Changes for page data-curation-copy

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

From 151.1 to 150.1 From 168.2 to 168.1

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

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To version 151.1

edited by ingrreit
on 2023/06/05 10:37

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--
--
  == Publishing neuroscience data, models and software via EBRAINS ==
@@ -27,6 +27,7 @@
  {{toc depth="3" start="2"/}}
  {{/box}}
++
  == **Information to get started** ==
  **[[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. **
@@ -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
  )))
  ----
@@ -73,19 +73,13 @@
  [[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/]]
++====   ====
--
--)))
++(% style="width:1841.22px" %)
++|(% style="width:344px" %)(((
++[[[[image:image-20230324171114-2.png||height="219" width="155"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
++)))|(% style="width:1493px" %)//We have collected 'all you need to know to share data on EBRAINS' in an infographic. //
--
  ==== **1. Provide some general information about your dataset** ====
@@ -98,9 +98,7 @@
  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 ** ====
@@ -120,12 +120,12 @@
  If a data collection is already uploaded elsewhere, we may link to the already existing repository.
--==== **3. Submit metadata** ====
++(% style="color:#1a202c; font-family:inherit; font-size:23px" %)**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:
@@ -136,6 +136,17 @@
  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]]** . **
@@ -148,17 +148,9 @@
  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).
@@ -209,33 +209,25 @@
  === Step by Step - Software ===
--[[[[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="315" style="float:right" width="215"]]>>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** ==
@@ -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" %)(((
@@ -323,7 +323,7 @@
  (% 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" %) |
  ----
@@ -331,6 +331,17 @@
  == **Add practical value to your shared data, model or software** ==
++==== **Add a tutorial or learning resource ** ====
++
++(% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
++(% style="color:#000000" %)//More information will follow//
++
++
++==== **Create a workflow** ====
++
++(% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
++(% style="color:#000000" %)//More information will follow//
++
  ----
  === **Showcase shared data, models or software in other services** ===
@@ -355,19 +355,6 @@
  ----
--==== **Add a tutorial or learning resource ** ====
--
--(% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
--(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
--
--
--==== **Create a workflow** ====
--
--(% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
--(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
--
------
--
  === **The benefits of sharing data ** ===
  By sharing your data via EBRAINS, you gain access to the following benefits:
@@ -376,14 +376,17 @@
--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.
++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.
++
  ----
++===   ===
++
  === **Frequently asked questions ** ===
  (((
--====  ====
++====   ====
  (((
  >The curation process is time consuming and difficult

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