Changes for page data-curation-copy

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

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edited by eapapp
on 2023/06/06 13:58

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edited by ingrreit
on 2023/06/05 10:22

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--    <form title="Search in this collab" target="_blank" action="https://wiki.ebrains.eu/bin/view/Main/Search">
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--
--
  == Publishing neuroscience data, models and software via EBRAINS ==
@@ -27,10 +27,16 @@
  {{toc depth="3" start="2"/}}
  {{/box}}
++
  == **Information to get started** ==
++(% style="text-align: center;" %)
++**Get started! **
++
++(% style="text-align: center;" %)
  **[[REQUEST CURATION>>https://nettskjema.no/a/277393#/]] to share data, simulations, computational models, and software, - or to add a new version of an existing one. **
++(% style="text-align: center;" %)
  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.
@@ -48,7 +48,7 @@
  (% class="box successmessage" %)
  (((
--**Particular needs? Contact us! **The workflows for sharing can be modified for researchers or research groups aiming to frequently publish larger numbers of their research products through EBRAINS. Please contact the curation service team in such cases. Reach us at [[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
++**Particular needs? Contact us! **The workflows for sharing can be modified for researchers or research groups aiming to frequently publish larger numbers of their research products through EBRAINS. Please contact the curation service team in such cases
  )))
  ----
@@ -73,40 +73,22 @@
  [[image:image-20230326054341-1.png]]
--(% class="box floatinginfobox" id="share-data-infographic" %)
--(((
--(% style="text-align:center" %)
--//Download our infographic//
--//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/]]
++====   ====
--
--)))
--
--
  ==== **1. Provide some general information about your dataset** ====
--[[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#/]]. **
++[[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#/]]. **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.
--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.
++[[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]]**. This form collects the necessary information needed for us to evaluate whether we can ethically and legally share the data via EBRAINS.
--[[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]]**.
--This form collects the necessary information needed for us to evaluate whether we can ethically and legally share the data via EBRAINS.
--
--See below for information about the ethical and legal aspects concerning sharing of human subject data.
--
--
  ==== **2. Upload data ** ====
--[[image:https://lh5.googleusercontent.com/sieKO-kW8O18iPaUyonwyo4UfHBmtc2E9BDnjbx52j6J_uGmm-OzGAo7sloMk3sYwKa6QW3hYQsOA9N4H7uGQpca088Wrk0Nurpt_J3B0-NSbcaPNdZIh21otQcG6jnAxLGiKoEvkTyaDGTMk3fu7me8mQ=s2048||height="94px;" width="94px;"]]**Ensure data is structured consistently prior to upload. **
++[[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 documentation 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// //[[collection of guidelines on data organization>>https://drive.ebrains.eu/smart-link/25299f04-c4e5-4028-8f5f-3b8208f9a532/]] for further guidance.
  [[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).**
@@ -123,9 +123,9 @@
  ==== **3. Submit metadata** ====
--[[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) **
++[[image:https://lh5.googleusercontent.com/WS4T2LhF9znWWChn3Z550agLrrb-KTWdYVsJSv0lh4cGjKbjuN1WV68WER9xkYqi1UqN7KYZz7bImYz3_TpOuTuvma7T192QUiUZoyJVPk1fj5NSDSQh_kpIeBufAOdDtsDRpPKK_P5EDPqRCTAaOTNyCw=s2048||height="91px;" width="91px;"]]**Submit metadata using our **[[EBRAINS Metadata wizard>>https://ebrains-metadata-wizard.apps.hbp.eu/]]** (opt. 1), or through direct interaction with the Knowledge Graph (opt. 2) **
--//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
++//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
  //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:
@@ -133,32 +133,35 @@
  * [[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.
  * [[KG Core Python SDK>>https://github.com/HumanBrainProject/kg-core-sdks]]: This python package gives you full freedom in interacting with he KG. It allows you to upload any JSON-LD with metadata into your private space. Note, for dataset publications in EBRAINS, the JSON-LD metadata files have to comply to openMINDS.
++
  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.
++**The openMINDS metadata framework**
++
++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
++
++* the support-email: [[openminds@ebrains.eu>>path:mailto:openminds@ebrains.eu]]
++* the [[GitHub issue tracker>>url:https://github.com/HumanBrainProject/openMINDS/issues]]
++* the INCF NeuroStars [[openMINDS Community Forum>>url:https://neurostars.org/t/openminds-community-forum-virtual/20156]]
++
++
  ==== **4. Write a Data Descriptor ** ====
--[[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]]** . **
--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.
++[[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]]** . **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.
--See our infographic about the data descriptor for inspiration or guidance.
--Check out previous examples in the KG Search. See e.g., the data descriptor for the dataset "[[Anterogradely labeled axonal projections from the orbitofrontal cortex in rat>>https://doi.org/10.25493/2MX9-3XF]]".
++Check out previous examples in the KG Search! See e.g., the data descriptor for the dataset "[[Anterogradely labeled axonal projections from the orbitofrontal cortex in rat>>https://doi.org/10.25493/2MX9-3XF]]".
  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.
--(% class="box floatinginfobox" id="data-descriptor-infographic" %)
--(((
--(% style="text-align:center" %)
--//Download our infographic: //
--//The EBRAINS Data//
--//Descriptor at a glance//
--// //
--[[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
--
--)))
++|(% style="width:175px" %)[[[[image:image-20230324171109-1.png||height="154" width="109"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]|(% style="width:1662px" %)The EBRAINS Data descriptor at-a-glance
++
++
  ==== **5. Preview and publish ** ====
@@ -167,24 +167,20 @@
  ----
--==== **Sharing human subject data ** ====
++==== **Sharing human 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)//
--// //
++**Human subject data that can be shared on EBRAINS consists of:**
--(% 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.//
++- 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 classify as any of the above, please get in touch 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]].
++Human 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).
@@ -207,35 +207,27 @@
  ----
--=== Step by Step - Software ===
++=== Step by Step - Code ===
--[[[[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"]]
++[[[[image:swc-flow-no-header.png||alt="swc-flow.png"]]>>https://www.ebrains.eu/tools/ebrains-curation-request-form||rel="noopener noreferrer" target="_blank"]]
--~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.
++~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.
 . 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.
--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.
++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.[[[[image:Thumb.png||alt="EBRAINS-Share-Software.pdf" height="286" style="float:right" width="195"]]>>attach:EBRAINS-Share-Software.pdf]]
  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]].
--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.
++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.
--(% style="text-align: right;" %)
--==== //Software curation at a glance          //[[[[image:Thumb2.png||alt="EBRAINS-Share-Software.pdf" height="287" width="197"]]>>attach:EBRAINS-Share-Software-4.pdf]] ====
------
--== **The openMINDS metadata framework** ==
--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
--* the support-email: [[openminds@ebrains.eu>>path:mailto:openminds@ebrains.eu]]
--* the [[GitHub issue tracker>>url:https://github.com/HumanBrainProject/openMINDS/issues]]
--* the INCF NeuroStars [[openMINDS Community Forum>>url:https://neurostars.org/t/openminds-community-forum-virtual/20156]]
++
  ----
  == **The curation team: meet the curators** ==
@@ -242,6 +242,7 @@
  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.
@@ -254,7 +254,7 @@
  (% class="small" %)Curation Scientist
  Neuroscience (PhD)(%%)
--(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Behavioral neuroscience and microscopy**
++(% class="small" style="color:#4a5568" %)**Behavioral neuroscience and microscopy**
  )))|(% style="width:303px" %)(((
  [[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
@@ -263,7 +263,7 @@
  (% class="small" %)Curation Scientist,
  Phd Student
  Neuroscience (M. Sc.)(%%)
--(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and data integration**
++(% class="small" style="color:#4a5568" %)**Neuroanatomy and data integration**
  )))|(% style="width:303px" %)(((
  [[image:My project (1).jpg||height="209" width="167"]]
@@ -272,7 +272,7 @@
  (% class="small" %)Curation Scientist,
  Phd Student
  Neuroscience (M. Sc.)(%%)
--(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and structural connectivity**
++(% class="small" style="color:#4a5568" %)**Neuroanatomy and structural connectivity**
  )))|(% style="width:303px" %)(((
  [[image:My project1.jpg||height="209" width="167"]]
@@ -280,7 +280,7 @@
  (% class="small" %)Curation Scientist
  Neurocognitive Psychology (M. Sc.)(%%)
--(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroimaging **
++(% class="small" style="color:#4a5568" %)**Neuroimaging **
  )))
  |(% style="width:303px" %)(((
@@ -291,7 +291,7 @@
  (% class="small" %)Curation Scientist,
  Phd Student
  Neuroscience (M. Sc.)(%%)
--(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and brain atlases**
++(% class="small" style="color:#4a5568" %)**Neuroanatomy and brain atlases**
  )))| | |
@@ -305,7 +305,7 @@
  (% class="small" %)Curation Scientist,
  Phd Student
  Sensors and Cognitive Psychology (M. Sc.)(%%)
--(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Human-Computer Interaction**
++(% class="small" style="color:#4a5568" %)**Human-Computer Interaction**
  )))|(% style="width:303px" %)(((
@@ -323,67 +323,78 @@
  (% 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**
++(% class="small" style="color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
  )))|(% style="width:303px" %) |
  ----
--== **Add practical value to your shared data, model or software** ==
++== **Information and resources for researchers looking to share data** ==
++Below you can find some resources that can come in handy if you are looking to share data via EBRAINS, or in general.
  ----
--=== **Showcase shared data, models or software in other services** ===
++=== **Improve your research product ** ===
--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.
++(% class="wikigeneratedid" %)
++**{{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-fkdv6h"/}}**
--**Viewer for 2D images **
++==== **Add a tutorial or learning resource to your research product ** ====
--* 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="color:#e74c3c" %)- Learning resource [information](%%) ====
--**Viewer for sequential atlas-registered 2D images with annotation options**
--* 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]].
++==== **Create a workflow for .... ? ** ====
--**Use your research product in an interactive publication **
++==== (% style="color:#e74c3c" %)- Workflows [information](%%) ====
--* 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]].
++----
--**Interactive 3D atlas viewer with options for data visualization**
++=== **Integrate your data, models or software with other services** ===
--* 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]].
++EBRAINS supports further integration for a variety of data, and is continuously looking to increase the number of interoperable services.
++* 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]].
++* 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]].
++* Add your data, models or software to a// Live paper//: (% style="color:#e74c3c" %)[description] {{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-62mbgl"/}}
++* Integrate 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 integrate your data to atlases, check out the [[Atlas services>>https://ebrains.eu/services/atlases#Integratedatatoanatlas]] on ebrains.eu.
++
  ----
--==== **Add a tutorial or learning resource ** ====
++=== **The benefits of sharing data ** ===
--(% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
--(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
++(% style="color:#000000" %)Sharing your data, models or code (research products) via EBRAINS makes it discoverable amongst other research products available in the (%%)[[(% style="color:#000000" %)EBRAINS Knowledge Graph>>https://kg.ebrains.eu/]](%%). This is made possible by the highly flexible metadata framework describing neuroscience data in detail.
++(% style="color:#000000" %)EBRAINS is gradually implementing interconnected tools and analysis workflows developed in the Human Brain Project (HBP) to further enhance the output from adding your dataset to the database.
--==== **Create a workflow** ====
--(% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
--(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
++By sharing your data via EBRAINS, you gain access to the following benefits:
------
++[[image:image-20230324170841-3.png]]
--=== **The benefits of sharing data ** ===
--By sharing your data via EBRAINS, you gain access to the following benefits:
--[[image:image-20230324170841-3.png]]
++We support you to better follow the FAIR^^ ^^guiding principles 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.
++----
--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.
++=== **At a glance: "Sharing experimental data on EBRAINS" ** ===
++
++|(% style="width:439px" %)(((
++[[[[image:image-20230324171114-2.png||height="354" width="250"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
++)))|(% style="width:461px" %)(((
++
++)))|(% style="width:416px" %)[[[[image:image-20230330120354-1.png||height="352" width="250"]]>>https://drive.ebrains.eu/f/707147a883b94fae8e69/]]
++|(% style="width:439px" %)//Collection of useful information for researchers looking to share experimental data on EBRAINS.//|(% style="width:461px" %)//The EBRAINS data descriptor: a general overview //|(% style="width:416px" %)//Introduction to data organization: A [[collection of guidelines>>https://drive.ebrains.eu/smart-link/25299f04-c4e5-4028-8f5f-3b8208f9a532/]] on how to organise files and folders to ensure consistency and reproducibility in the future. //
++
  ----
--=== **Frequently asked questions ** ===
++=== **Common concerns - and answers ** ===
  (((
--====  ====
++====   ====
  (((
  >The curation process is time consuming and difficult

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