Changes for page data-curation-copy

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

From 150.1 to 151.1 From 170.1 to 171.1

From version 151.1

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

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To version 170.1

edited by eapapp
on 2023/06/06 16:26

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--XWiki.ingrreit
++XWiki.eapapp

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++{{html clean="false"}}
++<div style="float:right;margin-left:1em;margin-bottom:1em">
++    <form title="Search in this collab" target="_blank" action="https://wiki.ebrains.eu/bin/view/Main/Search">
++        <input type="hidden" name="sort" value="score">
++        <input type="hidden" name="sortOrder" value="desc">
++        <input type="hidden" name="highlight" value="true">
++        <input type="hidden" name="facet" value="true">
++        <input type="hidden" name="r" value="1">
++        <input type="hidden" name="f_locale" value="en">
++        <input type="hidden" name="f_space_facet" value="1/Collabs.test-ir2.">
++        <input type="hidden" name="l_space_facet" value="100">
++        <input type="hidden" name="f_type" value="DOCUMENT">
++        <input type="text" name="text" placeholder="Search here..." size="25" id="searchbox" />
++        <input type="submit" value="&#x1F50E;&#xFE0E;"  id="submit"/>
++    </form>
++</div>
++{{/html}}
++
++
  == Publishing neuroscience data, models and software via EBRAINS ==
@@ -8,7 +8,6 @@
  {{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. **
@@ -30,7 +30,7 @@
  (% 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
++**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]]
  )))
  ----
@@ -55,13 +55,19 @@
  [[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** ====
@@ -74,7 +74,9 @@
  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 ** ====
@@ -94,12 +94,12 @@
  If a data collection is already uploaded elsewhere, we may link to the already existing repository.
--(% style="color:#1a202c; font-family:inherit; font-size:23px" %)**3. Submit metadata**
++==== **3. Submit metadata** ====
--[[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) **
++[[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) **
--//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. 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. 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:
@@ -110,17 +110,6 @@
  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]]** . **
@@ -133,9 +133,17 @@
  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 ** ====
@@ -144,20 +144,24 @@
  ----
--==== **Sharing human data ** ====
++==== **Sharing human subject data ** ====
  (% class="box floatinginfobox" %)
  (((
--**Human subject data that can be shared on EBRAINS consists of:**
++**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)//
++// //
--- 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. //
++(% 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 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 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).
@@ -182,25 +182,38 @@
  === Step by Step - Software ===
--[[[[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.
++(% class="box floatinginfobox" id="software-curation-infographic" %)
++(((
++(% style="text-align:center" %)
++//Software curation at a glance//
++// //
++[[[[image:Thumb2.png||alt="EBRAINS-Share-Software.pdf" height="287" width="197"]]>>attach:EBRAINS-Share-Software-4.pdf]]
++)))
--2. 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.
++(% style="margin-left:15px" %)[[[[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"]]
--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]]
++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. 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.
++1. 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.
  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.
++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 on the right.
++----
++== **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** ==
@@ -219,7 +219,7 @@
  (% class="small" %)Curation Scientist
  Neuroscience (PhD)(%%)
--(% class="small" style="color:#4a5568" %)**Behavioral neuroscience and microscopy**
++(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Behavioral neuroscience and microscopy**
  )))|(% style="width:303px" %)(((
  [[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
@@ -228,7 +228,7 @@
  (% class="small" %)Curation Scientist,
  Phd Student
  Neuroscience (M. Sc.)(%%)
--(% class="small" style="color:#4a5568" %)**Neuroanatomy and data integration**
++(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and data integration**
  )))|(% style="width:303px" %)(((
  [[image:My project (1).jpg||height="209" width="167"]]
@@ -237,7 +237,7 @@
  (% class="small" %)Curation Scientist,
  Phd Student
  Neuroscience (M. Sc.)(%%)
--(% class="small" style="color:#4a5568" %)**Neuroanatomy and structural connectivity**
++(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and structural connectivity**
  )))|(% style="width:303px" %)(((
  [[image:My project1.jpg||height="209" width="167"]]
@@ -245,7 +245,7 @@
  (% class="small" %)Curation Scientist
  Neurocognitive Psychology (M. Sc.)(%%)
--(% class="small" style="color:#4a5568" %)**Neuroimaging **
++(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroimaging **
  )))
  |(% style="width:303px" %)(((
@@ -256,7 +256,7 @@
  (% class="small" %)Curation Scientist,
  Phd Student
  Neuroscience (M. Sc.)(%%)
--(% class="small" style="color:#4a5568" %)**Neuroanatomy and brain atlases**
++(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and brain atlases**
  )))| | |
@@ -270,8 +270,8 @@
  (% class="small" %)Curation Scientist,
  Phd Student
  Sensors and Cognitive Psychology (M. Sc.)(%%)
--(% class="small" style="color:#4a5568" %)**Human-Computer Interaction**
--)))|(% style="width:303px" %)(((
++(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Human-Computer Interaction**
++)))|(% style="width:328px" %)(((
@@ -279,17 +279,12 @@
--
--
--
--
--
  **Lyuba Zehl**
  (% class="small" %)Knowledge Systems Engineer
  Dr. rer. nat. (Systems Neuroscience)(%%)
--(% class="small" style="color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
--)))|(% style="width:303px" %) |
++(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
++)))|(% style="width:321px" %) |(% style="width:324px" %)
  ----
@@ -296,17 +296,6 @@
  == **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** ===
@@ -331,6 +331,19 @@
  ----
++==== **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:
@@ -339,57 +339,50 @@
--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.
--
  ----
--===   ===
--
  === **Frequently asked questions ** ===
  (((
--====   ====
++====  ====
  (((
-->The curation process is time consuming and difficult
++>Is the curation process time consuming and difficult?
  )))
  )))
++
  (% class="wikigeneratedid" id="HHowcanIshareA0models3F" %)
--Publishing your data naturally takes some time and effort but we will support you as much as possible. If communication is on a regular basis, we are able to finish basic curation - from the initial contact to dataset release - within two weeks.
++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.
-->Sharing my data is not beneficial for me - only for others
++>Is sharing my data also beneficial for me or only for others?
  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.
-->My data is too insignificant to share
++>Can my data be too insignificant to share?
--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.
++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.
-->My data can easily be misused if I share it with the world
++>Can my data be easily misused if I share it?
--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.
++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.
-->I don't think I'm allowed to share my data
++>Can I share my data before my paper is published?
--Many institutions are still very careful about what can be shared and how, but the situation is constantly evolving. As a researcher providing data, you will be asked to fill out an ethics compliance survey which survey to ensure that data published through the EBRAINS platform has been collected according to EU regulations. We are working on solutions for sharing anonymised human data that complies with GDPR standards to protect the identity of research subjects.
++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.
-->I can't share my data before my paper is published
++>Can I lose my competitive edge if I share my data before I publish the associated paper?
--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.
++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.
-->If I share my data before I publish the associated paper, I will lose my competitive edge
--
--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.
--
--
  ----
  == Contact ==

EBRAINS-Share-Software-4.pdf

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