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Changes for page data-curation-copy

Last modified by eapapp on 2023/07/04 16:46
From version 201.1
edited by ingrreit
on 2023/06/26 13:34
Change comment: There is no comment for this version
To version 170.1
edited by eapapp
on 2023/06/06 16:26
Change comment: There is no comment for this version

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17 17  {{/html}}
18 18  
19 19  
20 -(% class="wikigeneratedid" id="HPublishingneurosciencedata2CmodelsandsoftwareviaEBRAINS" %)
21 -(% style="font-size:2em" %)**Publishing neuroscience data, models and software via EBRAINS**
20 +== Publishing neuroscience data, models and software via EBRAINS ==
22 22  
22 +
23 23  (% class="wikigeneratedid" %)
24 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 25  
... ... @@ -34,10 +34,8 @@
34 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 35  
36 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 -)))
37 +(% style="text-align: center;" %)
38 +Search existing data, models and software in [[the EBRAINS Knowledge Graph Search>>https://kg.ebrains.eu/search/?facet_type[0]=Dataset]]
41 41  
42 42  
43 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. 
... ... @@ -83,6 +83,8 @@
83 83  //to share data on EBRAINS: //
84 84  // //
85 85  [[[[image:image-20230324171114-2.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
84 +
85 +
86 86  )))
87 87  
88 88  
... ... @@ -89,13 +89,12 @@
89 89  ==== **1. Provide some general information about your dataset** ====
90 90  
91 91  
92 +[[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#/]]. **
92 92  
93 -(% 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#/]]. **
94 -
95 95  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.
96 96  
97 97  
98 -(% 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]]**.
97 +[[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]]**.
99 99  
100 100  This form collects the necessary information needed for us to evaluate whether we can ethically and legally share the data via EBRAINS.
101 101  
... ... @@ -104,28 +104,18 @@
104 104  
105 105  ==== **2. Upload data ** ====
106 106  
107 -(% class="box floatinginfobox" id="share-data-infographic" %)
108 -(((
109 -(% style="text-align:center" %)
110 -//Download our infographic//
111 -//with guidelines
112 -on data organization: //
113 113  
114 -(% style="text-align:center" %)
115 -[[[[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/]]
116 -)))
107 +[[image:https://lh5.googleusercontent.com/sieKO-kW8O18iPaUyonwyo4UfHBmtc2E9BDnjbx52j6J_uGmm-OzGAo7sloMk3sYwKa6QW3hYQsOA9N4H7uGQpca088Wrk0Nurpt_J3B0-NSbcaPNdZIh21otQcG6jnAxLGiKoEvkTyaDGTMk3fu7me8mQ=s2048||height="94px;" width="94px;"]]**Ensure data is structured consistently prior to upload. **
117 117  
118 -(% 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. **
109 +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.
119 119  
120 -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.
111 +[[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).**
121 121  
122 -(% 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).**
113 +//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.
123 123  
124 -**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.
115 +//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.
125 125  
126 -**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.
127 127  
128 -
129 129  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. 
130 130  
131 131  If a data collection is already uploaded elsewhere, we may link to the already existing repository.
... ... @@ -134,11 +134,11 @@
134 134  ==== **3. Submit metadata** ====
135 135  
136 136  
137 -(% 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) **
126 +[[image:https://lh5.googleusercontent.com/WS4T2LhF9znWWChn3Z550agLrrb-KTWdYVsJSv0lh4cGjKbjuN1WV68WER9xkYqi1UqN7KYZz7bImYz3_TpOuTuvma7T192QUiUZoyJVPk1fj5NSDSQh_kpIeBufAOdDtsDRpPKK_P5EDPqRCTAaOTNyCw=s2048||height="91px;" width="91px;"]]**Submit metadata using the **[[EBRAINS Wizard>>https://ebrains-metadata-wizard.apps.hbp.eu/]]** (opt. 1), or through direct interaction with the Knowledge Graph (opt. 2) **
138 138  
139 -**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
128 +//Opt. 1.// Manually submit the minimal required metadata via the [[EBRAINS 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
140 140  
141 -**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:
130 +//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:
142 142  
143 143  * 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.
144 144  * [[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.
... ... @@ -147,12 +147,10 @@
147 147  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.
148 148  
149 149  
150 -==== **4. Write a Data Descriptor** ====
139 +==== **4. Write a Data Descriptor ** ====
151 151  
141 +[[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]]** . **
152 152  
153 -
154 -(% 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]]**.**
155 -
156 156  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. 
157 157  
158 158  See our infographic about the data descriptor for inspiration or guidance.
... ... @@ -161,31 +161,27 @@
161 161  
162 162  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.
163 163  
164 -
165 165  (% class="box floatinginfobox" id="data-descriptor-infographic" %)
166 166  (((
167 167  (% style="text-align:center" %)
168 -//Download our infographic
169 -about the EBRAINS Data//
170 -//Descriptor//
154 +//Download our infographic: //
155 +//The EBRAINS Data//
156 +//Descriptor at a glance//
171 171  // //
172 172  [[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
159 +
173 173  )))
174 174  
175 -==== **5. Preview and publish** ====
162 +==== **5. Preview and publish ** ====
176 176  
177 177  
178 -(% 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. **
165 +[[image:https://lh4.googleusercontent.com/XqT26Q4yWJK26cjtjhI4ToXoZZMxhT9LimG4Hk9mePxy0-KPKgpVIzcuiP5mOQowBgf2JjkrWUq2VbCmafWWZPJplEZALnFOlCZHLlQgzOx7fFwoBteyi_IlMLkPBS9vtOcdNIZ59HyLnQz4RsTQ0lUrSw=s2048||height="91px;" width="91px;"]]**Preview and approve the release of your dataset. **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.
179 179  
180 -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.
181 181  
182 -
183 183  ----
184 184  
185 -==== ====
170 +==== **Sharing human subject data ** ====
186 186  
187 -==== **Sharing human subject data** ====
188 -
189 189  (% class="box floatinginfobox" %)
190 190  (((
191 191  **Human subject data that can be shared on EBRAINS:**
... ... @@ -201,7 +201,6 @@
201 201  //please [[get in touch>>https://www.ebrains.eu/contact/]] and we will clarify the available options.//
202 202  )))
203 203  
204 -
205 205  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]].
206 206  
207 207  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).
... ... @@ -218,89 +218,11 @@
218 218  === Step by Step - Models ===
219 219  
220 220  
221 -==== 1. Start early ====
203 +~1. Request curation using the [[Curation request form>>https://nettskjema.no/a/277393#/]]. You will be contacted by a curator with more information.
222 222  
223 -It is not necessary to wait until you are ready to publish to register your model with EBRAINS.
224 224  
225 -By registering a model early in your project, you can take advantage of EBRAINS tools
226 -to keep track of simulations and to share them with your collaborators.
206 +//Additional information will be added soon.//
227 227  
228 -==== 2. Create/choose a Collab workspace ====
229 -
230 -We use EBRAINS Collaboratory "collab" workspaces to help manage the model curation process.
231 -
232 -In particular, we use collab membership (the "Team") to control who can view or edit your model metadata prior to publication.
233 -
234 -It is up to you whether you create a new collab for each model, or reuse an existing collab
235 -(it is no problem to have multiple models associated with a single collab).
236 -
237 -Collabs are also useful for storing simulation results, adding documentation for your model,
238 -and/or providing tutorials in Jupyter notebooks.
239 -
240 -==== 3. Upload code ====
241 -
242 -We recommend storing model code and/or configuration files in an online Git repository, for example on GitHub.
243 -This repository should be public when you publish the model, but a private repository can be used for model development.
244 -
245 -Alternatively, you can upload code to the Collab Drive or Bucket storage.
246 -
247 -==== 4.Submit metadata ====
248 -
249 -We recommend submitting metadata using the Model Catalog app, installed in your collab.
250 -
251 -To install it:
252 -
253 -1. click the "+ Create" button
254 -1. in the "Create Page" form, add a title, such as "Model Catalog", and select "Community App", then click "Create"
255 -1. scroll down until you find the "Model Catalog" app, click "Select", then "Save & View"
256 -
257 -You will then see a table of all the models and validation tests associated with this collab.
258 -If this is your first time using the app, the table will probably be empty.
259 -To add your model, click "+", fill in the form, then click "Add model".
260 -
261 -As development of your model proceeds, you can easily register new versions of the code,
262 -and new parameterizations, by clicking "Add new version".
263 -
264 -If you prefer not to use the app, you can instead fill in the [[Curation request form>>https://nettskjema.no/a/277393#/]].,
265 -and you will be contacted by e-mail with further instructions.
266 -
267 -==== 5. Provide a reference dataset ====
268 -
269 -Once you're ready to publish your model entry in the EBRAINS Knowledge Graph,
270 -we encourage you to provide a dataset containing the simulation results produced by your model,
271 -following the process under "Step by step - Data" above.
272 -
273 -These reference data will be linked to the model, and will be helpful to anyone trying to
274 -reuse your model.
275 -
276 -We will soon introduce a "Reproducible" badge for all models that include a reference dataset,
277 -and whose simulation results can be reproduced by an EBRAINS curator.
278 -
279 -==== 6. Request publication, preview and publish ====
280 -
281 -Until you request your model entry to be published in the EBRAINS Knowledge Graph,
282 -only members of the collab will be able to view the model entry, in the Model Catalog app
283 -or using the Model Validation Python client.
284 -
285 -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.
286 -
287 -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.
288 -
289 -
290 -Curators will then perform a number of checks:
291 -
292 -1. Does the model description provide sufficient context to understand the purpose and use of the model?
293 -1. Does the code repository contain a licence file, explaining the conditions for reusing the code?
294 -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.
295 -
296 -The curators will also take a snapshot of your model code.
297 -
298 -* 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"]].
299 -* 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.
300 -
301 -Once this is done, you will be invited to review a preview of how the model entry will appear in the KG Search,
302 -and will have the opportunity to request modifications prior to approval and publication.
303 -
304 304  ----
305 305  
306 306  === Step by Step - Software ===
... ... @@ -329,11 +329,6 @@
329 329  
330 330  == **The openMINDS metadata framework** ==
331 331  
332 -(% class="box floatinginfobox" %)
333 -(((
334 -[[[[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]]
335 -)))
336 -
337 337  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]].
338 338  
339 339  For feedback, requests, or contributions, please get in touch with the openMINDS development team via
... ... @@ -412,15 +412,20 @@
412 412  Phd Student
413 413  Sensors and Cognitive Psychology (M. Sc.)(%%)
414 414  (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Human-Computer Interaction**
415 -)))|(% style="width:303px" %)(((
416 -[[image:Lyuba.jpg||height="209" width="167"]]
314 +)))|(% style="width:328px" %)(((
315 +
417 417  
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318 +
319 +
320 +
321 +
418 418  **Lyuba Zehl**
419 419  
420 420  (% class="small" %)Knowledge Systems Engineer
421 421  Dr. rer. nat. (Systems Neuroscience)(%%)
422 422  (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
423 -)))|(% style="width:303px" %) |(% style="width:303px" %)
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424 424  
425 425  ----
426 426  
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431 431  
432 432  === **Showcase shared data, models or software in other services** ===
433 433  
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.
338 +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.
435 435  
340 +**Viewer for 2D images **
436 436  
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]].
342 +* 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]].
445 445  
344 +**Viewer for sequential atlas-registered 2D images with annotation options**
345 +
346 +* 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]].
347 +
348 +**Use your research product in an interactive publication **
349 +
350 +* 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]].
351 +
352 +**Interactive 3D atlas viewer with options for data visualization**
353 +
354 +* 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]].
355 +
446 446  ----
447 447  
448 448  ==== **Add a tutorial or learning resource ** ====
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480 480  )))
481 481  )))
482 482  
393 +
394 +(% class="wikigeneratedid" id="HHowcanIshareA0models3F" %)
483 483  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.
484 484  
485 485  >Is sharing my data also beneficial for me or only for others?
486 486  
399 +
487 487  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.
488 488  
489 489  >Can my data be too insignificant to share?
490 490  
404 +
491 491  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.
492 492  
493 493  >Can my data be easily misused if I share it?
494 494  
409 +
495 495  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.
496 496  
497 497  >Can I share my data before my paper is published?
498 498  
414 +
499 499  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.
500 500  
501 501  >Can I lose my competitive edge if I share my data before I publish the associated paper?
502 502  
419 +
503 503  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.
504 504  
505 505  
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510 510  [[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
511 511  
512 512  
513 -== References ==
514 -
515 515  {{putFootnotes/}}
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