Changes for page Data Curation

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edited by spieschnik
on 2025/11/17 10:45

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edited by adavison
on 2024/07/05 18:52

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- EBRAINS-Share-Software-4.pdf
- EBRAINS-Share-Software.pdf

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--XWiki.spieschnik
++XWiki.adavison

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@@ -84,7 +84,7 @@
  //with all you need to know//
  //to share data on EBRAINS: //
  // //
--[[~[~[image:image-20230324171114-2.png~|~|height="150" width="106"~]~]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
++[[[[image:image-20230324171114-2.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
  )))
@@ -108,7 +108,8 @@
  //with guidelines
  on data organization: //
--[[~[~[image:image-20230621121014-1.png~|~|data-xwiki-image-style-alignment="center" height="150" width="106"~]~]>>https://drive.ebrains.eu/lib/f5cf4964-f095-49bd-8c34-e4ffda05a497/file/ebrains-infographic-data-organisation.pdf/]]
++(% 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. **
@@ -122,7 +122,7 @@
  **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.
--EBRAINS offers secure, long-term storage at FENIX Supercomputing Centres in Europe.
++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.
  If a data collection is already uploaded elsewhere, we may link to the already existing repository.
@@ -165,7 +165,7 @@
  about the EBRAINS Data//
  //Descriptor//
  // //
--[[~[~[image:image-20230324171109-1.png~|~|height="150" width="106"~]~]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
++[[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
  )))
  ==== **5. Preview and publish** ====
@@ -207,7 +207,7 @@
  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.
--Alternatively, you can upload code to the Collab Drive (in this case, curators will copy it to a read-only Bucket upon publication) or Bucket storage.
++Alternatively, you can upload code to the Collab Drive or Bucket storage.
  ==== 4. Submit metadata ====
@@ -260,7 +260,7 @@
  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"]] (via the updateSWH extension).
++* 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,
@@ -286,21 +286,29 @@
  (% class="box floatinginfobox" %)
  (((
  **Human subject data that can be shared on EBRAINS:**
--// - Anonymized data//
++// //
  // - Post-mortem data//
--// - Aggregated 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 the [[GDPR >>https://gdpr-info.eu/]]and relevant [[EU directives>>https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=celex%3A32010L0063]]. The necessary information to assess this compliance is collected via our [[curation request form>>https://www.ebrains.eu/tools/ebrains-curation-request-form]].
--Anonymous data, including post-mortem and aggregated data, can be shared openly on the condition that subject identifiers are removed from the metadata. Such identifiers must not be shared with the curation team when submitting metadata for curation.
++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]].
--Identifiable or sensitive data are shared under restricted access and cannot be stored on the EBRAINS data storage. While the dataset as a whole is discoverable through anonymous metadata published on EBRAINS, access to the actual data files is managed via the [[EBRAINS Trusted Research Environments>>https://wiki.ebrains.eu/bin/view/Collabs/trusted-research-environments]]. The data custodian is required to comply with the[[ EBRAINS special terms for restricted access datasets>>https://drive.ebrains.eu/f/5a9bb3bd048446ae8ef6/?dl=1]].
++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** ==
@@ -307,7 +307,7 @@
  (% 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]]
++[[[[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 is a community-driven, open-source metadata framework for linked data, as used in graph database systems, such as the EBRAINS Knowledge Graph. It is composed of multiple metadata models with interlinked schemas, libraries of serviceable metadata instances, and supportive tooling (e.g., [[openMINDS Python>>https://github.com/openMetadataInitiative/openMINDS_Python]] or [[openMINDS Matlab>>https://github.com/openMetadataInitiative/openMINDS_MATLAB]]). A full documentation (for users and contributors) of the openMINDS framework can be found on [[ReadTheDocs>>https://openminds-documentation.readthedocs.io||rel="noopener noreferrer" target="_blank"]].
@@ -330,7 +330,7 @@
  |(% colspan="2" %)**Viewer for 2D images**
--|[[image:MIO_screenshot.PNG]]|Integrate image data with //SeriesZoom viewer//: EBRAINS 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 [[viewer links available for this dataset>>https://search.kg.ebrains.eu/?category=Dataset&q=nr2f1#9677359c-73fa-4425-b8fa-3de794e9017a]] as an example.
++|[[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**
@@ -403,6 +403,92 @@
  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.
++----
++
++== (% style="--darkreader-inline-color:#f1ede6; color:#1a202c; font-family:inherit; font-size:29px" %)**The curation team: meet the curators**(%%) ==
++
++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.
++
++The curators in EBRAINS are located in Oslo, Jülich, Trier and Paris.
++
++
++**Located in Norway**
++
++|(% style="width:303px" %)(((
++[[image:My project2.jpg||height="209" width="167"]]
++
++**Archana Golla**
++
++(% class="small" %)Curation Scientist
++Neuroscience (PhD)(%%)
++(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Behavioral neuroscience and microscopy**
++)))|(% style="width:303px" %)(((
++[[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
++
++**Camilla H. Blixhavn**
++
++(% class="small" %)Curation Scientist,
++Phd Student
++Neuroscience (M. Sc.)(%%)
++(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and data integration**
++)))|(% style="width:303px" %)(((
++[[image:My project (1).jpg||height="209" width="167"]]
++
++**Ingrid Reiten**
++
++(% class="small" %)Curation Scientist,
++Phd Student
++Neuroscience (M. Sc.)(%%)
++(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and structural connectivity**
++)))|(% style="width:303px" %)(((
++[[image:My project1.jpg||height="209" width="167"]]
++
++**Sophia Pieschnik**
++
++(% class="small" %)Curation Scientist
++Neurocognitive Psychology (M. Sc.)(%%)
++(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroimaging **
++)))
++
++|(% style="width:303px" %)(((
++[[image:My project.jpg||height="209" width="167"]]
++
++**Heidi Kleven**
++
++(% class="small" %)Curation Scientist,
++Phd Student
++Neuroscience (M. Sc.)(%%)
++(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and brain atlases**
++)))| | |
++
++
++\\**Located in Germany**
++
++|(% style="width:303px" %)(((
++[[image:My project (2).jpg||height="209" width="167"]]
++
++**Jan Gündling**
++
++(% class="small" %)Curation Scientist,
++Phd Student
++Sensors and Cognitive Psychology (M. Sc.)(%%)
++(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Human-Computer Interaction**
++)))|(% 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:#cac2b7; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
++)))|(% style="width:303px" %) |(% style="width:303px" %)
++
++----
++
++
++
++----
++
  == Contact ==
  [[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]

EBRAINS-Share-Software-4.pdf

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