Wiki source code of Data Curation

Version 212.1 by ingrreit on 2023/08/07 13:21

Show last authors
1 {{html clean="false"}}
2 <div style="float:right;margin-left:1em;margin-bottom:1em">
3 <form title="Search in this collab" target="_blank" action="https://wiki.ebrains.eu/bin/view/Main/Search">
4 <input type="hidden" name="sort" value="score">
5 <input type="hidden" name="sortOrder" value="desc">
6 <input type="hidden" name="highlight" value="true">
7 <input type="hidden" name="facet" value="true">
8 <input type="hidden" name="r" value="1">
9 <input type="hidden" name="f_locale" value="en">
10 <input type="hidden" name="f_space_facet" value="1/Collabs.test-ir2.">
11 <input type="hidden" name="l_space_facet" value="100">
12 <input type="hidden" name="f_type" value="DOCUMENT">
13 <input type="text" name="text" placeholder="Search here..." size="25" id="searchbox" />
14 <input type="submit" value="&#x1F50E;&#xFE0E;" id="submit"/>
15 </form>
16 </div>
17 {{/html}}
18
19
20 (% class="wikigeneratedid" id="HPublishingneurosciencedata2CmodelsandsoftwareviaEBRAINS" %)
21 (% style="font-size:2em" %)**Publishing neuroscience data, models and software via EBRAINS**
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 **Before you get started, make sure you[[ sign up for a free EBRAINS account>>https://www.ebrains.eu/page/sign-up]]. This is needed to complete the data sharing process. **
71
72
73 ----
74
75 === Step by step - Data ===
76
77
78 [[image:image-20230326054341-1.png]]
79
80 (% class="box floatinginfobox" id="share-data-infographic" %)
81 (((
82 (% style="text-align:center" %)
83 //Download our infographic//
84 //with all you need to know//
85 //to share data on EBRAINS: //
86 // //
87 [[[[image:image-20230324171114-2.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
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 (% class="box floatinginfobox" id="share-data-infographic" %)
110 (((
111 (% style="text-align:center" %)
112 //Download our infographic//
113 //with guidelines
114 on data organization: //
115
116 (% style="text-align:center" %)
117 [[[[image:image-20230621121014-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/lib/f5cf4964-f095-49bd-8c34-e4ffda05a497/file/ebrains-infographic-data-organisation.pdf/]]
118 )))
119
120 (% 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. **
121
122 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// //[[guidelines on data organization>>https://drive.ebrains.eu/smart-link/25299f04-c4e5-4028-8f5f-3b8208f9a532/]] for further guidance.
123
124 (% 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).**
125
126 **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.
127
128 **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.
129
130
131 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. 
132
133 If a data collection is already uploaded elsewhere, we may link to the already existing repository.
134
135
136 ==== **3. Submit metadata** ====
137
138
139 (% 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) **
140
141 **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
142
143 **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:
144
145 * 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.
146 * [[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.
147 * [[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.
148
149 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.
150
151
152 ==== **4. Write a Data Descriptor** ====
153
154
155
156 (% 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]]**.**
157
158 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. 
159
160 See our infographic about the data descriptor for inspiration or guidance.
161
162 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]]".
163
164 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.
165
166
167 (% class="box floatinginfobox" id="data-descriptor-infographic" %)
168 (((
169 (% style="text-align:center" %)
170 //Download our infographic
171 about the EBRAINS Data//
172 //Descriptor//
173 // //
174 [[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
175 )))
176
177 ==== **5. Preview and publish** ====
178
179
180 (% 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. **
181
182 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.
183
184
185
186
187 ----
188
189 === Step by Step - Models ===
190
191
192 ==== 1. Start early ====
193
194 It is not necessary to wait until you are ready to publish to register your model with EBRAINS.
195
196 By registering a model early in your project, you can take advantage of EBRAINS tools
197 to keep track of simulations and to share them with your collaborators.
198
199 ==== 2. Create/choose a Collab workspace ====
200
201 We use EBRAINS Collaboratory "collab" workspaces to help manage the model curation process.
202
203 In particular, we use collab membership (the "Team") to control who can view or edit your model metadata prior to publication.
204
205 It is up to you whether you create a new collab for each model, or reuse an existing collab
206 (it is no problem to have multiple models associated with a single collab).
207
208 Collabs are also useful for storing simulation results, adding documentation for your model,
209 and/or providing tutorials in Jupyter notebooks.
210
211 ==== 3. Upload code ====
212
213 We recommend storing model code and/or configuration files in an online Git repository, for example on GitHub.
214 This repository should be public when you publish the model, but a private repository can be used for model development.
215
216 Alternatively, you can upload code to the Collab Drive or Bucket storage.
217
218 ==== 4.Submit metadata ====
219
220 We recommend submitting metadata using the Model Catalog app, installed in your collab.
221
222 To install it:
223
224 1. click the "+ Create" button
225 1. in the "Create Page" form, add a title, such as "Model Catalog", and select "Community App", then click "Create"
226 1. scroll down until you find the "Model Catalog" app, click "Select", then "Save & View"
227
228 You will then see a table of all the models and validation tests associated with this collab.
229 If this is your first time using the app, the table will probably be empty.
230 To add your model, click "+", fill in the form, then click "Add model".
231
232 As development of your model proceeds, you can easily register new versions of the code,
233 and new parameterizations, by clicking "Add new version".
234
235 If you prefer not to use the app, you can instead fill in the [[Curation request form>>https://nettskjema.no/a/277393#/]].,
236 and you will be contacted by e-mail with further instructions.
237
238 ==== 5. Provide a reference dataset ====
239
240 Once you're ready to publish your model entry in the EBRAINS Knowledge Graph,
241 we encourage you to provide a dataset containing the simulation results produced by your model,
242 following the process under "Step by step - Data" above.
243
244 These reference data will be linked to the model, and will be helpful to anyone trying to
245 reuse your model.
246
247 We will soon introduce a "Reproducible" badge for all models that include a reference dataset,
248 and whose simulation results can be reproduced by an EBRAINS curator.
249
250 ==== 6. Request publication, preview and publish ====
251
252 Until you request your model entry to be published in the EBRAINS Knowledge Graph,
253 only members of the collab will be able to view the model entry, in the Model Catalog app
254 or using the Model Validation Python client.
255
256 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.
257
258 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.
259
260
261 Curators will then perform a number of checks:
262
263 1. Does the model description provide sufficient context to understand the purpose and use of the model?
264 1. Does the code repository contain a licence file, explaining the conditions for reusing the code?
265 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.
266
267 The curators will also take a snapshot of your model code.
268
269 * 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"]].
270 * 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.
271
272 Once this is done, you will be invited to review a preview of how the model entry will appear in the KG Search,
273 and will have the opportunity to request modifications prior to approval and publication.
274
275 ----
276
277 === Step by Step - Software ===
278
279
280 (% class="box floatinginfobox" id="software-curation-infographic" %)
281 (((
282 (% style="text-align:center" %)
283 //Software curation at a glance//
284 // //
285 [[[[image:Thumb2.png||alt="EBRAINS-Share-Software.pdf" height="287" width="197"]]>>attach:EBRAINS-Share-Software-4.pdf]]
286 )))
287
288 (% 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"]]
289
290 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.
291 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.
292 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.
293
294 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]].
295
296 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.
297
298
299 ----
300
301 === Sharing human subject data ===
302
303 (% class="box floatinginfobox" %)
304 (((
305 **Human subject data that can be shared on EBRAINS:**
306 // //
307 // - Post-mortem data//
308 // - Aggregated data//
309 // - Strongly pseudonymized or de-identified subject data//
310 // with a legal basis for sharing (e.g. Informed Consent)//
311 // //
312
313 (% class="small" %)
314 //If you have human data that does not qualify as any of the above,//
315 //please [[get in touch>>https://www.ebrains.eu/contact/]] and we will clarify the available options.//
316 )))
317
318
319 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]].
320
321 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).
322
323 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.
324
325 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.
326
327 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.
328
329 ----
330
331 == **The openMINDS metadata framework** ==
332
333 (% class="box floatinginfobox" %)
334 (((
335 [[[[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]]
336 )))
337
338 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]].
339
340 For feedback, requests, or contributions, please get in touch with the openMINDS development team via
341
342 * the support-email: [[openminds@ebrains.eu>>path:mailto:openminds@ebrains.eu]]
343 * the [[GitHub issue tracker>>url:https://github.com/HumanBrainProject/openMINDS/issues]]
344 * the INCF NeuroStars [[openMINDS Community Forum>>url:https://neurostars.org/t/openminds-community-forum-virtual/20156]]
345
346 ----
347
348 == **Add practical value to your shared data, model or software** ==
349
350
351 === **Showcase shared data, models or software in other services** ===
352
353 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.
354
355
356 |(% colspan="2" %)**Viewer for 2D images**
357 |[[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]].
358 |(% colspan="2" %)**Viewer for sequential atlas-registered 2D images with annotation options**
359 |[[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]].
360 |(% colspan="2" %)**Interactive 3D atlas viewer with options for data visualization**
361 |[[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]].
362 |(% colspan="2" %)**Use your research product in an interactive publication**
363 |[[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]].
364
365 ----
366
367 ==== **Add a tutorial or learning resource ** ====
368
369 (% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
370 (% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
371
372
373 ==== **Create a workflow** ====
374
375 (% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
376 (% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
377
378 ----
379
380 == **General benefits of sharing data ** ==
381
382 By sharing your data via EBRAINS, you gain access to the following benefits:
383
384 [[image:image-20230324170841-3.png]]
385
386
387
388 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.
389
390 ----
391
392 == **Frequently asked questions ** ==
393
394 >Is the curation process time consuming and difficult?
395
396 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.
397
398 >Is sharing my data also beneficial for me or only for others?
399
400 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.
401
402 >Can my data be too insignificant to share?
403
404 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.
405
406 >Can my data be easily misused if I share it?
407
408 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.
409
410 >Can I share my data before my paper is published?
411
412 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.
413
414 >Can I lose my competitive edge if I share my data before I publish the associated paper?
415
416 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.
417
418
419 ----
420
421 == (% style="color:#1a202c; font-family:inherit; font-size:29px" %)**The curation team: meet the curators**(%%) ==
422
423 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.
424
425 The curators in EBRAINS are located in Oslo, Jülich, Trier and Paris. 
426
427
428 **Located in Norway**
429
430 |(% style="width:303px" %)(((
431 [[image:My project2.jpg||height="209" width="167"]]
432
433 **Archana Golla**
434
435 (% class="small" %)Curation Scientist
436 Neuroscience (PhD)(%%)
437 (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Behavioral neuroscience and microscopy**
438 )))|(% style="width:303px" %)(((
439 [[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
440
441 **Camilla H. Blixhavn**
442
443 (% class="small" %)Curation Scientist,
444 Phd Student
445 Neuroscience (M. Sc.)(%%)
446 (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and data integration**
447 )))|(% style="width:303px" %)(((
448 [[image:My project (1).jpg||height="209" width="167"]]
449
450 **Ingrid Reiten**
451
452 (% class="small" %)Curation Scientist,
453 Phd Student
454 Neuroscience (M. Sc.)(%%)
455 (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and structural connectivity**
456 )))|(% style="width:303px" %)(((
457 [[image:My project1.jpg||height="209" width="167"]]
458
459 **Sophia Pieschnik**
460
461 (% class="small" %)Curation Scientist
462 Neurocognitive Psychology (M. Sc.)(%%)
463 (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroimaging **
464 )))
465
466 |(% style="width:303px" %)(((
467 [[image:My project.jpg||height="209" width="167"]]
468
469 **Heidi Kleven**
470
471 (% class="small" %)Curation Scientist,
472 Phd Student
473 Neuroscience (M. Sc.)(%%)
474 (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and brain atlases**
475 )))| | |
476
477
478 \\**Located in Germany**
479
480 |(% style="width:303px" %)(((
481 [[image:My project (2).jpg||height="209" width="167"]]
482
483 **Jan Gündling**
484
485 (% class="small" %)Curation Scientist,
486 Phd Student
487 Sensors and Cognitive Psychology (M. Sc.)(%%)
488 (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Human-Computer Interaction**
489 )))|(% style="width:303px" %)(((
490 [[image:Lyuba.jpg||height="209" width="167"]]
491
492 **Lyuba Zehl**
493
494 (% class="small" %)Knowledge Systems Engineer
495 Dr. rer. nat. (Systems Neuroscience)(%%)
496 (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
497 )))|(% style="width:303px" %) |(% style="width:303px" %)
498
499 ----
500
501
502
503 ----
504
505 == Contact ==
506
507 [[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
508
509 ----
510
511 == Affiliated laboratories ==
512
513 //Institute of Basic Medical Sciences,** **University of Oslo, Norway (PI: Jan G. Bjaalie, Trygve B. Leergaard)//
514
515 //Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Germany (PI: Timo Dicksheid)//
516
517 ----
518
519 == References ==
520
521 {{putFootnotes/}}
Public

Data Curation