbitofrontal cortex in rat>>https://doi.org/10.25493/2MX9-3XF]]".
153
154 Journal publications sufficiently describing the shared data, such as made available through [[Nature Scientific Data>>http://www.nature.com/sdata/about]], [[Elsevier Data in Brief>>http://www.journals.elsevier.com/data-in-brief/]], [[BMC Data note>>https://bmcresnotes.biomedcentral.com/submission-guidelines/preparing-your-manuscript/data-note]] and more, can replace the EBRAINS Data Descriptor.
155
156
157 (% class="box floatinginfobox" id="data-descriptor-infographic" %)
158 (((
159 (% style="text-align:center" %)
160 //Download our infographic: //
161 //The EBRAINS Data//
162 //Descriptor at a glance//
163 // //
164 [[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
165
166 )))
167
168 ==== **5. Preview and publish** ====
169
170
171 (% style="margin-right:10px" %)[[image:https://lh4.googleusercontent.com/XqT26Q4yWJK26cjtjhI4ToXoZZMxhT9LimG4Hk9mePxy0-KPKgpVIzcuiP5mOQowBgf2JjkrWUq2VbCmafWWZPJplEZALnFOlCZHLlQgzOx7fFwoBteyi_IlMLkPBS9vtOcdNIZ59HyLnQz4RsTQ0lUrSw=s2048||height="91px;" width="91px;"]](%%)**Preview and approve the release of your dataset. **
172
173 Once a Curator has assembled the dataset in the EBRAINS Knowledge Graph, combining the data, metadata and data descriptor, the data provider will receive a private URL for previewing the dataset prior to release. We need an official approval from the data custodian{{footnote}}The Data Custodian is responsible for the content and quality of the Data and metadata, and is the person to be contacted by EBRAINS CS in case of any misconduct related to the Data. It is the obligation of a Data Custodian to keep EBRAINS informed about changes in the contact information of the authors of the Datasets provided by them ([[EBRAINS Data Provision Protocol - version 1.1>>https://strapi-prod.sos-ch-dk-2.exo.io/EBRAINS_Data_Provision_Protocol_dfe0dcb104.pdf]]).{{/footnote}} to release the dataset. Once released, a [[DataCite DOI>>https://datacite.org/]] will be generated for the dataset. If the identical data collection has received a DOI elsewhere, we recommend re-using the already issued DOI.
174
175
176 ----
177
178 ==== ====
179
180 ==== **Sharing human subject data** ====
181
182 (% class="box floatinginfobox" %)
183 (((
184 **Human subject data that can be shared on EBRAINS:**
185 // //
186 // - Post-mortem data//
187 // - Aggregated data//
188 // - Strongly pseudonymized or de-identified subject data//
189 // with a legal basis for sharing (e.g. Informed Consent)//
190 // //
191
192 (% class="small" %)
193 //If you have human data that does not qualify as any of the above,//
194 //please [[get in touch>>https://www.ebrains.eu/contact/]] and we will clarify the available options.//
195 )))
196
197
198 Human subject data shared on EBRAINS must 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]].
199
200 Post-mortem and aggregated human data can be shared openly, given direct identifiers in the metadata are removed. Strongly pseudonymized and de-identified data can be shared via the Human Data Gateway (HDG).
201
202 The Human Data Gateway (HDG) was introduced in February 2021 as a response to the needs of multiple data providers who are bringing human subject data to EBRAINS. HDG covers the sharing of strongly pseudonymized or de-identified data, a limited range human subject data without direct identifiers and with very few indirect identifiers.
203
204 The HDG adds an an authentication layer on top of the data. This means that **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. **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.
205
206 The HDG 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.
207
208
209 ----
210
211 === Step by Step - Models ===
212
213
214 ==== 1. Start early ====
215
216 It is not necessary to wait until you are ready to publish to register your model with EBRAINS.
217
218 By registering a model early in your project, you can take advantage of EBRAINS tools
219 to keep track of simulations and to share them with your collaborators.
220
221 ==== 2. Create/choose a Collab workspace ====
222
223 We use EBRAINS Collaboratory "collab" workspaces to help manage the model curation process.
224
225 In particular, we use collab membership (the "Team") to control who can view or edit your model metadata prior to publication.
226
227 It is up to you whether you create a new collab for each model, or reuse an existing collab
228 (it is no problem to have multiple models associated with a single collab).
229
230 Collabs are also useful for storing simulation results, adding documentation for your model,
231 and/or providing tutorials in Jupyter notebooks.
232
233 ==== 3. Upload code ====
234
235 We recommend storing model code and/or configuration files in an online Git repository, for example on GitHub.
236 This repository should be public when you publish the model, but a private repository can be used for model development.
237
238 Alternatively, you can upload code to the Collab Drive or Bucket storage.
239
240 ==== 4.Submit metadata ====
241
242 We recommend submitting metadata using the Model Catalog app, installed in your collab.
243
244 To install it:
245
246 1. click the "+ Create" button
247 1. in the "Create Page" form, add a title, such as "Model Catalog", and select "Community App", then click "Create"
248 1. scroll down until you find the "Model Catalog" app, click "Select", then "Save & View"
249
250 You will then see a table of all the models and validation tests associated with this collab.
251 If this is your first time using the app, the table will probably be empty.
252 To add your model, click "+", fill in the form, then click "Add model".
253
254 As development of your model proceeds, you can easily register new versions of the code,
255 and new parameterizations, by clicking "Add new version".
256
257 If you prefer not to use the app, you can instead fill in the [[Curation request form>>https://nettskjema.no/a/277393#/]].,
258 and you will be contacted by e-mail with further instructions.
259
260 ==== 5. Provide a reference dataset ====
261
262 Once you're ready to publish your model entry in the EBRAINS Knowledge Graph,
263 we encourage you to provide a dataset containing the simulation results produced by your model,
264 following the process under "Step by step - Data" above.
265
266 These reference data will be linked to the model, and will be helpful to anyone trying to
267 reuse your model.
268
269 We will soon introduce a "Reproducible" badge for all models that include a reference dataset,
270 and whose simulation results can be reproduced by an EBRAINS curator.
271
272 ==== 6. Request publication, preview and publish ====
273
274 Until you request your model entry to be published in the EBRAINS Knowledge Graph,
275 only members of the collab will be able to view the model entry, in the Model Catalog app
276 or using the Model Validation Python client.
277
278 After publication, the model will appear in the [[EBRAINS public search results>>https://search.kg.ebrains.eu/?category=Model||rel="noopener noreferrer" target="_blank"]], and will receive a DOI.
279
280 To request publication, [[contact EBRAINS support>>https://ebrains.eu/support||rel="noopener noreferrer" target="_blank"]], providing the collab name and the model name or ID.
281
282
283 Curators will then perform a number of checks:
284
285 1. Does the model description provide sufficient context to understand the purpose and use of the model?
286 1. Does the code repository contain a licence file, explaining the conditions for reusing the code?
287 1. Does the model have a clearly defined version identifier (e.g. v1.0)? For models in a Git repository, the version identifier should match the name of a tag or release.
288
289 The curators will also take a snapshot of your model code.
290
291 * For models in public Git repositories, we archive a copy of the repository in [[Software Heritage>>https://www.softwareheritage.org/||rel=" noopener noreferrer" target="_blank"]].
292 * For models in a collab Bucket or Drive, we make a read-only copy of the code in a public container in the EBRAINS repository.
293
294 Once this is done, you will be invited to review a preview of how the model entry will appear in the KG Search,
295 and will have the opportunity to request modifications prior to approval and publication.
296
297 ----
298
299 === Step by Step - Software ===
300
301
302 (% class="box floatinginfobox" id="software-curation-infographic" %)
303 (((
304 (% style="text-align:center" %)
305 //Software curation at a glance//
306 // //
307 [[[[image:Thumb2.png||alt="EBRAINS-Share-Software.pdf" height="287" width="197"]]>>attach:EBRAINS-Share-Software-4.pdf]]
308 )))
309
310 (% style="margin-left:15px" %)[[[[image:Screenshot 2023-06-06 1122082.png||alt="swc-flow.png" height="136" width="637"]]>>https://www.ebrains.eu/tools/ebrains-curation-request-form||rel="noopener noreferrer" target="_blank"]]
311
312 1. Fill in the [[request form>>https://www.ebrains.eu/tools/ebrains-curation-request-form]]. You'll be contacted by a curator with further instructions. In these instructions, you will find the links to your software and software version entries in the Knowledge Graph.
313 1. Enter the metadata of your software in your private space of the [[Knowledge Graph Editor>>url:https://editor.kg.ebrains.eu/]] by using the links provided by the curator. Please provide the metadata for your software as complete as possible. This makes it easier for users to find and use your software. If you have questions feel free to contact the curation support. After you have finished editing your entries, please let the curators know by replying to your ticket. We curate your metadata and get back to you, if necessary.
314 1. After a quality check, we integrate and publish the information to the Knowledge Graph. Your software is then searchable and usable for the neuroscience community.
315
316 If you want to add a new version to an already curated software, please request this via the [[curation request form>>https://nettskjema.no/a/277393]].
317
318 For more information, visit our [[Guide to Software Curation in the EBRAINS Knowledge Graph>>url:https://wiki.ebrains.eu/bin/view/Collabs/swc-guide]] or see our infographic on the right.
319
320
321 ----
322
323 == **The openMINDS metadata framework** ==
324
325 (% class="box floatinginfobox" %)
326 (((
327 [[[[image:https://github.com/HumanBrainProject/openMINDS/raw/main/img/light_openMINDS-logo.png||alt="openMINDS logo" height="87" width="164"]]>>https://github.com/HumanBrainProject/openMINDS]]
328 )))
329
330 openMINDS (open Metadata Initiative for Neuroscience Data Structures) is a community-driven, open-source metadata framework for graph database systems, such as the EBRAINS Knowledge Graph. It is composed of linked metadata models, libraries of serviceable metadata instances, and supportive tooling ([[openMINDS Python>>url:https://pypi.org/project/openMINDS/]], openMINDS Matlab). For exploring the openMINDS schemas, go to the [[HTML documentation>>url:https://humanbrainproject.github.io/openMINDS/]]. For a full overview of the framework, go to [[the openMINDS collab>>url:https://wiki.ebrains.eu/bin/view/Collabs/openminds/]] or the [[GitHub repository>>https://github.com/HumanBrainProject/openMINDS]].
331
332 For feedback, requests, or contributions, please get in touch with the openMINDS development team via
333
334 * the support-email: [[openminds@ebrains.eu>>path:mailto:openminds@ebrains.eu]]
335 * the [[GitHub issue tracker>>url:https://github.com/HumanBrainProject/openMINDS/issues]]
336 * the INCF NeuroStars [[openMINDS Community Forum>>url:https://neurostars.org/t/openminds-community-forum-virtual/20156]]
337
338 ----
339
340 == **The curation team: meet the curators** ==
341
342 The EBRAINS curators help researchers publish their research using the EBRAINS Research Infrastructure. A curator’s job is similar to the job of an editor of a scientific journal, checking the data is organized, understandable, accessible and sufficiently described.
343
344 The curators in EBRAINS are located in Oslo, Jülich, Trier and Paris. 
345
346
347 **Located in Norway:**
348
349 |(% style="width:303px" %)(((
350 [[image:My project2.jpg||height="209" width="167"]]
351
352 **Archana Golla**
353
354 (% class="small" %)Curation Scientist
355 Neuroscience (PhD)(%%)
356 (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Behavioral neuroscience and microscopy**
357 )))|(% style="width:303px" %)(((
358 [[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
359
360 **Camilla H. Blixhavn**
361
362 (% class="small" %)Curation Scientist,
363 Phd Student
364 Neuroscience (M. Sc.)(%%)
365 (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and data integration**
366 )))|(% style="width:303px" %)(((
367 [[image:My project (1).jpg||height="209" width="167"]]
368
369 **Ingrid Reiten**
370
371 (% class="small" %)Curation Scientist,
372 Phd Student
373 Neuroscience (M. Sc.)(%%)
374 (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and structural connectivity**
375 )))|(% style="width:303px" %)(((
376 [[image:My project1.jpg||height="209" width="167"]]
377
378 **Sophia Pieschnik**
379
380 (% class="small" %)Curation Scientist
381 Neurocognitive Psychology (M. Sc.)(%%)
382 (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroimaging **
383 )))
384
385 |(% style="width:303px" %)(((
386 [[image:My project.jpg||height="209" width="167"]]
387
388 **Heidi Kleven**
389
390 (% class="small" %)Curation Scientist,
391 Phd Student
392 Neuroscience (M. Sc.)(%%)
393 (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and brain atlases**
394 )))| | |
395
396
397 \\**Located in Germany:**
398
399 |(% style="width:303px" %)(((
400 [[image:My project (2).jpg||height="209" width="167"]]
401
402 **Jan Gündling**
403
404 (% class="small" %)Curation Scientist,
405 Phd Student
406 Sensors and Cognitive Psychology (M. Sc.)(%%)
407 (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Human-Computer Interaction**
408 )))|(% style="width:328px" %)(((
409
410
411
412
413
414
415
416
417
418 **Lyuba Zehl**
419
420 (% class="small" %)Knowledge Systems Engineer
421 Dr. rer. nat. (Systems Neuroscience)(%%)
422 (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
423 )))|(% style="width:321px" %) |(% style="width:324px" %)
424
425 ----
426
427 == **Add practical value to your shared data, model or software** ==
428
429
430 ----
431
432 === **Showcase shared data, models or software in other services** ===
433
434 Below is a list of additional services that data, models or software shared via EBRAINS can benefit from. EBRAINS is continuously looking to increase the number of interoperable services.
435
436
437 |(% colspan="2" %)**Viewer for 2D images**
438 |[[image:MIO_screenshot.PNG]]|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]].
439 |(% colspan="2" %)**Viewer for sequential atlas-registered 2D images with annotation options**
440 |[[image:LZ_screenshot.PNG]]|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]].
441 |(% colspan="2" %)**Interactive 3D atlas viewer with options for data visualization**
442 |[[image:3Datlas_screenshot.PNG]]|Upload 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 register your data to atlases, read about the [[Atlas services on ebrains.eu>>https://ebrains.eu/services/atlases#Integratedatatoanatlas]].
443 |(% colspan="2" %)**Use your research product in an interactive publication**
444 |[[image:LivePaper_screenshot.PNG]]|Add your data, models or software to a// Live paper. //Read more about [[Live papers on ebrains.eu>>https://www.ebrains.eu/data/live-papers/live-papers]].
445
446 ----
447
448 ==== **Add a tutorial or learning resource ** ====
449
450 (% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
451 (% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
452
453
454 ==== **Create a workflow** ====
455
456 (% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
457 (% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
458
459 ----
460
461 === **The benefits of sharing data ** ===
462
463 By sharing your data via EBRAINS, you gain access to the following benefits:
464
465 [[image:image-20230324170841-3.png]]
466
467
468
469 We support you to better follow the [[FAIR^^ ^^guiding principles>>https://www.nature.com/articles/sdata201618]] 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.
470
471 ----
472
473 === **Frequently asked questions ** ===
474
475 (((
476 ==== ====
477
478 (((
479 >Is the curation process time consuming and difficult?
480 )))
481 )))
482
483 No, if communication is on a regular basis, we are able to finish curation within two weeks. Publishing your data naturally takes some effort but we will support you as much as possible.
484
485 >Is sharing my data also beneficial for me or only for others?
486
487 When you publish your data via EBRAINS, we provide comprehensive data management support and safe long term storage - all free of charge. Additionally, your data can be cited, just like a scientific journal article. Sharing your data may even lead to new funding opportunities. Many funders specifically support projects that are part of the “Open Science” initiative.
488
489 >Can my data be too insignificant to share?
490
491 No, there is no such thing as insignificant data. Data that is considered insignificant for a given topic, may have great significance for another. By making “insignificant” data publicly available, other researchers may find something interesting that was off-topic for your own purposes.
492
493 >Can my data be easily misused if I share it?
494
495 No, your data will be covered by a Creative Commons license of your choice. There are a variety of licenses available, enabling you to prevent use for specific purposes, e.g. commercial use.
496
497 >Can I share my data before my paper is published?
498
499 Yes, if you do not want to share your data before publishing the results in an article, you can publish your dataset with an embargo status. This will make it possible to find information about the data without making the data itself available, and give you a citeable DOI.
500
501 >Can I lose my competitive edge if I share my data before I publish the associated paper?
502
503 No, publishing your data does not mean that others can use it however they want. Use of your data will require citation, and by choosing an appropriate Creative Commons licence you decide what others are allowed to do with it. If you still feel worried, you can publish your data under embargo, and in this way delay the date of data release, but still make it possible for others to find the information about the data.
504
505
506 ----
507
508 == Contact ==
509
510 [[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
511
512
513 == References ==
514
515 {{putFootnotes/}}