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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="176" width="125"]]>>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 our **[[EBRAINS Metadata 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 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
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.
... ... @@ -118,32 +118,50 @@
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="191" width="135"]]>>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 data ** ====
178 +==== ====
133 133  
180 +==== **Sharing human subject data** ====
181 +
134 134  (% class="box floatinginfobox" %)
135 135  (((
136 -**Human subject data that can be shared on EBRAINS consists of:**
184 +**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  
145 -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]].
146 146  
198 +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]].
199 +
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).
148 148  
149 149  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.
... ... @@ -158,39 +158,125 @@
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.
235 +==== 3. Upload code ====
181 181  
182 -[[[[image:Thumb.png||alt="EBRAINS-Share-Software.pdf" height="203" style="float:left" width="139"]]>>attach:EBRAINS-Share-Software.pdf]]
237 +We recommend storing model code and/or configuration files in an online Git repository, for example on GitHub.
238 +This repository should be public when you publish the model, but a private repository can be used for model development.
183 183  
240 +Alternatively, you can upload code to the Collab Drive or Bucket storage.
184 184  
185 -==== //Software curation at a glance// ====
242 +==== 4.Submit metadata ====
186 186  
244 +We recommend submitting metadata using the Model Catalog app, installed in your collab.
187 187  
246 +To install it:
188 188  
248 +1. click the "+ Create" button
249 +1. in the "Create Page" form, add a title, such as "Model Catalog", and select "Community App", then click "Create"
250 +1. scroll down until you find the "Model Catalog" app, click "Select", then "Save & View"
189 189  
252 +You will then see a table of all the models and validation tests associated with this collab.
253 +If this is your first time using the app, the table will probably be empty.
254 +To add your model, click "+", fill in the form, then click "Add model".
255 +
256 +As development of your model proceeds, you can easily register new versions of the code,
257 +and new parameterizations by clicking "Add new version".
258 +
259 +If you prefer not to use the app, you can instead fill in the [[Curation request form>>https://nettskjema.no/a/277393#/]].,
260 +and you will be contacted by e-mail with further instructions.
261 +
262 +====
263 +5. Provide a reference dataset ====
264 +
265 +Once you're ready to publish your model entry in the EBRAINS Knowledge Graph,
266 +we encourage you to provide a dataset containing the simulation results produced by your model,
267 +following the process under "Step by step - Data" above.
268 +
269 +These reference data will be linked to the model, and will be helpful to anyone trying to
270 +reuse your model.
271 +
272 +We will soon introduce a "Reproducible" badge for all models that include a reference dataset,
273 +and whose simulation results can be reproduced by an EBRAINS curator.
274 +
275 +==== 6. Request publication, preview and publish ====
276 +
277 +Until you request your model entry to be published in the EBRAINS Knowledge Graph,
278 +only members of the collab will be able to view the model entry, in the Model Catalog app
279 +or using the Model Validation Python client.
280 +
281 +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.
282 +
283 +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.
284 +
285 +
286 +Curators will then perform a number of checks:
287 +
288 +1. Does the model description provide sufficient context to understand the purpose and use of the model?
289 +1. Does the code repository contain a licence file, explaining the conditions for reusing the code?
290 +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.
291 +
292 +The curators will also take a snapshot of your model code.
293 +
294 +* For models in public Git repositories, we archive a copy of the repository in Software Heritage.
295 +* 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.
296 +
297 +Once this is done, you will be invited to review a preview of how the model entry will appear in the KG Search,
298 +and will have the opportunity to request modifications prior to approval and publication.
299 +
190 190  ----
191 191  
302 +=== Step by Step - Software ===
303 +
304 +
305 +(% class="box floatinginfobox" id="software-curation-infographic" %)
306 +(((
307 +(% style="text-align:center" %)
308 +//Software curation at a glance//
309 +// //
310 +[[[[image:Thumb2.png||alt="EBRAINS-Share-Software.pdf" height="287" width="197"]]>>attach:EBRAINS-Share-Software-4.pdf]]
311 +)))
312 +
313 +(% 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"]]
314 +
315 +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.
316 +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.
317 +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.
318 +
319 +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]].
320 +
321 +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.
322 +
323 +
324 +----
325 +
192 192  == **The openMINDS metadata framework** ==
193 193  
328 +(% class="box floatinginfobox" %)
329 +(((
330 +[[[[image:https://github.com/HumanBrainProject/openMINDS/raw/main/img/light_openMINDS-logo.png||alt="openMINDS logo" height="87" width="164"]]>>https://github.com/HumanBrainProject/openMINDS]]
331 +)))
332 +
194 194  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]].
195 195  
196 196  For feedback, requests, or contributions, please get in touch with the openMINDS development team via
... ... @@ -217,7 +217,7 @@
217 217  
218 218  (% class="small" %)Curation Scientist
219 219  Neuroscience (PhD)(%%)
220 -(% class="small" style="color:#4a5568" %)**Behavioral neuroscience and microscopy**
359 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Behavioral neuroscience and microscopy**
221 221  )))|(% style="width:303px" %)(((
222 222  [[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
223 223  
... ... @@ -226,7 +226,7 @@
226 226  (% class="small" %)Curation Scientist,
227 227  Phd Student
228 228  Neuroscience (M. Sc.)(%%)
229 -(% class="small" style="color:#4a5568" %)**Neuroanatomy and data integration**
368 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and data integration**
230 230  )))|(% style="width:303px" %)(((
231 231  [[image:My project (1).jpg||height="209" width="167"]]
232 232  
... ... @@ -235,7 +235,7 @@
235 235  (% class="small" %)Curation Scientist,
236 236  Phd Student
237 237  Neuroscience (M. Sc.)(%%)
238 -(% class="small" style="color:#4a5568" %)**Neuroanatomy and structural connectivity**
377 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and structural connectivity**
239 239  )))|(% style="width:303px" %)(((
240 240  [[image:My project1.jpg||height="209" width="167"]]
241 241  
... ... @@ -243,7 +243,7 @@
243 243  
244 244  (% class="small" %)Curation Scientist
245 245  Neurocognitive Psychology (M. Sc.)(%%)
246 -(% class="small" style="color:#4a5568" %)**Neuroimaging **
385 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroimaging **
247 247  )))
248 248  
249 249  |(% style="width:303px" %)(((
... ... @@ -254,7 +254,7 @@
254 254  (% class="small" %)Curation Scientist,
255 255  Phd Student
256 256  Neuroscience (M. Sc.)(%%)
257 -(% class="small" style="color:#4a5568" %)**Neuroanatomy and brain atlases**
396 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and brain atlases**
258 258  )))| | |
259 259  
260 260  
... ... @@ -268,8 +268,8 @@
268 268  (% class="small" %)Curation Scientist,
269 269  Phd Student
270 270  Sensors and Cognitive Psychology (M. Sc.)(%%)
271 -(% class="small" style="color:#4a5568" %)**Human-Computer Interaction**
272 -)))|(% style="width:303px" %)(((
410 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Human-Computer Interaction**
411 +)))|(% style="width:328px" %)(((
273 273  
274 274  
275 275  
... ... @@ -279,15 +279,12 @@
279 279  
280 280  
281 281  
282 -
283 -
284 -
285 285  **Lyuba Zehl**
286 286  
287 287  (% class="small" %)Knowledge Systems Engineer
288 288  Dr. rer. nat. (Systems Neuroscience)(%%)
289 -(% class="small" style="color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
290 -)))|(% style="width:303px" %) |
425 +(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
426 +)))|(% style="width:321px" %) |(% style="width:324px" %)
291 291  
292 292  ----
293 293  
... ... @@ -294,38 +294,34 @@
294 294  == **Add practical value to your shared data, model or software** ==
295 295  
296 296  
297 -==== **Add a tutorial or learning resource ** ====
298 -
299 -(% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
300 -(% style="color:#000000" %)//More information will follow//
301 -
302 -
303 -==== **Create a workflow** ====
304 -
305 -(% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
306 -(% style="color:#000000" %)//More information will follow//
307 -
308 308  ----
309 309  
310 310  === **Showcase shared data, models or software in other services** ===
311 311  
312 -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.
437 +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.
313 313  
314 -**Viewer for 2D images **
315 315  
316 -* 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]].
440 +|(% colspan="2" %)**Viewer for 2D images**
441 +|[[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]].
442 +|(% colspan="2" %)**Viewer for sequential atlas-registered 2D images with annotation options**
443 +|[[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]].
444 +|(% colspan="2" %)**Interactive 3D atlas viewer with options for data visualization**
445 +|[[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]].
446 +|(% colspan="2" %)**Use your research product in an interactive publication**
447 +|[[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]].
317 317  
318 -**Viewer for sequential atlas-registered 2D images with annotation options**
449 +----
319 319  
320 -* 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]].
451 +==== **Add a tutorial or learning resource ** ====
321 321  
322 -**Use your research product in an interactive publication **
453 +(% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
454 +(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
323 323  
324 -* 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]].
325 325  
326 -**Interactive 3D atlas viewer with options for data visualization**
457 +==== **Create a workflow** ====
327 327  
328 -* 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]].
459 +(% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
460 +(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
329 329  
330 330  ----
331 331  
... ... @@ -337,7 +337,7 @@
337 337  
338 338  
339 339  
340 -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.
472 +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.
341 341  
342 342  ----
343 343  
... ... @@ -344,47 +344,36 @@
344 344  === **Frequently asked questions ** ===
345 345  
346 346  (((
347 -==== ====
479 +==== ====
348 348  
349 349  (((
350 ->The curation process is time consuming and difficult
482 +>Is the curation process time consuming and difficult?
351 351  )))
352 352  )))
353 353  
354 -(% class="wikigeneratedid" id="HHowcanIshareA0models3F" %)
355 -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.
486 +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.
356 356  
357 ->Sharing my data is not beneficial for me - only for others
488 +>Is sharing my data also beneficial for me or only for others?
358 358  
359 -
360 360  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.
361 361  
362 ->My data is too insignificant to share
492 +>Can my data be too insignificant to share?
363 363  
494 +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.
364 364  
365 -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.
496 +>Can my data be easily misused if I share it?
366 366  
367 ->My data can easily be misused if I share it with the world
498 +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.
368 368  
500 +>Can I share my data before my paper is published?
369 369  
370 -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.
502 +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.
371 371  
372 ->I don't think I'm allowed to share my data
504 +>Can I lose my competitive edge if I share my data before I publish the associated paper?
373 373  
506 +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.
374 374  
375 -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.
376 376  
377 ->I can't share my data before my paper is published
378 -
379 -
380 -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.
381 -
382 ->If I share my data before I publish the associated paper, I will lose my competitive edge
383 -
384 -
385 -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.
386 -
387 -
388 388  ----
389 389  
390 390  == Contact ==
... ... @@ -392,8 +392,6 @@
392 392  [[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
393 393  
394 394  
516 +== References ==
517 +
395 395  {{putFootnotes/}}
396 -~)~)~)~)~)~)
397 -~)~)~)
398 -~)~)~)~)~)~)~)~)~)
399 -~)~)~)~)~)~)
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