Changes for page data-curation-copy

Last modified by eapapp on 2023/07/04 16:46

From 189.1 to 190.1 From 202.1 to 203.1

From version 190.1

edited by eapapp
on 2023/06/08 17:08

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To version 202.1

edited by ingrreit
on 2023/06/26 13:38

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  {{/html}}
--== Publishing neuroscience data, models and software via EBRAINS ==
++(% class="wikigeneratedid" id="HPublishingneurosciencedata2CmodelsandsoftwareviaEBRAINS" %)
++(% style="font-size:2em" %)**Publishing neuroscience data, models and software via EBRAINS**
--
  (% class="wikigeneratedid" %)
  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]].
@@ -83,8 +83,6 @@
  //to share data on EBRAINS: //
  // //
  [[[[image:image-20230324171114-2.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
--
--
  )))
@@ -106,10 +106,20 @@
  ==== **2. Upload data ** ====
++(% class="box floatinginfobox" id="share-data-infographic" %)
++(((
++(% style="text-align:center" %)
++//Download our infographic//
++//with guidelines
++on data organization: //
++(% style="text-align:center" %)
++[[[[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/]]
++)))
++
  (% 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. **
--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.
++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.
  (% 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).**
@@ -157,12 +157,11 @@
  (% class="box floatinginfobox" id="data-descriptor-infographic" %)
  (((
  (% style="text-align:center" %)
--//Download our infographic: //
--//The EBRAINS Data//
--//Descriptor at a glance//
++//Download our infographic
++about the EBRAINS Data//
++//Descriptor//
  // //
  [[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
--
  )))
  ==== **5. Preview and publish** ====
@@ -173,49 +173,96 @@
  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.
++
++
  ----
--====  ====
++=== Step by Step - Models ===
--==== **Sharing human subject data** ====
--(% class="box floatinginfobox" %)
--(((
--**Human subject data that can be shared on EBRAINS:**
--// //
--// - Post-mortem data//
--// - Aggregated data//
--// - Strongly pseudonymized or de-identified subject data//
--//   with a legal basis for sharing (e.g. Informed Consent)//
--// //
++==== 1. Start early ====
--(% class="small" %)
--//If you have human data that does not qualify as any of the above,//
--//please [[get in touch>>https://www.ebrains.eu/contact/]] and we will clarify the available options.//
--)))
++It is not necessary to wait until you are ready to publish to register your model with EBRAINS.
++By registering a model early in your project, you can take advantage of EBRAINS tools
++to keep track of simulations and to share them with your collaborators.
--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]].
++==== 2. Create/choose a Collab workspace ====
--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).
++We use EBRAINS Collaboratory "collab" workspaces to help manage the model curation process.
--The Human Data Gateway (HDG) was introduced in February 2021 as a response to the needs of multiple data providers who are bringing human subject data to EBRAINS. HDG covers the sharing of strongly pseudonymized or de-identified data, a limited range human subject data without direct identifiers and with very few indirect identifiers.
++In particular, we use collab membership (the "Team") to control who can view or edit your model metadata prior to publication.
--The HDG adds an an authentication layer on top of the data. This means that **data users **must request access to the data (via their EBRAINS account) and will receive access provided they actively accept the [[EBRAINS Access Policy>>https://ebrains.eu/terms#access-policy]], the [[EBRAINS General Terms of Use>>https://ebrains.eu/terms#general-terms-of-use]], and the [[EBRAINS Data Use Agreement>>https://ebrains.eu/terms#data-use-agreement]]. The account holder also have to accept that information about their request and access to specific data under HDG is being tracked and stored. **Data owners** must be aware that sharing under the HDG affects the legal responsibilities for the data. They must agree to joint control of the data (see the [[Data Provision Protocol v1>>url:https://strapi-prod.sos-ch-dk-2.exo.io/EBRAINS_Data_Provision_Protocol_dfe0dcb104.pdf]], section 1.4 - 1.5) and the Data Protection Officers of the responsible institutions must have accepted that the data can be shared under HDG.
++It is up to you whether you create a new collab for each model, or reuse an existing collab
++(it is no problem to have multiple models associated with a single collab).
--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.
++Collabs are also useful for storing simulation results, adding documentation for your model,
++and/or providing tutorials in Jupyter notebooks.
++==== 3. Upload code ====
------
++We recommend storing model code and/or configuration files in an online Git repository, for example on GitHub.
++This repository should be public when you publish the model, but a private repository can be used for model development.
--=== Step by Step - Models ===
++Alternatively, you can upload code to the Collab Drive or Bucket storage.
++==== 4.Submit metadata ====
--~1. Request curation using the [[Curation request form>>https://nettskjema.no/a/277393#/]]. You will be contacted by a curator with more information.
++We recommend submitting metadata using the Model Catalog app, installed in your collab.
++To install it:
--//Additional information will be added soon.//
++1. click the "+ Create" button
++1. in the "Create Page" form, add a title, such as "Model Catalog", and select "Community App", then click "Create"
++1. scroll down until you find the "Model Catalog" app, click "Select", then "Save & View"
++You will then see a table of all the models and validation tests associated with this collab.
++If this is your first time using the app, the table will probably be empty.
++To add your model, click "+", fill in the form, then click "Add model".
++
++As development of your model proceeds, you can easily register new versions of the code,
++and new parameterizations, by clicking "Add new version".
++
++If you prefer not to use the app, you can instead fill in the [[Curation request form>>https://nettskjema.no/a/277393#/]].,
++and you will be contacted by e-mail with further instructions.
++
++==== 5. Provide a reference dataset ====
++
++Once you're ready to publish your model entry in the EBRAINS Knowledge Graph,
++we encourage you to provide a dataset containing the simulation results produced by your model,
++following the process under "Step by step - Data" above.
++
++These reference data will be linked to the model, and will be helpful to anyone trying to
++reuse your model.
++
++We will soon introduce a "Reproducible" badge for all models that include a reference dataset,
++and whose simulation results can be reproduced by an EBRAINS curator.
++
++==== 6. Request publication, preview and publish ====
++
++Until you request your model entry to be published in the EBRAINS Knowledge Graph,
++only members of the collab will be able to view the model entry, in the Model Catalog app
++or using the Model Validation Python client.
++
++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.
++
++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.
++
++
++Curators will then perform a number of checks:
++
++1.  Does the model description provide sufficient context to understand the purpose and use of the model?
++1.  Does the code repository contain a licence file, explaining the conditions for reusing the code?
++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.
++
++The curators will also take a snapshot of your model code.
++
++* 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"]].
++* 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.
++
++Once this is done, you will be invited to review a preview of how the model entry will appear in the KG Search,
++and will have the opportunity to request modifications prior to approval and publication.
++
  ----
  === Step by Step - Software ===
@@ -242,8 +242,43 @@
  ----
++=== Sharing human subject data ===
++
++(% class="box floatinginfobox" %)
++(((
++**Human subject data that can be shared on EBRAINS:**
++// //
++// - Post-mortem data//
++// - Aggregated data//
++// - Strongly pseudonymized or de-identified subject data//
++//   with a legal basis for sharing (e.g. Informed Consent)//
++// //
++
++(% class="small" %)
++//If you have human data that does not qualify as any of the above,//
++//please [[get in touch>>https://www.ebrains.eu/contact/]] and we will clarify the available options.//
++)))
++
++
++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]].
++
++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).
++
++The Human Data Gateway (HDG) was introduced in February 2021 as a response to the needs of multiple data providers who are bringing human subject data to EBRAINS. HDG covers the sharing of strongly pseudonymized or de-identified data, a limited range human subject data without direct identifiers and with very few indirect identifiers.
++
++The HDG adds an an authentication layer on top of the data. This means that **data users **must request access to the data (via their EBRAINS account) and will receive access provided they actively accept the [[EBRAINS Access Policy>>https://ebrains.eu/terms#access-policy]], the [[EBRAINS General Terms of Use>>https://ebrains.eu/terms#general-terms-of-use]], and the [[EBRAINS Data Use Agreement>>https://ebrains.eu/terms#data-use-agreement]]. The account holder also have to accept that information about their request and access to specific data under HDG is being tracked and stored. **Data owners** must be aware that sharing under the HDG affects the legal responsibilities for the data. They must agree to joint control of the data (see the [[Data Provision Protocol v1>>url:https://strapi-prod.sos-ch-dk-2.exo.io/EBRAINS_Data_Provision_Protocol_dfe0dcb104.pdf]], section 1.4 - 1.5) and the Data Protection Officers of the responsible institutions must have accepted that the data can be shared under HDG.
++
++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.
++
++----
++
  == **The openMINDS metadata framework** ==
++(% class="box floatinginfobox" %)
++(((
++[[[[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]]
++)))
++
  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]].
  For feedback, requests, or contributions, please get in touch with the openMINDS development team via
@@ -322,22 +322,15 @@
  Phd Student
  Sensors and Cognitive Psychology (M. Sc.)(%%)
  (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Human-Computer Interaction**
--)))|(% style="width:328px" %)(((
--
++)))|(% style="width:303px" %)(((
++[[image:Lyuba.jpg||height="209" width="167"]]
--
--
--
--
--
--
--
  **Lyuba Zehl**
  (% class="small" %)Knowledge Systems Engineer
  Dr. rer. nat. (Systems Neuroscience)(%%)
  (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
--)))|(% style="width:321px" %) |(% style="width:324px" %)
++)))|(% style="width:303px" %) |(% style="width:303px" %)
  ----
@@ -350,12 +350,16 @@
  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.
--(% cellpadding="15" style="margin-right:auto" %)
--|(% colspan="2" %)**Viewer for 2D images**|(% colspan="2" rowspan="1" %)**Viewer for sequential atlas-registered 2D images with annotation options**
--|(% style="white-space:nowrap; width:320px" %)[[image:MIO_screenshot.PNG||alt="MIO viewer" height="242" style="float:left" width="300"]]|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]].|(% style="white-space:nowrap; width:320px" %)**[[image:LZ_screenshot.PNG||alt="LocaliZoom viewer" height="250" style="float:left" width="300"]]**|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]].
--|(% colspan="2" rowspan="1" %)**Use your research product in an interactive publication**|(% colspan="2" rowspan="1" %)**Interactive 3D atlas viewer with options for data visualization**
--|[[image:LivePaper_screenshot.PNG||alt="LivePaper" height="341" style="float:left" width="300"]]|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]].|[[image:3Datlas_screenshot.PNG||alt="Siibra explorer" height="204" style="float:left" width="300"]]|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]].
++|(% colspan="2" %)**Viewer for 2D images**
++|[[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]].
++|(% colspan="2" %)**Viewer for sequential atlas-registered 2D images with annotation options**
++|[[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]].
++|(% colspan="2" %)**Interactive 3D atlas viewer with options for data visualization**
++|[[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]].
++|(% colspan="2" %)**Use your research product in an interactive publication**
++|[[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]].
++
  ----
  ==== **Add a tutorial or learning resource ** ====

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