Changes for page Data Curation

Last modified by abonard on 2025/06/03 10:55
From version 147.4
edited by ingrreit
on 2023/06/05 10:17
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To version 228.1
edited by puchades
on 2025/05/07 15:03
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1 +Data Curation
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1 -== Publishing neuroscience data, models and software via EBRAINS ==
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2 2  
3 3  
20 +(% class="wikigeneratedid" id="HPublishingneurosciencedata2CmodelsandsoftwareviaEBRAINS" %)
21 +(% style="font-size:2em" %)**Publishing neuroscience data, models and software via EBRAINS**
22 +
4 4  (% class="wikigeneratedid" %)
5 5  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]].
6 6  
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8 8  {{toc depth="3" start="2"/}}
9 9  {{/box}}
10 10  
11 -
12 12  == **Information to get started** ==
13 13  
14 -(% style="text-align: center;" %)
15 -**Get started! **
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. **
16 16  
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;" %)
21 21  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.
22 22  
23 23  
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]]
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 +)))
26 26  
27 27  
28 28  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. 
... ... @@ -35,7 +35,7 @@
35 35  
36 36  (% class="box successmessage" %)
37 37  (((
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
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]]
39 39  )))
40 40  
41 41  ----
... ... @@ -52,7 +52,9 @@
52 52  
53 53  The curation of data, models and software is different. Thus, below we explain the process for sharing for each research product separately.
54 54  
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. **
55 55  
72 +
56 56  ----
57 57  
58 58  === Step by step - Data ===
... ... @@ -60,32 +60,53 @@
60 60  
61 61  [[image:image-20230326054341-1.png]]
62 62  
63 -==== ====
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 +)))
64 64  
90 +
65 65  ==== **1. Provide some general information about your dataset** ====
66 66  
67 67  
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.
69 69  
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]]. **
70 70  
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.
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.
72 72  
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.
73 73  
101 +
74 74  ==== **2. Upload data ** ====
75 75  
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: //
76 76  
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.
111 +[[~[~[image:image-20230621121014-1.png~|~|data-xwiki-image-style-alignment="center" height="150" width="106"~]~]>>https://drive.ebrains.eu/lib/f5cf4964-f095-49bd-8c34-e4ffda05a497/file/ebrains-infographic-data-organisation.pdf/]]
112 +)))
78 78  
114 +(% 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. **
79 79  
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).**
116 +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.
81 81  
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.
118 +(% 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).**
83 83  
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.
120 +**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.
85 85  
122 +**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.
86 86  
87 -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. 
88 88  
125 +EBRAINS offers secure, long-term storage at FENIX Supercomputing Centres in Europe.
126 +
89 89  If a data collection is already uploaded elsewhere, we may link to the already existing repository.
90 90  
91 91  
... ... @@ -92,235 +92,250 @@
92 92  ==== **3. Submit metadata** ====
93 93  
94 94  
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) **
133 +(% 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) **
96 96  
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
135 +**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
98 98  
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:
137 +**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:
100 100  
101 101  * 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.
102 102  * [[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.
103 103  * [[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.
104 104  
143 +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.
105 105  
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.
107 107  
146 +==== **4. Write a Data Descriptor** ====
108 108  
109 -**The openMINDS metadata framework**
110 110  
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]].
112 112  
113 -For feedback, requests, or contributions, please get in touch with the openMINDS development team via
150 +(% 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]]**.**
114 114  
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]]
152 +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. 
118 118  
154 +See our infographic about the data descriptor for inspiration or guidance.
119 119  
120 -==== **4. Write a Data Descriptor ** ====
156 +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]]".
121 121  
158 +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.
122 122  
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. 
124 124  
161 +(% class="box floatinginfobox" id="data-descriptor-infographic" %)
162 +(((
163 +(% style="text-align:center" %)
164 +//Download our infographic
165 +about the EBRAINS Data//
166 +//Descriptor//
167 +// //
168 +[[~[~[image:image-20230324171109-1.png~|~|height="150" width="106"~]~]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
169 +)))
125 125  
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]]".
171 +==== **5. Preview and publish** ====
127 127  
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.
129 129  
174 +(% 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. **
130 130  
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
176 +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.
132 132  
133 133  
134 -==== **5. Preview and publish ** ====
135 135  
136 136  
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.
138 -
139 -
140 140  ----
141 141  
142 -==== **Sharing human data ** ====
183 +=== Step by Step - Models ===
143 143  
144 -(% class="box floatinginfobox" %)
145 -(((
146 -**Human subject data that can be shared on EBRAINS consists of:**
147 147  
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)
186 +==== 1. Start early ====
151 151  
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 -)))
188 +It is not necessary to wait until you are ready to publish to register your model with EBRAINS.
154 154  
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]].
190 +By registering a model early in your project, you can take advantage of EBRAINS tools
191 +to keep track of simulations and to share them with your collaborators.
156 156  
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).
193 +==== 2. Create/choose a Collab workspace ====
158 158  
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.
195 +We use EBRAINS Collaboratory "collab" workspaces to help manage the model curation process.
160 160  
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.
197 +In particular, we use collab membership (the "Team") to control who can view or edit your model metadata prior to publication.
162 162  
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.
199 +It is up to you whether you create a new collab for each model, or reuse an existing collab
200 +(it is no problem to have multiple models associated with a single collab).
164 164  
202 +Collabs are also useful for storing simulation results, adding documentation for your model,
203 +and/or providing tutorials in Jupyter notebooks.
165 165  
166 -----
205 +==== 3. Upload code ====
167 167  
168 -=== Step by Step - Models ===
207 +We recommend storing model code and/or configuration files in an online Git repository, for example on GitHub.
208 +This repository should be public when you publish the model, but a private repository can be used for model development.
169 169  
210 +Alternatively, you can upload code to the Collab Drive or Bucket storage.
170 170  
171 -~1. Request curation using the [[Curation request form>>https://nettskjema.no/a/277393#/]]. You will be contacted by a curator with more information.
212 +==== 4. Submit metadata ====
172 172  
214 +We recommend submitting metadata using the Model Catalog app, installed in your collab.
173 173  
174 -//Additional information will be added soon.//
216 +To install it:
175 175  
176 -----
218 +1. click the "+ Create" button
219 +1. in the "Create Page" form, add a title, such as "Model Catalog", and select "Community App", then click "Create"
220 +1. scroll down until you find the "Model Catalog" app, click "Select", then "Save & View"
177 177  
178 -=== Step by Step - Code ===
222 +You will then see a table of all the models and validation tests associated with this collab.
223 +If this is your first time using the app, the table will probably be empty.
224 +To add your model, click "+", fill in the form, then click "Add model".
179 179  
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"]]
226 +As development of your model proceeds, you can easily register new versions of the code,
227 +and new parameterizations, by clicking "Add new version".
181 181  
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.
229 +If you prefer not to use the app, you can instead fill in the [[EBRAINS Curation Request Form>>https://nettskjema.no/a/386195]].,
230 +and you will be contacted by e-mail with further instructions.
187 187  
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]].
232 +==== 5. Provide a reference dataset ====
190 190  
191 -----
234 +Once you're ready to publish your model entry in the EBRAINS Knowledge Graph,
235 +we encourage you to provide a dataset containing the simulation results produced by your model,
236 +following the process under "Step by step - Data" above.
192 192  
193 -== **The curation team: meet the curators** ==
238 +These reference data will be linked to the model, and will be helpful to anyone trying to
239 +reuse your model.
194 194  
195 -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.
241 +We will soon introduce a "Reproducible" badge for all models that include a reference dataset,
242 +and whose simulation results can be reproduced by an EBRAINS curator.
196 196  
244 +==== 6. Request publication, preview and publish ====
197 197  
198 -The curators in EBRAINS are located in Oslo, Jülich, Trier and Paris. 
199 -
246 +Until you request your model entry to be published in the EBRAINS Knowledge Graph,
247 +only members of the collab will be able to view the model entry, in the Model Catalog app
248 +or using the Model Validation Python client.
200 200  
201 -**Located in Norway:**
250 +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.
202 202  
203 -|(% style="width:303px" %)(((
204 -[[image:My project2.jpg||height="209" width="167"]]
252 +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.
205 205  
206 -**Archana Golla**
207 207  
208 -(% class="small" %)Curation Scientist
209 -Neuroscience (PhD)(%%)
210 -(% class="small" style="color:#4a5568" %)**Behavioral neuroscience and microscopy**
211 -)))|(% style="width:303px" %)(((
212 -[[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
255 +Curators will then perform a number of checks:
213 213  
214 -**Camilla H. Blixhavn**
257 +1. Does the model description provide sufficient context to understand the purpose and use of the model?
258 +1. Does the code repository contain a licence file, explaining the conditions for reusing the code?
259 +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.
215 215  
216 -(% class="small" %)Curation Scientist,
217 -Phd Student
218 -Neuroscience (M. Sc.)(%%)
219 -(% class="small" style="color:#4a5568" %)**Neuroanatomy and data integration**
220 -)))|(% style="width:303px" %)(((
221 -[[image:My project (1).jpg||height="209" width="167"]]
261 +The curators will also take a snapshot of your model code.
222 222  
223 -**Ingrid Reiten**
263 +* 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"]].
264 +* 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.
224 224  
225 -(% class="small" %)Curation Scientist,
226 -Phd Student
227 -Neuroscience (M. Sc.)(%%)
228 -(% class="small" style="color:#4a5568" %)**Neuroanatomy and structural connectivity**
229 -)))|(% style="width:303px" %)(((
230 -[[image:My project1.jpg||height="209" width="167"]]
266 +Once this is done, you will be invited to review a preview of how the model entry will appear in the KG Search,
267 +and will have the opportunity to request modifications prior to approval and publication.
231 231  
232 -**Sophia Pieschnik**
269 +----
233 233  
234 -(% class="small" %)Curation Scientist
235 -Neurocognitive Psychology (M. Sc.)(%%)
236 -(% class="small" style="color:#4a5568" %)**Neuroimaging **
237 -)))
271 +=== Step by Step - Software ===
238 238  
239 -|(% style="width:303px" %)(((
240 -[[image:My project.jpg||height="209" width="167"]]
273 +We ask software developers to provide their metadata in the "CodeMeta" format. [[CodeMeta>>https://codemeta.github.io/]] is a common format for software metadata, supported by GitHub, Zenodo, FigShare, DataCite, and the US National Science Foundation.
241 241  
242 -**Heidi Kleven**
275 +1. Create a codemeta.json file for your software. There are several [[tools>>https://codemeta.github.io/tools/]] to help you do this, for example the [[CodeMeta generator>>https://codemeta.github.io/codemeta-generator]] app. Please fill in as many of the fields as possible.
276 +1. Place this file in the root folder of your code repository.
277 +1. Contact [[EBRAINS support>>https://www.ebrains.eu/contact/]] to request curation of your software, letting us know the URL of your code repository. If you need help hosting your code online, please also let us know.
278 +1. After a quality check, we integrate and publish the information contained in your codemeta.json file to the Knowledge Graph. Your software is then searchable and usable for the neuroscience community.
243 243  
244 -(% class="small" %)Curation Scientist,
245 -Phd Student
246 -Neuroscience (M. Sc.)(%%)
247 -(% class="small" style="color:#4a5568" %)**Neuroanatomy and brain atlases**
248 -)))| | |
280 +When you release a new version of your software, just update the codemeta.json file in your repository. We will check the repository on a regular basis, and if the version identifier has changed the Knowledge Graph will be updated accordingly.
249 249  
250 -
251 -\\**Located in Germany:**
282 +----
252 252  
253 -|(% style="width:303px" %)(((
254 -[[image:My project (2).jpg||height="209" width="167"]]
284 +=== Sharing human subject data ===
255 255  
256 -**Jan Gündling**
286 +(% class="box floatinginfobox" %)
287 +(((
288 +**Human subject data that can be shared on EBRAINS:**
289 +// //
290 +// - Post-mortem data//
291 +// - Aggregated data//
292 +// - Strongly pseudonymized or de-identified subject data//
293 +// with a legal basis for sharing (e.g. Informed Consent)//
294 +// //
257 257  
258 -(% class="small" %)Curation Scientist,
259 -Phd Student
260 -Sensors and Cognitive Psychology (M. Sc.)(%%)
261 -(% class="small" style="color:#4a5568" %)**Human-Computer Interaction**
262 -)))|(% style="width:303px" %)(((
263 -
296 +(% class="small" %)
297 +//If you have human data that does not qualify as any of the above,//
298 +//please [[get in touch>>https://www.ebrains.eu/contact/]] and we will clarify the available options.//
299 +)))
264 264  
265 265  
302 +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]].
266 266  
304 +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).
267 267  
306 +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.
268 268  
308 +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.
269 269  
310 +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.
270 270  
312 +----
271 271  
314 +== **The openMINDS metadata framework** ==
272 272  
316 +(% class="box floatinginfobox" %)
317 +(((
318 +[[~[~[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]]
319 +)))
273 273  
321 +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"]].
274 274  
275 -**Lyuba Zehl**
323 +For feedback, requests, or contributions, please get in touch with the openMINDS development team via
276 276  
277 -(% class="small" %)Knowledge Systems Engineer
278 -Dr. rer. nat. (Systems Neuroscience)(%%)
279 -(% class="small" style="color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
280 -)))|(% style="width:303px" %) |
325 +* [[support@openmetadatainitiative.org>>mailto:mailto:support@openmetadatainitiative.org]]
326 +* [[GitHub Issues>>https://github.com/openMetadataInitiative/openMINDS/issues]] (for metadata schemas)
327 +* [[GitHub Issues>>https://github.com/openMetadataInitiative/openMINDS_instances/issues]] (for metadata instances)
328 +* [[openMINDS Community Forum>>https://neurostars.org/t/openminds-community-forum-virtual]]
281 281  
282 282  ----
283 283  
284 -== **Information and resources for researchers looking to share data** ==
332 +== **Add practical value to your shared data, model or software** ==
285 285  
286 -Below you can find some resources that can come in handy if you are looking to share data via EBRAINS, or in general.
287 287  
288 -----
335 +=== **Showcase shared data, models or software in other services** ===
289 289  
290 -=== **Improve your research product ** ===
337 +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.
291 291  
292 -(% class="wikigeneratedid" %)
293 -**{{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-fkdv6h"/}}**
294 294  
295 -==== **Add a tutorial or learning resource to your research product ** ====
340 +|(% colspan="2" %)**Viewer for 2D images**
341 +|[[image:MIO_screenshot.PNG]]|Integrate image data with //SeriesZoom viewer//: EBRAINS viewer provides an intuitive way of navigating high-resolution 2D image series. It has browser-based classic pan and zoom capabilities. A collection can be displayed as a filmstrip (Filmstrip Mode) or as a table (Collection Mode) with adjustable number of row and columns. See [[viewer links available for this dataset>>https://search.kg.ebrains.eu/?category=Dataset&q=nr2f1#9677359c-73fa-4425-b8fa-3de794e9017a]] as an example.
342 +|(% colspan="2" %)**Viewer for sequential atlas-registered 2D images with annotation options**
343 +|[[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]].
344 +|(% colspan="2" %)**Interactive 3D atlas viewer with options for data visualization**
345 +|[[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]].
346 +|(% colspan="2" %)**Use your research product in an interactive publication**
347 +|[[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]].
296 296  
297 -==== (% style="color:#e74c3c" %)- Learning resource [information](%%) ====
349 +----
298 298  
351 +==== **Add a tutorial or learning resource ** ====
299 299  
300 -==== **Create a workflow for .... ? ** ====
353 +(% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
354 +(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
301 301  
302 -==== (% style="color:#e74c3c" %)- Workflows [information](%%) ====
303 303  
304 -----
357 +==== **Create a workflow** ====
305 305  
306 -=== **Integrate your data, models or software with other services** ===
359 +(% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
360 +(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
307 307  
308 -EBRAINS supports further integration for a variety of data, and is continuously looking to increase the number of interoperable services.
362 +----
309 309  
310 -* 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]].
311 -* 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]].
312 -* 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"/}}
313 -* 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.
364 +== **EBRAINS commits to the FAIR principles** ==
314 314  
315 -----
366 +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.
316 316  
317 -=== **The benefits of sharing data ** ===
368 +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.
318 318  
319 -(% 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.
370 +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]]. **
320 320  
321 -(% 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.
322 322  
373 +----
323 323  
375 +== **General benefits of sharing data ** ==
376 +
324 324  By sharing your data via EBRAINS, you gain access to the following benefits:
325 325  
326 326  [[image:image-20230324170841-3.png]]
... ... @@ -327,76 +327,53 @@
327 327  
328 328  
329 329  
330 -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.
383 +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.
331 331  
332 -
333 333  ----
334 334  
335 -=== **At a glance: "Sharing experimental data on EBRAINS" ** ===
387 +== **Frequently asked questions ** ==
336 336  
389 +>Is the curation process time consuming and difficult?
337 337  
338 -|(% style="width:439px" %)(((
339 -[[[[image:image-20230324171114-2.png||height="354" width="250"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
340 -)))|(% style="width:461px" %)(((
341 -
342 -)))|(% style="width:416px" %)[[[[image:image-20230330120354-1.png||height="352" width="250"]]>>https://drive.ebrains.eu/f/707147a883b94fae8e69/]]
343 -|(% 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. //
391 +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.
344 344  
345 -----
393 +>Is sharing my data also beneficial for me or only for others?
346 346  
347 -=== **Common concerns - and answers ** ===
348 -
349 -(((
350 -==== ====
351 -
352 -(((
353 ->The curation process is time consuming and difficult
354 -)))
355 -)))
356 -
357 -(% class="wikigeneratedid" id="HHowcanIshareA0models3F" %)
358 -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.
359 -
360 ->Sharing my data is not beneficial for me - only for others
361 -
362 -
363 363  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.
364 364  
365 ->My data is too insignificant to share
397 +>Can my data be too insignificant to share?
366 366  
399 +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.
367 367  
368 -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.
401 +>Can my data be easily misused if I share it?
369 369  
370 ->My data can easily be misused if I share it with the world
403 +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.
371 371  
405 +>Can I share my data before my paper is published?
372 372  
373 -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.
407 +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.
374 374  
375 ->I don't think I'm allowed to share my data
409 +>Can I lose my competitive edge if I share my data before I publish the associated paper?
376 376  
411 +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.
377 377  
378 -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.
379 379  
380 ->I can't share my data before my paper is published
414 +== Contact ==
381 381  
416 +[[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
382 382  
383 -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.
418 +----
384 384  
385 ->If I share my data before I publish the associated paper, I will lose my competitive edge
420 +== Affiliated laboratories ==
386 386  
422 +//Institute of Basic Medical Sciences,** **University of Oslo, Norway (PI: Jan G. Bjaalie, Trygve B. Leergaard)//
387 387  
388 -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 +//Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Germany (PI: Timo Dicksheid)//
389 389  
426 +//Paris-Saclay Institute of Neuroscience, CNRS, Université Paris-Saclay, France (PI: Andrew P. Davison)//
390 390  
391 391  ----
392 392  
393 -== Contact ==
430 +== References ==
394 394  
395 -[[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
396 -
397 -
398 398  {{putFootnotes/}}
399 -~)~)~)~)~)~)
400 -~)~)~)
401 -~)~)~)~)~)~)~)~)~)
402 -~)~)~)~)~)~)
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Data Curation