Changes for page data-curation-copy

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18 -
19 -
20 20  == Publishing neuroscience data, models and software via EBRAINS ==
21 21  
22 22  
... ... @@ -27,17 +27,21 @@
27 27  {{toc depth="3" start="2"/}}
28 28  {{/box}}
29 29  
11 +
30 30  == **Information to get started** ==
31 31  
14 +(% style="text-align: center;" %)
15 +**Get started! **
16 +
17 +(% style="text-align: center;" %)
32 32  **[[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. **
33 33  
20 +(% style="text-align: center;" %)
34 34  Have you already published your data somewhere else? You can increase the exposure and impact of your shared dataset by also listing it on EBRAINS.
35 35  
36 36  
37 -(% class="box" style="text-align: center; font-size: 1.2em" %)
38 -(((
39 -Search existing data, models and software in the [[EBRAINS Knowledge Graph>>https://kg.ebrains.eu/search/?facet_type[0]=Dataset]]
40 -)))
24 +(% style="text-align: center;" %)
25 +Search existing data, models and software in [[the EBRAINS Knowledge Graph Search>>https://kg.ebrains.eu/search/?facet_type[0]=Dataset]]
41 41  
42 42  
43 43  EBRAINS accepts data from all modalities and from all species, as well as models, software, web services and metadata models (collectively referred to as research products) for sharing. You'll find detailed information about how to share each research product below. 
... ... @@ -50,7 +50,7 @@
50 50  
51 51  (% class="box successmessage" %)
52 52  (((
53 -**Particular needs? Contact us! **The workflows for sharing can be modified for researchers or research groups aiming to frequently publish larger numbers of their research products through EBRAINS. Please contact the curation service team in such cases. Reach us at [[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
38 +**Particular needs? Contact us! **The workflows for sharing can be modified for researchers or research groups aiming to frequently publish larger numbers of their research products through EBRAINS. Please contact the curation service team in such cases
54 54  )))
55 55  
56 56  ----
... ... @@ -70,188 +70,122 @@
70 70  
71 71  ----
72 72  
73 -=== Step by step - Data ===
58 +=== Step by step - Experimental data ===
74 74  
75 75  
76 76  [[image:image-20230326054341-1.png]]
77 77  
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/]]
63 +==== ====
86 86  
87 -
88 -)))
89 -
90 -
91 91  ==== **1. Provide some general information about your dataset** ====
92 92  
93 -(% 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#/]]. **
67 +The [[Curation request form>>https://nettskjema.no/a/277393#/]] collects preliminary information about your data, allowing us to assess whether the dataset fits within the scope of EBRAINS. The submission generates a curation ID allowing us to track the case.
94 94  
95 -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 +The [[Ethics and Regulatory compliance form>>https://nettskjema.no/a/224765]] collects the necessary information needed for us to evaluate whether we can safely and legally share the data on the EBRAINS platforms.
96 96  
97 97  
98 -(% 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]]**.
99 -
100 -This form collects the necessary information needed for us to evaluate whether we can ethically and legally share the data via EBRAINS.
101 -
102 -See below for information about the ethical and legal aspects concerning sharing of human subject data.
103 -
104 -
105 105  ==== **2. Upload data ** ====
106 106  
74 +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. The data must be consistently structured prior to upload. 
107 107  
108 -(% 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. **
76 +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.
109 109  
110 -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.
78 +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.
111 111  
112 -(% 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).**
113 113  
114 -//**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.
115 -
116 -//**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.
117 -
118 -
119 -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. 
120 -
121 121  If a data collection is already uploaded elsewhere, we may link to the already existing repository.
122 122  
123 123  
124 124  ==== **3. Submit metadata** ====
125 125  
86 +Easily submit openMINDS-compatible metadata via our [[metadata wizard>>https://ebrains-metadata-wizard.apps.hbp.eu/]]. This form covers all the required metadata for sharing data via EBRAINS. When you're ready to 'Submit', the metadata and all uploaded files will be sent to the Curation team.
126 126  
127 -(% 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 through direct interaction with the Knowledge Graph (opt. 2) **
88 +For power-users interested in exploring the full span of the openMINDS framework, please check out the [[openMINDS GitHub>>https://github.com/HumanBrainProject/openMINDS]] to learn more about how to programmatically gather your metadata. A stable version of the openMINDS package can be found on [[PyPi>>https://pypi.org/project/openMINDS/]]. We accept openMINDS metadata as JSON-LD (share these with us via curation-support@ebrains.eu). Additional documentation of openMINDS metadata submodules and schemas can be found on [[the openMINDS GitHub Wiki>>https://humanbrainproject.github.io/openMINDS/]]. We have prepared [[a list of the metadata properties that are required>>https://drive.ebrains.eu/lib/47995dbc-f576-4008-a76c-eefbfd818529/file/ebrains-minimum-required-metadata.xlsx]] for publishing data on EBRAINS.
128 128  
129 -//**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
130 130  
131 -//**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:
132 -
133 -* 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.
134 -* [[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.
135 -* [[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.
136 -
137 -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.
138 -
139 -
140 140  ==== **4. Write a Data Descriptor ** ====
141 141  
142 -(% 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]]** . **
143 -
144 144  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. 
145 145  
146 -See our infographic about the data descriptor for inspiration or guidance.
95 +[[The template >>https://drive.ebrains.eu/f/a2e07c95b1a54090bbbc/?dl=1]]safely guides you through the process of making one. Check out previous examples in the KG Search, e.g. the Data Descriptor for a dataset containing histology images of the rat brain stained for an anterograde tracer (see [[an example>>https://doi.org/10.25493/2MX9-3XF]]).
147 147  
148 -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]]".
149 149  
150 150  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.
151 151  
152 -(% class="box floatinginfobox" id="data-descriptor-infographic" %)
153 -(((
154 -(% style="text-align:center" %)
155 -//Download our infographic: //
156 -//The EBRAINS Data//
157 -//Descriptor at a glance//
158 -// //
159 -[[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
160 -
161 -)))
162 162  
163 163  ==== **5. Preview and publish ** ====
164 164  
103 +A Curator will assemble a dataset in the EBRAINS Knowledge Graph that combines the data, metadata and data descriptor. Once ready, 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.
165 165  
166 -(% 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. **
167 -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.
168 168  
169 -
170 170  ----
171 171  
172 -==== **Sharing human subject data ** ====
108 +==== **Sharing human data ** ====
173 173  
174 174  (% class="box floatinginfobox" %)
175 175  (((
176 -**Human subject data that can be shared on EBRAINS:**
177 -// //
178 -// - Post-mortem data//
179 -// - Aggregated data//
180 -// - Strongly pseudonymized or de-identified subject data//
181 -// with a legal basis for sharing (e.g. Informed Consent)//
182 -// //
112 +For **Human subject data**, the data must be //either//
183 183  
184 -(% class="small" %)
185 -//If you have human data that does not qualify as any of the above,//
186 -//please [[get in touch>>https://www.ebrains.eu/contact/]] and we will clarify the available options.//
114 +- Post-mortem data
115 +- Aggregated data
116 +- Pseudonymized subject data with a legal basis for sharing (e.g. Informed Consent)
117 +
118 +(% class="small" %)//If you have human data that do not classify as any of the above, please get in touch and we will clarify the available options. //
187 187  )))
188 188  
189 -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]].
121 +We must ensure data shared on EBRAINS 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]].
190 190  
191 -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).
123 +Post-mortem and aggregated human data can be shared openly. Pseudonymized data is shared via the Human Data Gateway (HDG) due to GDPR regulations. The HDG adds an authentication layer to the data.
192 192  
193 -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.
125 +**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.
126 +\\**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.
127 +\\The Human Data Gateway (HDG) was introduced in February 2021 and developed across multiple teams in the HBP. The initiative to create the service and the initial design originated from EBRAINS Curation in close collaboration with the Data compliance team and the HBP Data Governance Working Group. HDG is a response to the needs of multiple data providers who are bringing data of human origin to EBRAINS. HDG covers the sharing of a limited range of data of human origin, i.e., data without direct identifiers and with very few indirect identifiers (strongly pseudonymized, de-identified). It 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.
194 194  
195 -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.
196 196  
197 -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.
198 -
199 -
200 200  ----
201 201  
202 202  === Step by Step - Models ===
203 203  
134 +(% style="color:#e74c3c" %){{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-1rb0hn"/}}
204 204  
205 -~1. Request curation using the [[Curation request form>>https://nettskjema.no/a/277393#/]]. You will be contacted by a curator with more information.
136 +[place-holder-process-diagram]
206 206  
138 +==== **1. model step 1 ** ====
207 207  
208 -//Additional information will be added soon.//
140 +Text
209 209  
210 -----
211 211  
212 -=== Step by Step - Software ===
143 +==== **2. model step 2** ====
213 213  
145 +Text
214 214  
215 -(% class="box floatinginfobox" id="software-curation-infographic" %)
216 -(((
217 -(% style="text-align:center" %)
218 -//Software curation at a glance//
219 -// //
220 -[[[[image:Thumb2.png||alt="EBRAINS-Share-Software.pdf" height="287" width="197"]]>>attach:EBRAINS-Share-Software-4.pdf]]
221 -)))
222 222  
223 -(% 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"]]
148 +----
224 224  
225 -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.
226 -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.
227 -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.
150 +=== Step by Step - Code ===
228 228  
229 -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]].
152 +[[[[image:swc-flow-no-header.png||alt="swc-flow.png"]]>>https://www.ebrains.eu/tools/ebrains-curation-request-form||rel="noopener noreferrer" target="_blank"]]
230 230  
231 -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.
154 +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]]
155 +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.
156 +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.
157 +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.
158 +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.
232 232  
160 +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/]]
161 +For more information, visit our [[guide>>url:https://wiki.ebrains.eu/bin/view/Collabs/swc-guide]].
233 233  
234 234  ----
235 235  
236 -== **The openMINDS metadata framework** ==
165 +=== Webservices and metadata models ===
237 237  
238 -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]].
167 +(% class="wikigeneratedid" id="HContact...." %)
168 +(% style="color:#e74c3c; font-size:16px" %){{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-np253c"/}}(% style="color:#4a5568; font-size:16px" %)
239 239  
240 -For feedback, requests, or contributions, please get in touch with the openMINDS development team via
241 -
242 -* the support-email: [[openminds@ebrains.eu>>path:mailto:openminds@ebrains.eu]]
243 -* the [[GitHub issue tracker>>url:https://github.com/HumanBrainProject/openMINDS/issues]]
244 -* the INCF NeuroStars [[openMINDS Community Forum>>url:https://neurostars.org/t/openminds-community-forum-virtual/20156]]
245 -
246 246  ----
247 247  
248 248  == **The curation team: meet the curators** ==
249 249  
250 -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.
251 -
252 -The curators in EBRAINS are located in Oslo, Jülich, Trier and Paris. 
253 -
254 -
255 255  **Located in Norway:**
256 256  
257 257  |(% style="width:303px" %)(((
... ... @@ -261,7 +261,7 @@
261 261  
262 262  (% class="small" %)Curation Scientist
263 263  Neuroscience (PhD)(%%)
264 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Behavioral neuroscience and microscopy**
183 +(% class="small" style="color:#4a5568" %)**Behavioral neuroscience and microscopy**
265 265  )))|(% style="width:303px" %)(((
266 266  [[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
267 267  
... ... @@ -270,7 +270,7 @@
270 270  (% class="small" %)Curation Scientist,
271 271  Phd Student
272 272  Neuroscience (M. Sc.)(%%)
273 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and data integration**
192 +(% class="small" style="color:#4a5568" %)**Neuroanatomy and data integration**
274 274  )))|(% style="width:303px" %)(((
275 275  [[image:My project (1).jpg||height="209" width="167"]]
276 276  
... ... @@ -279,7 +279,7 @@
279 279  (% class="small" %)Curation Scientist,
280 280  Phd Student
281 281  Neuroscience (M. Sc.)(%%)
282 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and structural connectivity**
201 +(% class="small" style="color:#4a5568" %)**Neuroanatomy and structural connectivity**
283 283  )))|(% style="width:303px" %)(((
284 284  [[image:My project1.jpg||height="209" width="167"]]
285 285  
... ... @@ -287,7 +287,7 @@
287 287  
288 288  (% class="small" %)Curation Scientist
289 289  Neurocognitive Psychology (M. Sc.)(%%)
290 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroimaging **
209 +(% class="small" style="color:#4a5568" %)**Neuroimaging **
291 291  )))
292 292  
293 293  |(% style="width:303px" %)(((
... ... @@ -298,7 +298,7 @@
298 298  (% class="small" %)Curation Scientist,
299 299  Phd Student
300 300  Neuroscience (M. Sc.)(%%)
301 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and brain atlases**
220 +(% class="small" style="color:#4a5568" %)**Neuroanatomy and brain atlases**
302 302  )))| | |
303 303  
304 304  
... ... @@ -312,8 +312,8 @@
312 312  (% class="small" %)Curation Scientist,
313 313  Phd Student
314 314  Sensors and Cognitive Psychology (M. Sc.)(%%)
315 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Human-Computer Interaction**
316 -)))|(% style="width:328px" %)(((
234 +(% class="small" style="color:#4a5568" %)**Human-Computer Interaction**
235 +)))|(% style="width:303px" %)(((
317 317  
318 318  
319 319  
... ... @@ -321,107 +321,127 @@
321 321  
322 322  
323 323  
243 +
244 +
245 +
246 +
247 +
324 324  **Lyuba Zehl**
325 325  
326 326  (% class="small" %)Knowledge Systems Engineer
327 327  Dr. rer. nat. (Systems Neuroscience)(%%)
328 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
329 -)))|(% style="width:321px" %) |(% style="width:324px" %)
252 +(% class="small" style="color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
253 +)))|(% style="width:303px" %) |
330 330  
331 331  ----
332 332  
333 -== **Add practical value to your shared data, model or software** ==
257 +== **Information and resources for researchers looking to share data** ==
334 334  
259 +Below you can find some resources that can come in handy if you are looking to share data via EBRAINS, or in general.
335 335  
336 336  ----
337 337  
338 -=== **Showcase shared data, models or software in other services** ===
263 +=== **Improve your research product ** ===
339 339  
340 -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.
265 +(% class="wikigeneratedid" %)
266 +**{{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-fkdv6h"/}}**
341 341  
342 -**Viewer for 2D images **
268 +==== **Add a tutorial or learning resource to your research product ** ====
343 343  
344 -* 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]].
270 +==== (% style="color:#e74c3c" %)- Learning resource [information](%%) ====
345 345  
346 -**Viewer for sequential atlas-registered 2D images with annotation options**
347 347  
348 -* 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]].
273 +==== **Create a workflow for .... ? ** ====
349 349  
350 -**Use your research product in an interactive publication **
275 +==== (% style="color:#e74c3c" %)- Workflows [information](%%) ====
351 351  
352 -* 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]].
277 +----
353 353  
354 -**Interactive 3D atlas viewer with options for data visualization**
279 +=== **Integrate your data, models or software with other services** ===
355 355  
356 -* 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]].
281 +EBRAINS supports further integration for a variety of data, and is continuously looking to increase the number of interoperable services.
357 357  
283 +* 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]].
284 +* 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]].
285 +* 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"/}}
286 +* 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.
287 +
358 358  ----
359 359  
360 -==== **Add a tutorial or learning resource ** ====
290 +=== **The benefits of sharing data ** ===
361 361  
362 -(% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
363 -(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
292 +(% 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.
364 364  
294 +(% 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.
365 365  
366 -==== **Create a workflow** ====
367 367  
368 -(% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
369 -(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
297 +By sharing your data via EBRAINS, you gain access to the following benefits:
370 370  
371 -----
299 +[[image:image-20230324170841-3.png]]
372 372  
373 -=== **The benefits of sharing data ** ===
374 374  
375 -By sharing your data via EBRAINS, you gain access to the following benefits:
376 376  
377 -[[image:image-20230324170841-3.png]]
303 +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.
378 378  
379 379  
306 +----
380 380  
381 -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.
308 +=== **At a glance: "Sharing experimental data on EBRAINS" ** ===
382 382  
310 +
311 +|(% style="width:439px" %)(((
312 +[[[[image:image-20230324171114-2.png||height="354" width="250"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
313 +)))|(% style="width:461px" %)(((
314 +[[[[image:image-20230324171109-1.png||height="352" width="250"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
315 +)))|(% style="width:416px" %)[[[[image:image-20230330120354-1.png||height="352" width="250"]]>>https://drive.ebrains.eu/f/707147a883b94fae8e69/]]
316 +|(% 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. //
317 +
383 383  ----
384 384  
385 -=== **Frequently asked questions ** ===
320 +=== **Common concerns - and answers ** ===
386 386  
387 387  (((
388 -==== ====
323 +==== ====
389 389  
390 390  (((
391 ->Is the curation process time consuming and difficult?
326 +>The curation process is time consuming and difficult
392 392  )))
393 393  )))
394 394  
395 -
396 396  (% class="wikigeneratedid" id="HHowcanIshareA0models3F" %)
397 -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.
331 +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.
398 398  
399 ->Is sharing my data also beneficial for me or only for others?
333 +>Sharing my data is not beneficial for me - only for others
400 400  
401 401  
402 402  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.
403 403  
404 ->Can my data be too insignificant to share?
338 +>My data is too insignificant to share
405 405  
406 406  
407 -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.
341 +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.
408 408  
409 ->Can my data be easily misused if I share it?
343 +>My data can easily be misused if I share it with the world
410 410  
411 411  
412 -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.
346 +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.
413 413  
414 ->Can I share my data before my paper is published?
348 +>I don't think I'm allowed to share my data
415 415  
416 416  
417 -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.
351 +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.
418 418  
419 ->Can I lose my competitive edge if I share my data before I publish the associated paper?
353 +>I can't share my data before my paper is published
420 420  
421 421  
422 -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.
356 +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.
423 423  
358 +>If I share my data before I publish the associated paper, I will lose my competitive edge
424 424  
360 +
361 +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.
362 +
363 +
425 425  ----
426 426  
427 427  == Contact ==
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