Changes for page data-curation-copy

Last modified by eapapp on 2023/07/04 16:46
From version 157.1
edited by ingrreit
on 2023/06/05 10:48
Change comment: There is no comment for this version
To version 194.2
edited by adavison
on 2023/06/14 14:59
Change comment: There is no comment for this version

Summary

Details

Page properties
Author
... ... @@ -1,1 +1,1 @@
1 -XWiki.ingrreit
1 +XWiki.adavison
Content
... ... @@ -1,3 +1,22 @@
1 +{{html clean="false"}}
2 +<div style="float:right;margin-left:1em;margin-bottom:1em">
3 + <form title="Search in this collab" target="_blank" action="https://wiki.ebrains.eu/bin/view/Main/Search">
4 + <input type="hidden" name="sort" value="score">
5 + <input type="hidden" name="sortOrder" value="desc">
6 + <input type="hidden" name="highlight" value="true">
7 + <input type="hidden" name="facet" value="true">
8 + <input type="hidden" name="r" value="1">
9 + <input type="hidden" name="f_locale" value="en">
10 + <input type="hidden" name="f_space_facet" value="1/Collabs.test-ir2.">
11 + <input type="hidden" name="l_space_facet" value="100">
12 + <input type="hidden" name="f_type" value="DOCUMENT">
13 + <input type="text" name="text" placeholder="Search here..." size="25" id="searchbox" />
14 + <input type="submit" value="&#x1F50E;&#xFE0E;" id="submit"/>
15 + </form>
16 +</div>
17 +{{/html}}
18 +
19 +
1 1  == Publishing neuroscience data, models and software via EBRAINS ==
2 2  
3 3  
... ... @@ -8,7 +8,6 @@
8 8  {{toc depth="3" start="2"/}}
9 9  {{/box}}
10 10  
11 -
12 12  == **Information to get started** ==
13 13  
14 14  **[[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. **
... ... @@ -16,8 +16,10 @@
16 16  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.
17 17  
18 18  
19 -(% style="text-align: center;" %)
20 -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 +)))
21 21  
22 22  
23 23  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. 
... ... @@ -30,7 +30,7 @@
30 30  
31 31  (% class="box successmessage" %)
32 32  (((
33 -**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]]
34 34  )))
35 35  
36 36  ----
... ... @@ -55,34 +55,47 @@
55 55  
56 56  [[image:image-20230326054341-1.png]]
57 57  
58 -==== [[[[image:image-20230324171114-2.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]//All you need to know to share data on EBRAINS.// ====
78 +(% class="box floatinginfobox" id="share-data-infographic" %)
79 +(((
80 +(% style="text-align:center" %)
81 +//Download our infographic//
82 +//with all you need to know//
83 +//to share data on EBRAINS: //
84 +// //
85 +[[[[image:image-20230324171114-2.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
59 59  
87 +
88 +)))
60 60  
90 +
61 61  ==== **1. Provide some general information about your dataset** ====
62 62  
63 63  
64 -[[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#/]]. **
65 65  
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 [[Curation request form>>https://nettskjema.no/a/277393#/]]. **
96 +
66 66  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.
67 67  
68 68  
69 -[[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]]**.
100 +(% style="margin-right:10px" %)[[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]]**.
70 70  
71 71  This form collects the necessary information needed for us to evaluate whether we can ethically and legally share the data via EBRAINS.
72 72  
104 +See below for information about the ethical and legal aspects concerning sharing of human subject data.
73 73  
106 +
74 74  ==== **2. Upload data ** ====
75 75  
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. **
110 +(% 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. **
78 78  
79 79  We look for organized data, not organized according to our standard. This is to support the broadest degree of sharing possible. We do however require that the data is organized in a consistent and precise manner. Please see our// //[[collection of guidelines on data organization>>https://drive.ebrains.eu/smart-link/25299f04-c4e5-4028-8f5f-3b8208f9a532/]] for further guidance.
80 80  
81 -[[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).**
114 +(% 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 82  
83 -//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.
116 +**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 84  
85 -//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.
118 +**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 87  
88 88  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. 
... ... @@ -90,14 +90,14 @@
90 90  If a data collection is already uploaded elsewhere, we may link to the already existing repository.
91 91  
92 92  
93 -(% style="color:#1a202c; font-family:inherit; font-size:23px" %)**3. Submit metadata**
126 +==== **3. Submit metadata** ====
94 94  
95 95  
96 -[[image:https://lh5.googleusercontent.com/WS4T2LhF9znWWChn3Z550agLrrb-KTWdYVsJSv0lh4cGjKbjuN1WV68WER9xkYqi1UqN7KYZz7bImYz3_TpOuTuvma7T192QUiUZoyJVPk1fj5NSDSQh_kpIeBufAOdDtsDRpPKK_P5EDPqRCTAaOTNyCw=s2048||height="91px;" width="91px;"]]**Submit metadata using the **[[EBRAINS Wizard>>https://ebrains-metadata-wizard.apps.hbp.eu/]]** (opt. 1), or through direct interaction with the Knowledge Graph (opt. 2) **
129 +(% 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) **
97 97  
98 -//Opt. 1.// Manually submit the minimal required metadata via the [[EBRAINS Wizard>>https://ebrains-metadata-wizard.apps.hbp.eu/]]. The minimal required metadata covers extended bibliographic information necessary to publish your dataset on EBRAINS. The submitted information, including uploaded files, will be sent to the Curation team automatically
131 +**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
99 99  
100 -//Opt. 2.// To go beyond the minimal required metadata, you can directly interact with the Knowledge Graph (KG) in your private space. Within the private space, you can upload metadata and interact with them, moreover you can connect your metadata to existing publicly accessible entries. Access to your private space is granted upon the initiation of the curation process. You can access your private space via:
133 +**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:
101 101  
102 102  * 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.
103 103  * [[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.
... ... @@ -106,10 +106,12 @@
106 106  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  
108 108  
109 -==== **4. Write a Data Descriptor ** ====
142 +==== **4. Write a Data Descriptor** ====
110 110  
111 -[[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]]** . **
112 112  
145 +
146 +(% 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]]**.**
147 +
113 113  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. 
114 114  
115 115  See our infographic about the data descriptor for inspiration or guidance.
... ... @@ -118,30 +118,48 @@
118 118  
119 119  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.
120 120  
121 -==== [[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]//The EBRAINS Data descriptor at-a-glance// ====
122 122  
157 +(% class="box floatinginfobox" id="data-descriptor-infographic" %)
158 +(((
159 +(% style="text-align:center" %)
160 +//Download our infographic: //
161 +//The EBRAINS Data//
162 +//Descriptor at a glance//
163 +// //
164 +[[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
165 +
166 +)))
123 123  
124 -==== **5. Preview and publish ** ====
168 +==== **5. Preview and publish** ====
125 125  
126 126  
127 -[[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.
171 +(% 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. **
128 128  
173 +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.
129 129  
175 +
130 130  ----
131 131  
132 -==== **Sharing human subject data ** ====
178 +==== ====
133 133  
180 +==== **Sharing human subject data** ====
181 +
134 134  (% class="box floatinginfobox" %)
135 135  (((
136 136  **Human subject data that can be shared on EBRAINS:**
185 +// //
186 +// - Post-mortem data//
187 +// - Aggregated data//
188 +// - Strongly pseudonymized or de-identified subject data//
189 +// with a legal basis for sharing (e.g. Informed Consent)//
190 +// //
137 137  
138 -- Post-mortem data
139 -- Aggregated data
140 -- Strongly pseudonymized or de-identified subject data with a legal basis for sharing (e.g. Informed Consent)
141 -
142 -(% 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. //
192 +(% class="small" %)
193 +//If you have human data that does not qualify as any of the above,//
194 +//please [[get in touch>>https://www.ebrains.eu/contact/]] and we will clarify the available options.//
143 143  )))
144 144  
197 +
145 145  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]].
146 146  
147 147  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).
... ... @@ -158,40 +158,68 @@
158 158  === Step by Step - Models ===
159 159  
160 160  
161 -~1. Request curation using the [[Curation request form>>https://nettskjema.no/a/277393#/]]. You will be contacted by a curator with more information.
162 162  
163 163  
164 -//Additional information will be added soon.//
216 +==== 1. Start early ====
165 165  
166 -----
218 +It is not necessary to wait until you are ready to publish to register your model with EBRAINS.
167 167  
168 -=== Step by Step - Software ===
220 +By registering a model early in your project, you can take advantage of EBRAINS tools
221 +to keep track of simulations and to share them with your collaborators.
169 169  
170 -[[[[image:swc-flow-no-header.png||alt="swc-flow.png"]]>>https://www.ebrains.eu/tools/ebrains-curation-request-form||rel="noopener noreferrer" target="_blank"]]
223 +==== 2. Create/choose a Collab workspace ====
171 171  
172 -~1. Fill in the [[request form>>https://www.ebrains.eu/tools/ebrains-curation-request-form]]. You'll be contacted by a curator with further instructions. In these instructions you will find the links to your software and software version entries in the Knowledge Graph.
225 +We use EBRAINS Collaboratory "collab" workspaces to help manage the model curation process.
173 173  
174 -2. Enter the metadata of your software in your private space of the [[Knowledge Graph Editor>>url:https://editor.kg.ebrains.eu/]] by using the links provided by the curator. Please provide the metadata for your software as complete as possible. This makes it easier for users to find and use your software. If you have questions feel free to contact the curation support. After you have finished editing your entries, please let the curators know by replying to your ticket. We curate your metadata and get back to you, if necessary.
227 +In particular, we use collab membership (the "Team") to control who can view or edit your model metadata prior to publication.
175 175  
176 -3. After a quality check, we integrate and publish the information to the Knowledge Graph. Your software is then searchable and usable for the neuroscience community.
229 +It is up to you whether you create a new collab for each model, or reuse an existing collab
230 +(it is no problem to have multiple models associated with a single collab).
177 177  
178 -If you want to add a new version to an already curated software, please request this via the [[curation request form>>https://nettskjema.no/a/277393]].
232 +Collabs are also useful for storing simulation results, adding documentation for your model,
233 +and/or providing tutorials in Jupyter notebooks.
179 179  
180 -For more information, visit our [[Guide to Software Curation in the EBRAINS Knowledge Graph>>url:https://wiki.ebrains.eu/bin/view/Collabs/swc-guide]] or see our infographic below.
181 181  
182 -[[[[image:Thumb.png||alt="EBRAINS-Share-Software.pdf" height="155" style="float:left" width="106"]]>>attach:EBRAINS-Share-Software.pdf]]
183 183  
184 184  
238 +~1. Request curation using the [[Curation request form>>https://nettskjema.no/a/277393#/]]. You will be contacted by a curator with more information.
185 185  
186 -==== //Software curation at a glance// ====
187 187  
241 +//Additional information will be added soon.//
188 188  
243 +----
189 189  
245 +=== Step by Step - Software ===
190 190  
247 +
248 +(% class="box floatinginfobox" id="software-curation-infographic" %)
249 +(((
250 +(% style="text-align:center" %)
251 +//Software curation at a glance//
252 +// //
253 +[[[[image:Thumb2.png||alt="EBRAINS-Share-Software.pdf" height="287" width="197"]]>>attach:EBRAINS-Share-Software-4.pdf]]
254 +)))
255 +
256 +(% 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"]]
257 +
258 +1. Fill in the [[request form>>https://www.ebrains.eu/tools/ebrains-curation-request-form]]. You'll be contacted by a curator with further instructions. In these instructions, you will find the links to your software and software version entries in the Knowledge Graph.
259 +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.
260 +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.
261 +
262 +If you want to add a new version to an already curated software, please request this via the [[curation request form>>https://nettskjema.no/a/277393]].
263 +
264 +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.
265 +
266 +
191 191  ----
192 192  
193 193  == **The openMINDS metadata framework** ==
194 194  
271 +(% class="box floatinginfobox" %)
272 +(((
273 +[[[[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]]
274 +)))
275 +
195 195  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]].
196 196  
197 197  For feedback, requests, or contributions, please get in touch with the openMINDS development team via
... ... @@ -218,7 +218,7 @@
218 218  
219 219  (% class="small" %)Curation Scientist
220 220  Neuroscience (PhD)(%%)
221 -(% class="small" style="color:#4a5568" %)**Behavioral neuroscience and microscopy**
302 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Behavioral neuroscience and microscopy**
222 222  )))|(% style="width:303px" %)(((
223 223  [[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
224 224  
... ... @@ -227,7 +227,7 @@
227 227  (% class="small" %)Curation Scientist,
228 228  Phd Student
229 229  Neuroscience (M. Sc.)(%%)
230 -(% class="small" style="color:#4a5568" %)**Neuroanatomy and data integration**
311 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and data integration**
231 231  )))|(% style="width:303px" %)(((
232 232  [[image:My project (1).jpg||height="209" width="167"]]
233 233  
... ... @@ -236,7 +236,7 @@
236 236  (% class="small" %)Curation Scientist,
237 237  Phd Student
238 238  Neuroscience (M. Sc.)(%%)
239 -(% class="small" style="color:#4a5568" %)**Neuroanatomy and structural connectivity**
320 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and structural connectivity**
240 240  )))|(% style="width:303px" %)(((
241 241  [[image:My project1.jpg||height="209" width="167"]]
242 242  
... ... @@ -244,7 +244,7 @@
244 244  
245 245  (% class="small" %)Curation Scientist
246 246  Neurocognitive Psychology (M. Sc.)(%%)
247 -(% class="small" style="color:#4a5568" %)**Neuroimaging **
328 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroimaging **
248 248  )))
249 249  
250 250  |(% style="width:303px" %)(((
... ... @@ -255,7 +255,7 @@
255 255  (% class="small" %)Curation Scientist,
256 256  Phd Student
257 257  Neuroscience (M. Sc.)(%%)
258 -(% class="small" style="color:#4a5568" %)**Neuroanatomy and brain atlases**
339 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and brain atlases**
259 259  )))| | |
260 260  
261 261  
... ... @@ -269,8 +269,8 @@
269 269  (% class="small" %)Curation Scientist,
270 270  Phd Student
271 271  Sensors and Cognitive Psychology (M. Sc.)(%%)
272 -(% class="small" style="color:#4a5568" %)**Human-Computer Interaction**
273 -)))|(% style="width:303px" %)(((
353 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Human-Computer Interaction**
354 +)))|(% style="width:328px" %)(((
274 274  
275 275  
276 276  
... ... @@ -280,15 +280,12 @@
280 280  
281 281  
282 282  
283 -
284 -
285 -
286 286  **Lyuba Zehl**
287 287  
288 288  (% class="small" %)Knowledge Systems Engineer
289 289  Dr. rer. nat. (Systems Neuroscience)(%%)
290 -(% class="small" style="color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
291 -)))|(% style="width:303px" %) |
368 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
369 +)))|(% style="width:321px" %) |(% style="width:324px" %)
292 292  
293 293  ----
294 294  
... ... @@ -295,38 +295,34 @@
295 295  == **Add practical value to your shared data, model or software** ==
296 296  
297 297  
298 -==== **Add a tutorial or learning resource ** ====
299 -
300 -(% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
301 -(% style="color:#000000" %)//More information will follow//
302 -
303 -
304 -==== **Create a workflow** ====
305 -
306 -(% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
307 -(% style="color:#000000" %)//More information will follow//
308 -
309 309  ----
310 310  
311 311  === **Showcase shared data, models or software in other services** ===
312 312  
313 -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.
380 +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.
314 314  
315 -**Viewer for 2D images **
316 316  
317 -* 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]].
383 +|(% colspan="2" %)**Viewer for 2D images**
384 +|[[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]].
385 +|(% colspan="2" %)**Viewer for sequential atlas-registered 2D images with annotation options**
386 +|[[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]].
387 +|(% colspan="2" %)**Interactive 3D atlas viewer with options for data visualization**
388 +|[[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]].
389 +|(% colspan="2" %)**Use your research product in an interactive publication**
390 +|[[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]].
318 318  
319 -**Viewer for sequential atlas-registered 2D images with annotation options**
392 +----
320 320  
321 -* 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]].
394 +==== **Add a tutorial or learning resource ** ====
322 322  
323 -**Use your research product in an interactive publication **
396 +(% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
397 +(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
324 324  
325 -* 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]].
326 326  
327 -**Interactive 3D atlas viewer with options for data visualization**
400 +==== **Create a workflow** ====
328 328  
329 -* 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]].
402 +(% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
403 +(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
330 330  
331 331  ----
332 332  
... ... @@ -338,7 +338,7 @@
338 338  
339 339  
340 340  
341 -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.
415 +We support you to better follow the [[FAIR^^ ^^guiding principles>>https://www.nature.com/articles/sdata201618]] for data management and stewardship{{footnote}}Wilkinson, M., Dumontier, M., Aalbersberg, I. et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data 3, 160018 (2016). https://doi.org/10.1038/sdata.2016.18 {{/footnote}}.  Publishing data, models or code via EBRAINS will provide you with a citeable [[DataCite DOI>>https://www.doi.org/the-identifier/resources/handbook/]] for your research product.
342 342  
343 343  ----
344 344  
... ... @@ -345,47 +345,36 @@
345 345  === **Frequently asked questions ** ===
346 346  
347 347  (((
348 -==== ====
422 +==== ====
349 349  
350 350  (((
351 ->The curation process is time consuming and difficult
425 +>Is the curation process time consuming and difficult?
352 352  )))
353 353  )))
354 354  
355 -(% class="wikigeneratedid" id="HHowcanIshareA0models3F" %)
356 -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.
429 +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.
357 357  
358 ->Sharing my data is not beneficial for me - only for others
431 +>Is sharing my data also beneficial for me or only for others?
359 359  
360 -
361 361  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.
362 362  
363 ->My data is too insignificant to share
435 +>Can my data be too insignificant to share?
364 364  
437 +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.
365 365  
366 -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.
439 +>Can my data be easily misused if I share it?
367 367  
368 ->My data can easily be misused if I share it with the world
441 +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.
369 369  
443 +>Can I share my data before my paper is published?
370 370  
371 -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.
445 +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.
372 372  
373 ->I don't think I'm allowed to share my data
447 +>Can I lose my competitive edge if I share my data before I publish the associated paper?
374 374  
449 +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.
375 375  
376 -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.
377 377  
378 ->I can't share my data before my paper is published
379 -
380 -
381 -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.
382 -
383 ->If I share my data before I publish the associated paper, I will lose my competitive edge
384 -
385 -
386 -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.
387 -
388 -
389 389  ----
390 390  
391 391  == Contact ==
... ... @@ -393,8 +393,6 @@
393 393  [[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
394 394  
395 395  
459 +== References ==
460 +
396 396  {{putFootnotes/}}
397 -~)~)~)~)~)~)
398 -~)~)~)
399 -~)~)~)~)~)~)~)~)~)
400 -~)~)~)~)~)~)
3Datlas_screenshot.PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.eapapp
Size
... ... @@ -1,0 +1,1 @@
1 +410.7 KB
Content
EBRAINS-Share-Software-4.pdf
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.jan
Size
... ... @@ -1,0 +1,1 @@
1 +1.2 MB
Content
LZ_screenshot.PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.eapapp
Size
... ... @@ -1,0 +1,1 @@
1 +1.8 MB
Content
LivePaper_screenshot.PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.eapapp
Size
... ... @@ -1,0 +1,1 @@
1 +120.9 KB
Content
MIO_screenshot.PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.eapapp
Size
... ... @@ -1,0 +1,1 @@
1 +607.0 KB
Content
Screenshot 2023-06-06 112208.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.jan
Size
... ... @@ -1,0 +1,1 @@
1 +138.1 KB
Content
Screenshot 2023-06-06 1122082.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.jan
Size
... ... @@ -1,0 +1,1 @@
1 +123.6 KB
Content
Thumb2.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.jan
Size
... ... @@ -1,0 +1,1 @@
1 +165.5 KB
Content