Changes for page data-curation-copy

Last modified by eapapp on 2023/07/04 16:46
From version 167.1
edited by eapapp
on 2023/06/06 13:46
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To version 209.1
edited by ingrreit
on 2023/07/04 16:11
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1 -XWiki.eapapp
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17 17  {{/html}}
18 18  
19 19  
20 -== Publishing neuroscience data, models and software via EBRAINS ==
20 +(% class="wikigeneratedid" id="HPublishingneurosciencedata2CmodelsandsoftwareviaEBRAINS" %)
21 +(% style="font-size:2em" %)**Publishing neuroscience data, models and software via EBRAINS**
21 21  
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  
... ... @@ -34,8 +34,10 @@
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 -(% 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]]
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 +)))
39 39  
40 40  
41 41  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. 
... ... @@ -80,7 +80,7 @@
80 80  //with all you need to know//
81 81  //to share data on EBRAINS: //
82 82  // //
83 -[[[[image:image-20230324171114-2.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]//
85 +[[[[image:image-20230324171114-2.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
84 84  )))
85 85  
86 86  
... ... @@ -87,12 +87,13 @@
87 87  ==== **1. Provide some general information about your dataset** ====
88 88  
89 89  
90 -[[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#/]]. **
91 91  
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 +
92 92  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.
93 93  
94 94  
95 -[[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]]**.
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]]**.
96 96  
97 97  This form collects the necessary information needed for us to evaluate whether we can ethically and legally share the data via EBRAINS.
98 98  
... ... @@ -101,18 +101,28 @@
101 101  
102 102  ==== **2. Upload data ** ====
103 103  
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: //
104 104  
105 -[[image:https://lh5.googleusercontent.com/sieKO-kW8O18iPaUyonwyo4UfHBmtc2E9BDnjbx52j6J_uGmm-OzGAo7sloMk3sYwKa6QW3hYQsOA9N4H7uGQpca088Wrk0Nurpt_J3B0-NSbcaPNdZIh21otQcG6jnAxLGiKoEvkTyaDGTMk3fu7me8mQ=s2048||height="94px;" width="94px;"]]**Ensure data is structured consistently prior to upload. **
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 +)))
106 106  
107 -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.
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. **
108 108  
109 -[[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).**
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.
110 110  
111 -//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.
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).**
112 112  
113 -//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.
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.
114 114  
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.
115 115  
128 +
116 116  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. 
117 117  
118 118  If a data collection is already uploaded elsewhere, we may link to the already existing repository.
... ... @@ -121,11 +121,11 @@
121 121  ==== **3. Submit metadata** ====
122 122  
123 123  
124 -[[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) **
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) **
125 125  
126 -//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
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
127 127  
128 -//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:
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:
129 129  
130 130  * 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.
131 131  * [[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.
... ... @@ -134,10 +134,12 @@
134 134  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.
135 135  
136 136  
137 -==== **4. Write a Data Descriptor ** ====
150 +==== **4. Write a Data Descriptor** ====
138 138  
139 -[[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]]** . **
140 140  
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 +
141 141  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. 
142 142  
143 143  See our infographic about the data descriptor for inspiration or guidance.
... ... @@ -146,30 +146,159 @@
146 146  
147 147  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.
148 148  
149 -==== [[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]//The EBRAINS Data descriptor at-a-glance// ====
150 150  
165 +(% class="box floatinginfobox" id="data-descriptor-infographic" %)
166 +(((
167 +(% style="text-align:center" %)
168 +//Download our infographic
169 +about the EBRAINS Data//
170 +//Descriptor//
171 +// //
172 +[[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
173 +)))
151 151  
152 -==== **5. Preview and publish ** ====
175 +==== **5. Preview and publish** ====
153 153  
154 154  
155 -[[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.
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. **
156 156  
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.
157 157  
182 +
183 +
184 +
158 158  ----
159 159  
160 -==== **Sharing human subject data ** ====
187 +=== Step by Step - Models ===
161 161  
189 +
190 +==== 1. Start early ====
191 +
192 +It is not necessary to wait until you are ready to publish to register your model with EBRAINS.
193 +
194 +By registering a model early in your project, you can take advantage of EBRAINS tools
195 +to keep track of simulations and to share them with your collaborators.
196 +
197 +==== 2. Create/choose a Collab workspace ====
198 +
199 +We use EBRAINS Collaboratory "collab" workspaces to help manage the model curation process.
200 +
201 +In particular, we use collab membership (the "Team") to control who can view or edit your model metadata prior to publication.
202 +
203 +It is up to you whether you create a new collab for each model, or reuse an existing collab
204 +(it is no problem to have multiple models associated with a single collab).
205 +
206 +Collabs are also useful for storing simulation results, adding documentation for your model,
207 +and/or providing tutorials in Jupyter notebooks.
208 +
209 +==== 3. Upload code ====
210 +
211 +We recommend storing model code and/or configuration files in an online Git repository, for example on GitHub.
212 +This repository should be public when you publish the model, but a private repository can be used for model development.
213 +
214 +Alternatively, you can upload code to the Collab Drive or Bucket storage.
215 +
216 +==== 4.Submit metadata ====
217 +
218 +We recommend submitting metadata using the Model Catalog app, installed in your collab.
219 +
220 +To install it:
221 +
222 +1. click the "+ Create" button
223 +1. in the "Create Page" form, add a title, such as "Model Catalog", and select "Community App", then click "Create"
224 +1. scroll down until you find the "Model Catalog" app, click "Select", then "Save & View"
225 +
226 +You will then see a table of all the models and validation tests associated with this collab.
227 +If this is your first time using the app, the table will probably be empty.
228 +To add your model, click "+", fill in the form, then click "Add model".
229 +
230 +As development of your model proceeds, you can easily register new versions of the code,
231 +and new parameterizations, by clicking "Add new version".
232 +
233 +If you prefer not to use the app, you can instead fill in the [[Curation request form>>https://nettskjema.no/a/277393#/]].,
234 +and you will be contacted by e-mail with further instructions.
235 +
236 +==== 5. Provide a reference dataset ====
237 +
238 +Once you're ready to publish your model entry in the EBRAINS Knowledge Graph,
239 +we encourage you to provide a dataset containing the simulation results produced by your model,
240 +following the process under "Step by step - Data" above.
241 +
242 +These reference data will be linked to the model, and will be helpful to anyone trying to
243 +reuse your model.
244 +
245 +We will soon introduce a "Reproducible" badge for all models that include a reference dataset,
246 +and whose simulation results can be reproduced by an EBRAINS curator.
247 +
248 +==== 6. Request publication, preview and publish ====
249 +
250 +Until you request your model entry to be published in the EBRAINS Knowledge Graph,
251 +only members of the collab will be able to view the model entry, in the Model Catalog app
252 +or using the Model Validation Python client.
253 +
254 +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.
255 +
256 +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.
257 +
258 +
259 +Curators will then perform a number of checks:
260 +
261 +1. Does the model description provide sufficient context to understand the purpose and use of the model?
262 +1. Does the code repository contain a licence file, explaining the conditions for reusing the code?
263 +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.
264 +
265 +The curators will also take a snapshot of your model code.
266 +
267 +* 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"]].
268 +* 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.
269 +
270 +Once this is done, you will be invited to review a preview of how the model entry will appear in the KG Search,
271 +and will have the opportunity to request modifications prior to approval and publication.
272 +
273 +----
274 +
275 +=== Step by Step - Software ===
276 +
277 +
278 +(% class="box floatinginfobox" id="software-curation-infographic" %)
279 +(((
280 +(% style="text-align:center" %)
281 +//Software curation at a glance//
282 +// //
283 +[[[[image:Thumb2.png||alt="EBRAINS-Share-Software.pdf" height="287" width="197"]]>>attach:EBRAINS-Share-Software-4.pdf]]
284 +)))
285 +
286 +(% 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"]]
287 +
288 +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.
289 +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.
290 +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.
291 +
292 +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]].
293 +
294 +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.
295 +
296 +
297 +----
298 +
299 +=== Sharing human subject data ===
300 +
162 162  (% class="box floatinginfobox" %)
163 163  (((
164 164  **Human subject data that can be shared on EBRAINS:**
304 +// //
305 +// - Post-mortem data//
306 +// - Aggregated data//
307 +// - Strongly pseudonymized or de-identified subject data//
308 +// with a legal basis for sharing (e.g. Informed Consent)//
309 +// //
165 165  
166 -- Post-mortem data
167 -- Aggregated data
168 -- Strongly pseudonymized or de-identified subject data with a legal basis for sharing (e.g. Informed Consent)
169 -
170 -(% class="small" %)//If you have human data that does not classify as any of the above, please get in touch and we will clarify the available options. //
311 +(% class="small" %)
312 +//If you have human data that does not qualify as any of the above,//
313 +//please [[get in touch>>https://www.ebrains.eu/contact/]] and we will clarify the available options.//
171 171  )))
172 172  
316 +
173 173  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]].
174 174  
175 175  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).
... ... @@ -180,51 +180,99 @@
180 180  
181 181  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.
182 182  
327 +----
183 183  
329 +== **The openMINDS metadata framework** ==
330 +
331 +(% class="box floatinginfobox" %)
332 +(((
333 +[[[[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]]
334 +)))
335 +
336 +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]].
337 +
338 +For feedback, requests, or contributions, please get in touch with the openMINDS development team via
339 +
340 +* the support-email: [[openminds@ebrains.eu>>path:mailto:openminds@ebrains.eu]]
341 +* the [[GitHub issue tracker>>url:https://github.com/HumanBrainProject/openMINDS/issues]]
342 +* the INCF NeuroStars [[openMINDS Community Forum>>url:https://neurostars.org/t/openminds-community-forum-virtual/20156]]
343 +
184 184  ----
185 185  
186 -=== Step by Step - Models ===
346 +== **Add practical value to your shared data, model or software** ==
187 187  
188 188  
189 -~1. Request curation using the [[Curation request form>>https://nettskjema.no/a/277393#/]]. You will be contacted by a curator with more information.
349 +=== **Showcase shared data, models or software in other services** ===
190 190  
351 +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.
191 191  
192 -//Additional information will be added soon.//
193 193  
354 +|(% colspan="2" %)**Viewer for 2D images**
355 +|[[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]].
356 +|(% colspan="2" %)**Viewer for sequential atlas-registered 2D images with annotation options**
357 +|[[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]].
358 +|(% colspan="2" %)**Interactive 3D atlas viewer with options for data visualization**
359 +|[[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]].
360 +|(% colspan="2" %)**Use your research product in an interactive publication**
361 +|[[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]].
362 +
194 194  ----
195 195  
196 -=== Step by Step - Software ===
365 +==== **Add a tutorial or learning resource ** ====
197 197  
198 -[[[[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"]]
367 +(% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
368 +(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
199 199  
200 -~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.
201 201  
202 -2. 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.
371 +==== **Create a workflow** ====
203 203  
204 -3. 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.
373 +(% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
374 +(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
205 205  
206 -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]].
376 +----
207 207  
208 -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 below.
378 +== **General benefits of sharing data ** ==
209 209  
210 -(% style="text-align: right;" %)
211 -==== //Software curation at a glance          //[[[[image:Thumb2.png||alt="EBRAINS-Share-Software.pdf" height="287" width="197"]]>>attach:EBRAINS-Share-Software-4.pdf]] ====
380 +By sharing your data via EBRAINS, you gain access to the following benefits:
212 212  
382 +[[image:image-20230324170841-3.png]]
383 +
384 +
385 +
386 +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.
387 +
213 213  ----
214 214  
215 -== **The openMINDS metadata framework** ==
390 +== **Frequently asked questions ** ==
216 216  
217 -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]].
392 +>Is the curation process time consuming and difficult?
218 218  
219 -For feedback, requests, or contributions, please get in touch with the openMINDS development team via
394 +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.
220 220  
221 -* the support-email: [[openminds@ebrains.eu>>path:mailto:openminds@ebrains.eu]]
222 -* the [[GitHub issue tracker>>url:https://github.com/HumanBrainProject/openMINDS/issues]]
223 -* the INCF NeuroStars [[openMINDS Community Forum>>url:https://neurostars.org/t/openminds-community-forum-virtual/20156]]
396 +>Is sharing my data also beneficial for me or only for others?
224 224  
398 +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.
399 +
400 +>Can my data be too insignificant to share?
401 +
402 +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.
403 +
404 +>Can my data be easily misused if I share it?
405 +
406 +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.
407 +
408 +>Can I share my data before my paper is published?
409 +
410 +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.
411 +
412 +>Can I lose my competitive edge if I share my data before I publish the associated paper?
413 +
414 +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.
415 +
416 +
225 225  ----
226 226  
227 -== **The curation team: meet the curators** ==
419 +== (% style="color:#1a202c; font-family:inherit; font-size:29px" %)**The curation team: meet the curators**(%%) ==
228 228  
229 229  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.
230 230  
... ... @@ -231,7 +231,7 @@
231 231  The curators in EBRAINS are located in Oslo, Jülich, Trier and Paris. 
232 232  
233 233  
234 -**Located in Norway:**
426 +**Located in Norway**
235 235  
236 236  |(% style="width:303px" %)(((
237 237  [[image:My project2.jpg||height="209" width="167"]]
... ... @@ -281,7 +281,7 @@
281 281  )))| | |
282 282  
283 283  
284 -\\**Located in Germany:**
476 +\\**Located in Germany**
285 285  
286 286  |(% style="width:303px" %)(((
287 287  [[image:My project (2).jpg||height="209" width="167"]]
... ... @@ -293,132 +293,35 @@
293 293  Sensors and Cognitive Psychology (M. Sc.)(%%)
294 294  (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Human-Computer Interaction**
295 295  )))|(% style="width:303px" %)(((
296 -
488 +[[image:Lyuba.jpg||height="209" width="167"]]
297 297  
298 -
299 -
300 -
301 -
302 -
303 -
304 -
305 -
306 -
307 -
308 308  **Lyuba Zehl**
309 309  
310 310  (% class="small" %)Knowledge Systems Engineer
311 311  Dr. rer. nat. (Systems Neuroscience)(%%)
312 312  (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
313 -)))|(% style="width:303px" %) |
495 +)))|(% style="width:303px" %) |(% style="width:303px" %)
314 314  
315 315  ----
316 316  
317 -== **Add practical value to your shared data, model or software** ==
318 318  
319 319  
320 320  ----
321 321  
322 -=== **Showcase shared data, models or software in other services** ===
503 +== Contact ==
323 323  
324 -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.
505 +[[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
325 325  
326 -**Viewer for 2D images **
327 -
328 -* 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]].
329 -
330 -**Viewer for sequential atlas-registered 2D images with annotation options**
331 -
332 -* 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]].
333 -
334 -**Use your research product in an interactive publication **
335 -
336 -* 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]].
337 -
338 -**Interactive 3D atlas viewer with options for data visualization**
339 -
340 -* 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]].
341 -
342 342  ----
343 343  
344 -==== **Add a tutorial or learning resource ** ====
509 +== Affiliated laboratories ==
345 345  
346 -(% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
347 -(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
511 +//Institute of Basic Medical Sciences,** **University of Oslo, Norway (PI: Jan G. Bjaalie, Trygve B. Leergaard)//
348 348  
513 +//Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Germany (PI: Timo Dicksheid)//
349 349  
350 -==== **Create a workflow** ====
351 -
352 -(% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
353 -(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
354 -
355 355  ----
356 356  
357 -=== **The benefits of sharing data ** ===
517 +== References ==
358 358  
359 -By sharing your data via EBRAINS, you gain access to the following benefits:
360 -
361 -[[image:image-20230324170841-3.png]]
362 -
363 -
364 -
365 -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.
366 -
367 -----
368 -
369 -=== **Frequently asked questions ** ===
370 -
371 -(((
372 -==== ====
373 -
374 -(((
375 ->The curation process is time consuming and difficult
376 -)))
377 -)))
378 -
379 -(% class="wikigeneratedid" id="HHowcanIshareA0models3F" %)
380 -Publishing your data naturally takes some time and effort but we will support you as much as possible. If communication is on a regular basis, we are able to finish basic curation - from the initial contact to dataset release - within two weeks.
381 -
382 ->Sharing my data is not beneficial for me - only for others
383 -
384 -
385 -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.
386 -
387 ->My data is too insignificant to share
388 -
389 -
390 -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.
391 -
392 ->My data can easily be misused if I share it with the world
393 -
394 -
395 -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.
396 -
397 ->I don't think I'm allowed to share my data
398 -
399 -
400 -Many institutions are still very careful about what can be shared and how, but the situation is constantly evolving. As a researcher providing data, you will be asked to fill out an ethics compliance survey which survey to ensure that data published through the EBRAINS platform has been collected according to EU regulations. We are working on solutions for sharing anonymised human data that complies with GDPR standards to protect the identity of research subjects.
401 -
402 ->I can't share my data before my paper is published
403 -
404 -
405 -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.
406 -
407 ->If I share my data before I publish the associated paper, I will lose my competitive edge
408 -
409 -
410 -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.
411 -
412 -
413 -----
414 -
415 -== Contact ==
416 -
417 -[[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
418 -
419 -
420 420  {{putFootnotes/}}
421 -~)~)~)~)~)~)
422 -~)~)~)
423 -~)~)~)~)~)~)~)~)~)
424 -~)~)~)~)~)~)
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