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ingrreit 201.1 20 (% class="wikigeneratedid" id="HPublishingneurosciencedata2CmodelsandsoftwareviaEBRAINS" %)
21 (% style="font-size:2em" %)**Publishing neuroscience data, models and software via EBRAINS**
ingrreit 10.1 22
ingrreit 146.1 23 (% class="wikigeneratedid" %)
ingrreit 146.2 24 The aim of this collab is to provide you with detailed information about publishing data, simulations, computational models, and software via EBRAINS. If you want a quick overview of the sharing process, see [[https:~~/~~/ebrains.eu/service/share-data>>https://ebrains.eu/service/share-data]].
ingrreit 146.1 25
ingrreit 10.1 26 {{box title="**Contents**"}}
27 {{toc depth="3" start="2"/}}
28 {{/box}}
29
ingrreit 146.2 30 == **Information to get started** ==
ingrreit 10.1 31
ingrreit 147.2 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
ingrreit 146.2 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.
ingrreit 10.1 35
36
eapapp 171.1 37 (% class="box" style="text-align: center; font-size: 1.2em" %)
38 (((
eapapp 172.1 39 Search existing data, models and software in the [[EBRAINS Knowledge Graph>>https://kg.ebrains.eu/search/?facet_type[0]=Dataset]]
eapapp 171.1 40 )))
ingrreit 146.2 41
42
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. 
44
45
46 (% class="box infomessage" %)
47 (((
48 We strongly recommend to **start preparing for data sharing as early as possible**. With a structured data repository and adequate notes on how the data was acquired, you greatly minimize the effort required to publish your data. The time it takes to share data on EBRAINS heavily depends on on the engagement from the researcher and how well the data and metadata is prepared before-hand. Contact us for personalised guidance on how to prepare for sharing.
49 )))
50
51 (% class="box successmessage" %)
52 (((
ingrreit 159.1 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]]
ingrreit 146.2 54 )))
55
ingrreit 10.1 56 ----
57
ingrreit 30.1 58 == **The EBRAINS curation process** ==
ingrreit 10.1 59
ingrreit 29.1 60 In EBRAINS, multimodal and heterogenous neuroscience data, models and software are categorised and described in a standardised manner so that they can be effectively searched, compared, and analysed. This effort is referred to as curation. 
ingrreit 10.1 61
ingrreit 30.1 62 >The EBRAINS curation process involves organising and annotating neuroscientific data to make the data discoverable and reusable.
ingrreit 10.1 63
ingrreit 30.1 64 Behind this process is the EBRAINS Curation team. Our mandate is to support you in sharing your data in line with the [[**FAIR principles**>>https://www.go-fair.org/fair-principles/]], whether you choose to describe only the key aspects of your data, or can invest in adding more detailed metadata.
ingrreit 10.1 65
ingrreit 147.2 66 Curated data, models and software are made available in [[the EBRAINS Knowledge Graph>>https://kg.ebrains.eu/]]. This makes the data and metadata discoverable in the [[Knowledge Graph Search>>url:https://search.kg.ebrains.eu/]] and the [[Knowledge Graph API>>url:https://docs.kg.ebrains.eu/8387ccd27a186dea3dd0b949dc528842/api_endpoints.html]]. The data, models and software are integrated in the EBRAINS Knowledge Graph by interoperable metadata schemas defined in [[openMINDS>>url:https://github.com/HumanBrainProject/openMINDS/wiki]].Data and models are linked to and discoverable via the species-specific [[EBRAINS siibra atlas viewer>>url:https://ebrains.eu/services/atlases/brain-atlases]] by using interoperable metadata schemas as defined in [[SANDS>>url:https://github.com/HumanBrainProject/SANDS/wiki]].
ingrreit 34.1 67
ingrreit 147.2 68 The curation of data, models and software is different. Thus, below we explain the process for sharing for each research product separately.
ingrreit 47.3 69
ingrreit 10.1 70
ingrreit 34.1 71 ----
72
ingrreit 147.3 73 === Step by step - Data ===
ingrreit 10.1 74
75
ingrreit 23.2 76 [[image:image-20230326054341-1.png]]
ingrreit 10.1 77
eapapp 167.1 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 // //
eapapp 168.1 85 [[[[image:image-20230324171114-2.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
eapapp 167.1 86 )))
ingrreit 36.1 87
ingrreit 147.8 88
ingrreit 10.1 89 ==== **1. Provide some general information about your dataset** ====
90
eapapp 173.1 91
92
eapapp 172.1 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#/]]. **
ingrreit 10.1 94
ingrreit 151.1 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.
ingrreit 10.1 96
ingrreit 147.3 97
eapapp 172.1 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]]**.
ingrreit 147.3 99
ingrreit 151.1 100 This form collects the necessary information needed for us to evaluate whether we can ethically and legally share the data via EBRAINS.
101
ingrreit 158.1 102 See below for information about the ethical and legal aspects concerning sharing of human subject data.
ingrreit 151.1 103
ingrreit 158.1 104
ingrreit 10.1 105 ==== **2. Upload data ** ====
106
ingrreit 200.1 107 (% class="box floatinginfobox" id="share-data-infographic" %)
108 (((
109 (% style="text-align:center" %)
110 //Download our infographic//
111 //with guidelines
112 on data organization: //
ingrreit 10.1 113
ingrreit 200.1 114 (% style="text-align:center" %)
115 [[[[image:image-20230621121014-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/lib/f5cf4964-f095-49bd-8c34-e4ffda05a497/file/ebrains-infographic-data-organisation.pdf/]]
116 )))
117
eapapp 172.1 118 (% 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. **
ingrreit 10.1 119
ingrreit 200.1 120 We look for organized data, not organized according to our standard. This is to support the broadest degree of sharing possible. We do however require that the data is organized in a consistent and precise manner. Please see our// //[[guidelines on data organization>>https://drive.ebrains.eu/smart-link/25299f04-c4e5-4028-8f5f-3b8208f9a532/]] for further guidance.
ingrreit 151.1 121
eapapp 172.1 122 (% 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).**
ingrreit 10.1 123
eapapp 176.1 124 **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.
ingrreit 147.3 125
eapapp 176.1 126 **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.
ingrreit 147.3 127
128
129 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. 
130
ingrreit 10.1 131 If a data collection is already uploaded elsewhere, we may link to the already existing repository.
132
133
ingrreit 160.1 134 ==== **3. Submit metadata** ====
ingrreit 147.8 135
136
eapapp 174.1 137 (% 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) **
ingrreit 10.1 138
eapapp 175.1 139 **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
ingrreit 10.1 140
eapapp 175.1 141 **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:
ingrreit 147.3 142
143 * 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.
144 * [[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.
145 * [[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.
146
147 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.
148
149
eapapp 173.1 150 ==== **4. Write a Data Descriptor** ====
ingrreit 10.1 151
eapapp 173.1 152
153
eapapp 175.1 154 (% 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]]**.**
ingrreit 10.1 155
ingrreit 151.1 156 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. 
ingrreit 10.1 157
ingrreit 151.1 158 See our infographic about the data descriptor for inspiration or guidance.
ingrreit 10.1 159
ingrreit 151.1 160 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]]".
ingrreit 147.3 161
ingrreit 10.1 162 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.
163
eapapp 173.1 164
eapapp 168.1 165 (% class="box floatinginfobox" id="data-descriptor-infographic" %)
166 (((
167 (% style="text-align:center" %)
ingrreit 200.1 168 //Download our infographic
169 about the EBRAINS Data//
170 //Descriptor//
eapapp 168.1 171 // //
172 [[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
173 )))
ingrreit 10.1 174
eapapp 173.1 175 ==== **5. Preview and publish** ====
ingrreit 10.1 176
177
eapapp 172.1 178 (% 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. **
eapapp 173.1 179
eapapp 172.1 180 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.
ingrreit 10.1 181
ingrreit 147.3 182
ingrreit 10.1 183 ----
184
eapapp 173.1 185 ==== ====
ingrreit 10.1 186
eapapp 173.1 187 ==== **Sharing human subject data** ====
188
ingrreit 10.1 189 (% class="box floatinginfobox" %)
ingrreit 1.1 190 (((
ingrreit 156.1 191 **Human subject data that can be shared on EBRAINS:**
eapapp 168.1 192 // //
193 // - Post-mortem data//
194 // - Aggregated data//
195 // - Strongly pseudonymized or de-identified subject data//
196 // with a legal basis for sharing (e.g. Informed Consent)//
197 // //
ingrreit 1.1 198
eapapp 168.1 199 (% class="small" %)
200 //If you have human data that does not qualify as any of the above,//
201 //please [[get in touch>>https://www.ebrains.eu/contact/]] and we will clarify the available options.//
ingrreit 1.1 202 )))
203
eapapp 173.1 204
ingrreit 157.1 205 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]].
ingrreit 1.1 206
ingrreit 147.3 207 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).
ingrreit 128.1 208
ingrreit 147.3 209 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.
ingrreit 1.1 210
ingrreit 147.3 211 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.
ingrreit 1.1 212
ingrreit 147.3 213 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.
214
215
ingrreit 10.1 216 ----
217
218 === Step by Step - Models ===
219
ingrreit 127.1 220
adavison 194.2 221 ==== 1. Start early ====
222
223 It is not necessary to wait until you are ready to publish to register your model with EBRAINS.
224
225 By registering a model early in your project, you can take advantage of EBRAINS tools
226 to keep track of simulations and to share them with your collaborators.
227
228 ==== 2. Create/choose a Collab workspace ====
229
230 We use EBRAINS Collaboratory "collab" workspaces to help manage the model curation process.
231
232 In particular, we use collab membership (the "Team") to control who can view or edit your model metadata prior to publication.
233
234 It is up to you whether you create a new collab for each model, or reuse an existing collab
235 (it is no problem to have multiple models associated with a single collab).
236
237 Collabs are also useful for storing simulation results, adding documentation for your model,
238 and/or providing tutorials in Jupyter notebooks.
239
adavison 195.1 240 ==== 3. Upload code ====
adavison 194.2 241
adavison 195.1 242 We recommend storing model code and/or configuration files in an online Git repository, for example on GitHub.
243 This repository should be public when you publish the model, but a private repository can be used for model development.
adavison 194.2 244
adavison 195.1 245 Alternatively, you can upload code to the Collab Drive or Bucket storage.
adavison 194.2 246
adavison 195.1 247 ==== 4.Submit metadata ====
ingrreit 10.1 248
adavison 195.1 249 We recommend submitting metadata using the Model Catalog app, installed in your collab.
ingrreit 10.1 250
adavison 195.1 251 To install it:
ingrreit 10.1 252
adavison 195.1 253 1. click the "+ Create" button
254 1. in the "Create Page" form, add a title, such as "Model Catalog", and select "Community App", then click "Create"
255 1. scroll down until you find the "Model Catalog" app, click "Select", then "Save & View"
256
257 You will then see a table of all the models and validation tests associated with this collab.
258 If this is your first time using the app, the table will probably be empty.
259 To add your model, click "+", fill in the form, then click "Add model".
260
261 As development of your model proceeds, you can easily register new versions of the code,
adavison 196.1 262 and new parameterizations, by clicking "Add new version".
adavison 195.1 263
264 If you prefer not to use the app, you can instead fill in the [[Curation request form>>https://nettskjema.no/a/277393#/]].,
265 and you will be contacted by e-mail with further instructions.
266
adavison 195.2 267 ==== 5. Provide a reference dataset ====
adavison 195.1 268
269 Once you're ready to publish your model entry in the EBRAINS Knowledge Graph,
270 we encourage you to provide a dataset containing the simulation results produced by your model,
271 following the process under "Step by step - Data" above.
272
273 These reference data will be linked to the model, and will be helpful to anyone trying to
274 reuse your model.
275
276 We will soon introduce a "Reproducible" badge for all models that include a reference dataset,
277 and whose simulation results can be reproduced by an EBRAINS curator.
278
279 ==== 6. Request publication, preview and publish ====
280
281 Until you request your model entry to be published in the EBRAINS Knowledge Graph,
282 only members of the collab will be able to view the model entry, in the Model Catalog app
283 or using the Model Validation Python client.
284
adavison 195.2 285 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.
adavison 195.1 286
adavison 195.2 287 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.
adavison 195.1 288
289
290 Curators will then perform a number of checks:
291
292 1. Does the model description provide sufficient context to understand the purpose and use of the model?
293 1. Does the code repository contain a licence file, explaining the conditions for reusing the code?
adavison 196.1 294 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.
adavison 195.1 295
296 The curators will also take a snapshot of your model code.
297
spieschnik 198.1 298 * For models in public Git repositories, we archive a copy of the repository in [[Software Heritage>>https://www.softwareheritage.org/||rel="noopener noreferrer" target="_blank"]].
adavison 195.1 299 * 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.
300
301 Once this is done, you will be invited to review a preview of how the model entry will appear in the KG Search,
302 and will have the opportunity to request modifications prior to approval and publication.
303
ingrreit 10.1 304 ----
305
ingrreit 147.6 306 === Step by Step - Software ===
ingrreit 10.1 307
ingrreit 127.1 308
eapapp 170.1 309 (% class="box floatinginfobox" id="software-curation-infographic" %)
310 (((
311 (% style="text-align:center" %)
312 //Software curation at a glance//
313 // //
314 [[[[image:Thumb2.png||alt="EBRAINS-Share-Software.pdf" height="287" width="197"]]>>attach:EBRAINS-Share-Software-4.pdf]]
315 )))
ingrreit 10.1 316
eapapp 170.1 317 (% 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"]]
jan 130.1 318
eapapp 170.1 319 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.
320 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.
321 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.
ingrreit 147.5 322
323 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]].
324
eapapp 170.1 325 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.
ingrreit 147.5 326
327
ingrreit 10.1 328 ----
329
ingrreit 152.1 330 == **The openMINDS metadata framework** ==
331
ingrreit 193.1 332 (% class="box floatinginfobox" %)
333 (((
334 [[[[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]]
335 )))
336
ingrreit 152.1 337 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]].
338
339 For feedback, requests, or contributions, please get in touch with the openMINDS development team via
340
341 * the support-email: [[openminds@ebrains.eu>>path:mailto:openminds@ebrains.eu]]
342 * the [[GitHub issue tracker>>url:https://github.com/HumanBrainProject/openMINDS/issues]]
343 * the INCF NeuroStars [[openMINDS Community Forum>>url:https://neurostars.org/t/openminds-community-forum-virtual/20156]]
344
345 ----
346
ingrreit 147.4 347 == **The curation team: meet the curators** ==
ingrreit 27.2 348
ingrreit 147.4 349 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.
ingrreit 27.2 350
ingrreit 147.4 351 The curators in EBRAINS are located in Oslo, Jülich, Trier and Paris. 
352
ingrreit 55.1 353
spieschnik 72.1 354 **Located in Norway:**
ingrreit 55.1 355
spieschnik 98.1 356 |(% style="width:303px" %)(((
spieschnik 113.1 357 [[image:My project2.jpg||height="209" width="167"]]
spieschnik 97.2 358
spieschnik 105.1 359 **Archana Golla**
360
spieschnik 111.1 361 (% class="small" %)Curation Scientist
spieschnik 116.1 362 Neuroscience (PhD)(%%)
eapapp 166.1 363 (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Behavioral neuroscience and microscopy**
spieschnik 105.1 364 )))|(% style="width:303px" %)(((
spieschnik 142.2 365 [[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
spieschnik 98.1 366
spieschnik 122.1 367 **Camilla H. Blixhavn**
spieschnik 105.1 368
spieschnik 122.1 369 (% class="small" %)Curation Scientist,
370 Phd Student
371 Neuroscience (M. Sc.)(%%)
eapapp 166.1 372 (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and data integration**
spieschnik 126.1 373 )))|(% style="width:303px" %)(((
spieschnik 124.1 374 [[image:My project (1).jpg||height="209" width="167"]]
spieschnik 105.1 375
376 **Ingrid Reiten**
377
spieschnik 111.1 378 (% class="small" %)Curation Scientist,
spieschnik 112.1 379 Phd Student
spieschnik 117.1 380 Neuroscience (M. Sc.)(%%)
eapapp 166.1 381 (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and structural connectivity**
spieschnik 126.1 382 )))|(% style="width:303px" %)(((
spieschnik 124.1 383 [[image:My project1.jpg||height="209" width="167"]]
spieschnik 105.1 384
spieschnik 122.1 385 **Sophia Pieschnik**
spieschnik 105.1 386
spieschnik 122.1 387 (% class="small" %)Curation Scientist
388 Neurocognitive Psychology (M. Sc.)(%%)
eapapp 166.1 389 (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroimaging **
spieschnik 123.1 390 )))
spieschnik 72.1 391
spieschnik 143.2 392 |(% style="width:303px" %)(((
spieschnik 142.2 393 [[image:My project.jpg||height="209" width="167"]]
spieschnik 141.2 394
spieschnik 142.2 395 **Heidi Kleven**
spieschnik 141.2 396
spieschnik 142.2 397 (% class="small" %)Curation Scientist,
398 Phd Student
399 Neuroscience (M. Sc.)(%%)
eapapp 166.1 400 (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and brain atlases**
spieschnik 142.2 401 )))| | |
402
spieschnik 141.2 403
ingrreit 128.1 404 \\**Located in Germany:**
spieschnik 72.1 405
spieschnik 143.2 406 |(% style="width:303px" %)(((
spieschnik 115.1 407 [[image:My project (2).jpg||height="209" width="167"]]
spieschnik 72.1 408
409 **Jan Gündling**
410
spieschnik 143.2 411 (% class="small" %)Curation Scientist,
jan 131.2 412 Phd Student
spieschnik 117.1 413 Sensors and Cognitive Psychology (M. Sc.)(%%)
eapapp 166.1 414 (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Human-Computer Interaction**
spieschnik 198.1 415 )))|(% style="width:303px" %)(((
416 [[image:Lyuba.jpg||height="209" width="167"]]
spieschnik 72.1 417
spieschnik 143.2 418 **Lyuba Zehl**
419
420 (% class="small" %)Knowledge Systems Engineer
421 Dr. rer. nat. (Systems Neuroscience)(%%)
eapapp 166.1 422 (% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
spieschnik 198.1 423 )))|(% style="width:303px" %) |(% style="width:303px" %)
spieschnik 143.2 424
ingrreit 27.2 425 ----
426
ingrreit 147.6 427 == **Add practical value to your shared data, model or software** ==
ingrreit 10.1 428
429
ingrreit 147.6 430 ----
ingrreit 58.1 431
ingrreit 147.6 432 === **Showcase shared data, models or software in other services** ===
ingrreit 58.1 433
eapapp 190.1 434 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.
ingrreit 58.1 435
ingrreit 55.1 436
eapapp 192.1 437 |(% colspan="2" %)**Viewer for 2D images**
438 |[[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]].
439 |(% colspan="2" %)**Viewer for sequential atlas-registered 2D images with annotation options**
440 |[[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]].
441 |(% colspan="2" %)**Interactive 3D atlas viewer with options for data visualization**
442 |[[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]].
443 |(% colspan="2" %)**Use your research product in an interactive publication**
444 |[[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]].
445
ingrreit 60.1 446 ----
447
ingrreit 160.1 448 ==== **Add a tutorial or learning resource ** ====
449
450 (% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
eapapp 166.1 451 (% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
ingrreit 160.1 452
453
454 ==== **Create a workflow** ====
455
456 (% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
eapapp 166.1 457 (% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
ingrreit 160.1 458
459 ----
460
ingrreit 37.1 461 === **The benefits of sharing data ** ===
ingrreit 27.1 462
463 By sharing your data via EBRAINS, you gain access to the following benefits:
464
465 [[image:image-20230324170841-3.png]]
466
467
468
ingrreit 159.1 469 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.
ingrreit 27.1 470
471 ----
472
ingrreit 148.1 473 === **Frequently asked questions ** ===
ingrreit 10.1 474
ingrreit 1.1 475 (((
eapapp 166.1 476 ==== ====
ingrreit 1.1 477
ingrreit 23.2 478 (((
spieschnik 168.2 479 >Is the curation process time consuming and difficult?
ingrreit 1.1 480 )))
ingrreit 19.1 481 )))
ingrreit 10.1 482
spieschnik 168.2 483 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.
ingrreit 10.1 484
spieschnik 168.2 485 >Is sharing my data also beneficial for me or only for others?
ingrreit 10.1 486
487 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.
488
spieschnik 168.2 489 >Can my data be too insignificant to share?
ingrreit 10.1 490
spieschnik 168.2 491 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.
ingrreit 10.1 492
spieschnik 168.2 493 >Can my data be easily misused if I share it?
ingrreit 10.1 494
spieschnik 168.2 495 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.
ingrreit 10.1 496
spieschnik 168.2 497 >Can I share my data before my paper is published?
ingrreit 10.1 498
spieschnik 168.2 499 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.
ingrreit 10.1 500
spieschnik 168.2 501 >Can I lose my competitive edge if I share my data before I publish the associated paper?
ingrreit 10.1 502
spieschnik 168.2 503 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.
ingrreit 10.1 504
505
506 ----
507
508 == Contact ==
509
510 [[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
511
512
eapapp 177.1 513 == References ==
514
ingrreit 10.1 515 {{putFootnotes/}}