Changes for page Data Curation

Last modified by abonard on 2025/06/03 10:55
From version 221.1
edited by eapapp
on 2024/06/20 12:34
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To version 147.3
edited by ingrreit
on 2023/06/05 10:16
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1 -Data Curation
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1 -Collabs.WebHome
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2 -<div style="float:right;margin-left:1em;margin-bottom:1em">
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1 +== Publishing neuroscience data, models and software via EBRAINS ==
18 18  
19 19  
20 -(% class="wikigeneratedid" id="HPublishingneurosciencedata2CmodelsandsoftwareviaEBRAINS" %)
21 -(% style="font-size:2em" %)**Publishing neuroscience data, models and software via EBRAINS**
22 -
23 23  (% class="wikigeneratedid" %)
24 24  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]].
25 25  
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27 27  {{toc depth="3" start="2"/}}
28 28  {{/box}}
29 29  
11 +
30 30  == **Information to get started** ==
31 31  
32 -**[[REQUEST CURATION>>https://nettskjema.no/a/386195]] to share data, simulations, computational models, and software, - or to add a new version of an existing one. **
14 +(% style="text-align: center;" %)
15 +**Get started! **
33 33  
17 +(% style="text-align: center;" %)
18 +**[[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. **
19 +
20 +(% style="text-align: center;" %)
34 34  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.
35 35  
36 36  
37 -(% class="box" style="text-align: center; font-size: 1.2em" %)
38 -(((
39 -Search existing data, models and software in the [[EBRAINS Knowledge Graph>>https://kg.ebrains.eu/search/?facet_type[0]=Dataset]]
40 -)))
24 +(% style="text-align: center;" %)
25 +Search existing data, models and software in [[the EBRAINS Knowledge Graph Search>>https://kg.ebrains.eu/search/?facet_type[0]=Dataset]]
41 41  
42 42  
43 43  EBRAINS accepts data from all modalities and from all species, as well as models, software, web services and metadata models (collectively referred to as research products) for sharing. You'll find detailed information about how to share each research product below. 
... ... @@ -50,7 +50,7 @@
50 50  
51 51  (% class="box successmessage" %)
52 52  (((
53 -**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]]
38 +**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
54 54  )))
55 55  
56 56  ----
... ... @@ -67,9 +67,7 @@
67 67  
68 68  The curation of data, models and software is different. Thus, below we explain the process for sharing for each research product separately.
69 69  
70 -**Before you get started, make sure you[[ sign up for a free EBRAINS account>>https://www.ebrains.eu/page/sign-up]]. This is needed to complete the data sharing process. **
71 71  
72 -
73 73  ----
74 74  
75 75  === Step by step - Data ===
... ... @@ -77,52 +77,30 @@
77 77  
78 78  [[image:image-20230326054341-1.png]]
79 79  
80 -(% class="box floatinginfobox" id="share-data-infographic" %)
81 -(((
82 -(% style="text-align:center" %)
83 -//Download our infographic//
84 -//with all you need to know//
85 -//to share data on EBRAINS: //
86 -// //
87 -[[[[image:image-20230324171114-2.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
88 -)))
63 +==== ====
89 89  
90 -
91 91  ==== **1. Provide some general information about your dataset** ====
92 92  
93 93  
68 +[[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.
94 94  
95 -(% style="margin-right:10px" %)[[image:https://lh3.googleusercontent.com/zh7TvO6w04YGW9jIhfhmdT6CexdGs-AWOLfJXKRq7-tdHOu6ar1rOQx8o4rZevrjXqgPZ7-Ejv4b6X9XpgXuHpdUXi-mBTHIUnv5Vz-DktHt0sP-PZ3gE8XgZid3TV3swV1uTCBhHx11ge0pjP7RVxswGQ=s2048||height="85px;" width="91px;"]](%%)** Fill in the [[EBRAINS Curation Request Form>>https://nettskjema.no/a/386195]]. **
96 96  
97 -The form collects general 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 and follow up on incoming requests.
71 +[[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.
98 98  
99 -You will also be asked to fill in information related to ethics and regulatory compliance, so that we can evaluate whether we can ethically and legally share the data via EBRAINS (earlier, this was recorded via a [[separate form>>https://nettskjema.no/a/224765]]). See below for information about the ethical and legal aspects concerning sharing of human subject data.
100 100  
101 -
102 102  ==== **2. Upload data ** ====
103 103  
104 -(% class="box floatinginfobox" id="share-data-infographic" %)
105 -(((
106 -(% style="text-align:center" %)
107 -//Download our infographic//
108 -//with guidelines
109 -on data organization: //
110 110  
111 -(% style="text-align:center" %)
112 -[[[[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/]]
113 -)))
77 +[[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.
114 114  
115 -(% 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. **
116 116  
117 -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.
80 +[[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).**
118 118  
119 -(% 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).**
82 +//Opt. 1. //For smaller datasets with a reasonable amount of files, we recommend using the Collab-Bucket solution (drag-and-drop). A Collab Bucket must first be assigned to a dataset, which happens when a datasets is accepted for sharing.
120 120  
121 -**Opt. 1. **For smaller datasets with a reasonable amount of files, we recommend using the Collab-Bucket solution (drag-and-drop). A Collab Bucket must first be assigned to a dataset, which happens when a datasets is accepted for sharing.
84 +//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.
122 122  
123 -**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.
124 124  
125 -
126 126  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. 
127 127  
128 128  If a data collection is already uploaded elsewhere, we may link to the already existing repository.
... ... @@ -131,382 +131,303 @@
131 131  ==== **3. Submit metadata** ====
132 132  
133 133  
134 -(% style="margin-right:10px" %)[[image:https://lh5.googleusercontent.com/WS4T2LhF9znWWChn3Z550agLrrb-KTWdYVsJSv0lh4cGjKbjuN1WV68WER9xkYqi1UqN7KYZz7bImYz3_TpOuTuvma7T192QUiUZoyJVPk1fj5NSDSQh_kpIeBufAOdDtsDRpPKK_P5EDPqRCTAaOTNyCw=s2048||height="91px;" width="91px;"]](%%)**Submit metadata using the **[[EBRAINS Metadata Wizard>>https://ebrains-metadata-wizard.apps.hbp.eu/]]** (opt. 1), or directly via the Knowledge Graph (opt. 2) **
95 +[[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) **
135 135  
136 -**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
97 +//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
137 137  
138 -**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:
99 +//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:
139 139  
140 140  * Knowledge Graph Editor: This User Interface allows you to manually enter metadata into your KG space and validate metadata that are programmatically uploaded. The Editor contains a basic set of openMINDS metadata templates, but can be extended to the full openMINDS metadata model on request. Access is granted once the request is accepted.
141 141  * [[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.
142 142  * [[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.
143 143  
144 -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/f/3e226ad165054b35b456/||rel="noopener noreferrer" target="_blank"]] on EBRAINS.
145 145  
106 +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.
146 146  
147 -==== **4. Write a Data Descriptor** ====
148 148  
109 +**The openMINDS metadata framework**
149 149  
111 +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]].
150 150  
151 -(% style="margin-right:10px" %)[[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]]**.**
113 +For feedback, requests, or contributions, please get in touch with the openMINDS development team via
152 152  
153 -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. 
115 +* the support-email: [[openminds@ebrains.eu>>path:mailto:openminds@ebrains.eu]]
116 +* the [[GitHub issue tracker>>url:https://github.com/HumanBrainProject/openMINDS/issues]]
117 +* the INCF NeuroStars [[openMINDS Community Forum>>url:https://neurostars.org/t/openminds-community-forum-virtual/20156]]
154 154  
155 -See our infographic about the data descriptor for inspiration or guidance.
156 156  
157 -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]]".
120 +==== **4. Write a Data Descriptor ** ====
158 158  
159 -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.
160 160  
123 +[[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. 
161 161  
162 -(% class="box floatinginfobox" id="data-descriptor-infographic" %)
163 -(((
164 -(% style="text-align:center" %)
165 -//Download our infographic
166 -about the EBRAINS Data//
167 -//Descriptor//
168 -// //
169 -[[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
170 -)))
171 171  
172 -==== **5. Preview and publish** ====
126 +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]]".
173 173  
128 +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.
174 174  
175 -(% style="margin-right:10px" %)[[image:https://lh4.googleusercontent.com/XqT26Q4yWJK26cjtjhI4ToXoZZMxhT9LimG4Hk9mePxy0-KPKgpVIzcuiP5mOQowBgf2JjkrWUq2VbCmafWWZPJplEZALnFOlCZHLlQgzOx7fFwoBteyi_IlMLkPBS9vtOcdNIZ59HyLnQz4RsTQ0lUrSw=s2048||height="91px;" width="91px;"]](%%)**Preview and approve the release of your dataset. **
176 176  
177 -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.
131 +|(% 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
178 178  
179 179  
134 +==== **5. Preview and publish ** ====
180 180  
181 181  
182 -----
137 +[[image:https://lh4.googleusercontent.com/XqT26Q4yWJK26cjtjhI4ToXoZZMxhT9LimG4Hk9mePxy0-KPKgpVIzcuiP5mOQowBgf2JjkrWUq2VbCmafWWZPJplEZALnFOlCZHLlQgzOx7fFwoBteyi_IlMLkPBS9vtOcdNIZ59HyLnQz4RsTQ0lUrSw=s2048||height="91px;" width="91px;"]]**Preview and approve the release of your dataset. **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.
183 183  
184 -=== Step by Step - Models ===
185 185  
140 +----
186 186  
187 -==== 1. Start early ====
142 +==== **Sharing human data ** ====
188 188  
189 -It is not necessary to wait until you are ready to publish to register your model with EBRAINS.
144 +(% class="box floatinginfobox" %)
145 +(((
146 +**Human subject data that can be shared on EBRAINS consists of:**
190 190  
191 -By registering a model early in your project, you can take advantage of EBRAINS tools
192 -to keep track of simulations and to share them with your collaborators.
148 +- Post-mortem data
149 +- Aggregated data
150 +- Strongly pseudonymized or de-identified subject data with a legal basis for sharing (e.g. Informed Consent)
193 193  
194 -==== 2. Create/choose a Collab workspace ====
152 +(% 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. //
153 +)))
195 195  
196 -We use EBRAINS Collaboratory "collab" workspaces to help manage the model curation process.
155 +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]].
197 197  
198 -In particular, we use collab membership (the "Team") to control who can view or edit your model metadata prior to publication.
157 +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).
199 199  
200 -It is up to you whether you create a new collab for each model, or reuse an existing collab
201 -(it is no problem to have multiple models associated with a single collab).
159 +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.
202 202  
203 -Collabs are also useful for storing simulation results, adding documentation for your model,
204 -and/or providing tutorials in Jupyter notebooks.
161 +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.
205 205  
206 -==== 3. Upload code ====
163 +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.
207 207  
208 -We recommend storing model code and/or configuration files in an online Git repository, for example on GitHub.
209 -This repository should be public when you publish the model, but a private repository can be used for model development.
210 210  
211 -Alternatively, you can upload code to the Collab Drive or Bucket storage.
166 +----
212 212  
213 -==== 4. Submit metadata ====
168 +=== Step by Step - Models ===
214 214  
215 -We recommend submitting metadata using the Model Catalog app, installed in your collab.
216 216  
217 -To install it:
171 +~1. Request curation using the [[Curation request form>>https://nettskjema.no/a/277393#/]]. You will be contacted by a curator with more information.
218 218  
219 -1. click the "+ Create" button
220 -1. in the "Create Page" form, add a title, such as "Model Catalog", and select "Community App", then click "Create"
221 -1. scroll down until you find the "Model Catalog" app, click "Select", then "Save & View"
222 222  
223 -You will then see a table of all the models and validation tests associated with this collab.
224 -If this is your first time using the app, the table will probably be empty.
225 -To add your model, click "+", fill in the form, then click "Add model".
174 +//Additional information will be added soon.//
226 226  
227 -As development of your model proceeds, you can easily register new versions of the code,
228 -and new parameterizations, by clicking "Add new version".
176 +----
229 229  
230 -If you prefer not to use the app, you can instead fill in the [[EBRAINS Curation Request Form>>https://nettskjema.no/a/386195]].,
231 -and you will be contacted by e-mail with further instructions.
178 +=== Step by Step - Code ===
232 232  
233 -==== 5. Provide a reference dataset ====
180 +[[[[image:swc-flow-no-header.png||alt="swc-flow.png"]]>>https://www.ebrains.eu/tools/ebrains-curation-request-form||rel="noopener noreferrer" target="_blank"]]
234 234  
235 -Once you're ready to publish your model entry in the EBRAINS Knowledge Graph,
236 -we encourage you to provide a dataset containing the simulation results produced by your model,
237 -following the process under "Step by step - Data" above.
182 +1. Fill in the [[request form>>https://www.ebrains.eu/tools/ebrains-curation-request-form]].[[[[image:Thumb.png||alt="EBRAINS-Share-Software.pdf" height="377" style="float:right" width="257"]]>>attach:EBRAINS-Share-Software.pdf]]
183 +1. One of our creators will then open a ticket and contact you with futher instructions. In these instructions you will find the links to your software and software version entries in the Knowledge Graph.
184 +1. In the next step you need to enter the metadata of your software in the [[Knowledge Graph Editor>>url:https://editor.kg.ebrains.eu/]] by using the links provided in the ticket. The links will lead you to the space in the KG, which was created especially for you. You can start directly with the editing of your software. 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.
185 +1. 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.
186 +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.
238 238  
239 -These reference data will be linked to the model, and will be helpful to anyone trying to
240 -reuse your model.
188 +If you want to add a new version to an already curated software, please write to [[curation-support@humanbrainproject.eu>>path:mailto:curation-support@humanbrainproject.eu]] or open a ticket at [[https:~~/~~/support.humanbrainproject.eu/.>>url:https://support.humanbrainproject.eu/]]
189 +For more information, visit our [[guide>>url:https://wiki.ebrains.eu/bin/view/Collabs/swc-guide]].
241 241  
242 -We will soon introduce a "Reproducible" badge for all models that include a reference dataset,
243 -and whose simulation results can be reproduced by an EBRAINS curator.
191 +----
244 244  
245 -==== 6. Request publication, preview and publish ====
193 +=== Webservices and metadata models ===
246 246  
247 -Until you request your model entry to be published in the EBRAINS Knowledge Graph,
248 -only members of the collab will be able to view the model entry, in the Model Catalog app
249 -or using the Model Validation Python client.
195 +(% class="wikigeneratedid" id="HContact...." %)
196 +(% style="color:#e74c3c; font-size:16px" %){{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-np253c"/}}(% style="color:#4a5568; font-size:16px" %)
250 250  
251 -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.
198 +----
252 252  
253 -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.
200 +== **The curation team: meet the curators** ==
254 254  
202 +**Located in Norway:**
255 255  
256 -Curators will then perform a number of checks:
204 +|(% style="width:303px" %)(((
205 +[[image:My project2.jpg||height="209" width="167"]]
257 257  
258 -1. Does the model description provide sufficient context to understand the purpose and use of the model?
259 -1. Does the code repository contain a licence file, explaining the conditions for reusing the code?
260 -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.
207 +**Archana Golla**
261 261  
262 -The curators will also take a snapshot of your model code.
209 +(% class="small" %)Curation Scientist
210 +Neuroscience (PhD)(%%)
211 +(% class="small" style="color:#4a5568" %)**Behavioral neuroscience and microscopy**
212 +)))|(% style="width:303px" %)(((
213 +[[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
263 263  
264 -* 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"]].
265 -* 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.
215 +**Camilla H. Blixhavn**
266 266  
267 -Once this is done, you will be invited to review a preview of how the model entry will appear in the KG Search,
268 -and will have the opportunity to request modifications prior to approval and publication.
217 +(% class="small" %)Curation Scientist,
218 +Phd Student
219 +Neuroscience (M. Sc.)(%%)
220 +(% class="small" style="color:#4a5568" %)**Neuroanatomy and data integration**
221 +)))|(% style="width:303px" %)(((
222 +[[image:My project (1).jpg||height="209" width="167"]]
269 269  
270 -----
224 +**Ingrid Reiten**
271 271  
272 -=== Step by Step - Software ===
226 +(% class="small" %)Curation Scientist,
227 +Phd Student
228 +Neuroscience (M. Sc.)(%%)
229 +(% class="small" style="color:#4a5568" %)**Neuroanatomy and structural connectivity**
230 +)))|(% style="width:303px" %)(((
231 +[[image:My project1.jpg||height="209" width="167"]]
273 273  
233 +**Sophia Pieschnik**
274 274  
275 -(% class="box floatinginfobox" id="software-curation-infographic" %)
276 -(((
277 -(% style="text-align:center" %)
278 -//Software curation at a glance//
279 -// //
280 -[[[[image:Thumb2.png||alt="EBRAINS-Share-Software.pdf" height="287" width="197"]]>>attach:EBRAINS-Share-Software-4.pdf]]
235 +(% class="small" %)Curation Scientist
236 +Neurocognitive Psychology (M. Sc.)(%%)
237 +(% class="small" style="color:#4a5568" %)**Neuroimaging **
281 281  )))
282 282  
283 -(% 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"]]
240 +|(% style="width:303px" %)(((
241 +[[image:My project.jpg||height="209" width="167"]]
284 284  
285 -1. Fill in the [[EBRAINS Curation 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.
286 -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.
287 -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.
243 +**Heidi Kleven**
288 288  
289 -If you want to add a new version to an already curated software, please request this via the [[EBRAINS Curation Request Form>>https://www.ebrains.eu/tools/ebrains-curation-request-form]].
245 +(% class="small" %)Curation Scientist,
246 +Phd Student
247 +Neuroscience (M. Sc.)(%%)
248 +(% class="small" style="color:#4a5568" %)**Neuroanatomy and brain atlases**
249 +)))| | |
290 290  
291 -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.
251 +
252 +\\**Located in Germany:**
292 292  
254 +|(% style="width:303px" %)(((
255 +[[image:My project (2).jpg||height="209" width="167"]]
293 293  
294 -----
257 +**Jan Gündling**
295 295  
296 -=== Sharing human subject data ===
259 +(% class="small" %)Curation Scientist,
260 +Phd Student
261 +Sensors and Cognitive Psychology (M. Sc.)(%%)
262 +(% class="small" style="color:#4a5568" %)**Human-Computer Interaction**
263 +)))|(% style="width:303px" %)(((
264 +
297 297  
298 -(% class="box floatinginfobox" %)
299 -(((
300 -**Human subject data that can be shared on EBRAINS:**
301 -// //
302 -// - Post-mortem data//
303 -// - Aggregated data//
304 -// - Strongly pseudonymized or de-identified subject data//
305 -// with a legal basis for sharing (e.g. Informed Consent)//
306 -// //
307 307  
308 -(% class="small" %)
309 -//If you have human data that does not qualify as any of the above,//
310 -//please [[get in touch>>https://www.ebrains.eu/contact/]] and we will clarify the available options.//
311 -)))
312 312  
313 313  
314 -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]].
315 315  
316 -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).
317 317  
318 -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.
319 319  
320 -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.
321 321  
322 -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.
323 323  
324 -----
325 325  
326 -== **The openMINDS metadata framework** ==
327 327  
328 -(% class="box floatinginfobox" %)
329 -(((
330 -[[[[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]]
331 -)))
276 +**Lyuba Zehl**
332 332  
333 -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"]].
278 +(% class="small" %)Knowledge Systems Engineer
279 +Dr. rer. nat. (Systems Neuroscience)(%%)
280 +(% class="small" style="color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
281 +)))|(% style="width:303px" %) |
334 334  
335 -For feedback, requests, or contributions, please get in touch with the openMINDS development team via
336 -
337 -* [[support@openmetadatainitiative.org>>mailto:mailto:support@openmetadatainitiative.org]]
338 -* [[GitHub Issues>>https://github.com/openMetadataInitiative/openMINDS/issues]] (for metadata schemas)
339 -* [[GitHub Issues>>https://github.com/openMetadataInitiative/openMINDS_instances/issues]] (for metadata instances)
340 -* [[openMINDS Community Forum>>https://neurostars.org/t/openminds-community-forum-virtual]]
341 -
342 342  ----
343 343  
344 -== **Add practical value to your shared data, model or software** ==
285 +== **Information and resources for researchers looking to share data** ==
345 345  
287 +Below you can find some resources that can come in handy if you are looking to share data via EBRAINS, or in general.
346 346  
347 -=== **Showcase shared data, models or software in other services** ===
348 -
349 -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.
350 -
351 -
352 -|(% colspan="2" %)**Viewer for 2D images**
353 -|[[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]].
354 -|(% colspan="2" %)**Viewer for sequential atlas-registered 2D images with annotation options**
355 -|[[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]].
356 -|(% colspan="2" %)**Interactive 3D atlas viewer with options for data visualization**
357 -|[[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]].
358 -|(% colspan="2" %)**Use your research product in an interactive publication**
359 -|[[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]].
360 -
361 361  ----
362 362  
363 -==== **Add a tutorial or learning resource ** ====
291 +=== **Improve your research product ** ===
364 364  
365 -(% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
366 -(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
293 +(% class="wikigeneratedid" %)
294 +**{{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-fkdv6h"/}}**
367 367  
296 +==== **Add a tutorial or learning resource to your research product ** ====
368 368  
369 -==== **Create a workflow** ====
298 +==== (% style="color:#e74c3c" %)- Learning resource [information](%%) ====
370 370  
371 -(% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
372 -(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
373 373  
374 -----
301 +==== **Create a workflow for .... ? ** ====
375 375  
376 -== **EBRAINS commits to the FAIR principles** ==
303 +==== (% style="color:#e74c3c" %)- Workflows [information](%%) ====
377 377  
378 -In 2016, the 'FAIR Guiding Principles for the management and guardianship of scientific data'{{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}} were introduced to the scientific community. The objective of the authors was to provide a set of general recommendations aimed at enhancing the Findability, Accessibility, Interoperability, and Reusability of digital resources (data). They emphasize the importance of making data more open, discoverable, and usable, ultimately facilitating collaboration and knowledge sharing within the scientific community. Today, the FAIR principles are widely recognized and adopted as best practices in data management and stewardship across scientific fields.
379 -
380 -In EBRAINS, all datasets, models and software shared go through a streamlined curation process that ensures relevant annotation of the data using the [[openMINDS>>url:https://github.com/HumanBrainProject/openMINDS]] metadata framework and integration into the [[EBRAINS Knowledge Graph>>url:https://docs.kg.ebrains.eu/]] metadata management system. The research products are Findable and Accessible through the [[Knowledge Graph Search>>url:https://search.kg.ebrains.eu/?category=Dataset]] as dataset/model/software cards that display further information regarding the dataset's Interoperability and Reusability.
381 -
382 -To further specify how EBRAINS aligns with the FAIR principles, we have assessed the FAIRness of datasets shared in the EBRAINS Knowledge Graph following the [[FAIRsFAIR Data Object Assessment Metrics>>https://zenodo.org/record/6461229||style="background-color: rgb(255, 255, 255); --darkreader-inline-bgcolor: #1c1e1f;"]]: see our **[[FAIR assessment of EBRAINS datasets>>doc:.FAIR assessment of EBRAINS datasets.WebHome]]. **
383 -
384 -
385 385  ----
386 386  
387 -== **General benefits of sharing data ** ==
307 +=== **Integrate your data, models or software with other services** ===
388 388  
389 -By sharing your data via EBRAINS, you gain access to the following benefits:
309 +EBRAINS supports further integration for a variety of data, and is continuously looking to increase the number of interoperable services.
390 390  
391 -[[image:image-20230324170841-3.png]]
311 +* 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]].
312 +* 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]].
313 +* 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"/}}
314 +* 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.
392 392  
393 -
394 -
395 -We support you to better follow the [[FAIR^^ ^^guiding principles>>https://www.nature.com/articles/sdata201618]] for data management and stewardship. 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.
396 -
397 397  ----
398 398  
399 -== **Frequently asked questions ** ==
318 +=== **The benefits of sharing data ** ===
400 400  
401 ->Is the curation process time consuming and difficult?
320 +(% 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.
402 402  
403 -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.
322 +(% 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.
404 404  
405 ->Is sharing my data also beneficial for me or only for others?
406 406  
407 -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.
325 +By sharing your data via EBRAINS, you gain access to the following benefits:
408 408  
409 ->Can my data be too insignificant to share?
327 +[[image:image-20230324170841-3.png]]
410 410  
411 -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.
412 412  
413 ->Can my data be easily misused if I share it?
414 414  
415 -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.
331 +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.
416 416  
417 ->Can I share my data before my paper is published?
418 418  
419 -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.
334 +----
420 420  
421 ->Can I lose my competitive edge if I share my data before I publish the associated paper?
336 +=== **At a glance: "Sharing experimental data on EBRAINS" ** ===
422 422  
423 -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.
424 424  
339 +|(% style="width:439px" %)(((
340 +[[[[image:image-20230324171114-2.png||height="354" width="250"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
341 +)))|(% style="width:461px" %)(((
342 +
343 +)))|(% style="width:416px" %)[[[[image:image-20230330120354-1.png||height="352" width="250"]]>>https://drive.ebrains.eu/f/707147a883b94fae8e69/]]
344 +|(% 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. //
425 425  
426 426  ----
427 427  
428 -== (% style="--darkreader-inline-color:#f1ede6; color:#1a202c; font-family:inherit; font-size:29px" %)**The curation team: meet the curators**(%%) ==
348 +=== **Common concerns - and answers ** ===
429 429  
430 -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.
350 +(((
351 +==== ====
431 431  
432 -The curators in EBRAINS are located in Oslo, Jülich, Trier and Paris. 
433 -
353 +(((
354 +>The curation process is time consuming and difficult
355 +)))
356 +)))
434 434  
435 -**Located in Norway**
358 +(% class="wikigeneratedid" id="HHowcanIshareA0models3F" %)
359 +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.
436 436  
437 -|(% style="width:303px" %)(((
438 -[[image:My project2.jpg||height="209" width="167"]]
361 +>Sharing my data is not beneficial for me - only for others
439 439  
440 -**Archana Golla**
441 441  
442 -(% class="small" %)Curation Scientist
443 -Neuroscience (PhD)(%%)
444 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Behavioral neuroscience and microscopy**
445 -)))|(% style="width:303px" %)(((
446 -[[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
364 +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.
447 447  
448 -**Camilla H. Blixhavn**
366 +>My data is too insignificant to share
449 449  
450 -(% class="small" %)Curation Scientist,
451 -Phd Student
452 -Neuroscience (M. Sc.)(%%)
453 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and data integration**
454 -)))|(% style="width:303px" %)(((
455 -[[image:My project (1).jpg||height="209" width="167"]]
456 456  
457 -**Ingrid Reiten**
369 +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.
458 458  
459 -(% class="small" %)Curation Scientist,
460 -Phd Student
461 -Neuroscience (M. Sc.)(%%)
462 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and structural connectivity**
463 -)))|(% style="width:303px" %)(((
464 -[[image:My project1.jpg||height="209" width="167"]]
371 +>My data can easily be misused if I share it with the world
465 465  
466 -**Sophia Pieschnik**
467 467  
468 -(% class="small" %)Curation Scientist
469 -Neurocognitive Psychology (M. Sc.)(%%)
470 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroimaging **
471 -)))
374 +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.
472 472  
473 -|(% style="width:303px" %)(((
474 -[[image:My project.jpg||height="209" width="167"]]
376 +>I don't think I'm allowed to share my data
475 475  
476 -**Heidi Kleven**
477 477  
478 -(% class="small" %)Curation Scientist,
479 -Phd Student
480 -Neuroscience (M. Sc.)(%%)
481 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and brain atlases**
482 -)))| | |
379 +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.
483 483  
484 -
485 -\\**Located in Germany**
381 +>I can't share my data before my paper is published
486 486  
487 -|(% style="width:303px" %)(((
488 -[[image:My project (2).jpg||height="209" width="167"]]
489 489  
490 -**Jan Gündling**
384 +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.
491 491  
492 -(% class="small" %)Curation Scientist,
493 -Phd Student
494 -Sensors and Cognitive Psychology (M. Sc.)(%%)
495 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Human-Computer Interaction**
496 -)))|(% style="width:303px" %)(((
497 -[[image:Lyuba.jpg||height="209" width="167"]]
386 +>If I share my data before I publish the associated paper, I will lose my competitive edge
498 498  
499 -**Lyuba Zehl**
500 500  
501 -(% class="small" %)Knowledge Systems Engineer
502 -Dr. rer. nat. (Systems Neuroscience)(%%)
503 -(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
504 -)))|(% style="width:303px" %) |(% style="width:303px" %)
389 +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.
505 505  
506 -----
507 507  
508 -
509 -
510 510  ----
511 511  
512 512  == Contact ==
... ... @@ -513,16 +513,9 @@
513 513  
514 514  [[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
515 515  
516 -----
517 517  
518 -== Affiliated laboratories ==
519 -
520 -//Institute of Basic Medical Sciences,** **University of Oslo, Norway (PI: Jan G. Bjaalie, Trygve B. Leergaard)//
521 -
522 -//Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Germany (PI: Timo Dicksheid)//
523 -
524 -----
525 -
526 -== References ==
527 -
528 528  {{putFootnotes/}}
400 +~)~)~)~)~)~)
401 +~)~)~)
402 +~)~)~)~)~)~)~)~)~)
403 +~)~)~)~)~)~)
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Data Curation