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Changes for page data-curation-copy

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1 1  == Publishing neuroscience data, models and software via EBRAINS ==
2 2  
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.
4 4  
4 +(% class="wikigeneratedid" %)
5 +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]].
6 +
5 5  {{box title="**Contents**"}}
6 6  {{toc depth="3" start="2"/}}
7 7  {{/box}}
8 8  
9 9  
10 -(% style="text-align: center;" %)
11 -**Get started! **
12 +== **Information to get started** ==
12 12  
13 -(% style="text-align: center;" %)
14 -**[[REQUEST CURATION>>https://nettskjema.no/a/277393#/]] **
14 +**[[REQUEST CURATION>>https://nettskjema.no/a/277393#/]] to share data, simulations, computational models, and software, - or to add a new version of an existing one. **
15 15  
16 +Have you already published your data somewhere else? You can increase the exposure and impact of your shared dataset by also listing it on EBRAINS.
17 +
18 +
16 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]]
20 +Search existing data, models and software in [[the EBRAINS Knowledge Graph Search>>https://kg.ebrains.eu/search/?facet_type[0]=Dataset]]
18 18  
19 19  
23 +EBRAINS accepts data from all modalities and from all species, as well as models, software, web services and metadata models (collectively referred to as research products) for sharing. You'll find detailed information about how to share each research product below. 
24 +
25 +
26 +(% class="box infomessage" %)
27 +(((
28 +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.
29 +)))
30 +
31 +(% class="box successmessage" %)
32 +(((
33 +**Particular needs? Contact us! **The workflows for sharing can be modified for researchers or research groups aiming to frequently publish larger numbers of their research products through EBRAINS. Please contact the curation service team in such cases
34 +)))
35 +
20 20  ----
21 21  
22 22  == **The EBRAINS curation process** ==
... ... @@ -27,203 +27,311 @@
27 27  
28 28  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.
29 29  
30 -=== About the curation team ===
46 +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]].
31 31  
32 -[[image:fb6d6429-709e-4f4d-be3b-eab0a46695bd.JPG||height="184" width="137"]]
48 +The curation of data, models and software is different. Thus, below we explain the process for sharing for each research product separately.
33 33  
34 -**Sophia Pieschnik**
35 -Biology (B.Sc.)
36 -Neurocognitive Psychology (M.Sc.)
37 37  
51 +----
38 38  
39 -(% class="box successmessage" %)
40 -(((
41 -**Particular needs? Contact us! **The process of sharing data can be modified to fit the needs of researchers and large-scale projects. Contact us if you have such requests and we'll be happy to work with you to find a solution that suits us both.
42 -)))
53 +=== Step by step - Data ===
43 43  
44 -(% class="box floatinginfobox" %)
45 -(((
46 -**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]]. **
47 -)))
48 48  
56 +[[image:image-20230326054341-1.png]]
49 49  
58 +==== ====
50 50  
60 +(% style="width:1841.22px" %)
61 +|(% style="width:344px" %)(((
62 +[[[[image:image-20230324171114-2.png||height="219" width="155"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
63 +)))|(% style="width:1493px" %)//We have collected 'all you need to know to share data on EBRAINS' in an infographic. //
51 51  
65 +==== **1. Provide some general information about your dataset** ====
52 52  
53 -We promote sharing of experimental data, models, software, web services, metadata models,
54 54  
68 +[[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#/]]. **
55 55  
56 -----
70 +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.
57 57  
58 -=== Step by step - Experimental data ===
59 59  
73 +[[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]]**.
60 60  
61 -[[image:image-20230326054341-1.png]]
75 +This form collects the necessary information needed for us to evaluate whether we can ethically and legally share the data via EBRAINS.
62 62  
63 -==== ====
64 64  
65 -==== **1. Provide some general information about your dataset** ====
78 +==== **2. Upload data ** ====
66 66  
67 -The [[Curation request form>>https://nettskjema.no/a/277393#/]] collects preliminary information about your data, allowing us to assess whether the dataset fits within the scope of EBRAINS. The submission generates a curation ID allowing us to track the case.
68 68  
69 -The [[Ethics and Regulatory compliance form>>https://nettskjema.no/a/224765]] collects the necessary information needed for us to evaluate whether we can safely and legally share the data on the EBRAINS platforms.
81 +[[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 70  
83 +We look for organized data, not organized according to our standard. This is to support the broadest degree of sharing possible. We do however require that the data is organized in a consistent and precise manner. Please see our// //[[collection of guidelines on data organization>>https://drive.ebrains.eu/smart-link/25299f04-c4e5-4028-8f5f-3b8208f9a532/]] for further guidance.
71 71  
72 -==== **2. Upload data ** ====
85 +[[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).**
73 73  
74 -EBRAINS offers secure, long-term storage at [[CSCS Swiss National Supercomputing Centre>>url:https://www.cscs.ch/]], with currently no upper limit of storage capacity. The data must be consistently structured prior to upload. 
87 +//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.
75 75  
76 -For smaller datasets with a reasonable amount of files, we recommend using the Collab-Bucket solution (drag-and-drop). A Collab Bucket must first be assigned to a dataset, which happens when a datasets is accepted for sharing.
89 +//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.
77 77  
78 -For larger datasets or datasets with a large amount of files, we recommend using a programmatic approach. The [[python script>>https://github.com/eapapp/ebrains-data-storage/tree/main/data-proxy]] is interactive and does not require any additional programming.
79 79  
92 +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. 
80 80  
81 81  If a data collection is already uploaded elsewhere, we may link to the already existing repository.
82 82  
83 83  
84 -==== **3. Submit metadata** ====
97 +(% style="color:#1a202c; font-family:inherit; font-size:23px" %)**3. Submit metadata**
85 85  
86 -Easily submit openMINDS-compatible metadata via our [[metadata wizard>>https://ebrains-metadata-wizard.apps.hbp.eu/]]. This form covers all the required metadata for sharing data via EBRAINS. When you're ready to 'Submit', the metadata and all uploaded files will be sent to the Curation team.
87 87  
88 -For power-users interested in exploring the full span of the openMINDS framework, please check out the [[openMINDS GitHub>>https://github.com/HumanBrainProject/openMINDS]] to learn more about how to programmatically gather your metadata. A stable version of the openMINDS package can be found on [[PyPi>>https://pypi.org/project/openMINDS/]]. We accept openMINDS metadata as JSON-LD (share these with us via curation-support@ebrains.eu). Additional documentation of openMINDS metadata submodules and schemas can be found on [[the openMINDS GitHub Wiki>>https://humanbrainproject.github.io/openMINDS/]].
100 +[[image:https://lh5.googleusercontent.com/WS4T2LhF9znWWChn3Z550agLrrb-KTWdYVsJSv0lh4cGjKbjuN1WV68WER9xkYqi1UqN7KYZz7bImYz3_TpOuTuvma7T192QUiUZoyJVPk1fj5NSDSQh_kpIeBufAOdDtsDRpPKK_P5EDPqRCTAaOTNyCw=s2048||height="91px;" width="91px;"]]**Submit metadata using our **[[EBRAINS Metadata wizard>>https://ebrains-metadata-wizard.apps.hbp.eu/]]** (opt. 1), or through direct interaction with the Knowledge Graph (opt. 2) **
89 89  
102 +//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
90 90  
104 +//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:
105 +
106 +* 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.
107 +* [[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.
108 +* [[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.
109 +
110 +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.
111 +
112 +
113 +**The openMINDS metadata framework**
114 +
115 +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]].
116 +
117 +For feedback, requests, or contributions, please get in touch with the openMINDS development team via
118 +
119 +* the support-email: [[openminds@ebrains.eu>>path:mailto:openminds@ebrains.eu]]
120 +* the [[GitHub issue tracker>>url:https://github.com/HumanBrainProject/openMINDS/issues]]
121 +* the INCF NeuroStars [[openMINDS Community Forum>>url:https://neurostars.org/t/openminds-community-forum-virtual/20156]]
122 +
123 +
91 91  ==== **4. Write a Data Descriptor ** ====
92 92  
126 +[[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]]** . **
127 +
93 93  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. 
94 94  
95 -[[The template >>https://drive.ebrains.eu/f/a2e07c95b1a54090bbbc/?dl=1]]safely guides you through the process of making one. Check out previous examples in the KG Search, e.g. the Data Descriptor for a dataset containing histology images of the rat brain stained for an anterograde tracer (see [[an example>>https://doi.org/10.25493/2MX9-3XF]]).
130 +See our infographic about the data descriptor for inspiration or guidance.
96 96  
132 +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]]".
97 97  
98 98  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.
99 99  
100 100  
137 +|(% style="width:175px" %)[[[[image:image-20230324171109-1.png||height="154" width="109"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]|(% style="width:1662px" %)The EBRAINS Data descriptor at-a-glance
138 +
101 101  ==== **5. Preview and publish ** ====
102 102  
103 -A Curator will assemble a dataset in the EBRAINS Knowledge Graph that combines the data, metadata and data descriptor. Once ready, the data provider will receive a private URL for previewing the dataset prior to release. We need an official approval from the data custodian{{footnote}}The Data Custodian is responsible for the content and quality of the Data and metadata, and is the person to be contacted by EBRAINS CS in case of any misconduct related to the Data. It is the obligation of a Data Custodian to keep EBRAINS informed about changes in the contact information of the authors of the Datasets provided by them ([[EBRAINS Data Provision Protocol - version 1.1>>https://strapi-prod.sos-ch-dk-2.exo.io/EBRAINS_Data_Provision_Protocol_dfe0dcb104.pdf]]).{{/footnote}} to release the dataset. Once released, a [[DataCite DOI>>https://datacite.org/]] will be generated for the dataset. If the identical data collection has received a DOI elsewhere, we recommend re-using the already issued DOI.
104 104  
142 +[[image:https://lh4.googleusercontent.com/XqT26Q4yWJK26cjtjhI4ToXoZZMxhT9LimG4Hk9mePxy0-KPKgpVIzcuiP5mOQowBgf2JjkrWUq2VbCmafWWZPJplEZALnFOlCZHLlQgzOx7fFwoBteyi_IlMLkPBS9vtOcdNIZ59HyLnQz4RsTQ0lUrSw=s2048||height="91px;" width="91px;"]]**Preview and approve the release of your dataset. **Once a Curator has assembled the dataset in the EBRAINS Knowledge Graph, combining the data, metadata and data descriptor, the data provider will receive a private URL for previewing the dataset prior to release. We need an official approval from the data custodian{{footnote}}The Data Custodian is responsible for the content and quality of the Data and metadata, and is the person to be contacted by EBRAINS CS in case of any misconduct related to the Data. It is the obligation of a Data Custodian to keep EBRAINS informed about changes in the contact information of the authors of the Datasets provided by them ([[EBRAINS Data Provision Protocol - version 1.1>>https://strapi-prod.sos-ch-dk-2.exo.io/EBRAINS_Data_Provision_Protocol_dfe0dcb104.pdf]]).{{/footnote}} to release the dataset. Once released, a [[DataCite DOI>>https://datacite.org/]] will be generated for the dataset. If the identical data collection has received a DOI elsewhere, we recommend re-using the already issued DOI.
105 105  
144 +
106 106  ----
107 107  
108 108  ==== **Sharing human data ** ====
109 109  
110 -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]].
111 -
112 112  (% class="box floatinginfobox" %)
113 113  (((
114 -For **Human subject data**, the data must be //either//
151 +**Human subject data that can be shared on EBRAINS consists of:**
115 115  
116 116  - Post-mortem data
117 -
118 118  - Aggregated data
155 +- Strongly pseudonymized or de-identified subject data with a legal basis for sharing (e.g. Informed Consent)
119 119  
120 -- Pseudonymized subject data with a legal basis for sharing (e.g. Informed Consent)
121 -
122 -(% 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. //
157 +(% class="small" %)//If you have human data that does not classify as any of the above, please get in touch and we will clarify the available options. //
123 123  )))
124 124  
125 -Pseudonymized data is shared via the Human Data Gateway (HDG) due to GDPR regulations. The HDG adds an authentication layer to the data.
160 +Human data shared on EBRAINS must comply with [[GDPR >>https://gdpr-info.eu/]]and [[EU directives>>https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=celex%3A32010L0063]]. The information we need to assess this is collected via our [[Ethics and Regulatory Compliance Survey>>https://nettskjema.no/a/224765]].
126 126  
127 -**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.
128 -\\**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.
129 -\\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.
162 +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).
130 130  
164 +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.
131 131  
166 +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.
167 +
168 +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.
169 +
170 +
132 132  ----
133 133  
134 134  === Step by Step - Models ===
135 135  
136 -[place-holder-process-diagram]
137 137  
138 -==== **1. model step 1 ** ====
176 +~1. Request curation using the [[Curation request form>>https://nettskjema.no/a/277393#/]]. You will be contacted by a curator with more information.
139 139  
140 -Text
141 141  
179 +//Additional information will be added soon.//
142 142  
143 -==== **2. model step 2** ====
181 +----
144 144  
145 -Text
183 +=== Step by Step - Software ===
146 146  
185 +[[[[image:swc-flow-no-header.png||alt="swc-flow.png"]]>>https://www.ebrains.eu/tools/ebrains-curation-request-form||rel="noopener noreferrer" target="_blank"]]
147 147  
148 -----
187 +~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.
149 149  
150 -=== Step by Step - Code ===
189 +2. Enter the metadata of your software in your private space of the [[Knowledge Graph Editor>>url:https://editor.kg.ebrains.eu/]] by using the links provided by the curator. Please provide the metadata for your software as complete as possible. This makes it easier for users to find and use your software. If you have questions feel free to contact the curation support. After you have finished editing your entries, please let the curators know by replying to your ticket. We curate your metadata and get back to you, if necessary.
151 151  
152 -[place-holder-process-diagram]
191 +3. After a quality check, we integrate and publish the information to the Knowledge Graph. Your software is then searchable and usable for the neuroscience community.[[[[image:Thumb.png||alt="EBRAINS-Share-Software.pdf" height="315" style="float:right" width="215"]]>>attach:EBRAINS-Share-Software.pdf]]
153 153  
154 -==== **1. code step 1 ** ====
193 +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]].
155 155  
156 -Text
195 +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.
157 157  
158 158  
159 -==== **2. code step 2** ====
160 160  
161 -Text
162 162  
163 -----
164 164  
165 -=== When you've completed the curation process ===
166 166  
167 -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]].
168 168  
169 -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]].
170 170  
171 171  ----
172 172  
173 -== **Information and resources for researchers looking to share data** ==
206 +== **The curation team: meet the curators** ==
174 174  
175 -Below you can find some resources that can come in handy if you are looking to share data via EBRAINS, or in general.
208 +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.
176 176  
177 -----
210 +The curators in EBRAINS are located in Oslo, Jülich, Trier and Paris. 
211 +
178 178  
179 -=== **The benefits of sharing data ** ===
213 +**Located in Norway:**
180 180  
181 -(% 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.
215 +|(% style="width:303px" %)(((
216 +[[image:My project2.jpg||height="209" width="167"]]
182 182  
183 -(% 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.
218 +**Archana Golla**
184 184  
220 +(% class="small" %)Curation Scientist
221 +Neuroscience (PhD)(%%)
222 +(% class="small" style="color:#4a5568" %)**Behavioral neuroscience and microscopy**
223 +)))|(% style="width:303px" %)(((
224 +[[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
185 185  
186 -By sharing your data via EBRAINS, you gain access to the following benefits:
226 +**Camilla H. Blixhavn**
187 187  
188 -[[image:image-20230324170841-3.png]]
228 +(% class="small" %)Curation Scientist,
229 +Phd Student
230 +Neuroscience (M. Sc.)(%%)
231 +(% class="small" style="color:#4a5568" %)**Neuroanatomy and data integration**
232 +)))|(% style="width:303px" %)(((
233 +[[image:My project (1).jpg||height="209" width="167"]]
189 189  
235 +**Ingrid Reiten**
190 190  
237 +(% class="small" %)Curation Scientist,
238 +Phd Student
239 +Neuroscience (M. Sc.)(%%)
240 +(% class="small" style="color:#4a5568" %)**Neuroanatomy and structural connectivity**
241 +)))|(% style="width:303px" %)(((
242 +[[image:My project1.jpg||height="209" width="167"]]
191 191  
192 -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.
244 +**Sophia Pieschnik**
193 193  
246 +(% class="small" %)Curation Scientist
247 +Neurocognitive Psychology (M. Sc.)(%%)
248 +(% class="small" style="color:#4a5568" %)**Neuroimaging **
249 +)))
194 194  
251 +|(% style="width:303px" %)(((
252 +[[image:My project.jpg||height="209" width="167"]]
253 +
254 +**Heidi Kleven**
255 +
256 +(% class="small" %)Curation Scientist,
257 +Phd Student
258 +Neuroscience (M. Sc.)(%%)
259 +(% class="small" style="color:#4a5568" %)**Neuroanatomy and brain atlases**
260 +)))| | |
261 +
262 +
263 +\\**Located in Germany:**
264 +
265 +|(% style="width:303px" %)(((
266 +[[image:My project (2).jpg||height="209" width="167"]]
267 +
268 +**Jan Gündling**
269 +
270 +(% class="small" %)Curation Scientist,
271 +Phd Student
272 +Sensors and Cognitive Psychology (M. Sc.)(%%)
273 +(% class="small" style="color:#4a5568" %)**Human-Computer Interaction**
274 +)))|(% style="width:303px" %)(((
275 +
276 +
277 +
278 +
279 +
280 +
281 +
282 +
283 +
284 +
285 +
286 +
287 +**Lyuba Zehl**
288 +
289 +(% class="small" %)Knowledge Systems Engineer
290 +Dr. rer. nat. (Systems Neuroscience)(%%)
291 +(% class="small" style="color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
292 +)))|(% style="width:303px" %) |
293 +
195 195  ----
196 196  
197 -(% style="font-family:inherit" %) (% style="color:#1a202c; font-family:inherit; font-size:26px" %)**What can I share on EBRAINS? **
296 +== **Add practical value to your shared data, model or software** ==
198 198  
199 -(% class="wikigeneratedid" id="H" %)
200 -[[image:image-20230324170829-2.png]]
201 201  
299 +==== **Add a tutorial or learning resource ** ====
202 202  
301 +(% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
302 +(% style="color:#000000" %)//More information will follow//
303 +
304 +
305 +==== **Create a workflow** ====
306 +
307 +(% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
308 +(% style="color:#000000" %)//More information will follow//
309 +
203 203  ----
204 204  
205 -=== **At a glance: "Sharing experimental data on EBRAINS" ** ===
312 +=== **Showcase shared data, models or software in other services** ===
206 206  
314 +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.
207 207  
208 -|(% style="width:439px" %)(((
209 -[[[[image:image-20230324171114-2.png||height="354" width="250"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
210 -)))|(% style="width:461px" %)(((
211 -[[[[image:image-20230324171109-1.png||height="352" width="250"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
212 -)))|(% style="width:416px" %)[[[[image:image-20230330120354-1.png||height="352" width="250"]]>>https://drive.ebrains.eu/f/707147a883b94fae8e69/]]
213 -|(% 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. //
316 +**Viewer for 2D images **
214 214  
318 +* 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]].
319 +
320 +**Viewer for sequential atlas-registered 2D images with annotation options**
321 +
322 +* 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]].
323 +
324 +**Use your research product in an interactive publication **
325 +
326 +* 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]].
327 +
328 +**Interactive 3D atlas viewer with options for data visualization**
329 +
330 +* 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]].
331 +
215 215  ----
216 216  
217 -=== **Integrate your data in the EBRAINS atlas services** ===
334 +=== **The benefits of sharing data ** ===
218 218  
219 -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.
336 +By sharing your data via EBRAINS, you gain access to the following benefits:
220 220  
221 -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.
338 +[[image:image-20230324170841-3.png]]
222 222  
340 +
341 +
342 +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.
343 +
344 +
223 223  ----
224 224  
225 -=== **Common concerns - and answers ** ===
347 +=== ===
226 226  
349 +=== **Frequently asked questions ** ===
350 +
227 227  (((
228 228  ==== ====
229 229  
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274 274  
275 275  
276 276  {{putFootnotes/}}
401 +~)~)~)~)~)~)
402 +~)~)~)
403 +~)~)~)~)~)~)~)~)~)
404 +~)~)~)~)~)~)
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