Changes for page data-curation-copy

Last modified by eapapp on 2023/07/04 16:46
From version 195.1
edited by adavison
on 2023/06/14 15:35
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To version 172.1
edited by eapapp
on 2023/06/06 16:39
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90 90  
91 91  ==== **1. Provide some general information about your dataset** ====
92 92  
93 -
94 -
95 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 96  
97 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.
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113 113  
114 114  (% style="margin-right:10px" %)[[image:https://lh5.googleusercontent.com/EWtYwfVlbeC-jqPasgmzidqc50GrkKIEgwXeUeql8aaMHIukmFdWEy0nufVWWATbxDDK3XwwZEDmASrbpCsBk1u0HpAd8x4ZgAMsMPRcWyrb9etlV6FgKE_QN2e6SqKxHE0rzkR8uI1rRW_5z21TFGYVnw=s2048||height="91px;" width="91px;"]](%%)**Upload data to EBRAINS Storage, either using a drag-and-drop solution (opt. 1) or an interactive python script (opt. 2).**
115 115  
116 -**Opt. 1. **For smaller datasets with a reasonable amount of files, we recommend using the Collab-Bucket solution (drag-and-drop). A Collab Bucket must first be assigned to a dataset, which happens when a datasets is accepted for sharing.
114 +//**Opt. 1. **//For smaller datasets with a reasonable amount of files, we recommend using the Collab-Bucket solution (drag-and-drop). A Collab Bucket must first be assigned to a dataset, which happens when a datasets is accepted for sharing.
117 117  
118 -**Opt. 2. **For larger datasets or datasets with a large amount of files, we recommend using a programmatic approach. The [[python script>>https://github.com/eapapp/ebrains-data-storage/tree/main/data-proxy]] is interactive and does not require any additional programming.
116 +//**Opt. 2. **//For larger datasets or datasets with a large amount of files, we recommend using a programmatic approach. The [[python script>>https://github.com/eapapp/ebrains-data-storage/tree/main/data-proxy]] is interactive and does not require any additional programming.
119 119  
120 120  
121 121  EBRAINS offers secure, long-term storage at [[CSCS Swiss National Supercomputing Centre>>url:https://www.cscs.ch/]], with currently no upper limit of storage capacity. 
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126 126  ==== **3. Submit metadata** ====
127 127  
128 128  
129 -(% style="margin-right:10px" %)[[image:https://lh5.googleusercontent.com/WS4T2LhF9znWWChn3Z550agLrrb-KTWdYVsJSv0lh4cGjKbjuN1WV68WER9xkYqi1UqN7KYZz7bImYz3_TpOuTuvma7T192QUiUZoyJVPk1fj5NSDSQh_kpIeBufAOdDtsDRpPKK_P5EDPqRCTAaOTNyCw=s2048||height="91px;" width="91px;"]](%%)**Submit metadata using the **[[EBRAINS Metadata Wizard>>https://ebrains-metadata-wizard.apps.hbp.eu/]]** (opt. 1), or directly via the Knowledge Graph (opt. 2) **
127 +(% 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 through direct interaction with the Knowledge Graph (opt. 2) **
130 130  
131 -**Opt. 1.** Manually submit the minimal required metadata via the [[EBRAINS Metadata Wizard>>https://ebrains-metadata-wizard.apps.hbp.eu/]]. The minimal required metadata covers extended bibliographic information necessary to publish your dataset on EBRAINS. The submitted information, including uploaded files, will be sent to the Curation team automatically
129 +//**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
132 132  
133 -**Opt. 2.** To go beyond the minimal required metadata, you can directly interact with the Knowledge Graph (KG) in your private space. Within the private space, you can upload metadata and interact with them, moreover you can connect your metadata to existing publicly accessible entries. Access to your private space is granted upon the initiation of the curation process. You can access your private space via:
131 +//**Opt. 2.**// To go beyond the minimal required metadata, you can directly interact with the Knowledge Graph (KG) in your private space. Within the private space, you can upload metadata and interact with them, moreover you can connect your metadata to existing publicly accessible entries. Access to your private space is granted upon the initiation of the curation process. You can access your private space via:
134 134  
135 135  * Knowledge Graph Editor: This User Interface allows you to manually enter metadata into your KG space and validate metadata that are programmatically uploaded. The Editor contains a basic set of openMINDS metadata templates, but can be extended to the full openMINDS metadata model on request. Access is granted once the request is accepted.
136 136  * [[Fairgraph>>https://fairgraph.readthedocs.io/en/stable/]]: This is the recommended software tool for programmatic interaction with the KG. It allows you to programmatically upload openMINDS compliant metadata into your KG space and interact with existing metadata.
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139 139  Datasets published through the EBRAINS Knowledge Graph have to be registered using **openMINDS compliant metadata** delivered as JSON-LD files. See this summary table for an overview of [[the minimally required openMINDS properties for publishing>>https://drive.ebrains.eu/lib/47995dbc-f576-4008-a76c-eefbfd818529/file/ebrains-minimum-required-metadata.xlsx]] on EBRAINS.
140 140  
141 141  
142 -==== **4. Write a Data Descriptor** ====
140 +==== **4. Write a Data Descriptor ** ====
143 143  
142 +(% 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]]** . **
144 144  
145 -
146 -(% style="margin-right:10px" %)[[image:https://lh4.googleusercontent.com/lMYEKOXzejbBydOdotWWteXQo7j363xRyntBGjcPZVEdtIU1CJYX7q1STpdr2JPZK4hpWWXk20UlkUOqDGL5kX6vnQVBSdrfUo6EGfXOwpuGq1Uygv0tTZJ0lRO6voJvg56QC2mufvjAcRXGfAKFOjtc6w=s2048||height="94px;" width="94px;"]](%%)**Write a data descriptor by filling in **[[this template>>https://drive.ebrains.eu/f/a2e07c95b1a54090bbbc/?dl=1]]**.**
147 -
148 148  The Data Descriptor is a document helping others interpret and reuse (and prevent misuse) of your data, and is critical to achieve a basic level of FAIR. The document will be uploaded in the repository of the data, shared as a PDF. 
149 149  
150 150  See our infographic about the data descriptor for inspiration or guidance.
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153 153  
154 154  Journal publications sufficiently describing the shared data, such as made available through [[Nature Scientific Data>>http://www.nature.com/sdata/about]], [[Elsevier Data in Brief>>http://www.journals.elsevier.com/data-in-brief/]], [[BMC Data note>>https://bmcresnotes.biomedcentral.com/submission-guidelines/preparing-your-manuscript/data-note]] and more, can replace the EBRAINS Data Descriptor.
155 155  
156 -
157 157  (% class="box floatinginfobox" id="data-descriptor-infographic" %)
158 158  (((
159 159  (% style="text-align:center" %)
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165 165  
166 166  )))
167 167  
168 -==== **5. Preview and publish** ====
163 +==== **5. Preview and publish ** ====
169 169  
170 170  
171 171  (% style="margin-right:10px" %)[[image:https://lh4.googleusercontent.com/XqT26Q4yWJK26cjtjhI4ToXoZZMxhT9LimG4Hk9mePxy0-KPKgpVIzcuiP5mOQowBgf2JjkrWUq2VbCmafWWZPJplEZALnFOlCZHLlQgzOx7fFwoBteyi_IlMLkPBS9vtOcdNIZ59HyLnQz4RsTQ0lUrSw=s2048||height="91px;" width="91px;"]](%%)**Preview and approve the release of your dataset. **
172 -
173 173  Once a Curator has assembled the dataset in the EBRAINS Knowledge Graph, combining the data, metadata and data descriptor, the data provider will receive a private URL for previewing the dataset prior to release. We need an official approval from the data custodian{{footnote}}The Data Custodian is responsible for the content and quality of the Data and metadata, and is the person to be contacted by EBRAINS CS in case of any misconduct related to the Data. It is the obligation of a Data Custodian to keep EBRAINS informed about changes in the contact information of the authors of the Datasets provided by them ([[EBRAINS Data Provision Protocol - version 1.1>>https://strapi-prod.sos-ch-dk-2.exo.io/EBRAINS_Data_Provision_Protocol_dfe0dcb104.pdf]]).{{/footnote}} to release the dataset. Once released, a [[DataCite DOI>>https://datacite.org/]] will be generated for the dataset. If the identical data collection has received a DOI elsewhere, we recommend re-using the already issued DOI.
174 174  
175 175  
176 176  ----
177 177  
178 -==== ====
172 +==== **Sharing human subject data ** ====
179 179  
180 -==== **Sharing human subject data** ====
181 -
182 182  (% class="box floatinginfobox" %)
183 183  (((
184 184  **Human subject data that can be shared on EBRAINS:**
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194 194  //please [[get in touch>>https://www.ebrains.eu/contact/]] and we will clarify the available options.//
195 195  )))
196 196  
197 -
198 198  Human subject data shared on EBRAINS must comply with [[GDPR >>https://gdpr-info.eu/]]and [[EU directives>>https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=celex%3A32010L0063]]. The information we need to assess this is collected via our [[Ethics and Regulatory Compliance Survey>>https://nettskjema.no/a/224765]].
199 199  
200 200  Post-mortem and aggregated human data can be shared openly, given direct identifiers in the metadata are removed. Strongly pseudonymized and de-identified data can be shared via the Human Data Gateway (HDG).
... ... @@ -211,92 +211,11 @@
211 211  === Step by Step - Models ===
212 212  
213 213  
205 +~1. Request curation using the [[Curation request form>>https://nettskjema.no/a/277393#/]]. You will be contacted by a curator with more information.
214 214  
215 215  
216 -==== 1. Start early ====
208 +//Additional information will be added soon.//
217 217  
218 -It is not necessary to wait until you are ready to publish to register your model with EBRAINS.
219 -
220 -By registering a model early in your project, you can take advantage of EBRAINS tools
221 -to keep track of simulations and to share them with your collaborators.
222 -
223 -==== 2. Create/choose a Collab workspace ====
224 -
225 -We use EBRAINS Collaboratory "collab" workspaces to help manage the model curation process.
226 -
227 -In particular, we use collab membership (the "Team") to control who can view or edit your model metadata prior to publication.
228 -
229 -It is up to you whether you create a new collab for each model, or reuse an existing collab
230 -(it is no problem to have multiple models associated with a single collab).
231 -
232 -Collabs are also useful for storing simulation results, adding documentation for your model,
233 -and/or providing tutorials in Jupyter notebooks.
234 -
235 -==== 3. Upload code ====
236 -
237 -We recommend storing model code and/or configuration files in an online Git repository, for example on GitHub.
238 -This repository should be public when you publish the model, but a private repository can be used for model development.
239 -
240 -Alternatively, you can upload code to the Collab Drive or Bucket storage.
241 -
242 -==== 4.Submit metadata ====
243 -
244 -We recommend submitting metadata using the Model Catalog app, installed in your collab.
245 -
246 -To install it:
247 -
248 -1. click the "+ Create" button
249 -1. in the "Create Page" form, add a title, such as "Model Catalog", and select "Community App", then click "Create"
250 -1. scroll down until you find the "Model Catalog" app, click "Select", then "Save & View"
251 -
252 -You will then see a table of all the models and validation tests associated with this collab.
253 -If this is your first time using the app, the table will probably be empty.
254 -To add your model, click "+", fill in the form, then click "Add model".
255 -
256 -As development of your model proceeds, you can easily register new versions of the code,
257 -and new parameterizations by clicking "Add new version".
258 -
259 -If you prefer not to use the app, you can instead fill in the [[Curation request form>>https://nettskjema.no/a/277393#/]].,
260 -and you will be contacted by e-mail with further instructions.
261 -
262 -====
263 -5. Provide a reference dataset ====
264 -
265 -Once you're ready to publish your model entry in the EBRAINS Knowledge Graph,
266 -we encourage you to provide a dataset containing the simulation results produced by your model,
267 -following the process under "Step by step - Data" above.
268 -
269 -These reference data will be linked to the model, and will be helpful to anyone trying to
270 -reuse your model.
271 -
272 -We will soon introduce a "Reproducible" badge for all models that include a reference dataset,
273 -and whose simulation results can be reproduced by an EBRAINS curator.
274 -
275 -==== 6. Request publication, preview and publish ====
276 -
277 -Until you request your model entry to be published in the EBRAINS Knowledge Graph,
278 -only members of the collab will be able to view the model entry, in the Model Catalog app
279 -or using the Model Validation Python client.
280 -
281 -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.
282 -
283 -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.
284 -
285 -
286 -Curators will then perform a number of checks:
287 -
288 -1. Does the model description provide sufficient context to understand the purpose and use of the model?
289 -1. Does the code repository contain a licence file, explaining the conditions for reusing the code?
290 -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.
291 -
292 -The curators will also take a snapshot of your model code.
293 -
294 -* For models in public Git repositories, we archive a copy of the repository in Software Heritage.
295 -* 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.
296 -
297 -Once this is done, you will be invited to review a preview of how the model entry will appear in the KG Search,
298 -and will have the opportunity to request modifications prior to approval and publication.
299 -
300 300  ----
301 301  
302 302  === Step by Step - Software ===
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325 325  
326 326  == **The openMINDS metadata framework** ==
327 327  
328 -(% class="box floatinginfobox" %)
329 -(((
330 -[[[[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]]
331 -)))
332 -
333 333  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]].
334 334  
335 335  For feedback, requests, or contributions, please get in touch with the openMINDS development team via
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416 416  
417 417  
418 418  
419 -
420 -
421 421  **Lyuba Zehl**
422 422  
423 423  (% class="small" %)Knowledge Systems Engineer
... ... @@ -434,18 +434,24 @@
434 434  
435 435  === **Showcase shared data, models or software in other services** ===
436 436  
437 -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.
340 +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.
438 438  
342 +**Viewer for 2D images **
439 439  
440 -|(% colspan="2" %)**Viewer for 2D images**
441 -|[[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]].
442 -|(% colspan="2" %)**Viewer for sequential atlas-registered 2D images with annotation options**
443 -|[[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]].
444 -|(% colspan="2" %)**Interactive 3D atlas viewer with options for data visualization**
445 -|[[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]].
446 -|(% colspan="2" %)**Use your research product in an interactive publication**
447 -|[[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]].
344 +* 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]].
448 448  
346 +**Viewer for sequential atlas-registered 2D images with annotation options**
347 +
348 +* 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]].
349 +
350 +**Use your research product in an interactive publication **
351 +
352 +* 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]].
353 +
354 +**Interactive 3D atlas viewer with options for data visualization**
355 +
356 +* 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]].
357 +
449 449  ----
450 450  
451 451  ==== **Add a tutorial or learning resource ** ====
... ... @@ -483,26 +483,33 @@
483 483  )))
484 484  )))
485 485  
395 +
396 +(% class="wikigeneratedid" id="HHowcanIshareA0models3F" %)
486 486  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.
487 487  
488 488  >Is sharing my data also beneficial for me or only for others?
489 489  
401 +
490 490  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.
491 491  
492 492  >Can my data be too insignificant to share?
493 493  
406 +
494 494  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.
495 495  
496 496  >Can my data be easily misused if I share it?
497 497  
411 +
498 498  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.
499 499  
500 500  >Can I share my data before my paper is published?
501 501  
416 +
502 502  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.
503 503  
504 504  >Can I lose my competitive edge if I share my data before I publish the associated paper?
505 505  
421 +
506 506  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.
507 507  
508 508  
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513 513  [[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
514 514  
515 515  
516 -== References ==
517 -
518 518  {{putFootnotes/}}
433 +~)~)~)~)~)~)
434 +~)~)~)
435 +~)~)~)~)~)~)~)~)~)
436 +~)~)~)~)~)~)
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