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1 +== Publishing neuroscience data, models and software via EBRAINS ==
18 18  
3 +The aim of this collab is to provide you with all the information you need to publish your experimental data, simulations, computational models, and software via EBRAINS. 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.
19 19  
20 -(% class="wikigeneratedid" id="HPublishingneurosciencedata2CmodelsandsoftwareviaEBRAINS" %)
21 -(% style="font-size:2em" %)**Publishing neuroscience data, models and software via EBRAINS**
22 -
23 -(% class="wikigeneratedid" %)
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]].
25 -
26 26  {{box title="**Contents**"}}
27 27  {{toc depth="3" start="2"/}}
28 28  {{/box}}
29 29  
30 -== **Information to get started** ==
31 31  
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. **
10 +(% style="text-align: center;" %)
11 +**Get started! **
33 33  
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.
13 +(% style="text-align: center;" %)
14 +**[[REQUEST CURATION>>https://nettskjema.no/a/277393#/]] **
35 35  
16 +(% style="text-align: center;" %)
17 + Search existing data, models and software in [[the EBRAINS Knowledge Graph Search>>https://kg.ebrains.eu/search/?facet_type[0]=Dataset]]
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 -)))
41 41  
20 +----
42 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 -
22 +== **The EBRAINS curation process** ==
45 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 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]]
26 +EBRAINS accepts **experimental data,** of all modalities and from all species, **models**, **software**, **web services **and **metadata models**. You'll find detailed information about each research product below.
54 54  )))
55 55  
56 -----
57 -
58 -== **The EBRAINS curation process** ==
59 -
60 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. 
61 61  
62 62  >The EBRAINS curation process involves organising and annotating neuroscientific data to make the data discoverable and reusable.
... ... @@ -63,297 +63,139 @@
63 63  
64 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.
65 65  
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]].
35 +Curated data, models and software are made available in the [[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 programmatically via 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 as 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]].
67 67  
68 -The curation of data, models and software is different. Thus, below we explain the process for sharing for each research product separately.
69 69  
38 +(% class="box infomessage" %)
39 +(((
40 +**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>>mailto:curation-support@ebrains.eu]]. **
41 +)))
70 70  
43 +(% class="box successmessage" %)
44 +(((
45 +**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.
46 +)))
47 +
71 71  ----
72 72  
73 -=== Step by step - Data ===
50 +=== 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/]]
86 -)))
55 +==== ====
87 87  
88 -
89 89  ==== **1. Provide some general information about your dataset** ====
90 90  
59 +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.
91 91  
61 +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.
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#/]]. **
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.
96 -
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  
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: //
66 +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. 
113 113  
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 -)))
68 +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.
117 117  
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. **
70 +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.
119 119  
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.
121 121  
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).**
123 -
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.
125 -
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.
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 -
131 131  If a data collection is already uploaded elsewhere, we may link to the already existing repository.
132 132  
133 133  
134 134  ==== **3. Submit metadata** ====
135 135  
78 +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.
136 136  
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) **
80 +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.
138 138  
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
140 140  
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:
83 +==== **4. Write a Data Descriptor ** ====
142 142  
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.
85 +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. 
146 146  
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.
87 +[[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]]).
148 148  
149 149  
150 -==== **4. Write a Data Descriptor** ====
90 +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  
152 152  
93 +==== **5. Preview and publish ** ====
153 153  
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]]**.**
95 +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.
155 155  
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. 
157 157  
158 -See our infographic about the data descriptor for inspiration or guidance.
98 +----
159 159  
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]]".
100 +==== **Sharing human data ** ====
161 161  
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.
102 +(% class="box floatinginfobox" %)
103 +(((
104 +For **Human subject data**, the data must be //either//
163 163  
106 +- Post-mortem data
107 +- Aggregated data
108 +- Pseudonymized subject data with a legal basis for sharing (e.g. Informed Consent)
164 164  
165 -(% class="box floatinginfobox" id="data-descriptor-infographic" %)
166 -(((
167 -(% style="text-align:center" %)
168 -//Download our infographic
169 -about the EBRAINS Data//
170 -//Descriptor//
171 -// //
172 -[[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
110 +(% 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. //
173 173  )))
174 174  
175 -==== **5. Preview and publish** ====
113 +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]].
176 176  
115 +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.
177 177  
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. **
117 +**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.
118 +\\**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.
119 +\\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.
179 179  
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.
181 181  
182 -
183 -
184 -
185 185  ----
186 186  
187 187  === Step by Step - Models ===
188 188  
126 +(% style="color:#e74c3c" %){{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-1rb0hn"/}}
189 189  
190 -==== 1. Start early ====
128 +[place-holder-process-diagram]
191 191  
192 -It is not necessary to wait until you are ready to publish to register your model with EBRAINS.
130 +==== **1. model step 1 ** ====
193 193  
194 -By registering a model early in your project, you can take advantage of EBRAINS tools
195 -to keep track of simulations and to share them with your collaborators.
132 +Text
196 196  
197 -==== 2. Create/choose a Collab workspace ====
198 198  
199 -We use EBRAINS Collaboratory "collab" workspaces to help manage the model curation process.
135 +==== **2. model step 2** ====
200 200  
201 -In particular, we use collab membership (the "Team") to control who can view or edit your model metadata prior to publication.
137 +Text
202 202  
203 -It is up to you whether you create a new collab for each model, or reuse an existing collab
204 -(it is no problem to have multiple models associated with a single collab).
205 205  
206 -Collabs are also useful for storing simulation results, adding documentation for your model,
207 -and/or providing tutorials in Jupyter notebooks.
208 -
209 -==== 3. Upload code ====
210 -
211 -We recommend storing model code and/or configuration files in an online Git repository, for example on GitHub.
212 -This repository should be public when you publish the model, but a private repository can be used for model development.
213 -
214 -Alternatively, you can upload code to the Collab Drive or Bucket storage.
215 -
216 -==== 4.Submit metadata ====
217 -
218 -We recommend submitting metadata using the Model Catalog app, installed in your collab.
219 -
220 -To install it:
221 -
222 -1. click the "+ Create" button
223 -1. in the "Create Page" form, add a title, such as "Model Catalog", and select "Community App", then click "Create"
224 -1. scroll down until you find the "Model Catalog" app, click "Select", then "Save & View"
225 -
226 -You will then see a table of all the models and validation tests associated with this collab.
227 -If this is your first time using the app, the table will probably be empty.
228 -To add your model, click "+", fill in the form, then click "Add model".
229 -
230 -As development of your model proceeds, you can easily register new versions of the code,
231 -and new parameterizations, by clicking "Add new version".
232 -
233 -If you prefer not to use the app, you can instead fill in the [[Curation request form>>https://nettskjema.no/a/277393#/]].,
234 -and you will be contacted by e-mail with further instructions.
235 -
236 -==== 5. Provide a reference dataset ====
237 -
238 -Once you're ready to publish your model entry in the EBRAINS Knowledge Graph,
239 -we encourage you to provide a dataset containing the simulation results produced by your model,
240 -following the process under "Step by step - Data" above.
241 -
242 -These reference data will be linked to the model, and will be helpful to anyone trying to
243 -reuse your model.
244 -
245 -We will soon introduce a "Reproducible" badge for all models that include a reference dataset,
246 -and whose simulation results can be reproduced by an EBRAINS curator.
247 -
248 -==== 6. Request publication, preview and publish ====
249 -
250 -Until you request your model entry to be published in the EBRAINS Knowledge Graph,
251 -only members of the collab will be able to view the model entry, in the Model Catalog app
252 -or using the Model Validation Python client.
253 -
254 -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.
255 -
256 -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.
257 -
258 -
259 -Curators will then perform a number of checks:
260 -
261 -1. Does the model description provide sufficient context to understand the purpose and use of the model?
262 -1. Does the code repository contain a licence file, explaining the conditions for reusing the code?
263 -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.
264 -
265 -The curators will also take a snapshot of your model code.
266 -
267 -* 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"]].
268 -* 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.
269 -
270 -Once this is done, you will be invited to review a preview of how the model entry will appear in the KG Search,
271 -and will have the opportunity to request modifications prior to approval and publication.
272 -
273 273  ----
274 274  
275 -=== Step by Step - Software ===
142 +=== Step by Step - Code ===
276 276  
144 +[[[[image:swc-flow-no-header.png||alt="swc-flow.png"]]>>https://www.ebrains.eu/tools/ebrains-curation-request-form||rel="noopener noreferrer" target="_blank"]]
277 277  
278 -(% class="box floatinginfobox" id="software-curation-infographic" %)
279 -(((
280 -(% style="text-align:center" %)
281 -//Software curation at a glance//
282 -// //
283 -[[[[image:Thumb2.png||alt="EBRAINS-Share-Software.pdf" height="287" width="197"]]>>attach:EBRAINS-Share-Software-4.pdf]]
284 -)))
285 -
286 -(% 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"]]
287 -
288 -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.
289 -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.
146 +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]]
147 +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.
148 +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.
149 +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.
290 290  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.
291 291  
292 -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 +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/]]
153 +For more information, visit our [[guide>>url:https://wiki.ebrains.eu/bin/view/Collabs/swc-guide]].
293 293  
294 -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.
295 -
296 -
297 297  ----
298 298  
299 -=== Sharing human subject data ===
157 +=== Webservices and metadata models ===
300 300  
301 -(% class="box floatinginfobox" %)
302 -(((
303 -**Human subject data that can be shared on EBRAINS:**
304 -// //
305 -// - Post-mortem data//
306 -// - Aggregated data//
307 -// - Strongly pseudonymized or de-identified subject data//
308 -// with a legal basis for sharing (e.g. Informed Consent)//
309 -// //
159 +(% class="wikigeneratedid" id="HContact...." %)
160 +(% style="color:#e74c3c; font-size:16px" %){{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-np253c"/}}(% style="color:#4a5568; font-size:16px" %)
310 310  
311 -(% class="small" %)
312 -//If you have human data that does not qualify as any of the above,//
313 -//please [[get in touch>>https://www.ebrains.eu/contact/]] and we will clarify the available options.//
314 -)))
315 -
316 -
317 -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]].
318 -
319 -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).
320 -
321 -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.
322 -
323 -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.
324 -
325 -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.
326 -
327 327  ----
328 328  
329 -== **The openMINDS metadata framework** ==
330 -
331 -(% class="box floatinginfobox" %)
332 -(((
333 -[[[[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]]
334 -)))
335 -
336 -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]].
337 -
338 -For feedback, requests, or contributions, please get in touch with the openMINDS development team via
339 -
340 -* the support-email: [[openminds@ebrains.eu>>path:mailto:openminds@ebrains.eu]]
341 -* the [[GitHub issue tracker>>url:https://github.com/HumanBrainProject/openMINDS/issues]]
342 -* the INCF NeuroStars [[openMINDS Community Forum>>url:https://neurostars.org/t/openminds-community-forum-virtual/20156]]
343 -
344 -----
345 -
346 346  == **The curation team: meet the curators** ==
347 347  
348 -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.
166 +**Located in Norway:**
349 349  
350 -The curators in EBRAINS are located in Oslo, Jülich, Trier and Paris. 
351 -
352 -
353 -**Located in Norway**
354 -
355 -//Institute of Basic Medical Sciences,** **University of Oslo, Norway (PI: Jan G. Bjaalie, Trygve B. Leergaard)//
356 -
357 357  |(% style="width:303px" %)(((
358 358  [[image:My project2.jpg||height="209" width="167"]]
359 359  
... ... @@ -361,7 +361,7 @@
361 361  
362 362  (% class="small" %)Curation Scientist
363 363  Neuroscience (PhD)(%%)
364 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Behavioral neuroscience and microscopy**
175 +(% class="small" style="color:#4a5568" %)**Behavioral neuroscience and microscopy**
365 365  )))|(% style="width:303px" %)(((
366 366  [[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
367 367  
... ... @@ -370,7 +370,7 @@
370 370  (% class="small" %)Curation Scientist,
371 371  Phd Student
372 372  Neuroscience (M. Sc.)(%%)
373 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and data integration**
184 +(% class="small" style="color:#4a5568" %)**Neuroanatomy and data integration**
374 374  )))|(% style="width:303px" %)(((
375 375  [[image:My project (1).jpg||height="209" width="167"]]
376 376  
... ... @@ -379,7 +379,7 @@
379 379  (% class="small" %)Curation Scientist,
380 380  Phd Student
381 381  Neuroscience (M. Sc.)(%%)
382 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and structural connectivity**
193 +(% class="small" style="color:#4a5568" %)**Neuroanatomy and structural connectivity**
383 383  )))|(% style="width:303px" %)(((
384 384  [[image:My project1.jpg||height="209" width="167"]]
385 385  
... ... @@ -387,7 +387,7 @@
387 387  
388 388  (% class="small" %)Curation Scientist
389 389  Neurocognitive Psychology (M. Sc.)(%%)
390 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroimaging **
201 +(% class="small" style="color:#4a5568" %)**Neuroimaging **
391 391  )))
392 392  
393 393  |(% style="width:303px" %)(((
... ... @@ -398,16 +398,12 @@
398 398  (% class="small" %)Curation Scientist,
399 399  Phd Student
400 400  Neuroscience (M. Sc.)(%%)
401 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and brain atlases**
212 +(% class="small" style="color:#4a5568" %)**Neuroanatomy and brain atlases**
402 402  )))| | |
403 403  
404 404  
405 -\\**Located in Germany**
216 +\\**Located in Germany:**
406 406  
407 -//Human-Computer Interaction, University of Trier, Germany  //
408 -
409 -//Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Germany (PI: Timo Dicksheid)//
410 -
411 411  |(% style="width:303px" %)(((
412 412  [[image:My project (2).jpg||height="209" width="167"]]
413 413  
... ... @@ -416,55 +416,69 @@
416 416  (% class="small" %)Curation Scientist,
417 417  Phd Student
418 418  Sensors and Cognitive Psychology (M. Sc.)(%%)
419 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Human-Computer Interaction**
226 +(% class="small" style="color:#4a5568" %)**Human-Computer Interaction**
420 420  )))|(% style="width:303px" %)(((
421 -[[image:Lyuba.jpg||height="209" width="167"]]
228 +
422 422  
230 +
231 +
232 +
233 +
234 +
235 +
236 +
237 +
238 +
239 +
423 423  **Lyuba Zehl**
424 424  
425 425  (% class="small" %)Knowledge Systems Engineer
426 426  Dr. rer. nat. (Systems Neuroscience)(%%)
427 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
428 -)))|(% style="width:303px" %) |(% style="width:303px" %)
244 +(% class="small" style="color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
245 +)))|(% style="width:303px" %) |
429 429  
430 430  ----
431 431  
432 -== **Add practical value to your shared data, model or software** ==
249 +== **Information and resources for researchers looking to share data** ==
433 433  
251 +Below you can find some resources that can come in handy if you are looking to share data via EBRAINS, or in general.
434 434  
435 435  ----
436 436  
437 -=== **Showcase shared data, models or software in other services** ===
255 +=== **Improve your research product ** ===
438 438  
439 -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.
257 +(% class="wikigeneratedid" %)
258 +**{{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-fkdv6h"/}}**
440 440  
260 +==== **Add a tutorial or learning resource to your research product ** ====
441 441  
442 -|(% colspan="2" %)**Viewer for 2D images**
443 -|[[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]].
444 -|(% colspan="2" %)**Viewer for sequential atlas-registered 2D images with annotation options**
445 -|[[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]].
446 -|(% colspan="2" %)**Interactive 3D atlas viewer with options for data visualization**
447 -|[[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]].
448 -|(% colspan="2" %)**Use your research product in an interactive publication**
449 -|[[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]].
262 +==== (% style="color:#e74c3c" %)- Learning resource [information](%%) ====
450 450  
451 -----
452 452  
453 -==== **Add a tutorial or learning resource ** ====
265 +==== **Create a workflow for .... ? ** ====
454 454  
455 -(% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
456 -(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
267 +==== (% style="color:#e74c3c" %)- Workflows [information](%%) ====
457 457  
269 +----
458 458  
459 -==== **Create a workflow** ====
271 +=== **Integrate your data, models or software with other services** ===
460 460  
461 -(% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
462 -(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
273 +EBRAINS supports further integration for a variety of data, and is continuously looking to increase the number of interoperable services.
463 463  
275 +* 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]].
276 +* 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]].
277 +* 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"/}}
278 +* 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.
279 +
464 464  ----
465 465  
466 466  === **The benefits of sharing data ** ===
467 467  
284 +(% 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.
285 +
286 +(% 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.
287 +
288 +
468 468  By sharing your data via EBRAINS, you gain access to the following benefits:
469 469  
470 470  [[image:image-20230324170841-3.png]]
... ... @@ -471,43 +471,67 @@
471 471  
472 472  
473 473  
474 -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.
295 +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.
475 475  
297 +
476 476  ----
477 477  
478 -=== **Frequently asked questions ** ===
300 +=== **At a glance: "Sharing experimental data on EBRAINS" ** ===
479 479  
302 +
303 +|(% style="width:439px" %)(((
304 +[[[[image:image-20230324171114-2.png||height="354" width="250"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
305 +)))|(% style="width:461px" %)(((
306 +[[[[image:image-20230324171109-1.png||height="352" width="250"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
307 +)))|(% style="width:416px" %)[[[[image:image-20230330120354-1.png||height="352" width="250"]]>>https://drive.ebrains.eu/f/707147a883b94fae8e69/]]
308 +|(% 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. //
309 +
310 +----
311 +
312 +=== **Common concerns - and answers ** ===
313 +
480 480  (((
481 -==== ====
315 +==== ====
482 482  
483 483  (((
484 ->Is the curation process time consuming and difficult?
318 +>The curation process is time consuming and difficult
485 485  )))
486 486  )))
487 487  
488 -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.
322 +(% class="wikigeneratedid" id="HHowcanIshareA0models3F" %)
323 +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.
489 489  
490 ->Is sharing my data also beneficial for me or only for others?
325 +>Sharing my data is not beneficial for me - only for others
491 491  
327 +
492 492  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.
493 493  
494 ->Can my data be too insignificant to share?
330 +>My data is too insignificant to share
495 495  
496 -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.
497 497  
498 ->Can my data be easily misused if I share it?
333 +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.
499 499  
500 -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.
335 +>My data can easily be misused if I share it with the world
501 501  
502 ->Can I share my data before my paper is published?
503 503  
504 -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.
338 +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.
505 505  
506 ->Can I lose my competitive edge if I share my data before I publish the associated paper?
340 +>I don't think I'm allowed to share my data
507 507  
508 -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.
509 509  
343 +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.
510 510  
345 +>I can't share my data before my paper is published
346 +
347 +
348 +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.
349 +
350 +>If I share my data before I publish the associated paper, I will lose my competitive edge
351 +
352 +
353 +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.
354 +
355 +
511 511  ----
512 512  
513 513  == Contact ==
... ... @@ -515,6 +515,8 @@
515 515  [[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
516 516  
517 517  
518 -== References ==
519 -
520 520  {{putFootnotes/}}
364 +~)~)~)~)~)~)
365 +~)~)~)
366 +~)~)~)~)~)~)~)~)~)
367 +~)~)~)~)~)~)
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