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Changes for page Data Curation

Last modified by abonard on 2025/06/03 10:55
From version 228.1
edited by puchades
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To version 14.1
edited by ingrreit
on 2023/03/24 17:11
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18 18  
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** ==
8 +== Publishing data via EBRAINS ==
31 31  
32 -**[[REQUEST CURATION>>https://nettskjema.no/a/386195]] to share data, simulations, computational models, and software, - or to add a new version of an existing one. **
10 +The aim of this collab is to provide you with all the information you need to publish your neuroscience data via the EBRAINS Knowledge Graph. By "neuroscience data," we mean experimental datasets collected from living organisms, but also simulations, computational models, and software. Have you already published your data somewhere else? You can increase the exposure and impact of your shared dataset by re-sharing its metadata via EBRAINS.
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.
35 35  
13 +(% style="text-align: center;" %)
14 +**Get started! **
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 -)))
16 +(% style="text-align: center;" %)
17 +**[[REQUEST CURATION>>https://nettskjema.no/a/277393#/]] **
41 41  
19 +(% style="text-align: center;" %)
20 + Search existing datasets on [[the Knowledge Graph>>https://kg.ebrains.eu/search/?facet_type[0]=Dataset]]
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 -
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 -)))
23 +----
50 50  
51 -(% class="box successmessage" %)
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]]
54 -)))
25 +=== **All neuroscience data are welcome** ===
55 55  
56 -----
27 +=== [[image:image-20230324170829-2.png]] ===
57 57  
58 -== **The EBRAINS curation process** ==
59 59  
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. 
30 +----
61 61  
62 ->The EBRAINS curation process involves organising and annotating neuroscientific data to make the data discoverable and reusable.
32 +=== **Benefits of sharing data ** ===
63 63  
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.
34 +By sharing your data via EBRAINS, you gain access to the following benefits:
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]].
36 +[[image:image-20230324170841-3.png]]
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  
70 -**Before you get started, make sure you[[ sign up for a free EBRAINS account>>https://www.ebrains.eu/page/sign-up]]. This is needed to complete the data sharing process. **
71 71  
40 +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}}.
72 72  
73 73  ----
74 74  
75 -=== Step by step - Data ===
44 +== **What is curation?** ==
76 76  
46 +>The EBRAINS data curation process involves organising and annotating neuroscientific data to make the data discoverable and reusable.
77 77  
78 -[[image:image-20230326054341-1.png]]
48 +Neuroscience data are multimodal, heterogenous, and organised in different ways. All these diverse data need to be categorised and described in a standardised manner so that they can be effectively searched, compared, and analysed by using the integrated tools and workflows on the EBRAINS platform. This effort is referred to as curation.
79 79  
80 -(% class="box floatinginfobox" id="share-data-infographic" %)
81 -(((
82 -(% style="text-align:center" %)
83 -//Download our infographic//
84 -//with all you need to know//
85 -//to share data on EBRAINS: //
86 -// //
87 -[[~[~[image:image-20230324171114-2.png~|~|height="150" width="106"~]~]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
88 -)))
89 89  
51 +Sharing your data, models or code via EBRAINS makes your data discoverable amongst other neuroscience research products available in [[the EBRAINS Knowledge Graph>>https://kg.ebrains.eu/]]. The data are easily discoverable in our online search engine: the [[EBRAINS Knowledge Graph Search>>https://search.kg.ebrains.eu/]] and can also be accessed programmatically. This search is made possible by the integration of the Knowledge Graph with a highly flexible metadata framework describing neuroscience data in detail, [[openMINDS>>https://github.com/HumanBrainProject/openMINDS]]. 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.
90 90  
91 -==== **1. Provide some general information about your dataset** ====
53 +----
92 92  
55 +== **The process** ==
93 93  
57 +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. 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.
94 94  
95 -(% style="margin-right:10px" %)[[image:https://lh3.googleusercontent.com/zh7TvO6w04YGW9jIhfhmdT6CexdGs-AWOLfJXKRq7-tdHOu6ar1rOQx8o4rZevrjXqgPZ7-Ejv4b6X9XpgXuHpdUXi-mBTHIUnv5Vz-DktHt0sP-PZ3gE8XgZid3TV3swV1uTCBhHx11ge0pjP7RVxswGQ=s2048||height="85px;" width="91px;"]](%%)** Fill in the [[EBRAINS Curation Request Form>>https://nettskjema.no/a/386195]]. **
96 96  
97 -The form collects general 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 and follow up on incoming requests.
60 +Data, models and code are integrated into the [[EBRAINS Knowledge Graph>>url:https://kg.ebrains.eu/]] by using interoperable metadata schemas as defined in [[openMINDS>>url:https://github.com/HumanBrainProject/openMINDS/wiki]]. This makes the data and metadata discoverable in the [[KG Search>>url:https://search.kg.ebrains.eu/]] and programmatically via the [[KG API>>url:https://docs.kg.ebrains.eu/8387ccd27a186dea3dd0b949dc528842/api_endpoints.html]].
98 98  
99 -You will also be asked to fill in information related to ethics and regulatory compliance, so that we can evaluate whether we can ethically and legally share the data via EBRAINS (earlier, this was recorded via a [[separate form>>https://nettskjema.no/a/224765]]). See below for information about the ethical and legal aspects concerning sharing of human subject data.
62 +Data and models are linked to and discoverable via the species-specific [[EBRAINS Interactive 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]].
100 100  
101 101  
102 -==== **2. Upload data ** ====
65 +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. 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. **Want to learn more about how to Prepare to Share? **Contact us!
103 103  
104 -(% class="box floatinginfobox" id="share-data-infographic" %)
105 -(((
106 -(% style="text-align:center" %)
107 -//Download our infographic//
108 -//with guidelines
109 -on data organization: //
67 +=== Step by step - Experimental data ===
110 110  
111 -[[~[~[image:image-20230621121014-1.png~|~|data-xwiki-image-style-alignment="center" height="150" width="106"~]~]>>https://drive.ebrains.eu/lib/f5cf4964-f095-49bd-8c34-e4ffda05a497/file/ebrains-infographic-data-organisation.pdf/]]
112 -)))
69 +=== [[image:image-20230324170858-4.png]] ===
113 113  
114 -(% 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. **
115 115  
116 -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.
72 +==== **1. Provide some general information about your dataset** ====
117 117  
118 -(% 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).**
74 +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.
119 119  
120 -**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.
76 +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.
121 121  
122 -**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.
123 123  
79 +==== **2. Upload data ** ====
124 124  
125 -EBRAINS offers secure, long-term storage at FENIX Supercomputing Centres in Europe.
81 +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. 
126 126  
127 -If a data collection is already uploaded elsewhere, we may link to the already existing repository.
83 +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.
128 128  
85 +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.
129 129  
130 -==== **3. Submit metadata** ====
131 131  
88 +If a data collection is already uploaded elsewhere, we may link to the already existing repository.
132 132  
133 -(% 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) **
134 134  
135 -**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
91 +==== **3. Submit metadata** ====
136 136  
137 -**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:
93 +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.
138 138  
139 -* 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.
140 -* [[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.
141 -* [[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.
95 +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/]].
142 142  
143 -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/f/3e226ad165054b35b456/||rel="noopener noreferrer" target="_blank"]] on EBRAINS.
144 144  
98 +==== **4. Write a Data Descriptor ** ====
145 145  
146 -==== **4. Write a Data Descriptor** ====
147 -
148 -
149 -
150 -(% 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]]**.**
151 -
152 152  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. 
153 153  
154 -See our infographic about the data descriptor for inspiration or guidance.
102 +[[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]]).
155 155  
156 -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]]".
157 157  
158 158  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.
159 159  
160 160  
161 -(% class="box floatinginfobox" id="data-descriptor-infographic" %)
162 -(((
163 -(% style="text-align:center" %)
164 -//Download our infographic
165 -about the EBRAINS Data//
166 -//Descriptor//
167 -// //
168 -[[~[~[image:image-20230324171109-1.png~|~|height="150" width="106"~]~]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
169 -)))
108 +==== **5. Preview and publish ** ====
170 170  
171 -==== **5. Preview and publish** ====
110 +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.
172 172  
173 173  
174 -(% 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. **
175 -
176 -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.
177 -
178 -
179 -
180 -
181 181  ----
182 182  
183 -=== Step by Step - Models ===
115 +==== **Sharing human data ** ====
184 184  
117 +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]].
185 185  
186 -==== 1. Start early ====
119 +(% class="box floatinginfobox" %)
120 +(((
121 +For **Human subject data**, the data must be //either//
187 187  
188 -It is not necessary to wait until you are ready to publish to register your model with EBRAINS.
123 +- Post-mortem data
189 189  
190 -By registering a model early in your project, you can take advantage of EBRAINS tools
191 -to keep track of simulations and to share them with your collaborators.
125 +- Aggregated data
192 192  
193 -==== 2. Create/choose a Collab workspace ====
127 +- Pseudonymized subject data with a legal basis for sharing (e.g. Informed Consent)
194 194  
195 -We use EBRAINS Collaboratory "collab" workspaces to help manage the model curation process.
129 +(% 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. //
130 +)))
196 196  
197 -In particular, we use collab membership (the "Team") to control who can view or edit your model metadata prior to publication.
132 +Pseudonymized data is shared via the Human Data Gateway (HDG) due to GDPR regulations. The HDG adds an authentication layer to the data.
198 198  
199 -It is up to you whether you create a new collab for each model, or reuse an existing collab
200 -(it is no problem to have multiple models associated with a single collab).
134 +**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.
135 +\\**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.
136 +\\**Human Data Gateway, Background**
137 +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.
201 201  
202 -Collabs are also useful for storing simulation results, adding documentation for your model,
203 -and/or providing tutorials in Jupyter notebooks.
204 204  
205 -==== 3. Upload code ====
140 +----
206 206  
207 -We recommend storing model code and/or configuration files in an online Git repository, for example on GitHub.
208 -This repository should be public when you publish the model, but a private repository can be used for model development.
142 +=== Step by Step - Models ===
209 209  
210 -Alternatively, you can upload code to the Collab Drive or Bucket storage.
144 +[place-holder-process-diagram]
211 211  
212 -==== 4. Submit metadata ====
146 +==== **1. model step 1 ** ====
213 213  
214 -We recommend submitting metadata using the Model Catalog app, installed in your collab.
148 +Text
215 215  
216 -To install it:
217 217  
218 -1. click the "+ Create" button
219 -1. in the "Create Page" form, add a title, such as "Model Catalog", and select "Community App", then click "Create"
220 -1. scroll down until you find the "Model Catalog" app, click "Select", then "Save & View"
151 +==== **2. model step 2** ====
221 221  
222 -You will then see a table of all the models and validation tests associated with this collab.
223 -If this is your first time using the app, the table will probably be empty.
224 -To add your model, click "+", fill in the form, then click "Add model".
153 +Text
225 225  
226 -As development of your model proceeds, you can easily register new versions of the code,
227 -and new parameterizations, by clicking "Add new version".
228 228  
229 -If you prefer not to use the app, you can instead fill in the [[EBRAINS Curation Request Form>>https://nettskjema.no/a/386195]].,
230 -and you will be contacted by e-mail with further instructions.
156 +----
231 231  
232 -==== 5. Provide a reference dataset ====
158 +=== Step by Step - Code ===
233 233  
234 -Once you're ready to publish your model entry in the EBRAINS Knowledge Graph,
235 -we encourage you to provide a dataset containing the simulation results produced by your model,
236 -following the process under "Step by step - Data" above.
160 +[place-holder-process-diagram]
237 237  
238 -These reference data will be linked to the model, and will be helpful to anyone trying to
239 -reuse your model.
162 +==== **1. code step 1 ** ====
240 240  
241 -We will soon introduce a "Reproducible" badge for all models that include a reference dataset,
242 -and whose simulation results can be reproduced by an EBRAINS curator.
164 +Text
243 243  
244 -==== 6. Request publication, preview and publish ====
245 245  
246 -Until you request your model entry to be published in the EBRAINS Knowledge Graph,
247 -only members of the collab will be able to view the model entry, in the Model Catalog app
248 -or using the Model Validation Python client.
167 +==== **2. code step 2** ====
249 249  
250 -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.
169 +Text
251 251  
252 -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.
253 -
254 -
255 -Curators will then perform a number of checks:
256 -
257 -1. Does the model description provide sufficient context to understand the purpose and use of the model?
258 -1. Does the code repository contain a licence file, explaining the conditions for reusing the code?
259 -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.
260 -
261 -The curators will also take a snapshot of your model code.
262 -
263 -* 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"]].
264 -* 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.
265 -
266 -Once this is done, you will be invited to review a preview of how the model entry will appear in the KG Search,
267 -and will have the opportunity to request modifications prior to approval and publication.
268 -
269 269  ----
270 270  
271 -=== Step by Step - Software ===
173 +== **Resources for researchers looking to share data** ==
272 272  
273 -We ask software developers to provide their metadata in the "CodeMeta" format. [[CodeMeta>>https://codemeta.github.io/]] is a common format for software metadata, supported by GitHub, Zenodo, FigShare, DataCite, and the US National Science Foundation.
175 +Below you can find some resources that can come in handy if you are looking to share data via EBRAINS, or in general.
274 274  
275 -1. Create a codemeta.json file for your software. There are several [[tools>>https://codemeta.github.io/tools/]] to help you do this, for example the [[CodeMeta generator>>https://codemeta.github.io/codemeta-generator]] app. Please fill in as many of the fields as possible.
276 -1. Place this file in the root folder of your code repository.
277 -1. Contact [[EBRAINS support>>https://www.ebrains.eu/contact/]] to request curation of your software, letting us know the URL of your code repository. If you need help hosting your code online, please also let us know.
278 -1. After a quality check, we integrate and publish the information contained in your codemeta.json file to the Knowledge Graph. Your software is then searchable and usable for the neuroscience community.
279 -
280 -When you release a new version of your software, just update the codemeta.json file in your repository. We will check the repository on a regular basis, and if the version identifier has changed the Knowledge Graph will be updated accordingly.
281 -
282 282  ----
283 283  
284 -=== Sharing human subject data ===
179 +=== **Useful information about sharing of experimental data on EBRAINS ** ===
285 285  
286 -(% class="box floatinginfobox" %)
287 -(((
288 -**Human subject data that can be shared on EBRAINS:**
289 -// //
290 -// - Post-mortem data//
291 -// - Aggregated data//
292 -// - Strongly pseudonymized or de-identified subject data//
293 -// with a legal basis for sharing (e.g. Informed Consent)//
294 -// //
295 295  
296 -(% class="small" %)
297 -//If you have human data that does not qualify as any of the above,//
298 -//please [[get in touch>>https://www.ebrains.eu/contact/]] and we will clarify the available options.//
182 +|(% style="width:593px" %)(((
183 +[[[[image:image-20230324171114-2.png]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
184 +)))|(% style="width:1240px" %)(((
185 +[[[[image:image-20230324171109-1.png]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
299 299  )))
187 +|(% style="width:593px" %)//Collection of useful information for researchers looking to share experimental data on EBRAINS.//|(% style="width:1240px" %)//The EBRAINS data descriptor//
300 300  
189 +----
301 301  
302 -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]].
191 +=== **Introduction to data organisation ** ===
303 303  
304 -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).
193 +Have you ever experienced not being able to find a file that you were sure you had somewhere? We have prepared a [[collection of guidelines>>https://drive.ebrains.eu/smart-link/25299f04-c4e5-4028-8f5f-3b8208f9a532/]] and [[advice>>https://drive.ebrains.eu/lib/f5cf4964-f095-49bd-8c34-e4ffda05a497/file/DataOrganisation.zip]] on how to organise files and folders to ensure consistency and reproducibility in the future.
305 305  
306 -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.
195 +* Why is data organisation important?
196 +* How to organise my data repository?
197 +* What is a Data Descriptor and why do I need one?
307 307  
308 -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.
309 -
310 -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.
311 -
312 312  ----
313 313  
314 -== **The openMINDS metadata framework** ==
201 +=== **Integrate your data in the EBRAINS atlas services** ===
315 315  
316 -(% class="box floatinginfobox" %)
317 -(((
318 -[[~[~[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]]
319 -)))
203 +EBRAINS supports viewers for a variety of data, and is continuously looking to improve the services for visualising data. For 2D histology image data that is registered to an EBRAINS supported brain atlas, the data and the overlying atlas plates can be uploaded to the LocaliZoom viewer. See for example the [[LocaliZoom links available for this dataset>>https://doi.org/10.25493/T686-7BX]] as an example.
320 320  
321 -openMINDS is a community-driven, open-source metadata framework for linked data, as used in graph database systems, such as the EBRAINS Knowledge Graph. It is composed of multiple metadata models with interlinked schemas, libraries of serviceable metadata instances, and supportive tooling (e.g., [[openMINDS Python>>https://github.com/openMetadataInitiative/openMINDS_Python]] or [[openMINDS Matlab>>https://github.com/openMetadataInitiative/openMINDS_MATLAB]]). A full documentation (for users and contributors) of the openMINDS framework can be found on [[ReadTheDocs>>https://openminds-documentation.readthedocs.io||rel="noopener noreferrer" target="_blank"]].
205 +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.
322 322  
323 -For feedback, requests, or contributions, please get in touch with the openMINDS development team via
324 -
325 -* [[support@openmetadatainitiative.org>>mailto:mailto:support@openmetadatainitiative.org]]
326 -* [[GitHub Issues>>https://github.com/openMetadataInitiative/openMINDS/issues]] (for metadata schemas)
327 -* [[GitHub Issues>>https://github.com/openMetadataInitiative/openMINDS_instances/issues]] (for metadata instances)
328 -* [[openMINDS Community Forum>>https://neurostars.org/t/openminds-community-forum-virtual]]
329 -
330 330  ----
331 331  
332 -== **Add practical value to your shared data, model or software** ==
209 +=== **Common concerns - and answers ** ===
333 333  
211 +(((
212 +==== ====
334 334  
335 -=== **Showcase shared data, models or software in other services** ===
214 +==== The curation process is time consuming and difficult ====
215 +)))
336 336  
337 -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.
217 +(% class="wikigeneratedid" id="HHowcanIshareA0models3F" %)
218 +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.
338 338  
220 +>Sharing my data is not beneficial for me - only for others
339 339  
340 -|(% colspan="2" %)**Viewer for 2D images**
341 -|[[image:MIO_screenshot.PNG]]|Integrate image data with //SeriesZoom viewer//: EBRAINS 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 [[viewer links available for this dataset>>https://search.kg.ebrains.eu/?category=Dataset&q=nr2f1#9677359c-73fa-4425-b8fa-3de794e9017a]] as an example.
342 -|(% colspan="2" %)**Viewer for sequential atlas-registered 2D images with annotation options**
343 -|[[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]].
344 -|(% colspan="2" %)**Interactive 3D atlas viewer with options for data visualization**
345 -|[[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]].
346 -|(% colspan="2" %)**Use your research product in an interactive publication**
347 -|[[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]].
348 348  
349 -----
223 +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.
350 350  
351 -==== **Add a tutorial or learning resource ** ====
225 +>My data is too insignificant to share
352 352  
353 -(% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
354 -(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
355 355  
228 +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.
356 356  
357 -==== **Create a workflow** ====
230 +>My data can easily be misused if I share it with the world
358 358  
359 -(% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
360 -(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
361 361  
362 -----
233 +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.
363 363  
364 -== **EBRAINS commits to the FAIR principles** ==
235 +>I don't think I'm allowed to share my data
365 365  
366 -In 2016, the 'FAIR Guiding Principles for the management and guardianship of scientific data'{{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}} were introduced to the scientific community. The objective of the authors was to provide a set of general recommendations aimed at enhancing the Findability, Accessibility, Interoperability, and Reusability of digital resources (data). They emphasize the importance of making data more open, discoverable, and usable, ultimately facilitating collaboration and knowledge sharing within the scientific community. Today, the FAIR principles are widely recognized and adopted as best practices in data management and stewardship across scientific fields.
367 367  
368 -In EBRAINS, all datasets, models and software shared go through a streamlined curation process that ensures relevant annotation of the data using the [[openMINDS>>url:https://github.com/HumanBrainProject/openMINDS]] metadata framework and integration into the [[EBRAINS Knowledge Graph>>url:https://docs.kg.ebrains.eu/]] metadata management system. The research products are Findable and Accessible through the [[Knowledge Graph Search>>url:https://search.kg.ebrains.eu/?category=Dataset]] as dataset/model/software cards that display further information regarding the dataset's Interoperability and Reusability.
238 +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.
369 369  
370 -To further specify how EBRAINS aligns with the FAIR principles, we have assessed the FAIRness of datasets shared in the EBRAINS Knowledge Graph following the [[FAIRsFAIR Data Object Assessment Metrics>>https://zenodo.org/record/6461229||style="background-color: rgb(255, 255, 255); --darkreader-inline-bgcolor: #1c1e1f;"]]: see our **[[FAIR assessment of EBRAINS datasets>>doc:.FAIR assessment of EBRAINS datasets.WebHome]]. **
240 +>I can't share my data before my paper is published
371 371  
372 372  
373 -----
243 +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.
374 374  
375 -== **General benefits of sharing data ** ==
245 +>If I share my data before I publish the associated paper, I will lose my competitive edge
376 376  
377 -By sharing your data via EBRAINS, you gain access to the following benefits:
378 378  
379 -[[image:image-20230324170841-3.png]]
248 +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.
380 380  
381 381  
382 -
383 -We support you to better follow the [[FAIR^^ ^^guiding principles>>https://www.nature.com/articles/sdata201618]] for data management and stewardship. 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.
384 -
385 385  ----
386 386  
387 -== **Frequently asked questions ** ==
388 -
389 ->Is the curation process time consuming and difficult?
390 -
391 -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.
392 -
393 ->Is sharing my data also beneficial for me or only for others?
394 -
395 -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.
396 -
397 ->Can my data be too insignificant to share?
398 -
399 -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.
400 -
401 ->Can my data be easily misused if I share it?
402 -
403 -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.
404 -
405 ->Can I share my data before my paper is published?
406 -
407 -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.
408 -
409 ->Can I lose my competitive edge if I share my data before I publish the associated paper?
410 -
411 -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.
412 -
413 -
414 414  == Contact ==
415 415  
416 416  [[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
417 417  
418 -----
419 419  
420 -== Affiliated laboratories ==
421 -
422 -//Institute of Basic Medical Sciences,** **University of Oslo, Norway (PI: Jan G. Bjaalie, Trygve B. Leergaard)//
423 -
424 -//Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Germany (PI: Timo Dicksheid)//
425 -
426 -//Paris-Saclay Institute of Neuroscience, CNRS, Université Paris-Saclay, France (PI: Andrew P. Davison)//
427 -
428 -----
429 -
430 -== References ==
431 -
432 432  {{putFootnotes/}}
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