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Changes for page data-curation-copy

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1 +== Publishing neuroscience data, models and software via EBRAINS ==
3 3  
3 +
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 +
4 4  {{box title="**Contents**"}}
5 5  {{toc depth="3" start="2"/}}
6 6  {{/box}}
7 7  
8 -== Publishing data via EBRAINS ==
9 9  
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.
12 +== **Information to get started** ==
11 11  
12 -
13 13  (% style="text-align: center;" %)
14 14  **Get started! **
15 15  
16 16  (% style="text-align: center;" %)
17 -**[[REQUEST CURATION>>https://nettskjema.no/a/277393#/]] **
18 +**[[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. **
18 18  
19 19  (% style="text-align: center;" %)
20 - Search existing data, models and code in [[the EBRAINS Knowledge Graph>>https://kg.ebrains.eu/search/?facet_type[0]=Dataset]]
21 +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.
21 21  
22 22  
23 -----
24 +(% style="text-align: center;" %)
25 +Search existing data, models and software in [[the EBRAINS Knowledge Graph Search>>https://kg.ebrains.eu/search/?facet_type[0]=Dataset]]
24 24  
25 -=== **All neuroscience data are welcome** ===
26 26  
27 -(% class="wikigeneratedid" id="H" %)
28 -[[image:image-20230324170829-2.png]]
28 +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. 
29 +
29 29  
31 +(% class="box infomessage" %)
32 +(((
33 +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.
34 +)))
35 +
36 +(% class="box successmessage" %)
37 +(((
38 +**Particular needs? Contact us! **The workflows for sharing can be modified for researchers or research groups aiming to frequently publish larger numbers of their research products through EBRAINS. Please contact the curation service team in such cases
39 +)))
40 +
30 30  ----
31 31  
32 -=== **Benefits of sharing data ** ===
43 +== **The EBRAINS curation process** ==
33 33  
34 -By sharing your data via EBRAINS, you gain access to the following benefits:
45 +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. 
35 35  
36 -[[image:image-20230324170841-3.png]]
47 +>The EBRAINS curation process involves organising and annotating neuroscientific data to make the data discoverable and reusable.
37 37  
49 +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.
38 38  
51 +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]].
39 39  
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}}.
53 +The curation of data, models and software is different. Thus, below we explain the process for sharing for each research product separately.
41 41  
55 +
42 42  ----
43 43  
44 -== **What is curation?** ==
58 +=== Step by step - Data ===
45 45  
46 ->The EBRAINS data curation process involves organising and annotating neuroscientific data to make the data discoverable and reusable.
47 47  
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.
61 +[[image:image-20230326054341-1.png]]
49 49  
63 +==== ====
50 50  
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 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.
65 +(% style="width:1841.22px" %)
66 +|(% style="width:344px" %)(((
67 +[[[[image:image-20230324171114-2.png||height="354" width="250"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
68 +)))|(% style="width:1493px" %)//Collection of useful information for researchers looking to share experimental data on EBRAINS.//
52 52  
53 -----
54 54  
55 -== **The process** ==
71 +==== **1. Provide some general information about your dataset** ====
56 56  
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.
58 58  
74 +[[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#/]]. **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.
59 59  
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]].
61 61  
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]].
77 +[[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]]**. This form collects the necessary information needed for us to evaluate whether we can ethically and legally share the data via EBRAINS.
63 63  
64 64  
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!
80 +==== **2. Upload data ** ====
66 66  
67 -=== Step by step - Experimental data ===
68 68  
83 +[[image:https://lh5.googleusercontent.com/sieKO-kW8O18iPaUyonwyo4UfHBmtc2E9BDnjbx52j6J_uGmm-OzGAo7sloMk3sYwKa6QW3hYQsOA9N4H7uGQpca088Wrk0Nurpt_J3B0-NSbcaPNdZIh21otQcG6jnAxLGiKoEvkTyaDGTMk3fu7me8mQ=s2048||height="94px;" width="94px;"]]**Ensure data is structured consistently prior to upload. **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.
69 69  
70 -[[image:image-20230326054341-1.png]]
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).**
71 71  
72 -==== **1. Provide some general information about your dataset** ====
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.
73 73  
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.
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.
75 75  
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.
77 77  
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. 
78 78  
79 -==== **2. Upload data ** ====
94 +If a data collection is already uploaded elsewhere, we may link to the already existing repository.
80 80  
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. 
82 82  
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.
84 84  
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.
98 +|(% style="width:369px" %) |(% style="width:1467px" %)
86 86  
87 87  
88 -If a data collection is already uploaded elsewhere, we may link to the already existing repository.
101 +==== **3. Submit metadata** ====
89 89  
90 90  
91 -==== **3. Submit metadata** ====
104 +[[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) **
92 92  
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.
106 +//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
94 94  
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/]].
108 +//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:
96 96  
110 +* 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.
111 +* [[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.
112 +* [[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.
97 97  
114 +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.
115 +
116 +
117 +**The openMINDS metadata framework**
118 +
119 +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]].
120 +
121 +For feedback, requests, or contributions, please get in touch with the openMINDS development team via
122 +
123 +* the support-email: [[openminds@ebrains.eu>>path:mailto:openminds@ebrains.eu]]
124 +* the [[GitHub issue tracker>>url:https://github.com/HumanBrainProject/openMINDS/issues]]
125 +* the INCF NeuroStars [[openMINDS Community Forum>>url:https://neurostars.org/t/openminds-community-forum-virtual/20156]]
126 +
98 98  ==== **4. Write a Data Descriptor ** ====
99 99  
100 -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. 
101 101  
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]]).
130 +[[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]]** . **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. 
103 103  
104 104  
133 +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]]".
134 +
105 105  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.
106 106  
107 107  
138 +|(% 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
139 +
108 108  ==== **5. Preview and publish ** ====
109 109  
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.
111 111  
143 +[[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.
112 112  
145 +
113 113  ----
114 114  
115 115  ==== **Sharing human data ** ====
116 116  
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]].
118 -
119 119  (% class="box floatinginfobox" %)
120 120  (((
121 -For **Human subject data**, the data must be //either//
152 +**Human subject data that can be shared on EBRAINS consists of:**
122 122  
123 123  - Post-mortem data
124 -
125 125  - Aggregated data
156 +- Strongly pseudonymized or de-identified subject data with a legal basis for sharing (e.g. Informed Consent)
126 126  
127 -- Pseudonymized subject data with a legal basis for sharing (e.g. Informed Consent)
128 -
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. //
158 +(% 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. //
130 130  )))
131 131  
132 -Pseudonymized data is shared via the Human Data Gateway (HDG) due to GDPR regulations. The HDG adds an authentication layer to the data.
161 +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]].
133 133  
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.
163 +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).
138 138  
165 +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.
139 139  
167 +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.
168 +
169 +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.
170 +
171 +
140 140  ----
141 141  
142 142  === Step by Step - Models ===
143 143  
144 -[place-holder-process-diagram]
145 145  
146 -==== **1. model step 1 ** ====
177 +~1. Request curation using the [[Curation request form>>https://nettskjema.no/a/277393#/]]. You will be contacted by a curator with more information.
147 147  
148 -Text
149 149  
180 +//Additional information will be added soon.//
150 150  
151 -==== **2. model step 2** ====
182 +----
152 152  
153 -Text
184 +=== Step by Step - Software ===
154 154  
186 +[[[[image:swc-flow-no-header.png||alt="swc-flow.png"]]>>https://www.ebrains.eu/tools/ebrains-curation-request-form||rel="noopener noreferrer" target="_blank"]]
155 155  
188 +~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.
189 +
190 +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.
191 +
192 +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]]
193 +
194 +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]].
195 +
196 +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.
197 +
198 +
199 +
200 +
201 +
202 +
203 +
204 +
156 156  ----
157 157  
158 -=== Step by Step - Code ===
207 +== **The curation team: meet the curators** ==
159 159  
160 -[place-holder-process-diagram]
209 +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.
161 161  
162 -==== **1. code step 1 ** ====
211 +The curators in EBRAINS are located in Oslo, Jülich, Trier and Paris. 
212 +
163 163  
164 -Text
214 +**Located in Norway:**
165 165  
216 +|(% style="width:303px" %)(((
217 +[[image:My project2.jpg||height="209" width="167"]]
166 166  
167 -==== **2. code step 2** ====
219 +**Archana Golla**
168 168  
169 -Text
221 +(% class="small" %)Curation Scientist
222 +Neuroscience (PhD)(%%)
223 +(% class="small" style="color:#4a5568" %)**Behavioral neuroscience and microscopy**
224 +)))|(% style="width:303px" %)(((
225 +[[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
170 170  
227 +**Camilla H. Blixhavn**
228 +
229 +(% class="small" %)Curation Scientist,
230 +Phd Student
231 +Neuroscience (M. Sc.)(%%)
232 +(% class="small" style="color:#4a5568" %)**Neuroanatomy and data integration**
233 +)))|(% style="width:303px" %)(((
234 +[[image:My project (1).jpg||height="209" width="167"]]
235 +
236 +**Ingrid Reiten**
237 +
238 +(% class="small" %)Curation Scientist,
239 +Phd Student
240 +Neuroscience (M. Sc.)(%%)
241 +(% class="small" style="color:#4a5568" %)**Neuroanatomy and structural connectivity**
242 +)))|(% style="width:303px" %)(((
243 +[[image:My project1.jpg||height="209" width="167"]]
244 +
245 +**Sophia Pieschnik**
246 +
247 +(% class="small" %)Curation Scientist
248 +Neurocognitive Psychology (M. Sc.)(%%)
249 +(% class="small" style="color:#4a5568" %)**Neuroimaging **
250 +)))
251 +
252 +|(% style="width:303px" %)(((
253 +[[image:My project.jpg||height="209" width="167"]]
254 +
255 +**Heidi Kleven**
256 +
257 +(% class="small" %)Curation Scientist,
258 +Phd Student
259 +Neuroscience (M. Sc.)(%%)
260 +(% class="small" style="color:#4a5568" %)**Neuroanatomy and brain atlases**
261 +)))| | |
262 +
263 +
264 +\\**Located in Germany:**
265 +
266 +|(% style="width:303px" %)(((
267 +[[image:My project (2).jpg||height="209" width="167"]]
268 +
269 +**Jan Gündling**
270 +
271 +(% class="small" %)Curation Scientist,
272 +Phd Student
273 +Sensors and Cognitive Psychology (M. Sc.)(%%)
274 +(% class="small" style="color:#4a5568" %)**Human-Computer Interaction**
275 +)))|(% style="width:303px" %)(((
276 +
277 +
278 +
279 +
280 +
281 +
282 +
283 +
284 +
285 +
286 +
287 +
288 +**Lyuba Zehl**
289 +
290 +(% class="small" %)Knowledge Systems Engineer
291 +Dr. rer. nat. (Systems Neuroscience)(%%)
292 +(% class="small" style="color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
293 +)))|(% style="width:303px" %) |
294 +
171 171  ----
172 172  
173 -== **Resources for researchers looking to share data** ==
297 +== **Add practical value to your shared data, model or software** ==
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.
176 176  
300 +==== **Add a tutorial or learning resource ** ====
301 +
302 +(% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
303 +(% style="color:#000000" %)//More information will follow//
304 +
305 +
306 +==== **Create a workflow** ====
307 +
308 +(% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
309 +(% style="color:#000000" %)//More information will follow//
310 +
177 177  ----
178 178  
179 -=== **Useful information about sharing of experimental data on EBRAINS ** ===
313 +=== **Showcase shared data, models or software in other services** ===
180 180  
315 +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.
181 181  
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/]]
186 -)))
187 -|(% style="width:593px" %)//Collection of useful information for researchers looking to share experimental data on EBRAINS.//|(% style="width:1240px" %)//The EBRAINS data descriptor//
317 +**Viewer for 2D images **
188 188  
319 +* 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]].
320 +
321 +**Viewer for sequential atlas-registered 2D images with annotation options**
322 +
323 +* 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]].
324 +
325 +**Use your research product in an interactive publication **
326 +
327 +* 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]].
328 +
329 +**Interactive 3D atlas viewer with options for data visualization**
330 +
331 +* 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]].
332 +
189 189  ----
190 190  
191 -=== **Introduction to data organisation ** ===
335 +=== **The benefits of sharing data ** ===
192 192  
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.
337 +By sharing your data via EBRAINS, you gain access to the following benefits:
194 194  
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?
339 +[[image:image-20230324170841-3.png]]
198 198  
341 +
342 +
343 +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.
344 +
345 +
199 199  ----
200 200  
201 -=== **Integrate your data in the EBRAINS atlas services** ===
348 +=== **At a glance: "Sharing experimental data on EBRAINS" ** ===
202 202  
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.
204 204  
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.
206 206  
207 207  ----
208 208  
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211 211  (((
212 212  ==== ====
213 213  
214 ->
215 -
216 216  (((
217 217  >The curation process is time consuming and difficult
218 218  )))
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260 260  
261 261  
262 262  {{putFootnotes/}}
406 +~)~)~)~)~)~)
407 +~)~)~)
408 +~)~)~)~)~)~)~)~)~)
409 +~)~)~)~)~)~)
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