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1		-XWiki.jan
	1	+XWiki.ingrreit

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1		-== Publishing neuroscience data, models and software via EBRAINS ==
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2	2
3	3
	20	+(% class="wikigeneratedid" id="HPublishingneurosciencedata2CmodelsandsoftwareviaEBRAINS" %)
	21	+(% style="font-size:2em" %)**Publishing neuroscience data, models and software via EBRAINS**
	22	+
4	4	(% class="wikigeneratedid" %)
5	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	6
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8	8	{{toc depth="3" start="2"/}}
9	9	{{/box}}
10	10
11		-
12	12	== **Information to get started** ==
13	13
14	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. **
...	...	@@ -16,8 +16,10 @@
16	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	17
18	18
19		-(% style="text-align: center;" %)
20		-Search existing data, models and software in [[the EBRAINS Knowledge Graph Search>>https://kg.ebrains.eu/search/?facet_type[0]=Dataset]]
	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	+)))
21	21
22	22
23	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.
...	...	@@ -55,18 +55,27 @@
55	55
56	56	[[image:image-20230326054341-1.png]]
57	57
58		-==== [[[[image:image-20230324171114-2.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]//All you need to know to share data on EBRAINS.// ====
	78	+(% class="box floatinginfobox" id="share-data-infographic" %)
	79	+(((
	80	+(% style="text-align:center" %)
	81	+//Download our infographic//
	82	+//with all you need to know//
	83	+//to share data on EBRAINS: //
	84	+// //
	85	+[[[[image:image-20230324171114-2.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
	86	+)))
59	59
60	60
61	61	==== **1. Provide some general information about your dataset** ====
62	62
63	63
64		-[[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#/]]. **
65	65
	93	+(% style="margin-right:10px" %)[[image:https://lh3.googleusercontent.com/zh7TvO6w04YGW9jIhfhmdT6CexdGs-AWOLfJXKRq7-tdHOu6ar1rOQx8o4rZevrjXqgPZ7-Ejv4b6X9XpgXuHpdUXi-mBTHIUnv5Vz-DktHt0sP-PZ3gE8XgZid3TV3swV1uTCBhHx11ge0pjP7RVxswGQ=s2048||height="85px;" width="91px;"]](%%)** Fill in the [[Curation request form>>https://nettskjema.no/a/277393#/]]. **
	94	+
66	66	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.
67	67
68	68
69		-[[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]]**.
	98	+(% style="margin-right:10px" %)[[image:https://lh6.googleusercontent.com/yw442oS6BwZOlY-_0BoVxyCW3DrdcJ5ogCes92iOD16_rgNEVk56aNMDaVWXFfBLYv24bHzmGgBF9wg0szjH70xzuRTqxoQAeuy3knNO7axCHoyZDXwtyTcMgFnYwbOYxOT29LK-zchrUKLW6Mle93kOkQ=s2048||height="94px;" width="94px;"]](%%)**Fill in the [[Ethics and Regulatory compliance form>>https://nettskjema.no/a/224765]]**.
70	70
71	71	This form collects the necessary information needed for us to evaluate whether we can ethically and legally share the data via EBRAINS.
72	72
...	...	@@ -75,18 +75,28 @@
75	75
76	76	==== **2. Upload data ** ====
77	77
	107	+(% class="box floatinginfobox" id="share-data-infographic" %)
	108	+(((
	109	+(% style="text-align:center" %)
	110	+//Download our infographic//
	111	+//with guidelines
	112	+on data organization: //
78	78
79		-[[image:https://lh5.googleusercontent.com/sieKO-kW8O18iPaUyonwyo4UfHBmtc2E9BDnjbx52j6J_uGmm-OzGAo7sloMk3sYwKa6QW3hYQsOA9N4H7uGQpca088Wrk0Nurpt_J3B0-NSbcaPNdZIh21otQcG6jnAxLGiKoEvkTyaDGTMk3fu7me8mQ=s2048||height="94px;" width="94px;"]]**Ensure data is structured consistently prior to upload. **
	114	+(% style="text-align:center" %)
	115	+[[[[image:image-20230621121014-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/lib/f5cf4964-f095-49bd-8c34-e4ffda05a497/file/ebrains-infographic-data-organisation.pdf/]]
	116	+)))
80	80
81		-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.
	118	+(% style="margin-right:10px" %)[[image:https://lh5.googleusercontent.com/sieKO-kW8O18iPaUyonwyo4UfHBmtc2E9BDnjbx52j6J_uGmm-OzGAo7sloMk3sYwKa6QW3hYQsOA9N4H7uGQpca088Wrk0Nurpt_J3B0-NSbcaPNdZIh21otQcG6jnAxLGiKoEvkTyaDGTMk3fu7me8mQ=s2048||height="94px;" width="94px;"]](%%)**Ensure data is structured consistently prior to upload. **
82	82
83		-[[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).**
	120	+We look for organized data, not organized according to our standard. This is to support the broadest degree of sharing possible. We do however require that the data is organized in a consistent and precise manner. Please see our// //[[guidelines on data organization>>https://drive.ebrains.eu/smart-link/25299f04-c4e5-4028-8f5f-3b8208f9a532/]] for further guidance.
84	84
85		-//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.
	122	+(% style="margin-right:10px" %)[[image:https://lh5.googleusercontent.com/EWtYwfVlbeC-jqPasgmzidqc50GrkKIEgwXeUeql8aaMHIukmFdWEy0nufVWWATbxDDK3XwwZEDmASrbpCsBk1u0HpAd8x4ZgAMsMPRcWyrb9etlV6FgKE_QN2e6SqKxHE0rzkR8uI1rRW_5z21TFGYVnw=s2048||height="91px;" width="91px;"]](%%)**Upload data to EBRAINS Storage, either using a drag-and-drop solution (opt. 1) or an interactive python script (opt. 2).**
86	86
87		-//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.
	124	+**Opt. 1. **For smaller datasets with a reasonable amount of files, we recommend using the Collab-Bucket solution (drag-and-drop). A Collab Bucket must first be assigned to a dataset, which happens when a datasets is accepted for sharing.
88	88
	126	+**Opt. 2. **For larger datasets or datasets with a large amount of files, we recommend using a programmatic approach. The [[python script>>https://github.com/eapapp/ebrains-data-storage/tree/main/data-proxy]] is interactive and does not require any additional programming.
89	89
	128	+
90	90	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.
91	91
92	92	If a data collection is already uploaded elsewhere, we may link to the already existing repository.
...	...	@@ -95,11 +95,11 @@
95	95	==== **3. Submit metadata** ====
96	96
97	97
98		-[[image:https://lh5.googleusercontent.com/WS4T2LhF9znWWChn3Z550agLrrb-KTWdYVsJSv0lh4cGjKbjuN1WV68WER9xkYqi1UqN7KYZz7bImYz3_TpOuTuvma7T192QUiUZoyJVPk1fj5NSDSQh_kpIeBufAOdDtsDRpPKK_P5EDPqRCTAaOTNyCw=s2048||height="91px;" width="91px;"]]**Submit metadata using the **[[EBRAINS Wizard>>https://ebrains-metadata-wizard.apps.hbp.eu/]]** (opt. 1), or through direct interaction with the Knowledge Graph (opt. 2) **
	137	+(% style="margin-right:10px" %)[[image:https://lh5.googleusercontent.com/WS4T2LhF9znWWChn3Z550agLrrb-KTWdYVsJSv0lh4cGjKbjuN1WV68WER9xkYqi1UqN7KYZz7bImYz3_TpOuTuvma7T192QUiUZoyJVPk1fj5NSDSQh_kpIeBufAOdDtsDRpPKK_P5EDPqRCTAaOTNyCw=s2048||height="91px;" width="91px;"]](%%)**Submit metadata using the **[[EBRAINS Metadata Wizard>>https://ebrains-metadata-wizard.apps.hbp.eu/]]** (opt. 1), or directly via the Knowledge Graph (opt. 2) **
99	99
100		-//Opt. 1.// Manually submit the minimal required metadata via the [[EBRAINS 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
	139	+**Opt. 1.** Manually submit the minimal required metadata via the [[EBRAINS Metadata Wizard>>https://ebrains-metadata-wizard.apps.hbp.eu/]]. The minimal required metadata covers extended bibliographic information necessary to publish your dataset on EBRAINS. The submitted information, including uploaded files, will be sent to the Curation team automatically
101	101
102		-//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:
	141	+**Opt. 2.** To go beyond the minimal required metadata, you can directly interact with the Knowledge Graph (KG) in your private space. Within the private space, you can upload metadata and interact with them, moreover you can connect your metadata to existing publicly accessible entries. Access to your private space is granted upon the initiation of the curation process. You can access your private space via:
103	103
104	104	* 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.
105	105	* [[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.
...	...	@@ -108,10 +108,12 @@
108	108	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.
109	109
110	110
111		-==== **4. Write a Data Descriptor ** ====
	150	+==== **4. Write a Data Descriptor** ====
112	112
113		-[[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]]** . **
114	114
	153	+
	154	+(% style="margin-right:10px" %)[[image:https://lh4.googleusercontent.com/lMYEKOXzejbBydOdotWWteXQo7j363xRyntBGjcPZVEdtIU1CJYX7q1STpdr2JPZK4hpWWXk20UlkUOqDGL5kX6vnQVBSdrfUo6EGfXOwpuGq1Uygv0tTZJ0lRO6voJvg56QC2mufvjAcRXGfAKFOjtc6w=s2048||height="94px;" width="94px;"]](%%)**Write a data descriptor by filling in **[[this template>>https://drive.ebrains.eu/f/a2e07c95b1a54090bbbc/?dl=1]]**.**
	155	+
115	115	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.
116	116
117	117	See our infographic about the data descriptor for inspiration or guidance.
...	...	@@ -120,74 +120,178 @@
120	120
121	121	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.
122	122
123		-==== [[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]//The EBRAINS Data descriptor at-a-glance// ====
124	124
	165	+(% class="box floatinginfobox" id="data-descriptor-infographic" %)
	166	+(((
	167	+(% style="text-align:center" %)
	168	+//Download our infographic
	169	+about the EBRAINS Data//
	170	+//Descriptor//
	171	+// //
	172	+[[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
	173	+)))
125	125
126		-==== **5. Preview and publish ** ====
	175	+==== **5. Preview and publish** ====
127	127
128	128
129		-[[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.
	178	+(% style="margin-right:10px" %)[[image:https://lh4.googleusercontent.com/XqT26Q4yWJK26cjtjhI4ToXoZZMxhT9LimG4Hk9mePxy0-KPKgpVIzcuiP5mOQowBgf2JjkrWUq2VbCmafWWZPJplEZALnFOlCZHLlQgzOx7fFwoBteyi_IlMLkPBS9vtOcdNIZ59HyLnQz4RsTQ0lUrSw=s2048||height="91px;" width="91px;"]](%%)**Preview and approve the release of your dataset. **
130	130
	180	+Once a Curator has assembled the dataset in the EBRAINS Knowledge Graph, combining the data, metadata and data descriptor, the data provider will receive a private URL for previewing the dataset prior to release. We need an official approval from the data custodian{{footnote}}The Data Custodian is responsible for the content and quality of the Data and metadata, and is the person to be contacted by EBRAINS CS in case of any misconduct related to the Data. It is the obligation of a Data Custodian to keep EBRAINS informed about changes in the contact information of the authors of the Datasets provided by them ([[EBRAINS Data Provision Protocol - version 1.1>>https://strapi-prod.sos-ch-dk-2.exo.io/EBRAINS_Data_Provision_Protocol_dfe0dcb104.pdf]]).{{/footnote}} to release the dataset. Once released, a [[DataCite DOI>>https://datacite.org/]] will be generated for the dataset. If the identical data collection has received a DOI elsewhere, we recommend re-using the already issued DOI.
131	131
	182	+
	183	+
	184	+
132	132	----
133	133
134		-==== **Sharing human subject data ** ====
	187	+=== Step by Step - Models ===
135	135
136		-(% class="box floatinginfobox" %)
137		-(((
138		-**Human subject data that can be shared on EBRAINS:**
139	139
140		-- Post-mortem data
141		-- Aggregated data
142		-- Strongly pseudonymized or de-identified subject data with a legal basis for sharing (e.g. Informed Consent)
	190	+==== 1. Start early ====
143	143
144		-(% 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. //
145		-)))
	192	+It is not necessary to wait until you are ready to publish to register your model with EBRAINS.
146	146
147		-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]].
	194	+By registering a model early in your project, you can take advantage of EBRAINS tools
	195	+to keep track of simulations and to share them with your collaborators.
148	148
149		-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).
	197	+==== 2. Create/choose a Collab workspace ====
150	150
151		-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.
	199	+We use EBRAINS Collaboratory "collab" workspaces to help manage the model curation process.
152	152
153		-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.
	201	+In particular, we use collab membership (the "Team") to control who can view or edit your model metadata prior to publication.
154	154
155		-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.
	203	+It is up to you whether you create a new collab for each model, or reuse an existing collab
	204	+(it is no problem to have multiple models associated with a single collab).
156	156
	206	+Collabs are also useful for storing simulation results, adding documentation for your model,
	207	+and/or providing tutorials in Jupyter notebooks.
157	157
158		-----
	209	+==== 3. Upload code ====
159	159
160		-=== Step by Step - Models ===
	211	+We recommend storing model code and/or configuration files in an online Git repository, for example on GitHub.
	212	+This repository should be public when you publish the model, but a private repository can be used for model development.
161	161
	214	+Alternatively, you can upload code to the Collab Drive or Bucket storage.
162	162
163		-~1. Request curation using the [[Curation request form>>https://nettskjema.no/a/277393#/]]. You will be contacted by a curator with more information.
	216	+==== 4.Submit metadata ====
164	164
	218	+We recommend submitting metadata using the Model Catalog app, installed in your collab.
165	165
166		-//Additional information will be added soon.//
	220	+To install it:
167	167
	222	+1. click the "+ Create" button
	223	+1. in the "Create Page" form, add a title, such as "Model Catalog", and select "Community App", then click "Create"
	224	+1. scroll down until you find the "Model Catalog" app, click "Select", then "Save & View"
	225	+
	226	+You will then see a table of all the models and validation tests associated with this collab.
	227	+If this is your first time using the app, the table will probably be empty.
	228	+To add your model, click "+", fill in the form, then click "Add model".
	229	+
	230	+As development of your model proceeds, you can easily register new versions of the code,
	231	+and new parameterizations, by clicking "Add new version".
	232	+
	233	+If you prefer not to use the app, you can instead fill in the [[Curation request form>>https://nettskjema.no/a/277393#/]].,
	234	+and you will be contacted by e-mail with further instructions.
	235	+
	236	+==== 5. Provide a reference dataset ====
	237	+
	238	+Once you're ready to publish your model entry in the EBRAINS Knowledge Graph,
	239	+we encourage you to provide a dataset containing the simulation results produced by your model,
	240	+following the process under "Step by step - Data" above.
	241	+
	242	+These reference data will be linked to the model, and will be helpful to anyone trying to
	243	+reuse your model.
	244	+
	245	+We will soon introduce a "Reproducible" badge for all models that include a reference dataset,
	246	+and whose simulation results can be reproduced by an EBRAINS curator.
	247	+
	248	+==== 6. Request publication, preview and publish ====
	249	+
	250	+Until you request your model entry to be published in the EBRAINS Knowledge Graph,
	251	+only members of the collab will be able to view the model entry, in the Model Catalog app
	252	+or using the Model Validation Python client.
	253	+
	254	+After publication, the model will appear in the [[EBRAINS public search results>>https://search.kg.ebrains.eu/?category=Model||rel="noopener noreferrer" target="_blank"]], and will receive a DOI.
	255	+
	256	+To request publication, [[contact EBRAINS support>>https://ebrains.eu/support||rel="noopener noreferrer" target="_blank"]], providing the collab name and the model name or ID.
	257	+
	258	+
	259	+Curators will then perform a number of checks:
	260	+
	261	+1. Does the model description provide sufficient context to understand the purpose and use of the model?
	262	+1. Does the code repository contain a licence file, explaining the conditions for reusing the code?
	263	+1. Does the model have a clearly defined version identifier (e.g. v1.0)? For models in a Git repository, the version identifier should match the name of a tag or release.
	264	+
	265	+The curators will also take a snapshot of your model code.
	266	+
	267	+* For models in public Git repositories, we archive a copy of the repository in [[Software Heritage>>https://www.softwareheritage.org/||rel="noopener noreferrer" target="_blank"]].
	268	+* For models in a collab Bucket or Drive, we make a read-only copy of the code in a public container in the EBRAINS repository.
	269	+
	270	+Once this is done, you will be invited to review a preview of how the model entry will appear in the KG Search,
	271	+and will have the opportunity to request modifications prior to approval and publication.
	272	+
168	168	----
169	169
170	170	=== Step by Step - Software ===
171	171
172		-[[[[image:Screenshot 2023-06-06 1122082.png||alt="swc-flow.png" height="136" width="637"]]>>https://www.ebrains.eu/tools/ebrains-curation-request-form||rel="noopener noreferrer" target="_blank"]]
173	173
174		-~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.
	278	+(% class="box floatinginfobox" id="software-curation-infographic" %)
	279	+(((
	280	+(% style="text-align:center" %)
	281	+//Software curation at a glance//
	282	+// //
	283	+[[[[image:Thumb2.png||alt="EBRAINS-Share-Software.pdf" height="287" width="197"]]>>attach:EBRAINS-Share-Software-4.pdf]]
	284	+)))
175	175
176		-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.
	286	+(% style="margin-left:15px" %)[[[[image:Screenshot 2023-06-06 1122082.png||alt="swc-flow.png" height="136" width="637"]]>>https://www.ebrains.eu/tools/ebrains-curation-request-form||rel="noopener noreferrer" target="_blank"]]
177	177
178		-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.
	288	+1. Fill in the [[request form>>https://www.ebrains.eu/tools/ebrains-curation-request-form]]. You'll be contacted by a curator with further instructions. In these instructions, you will find the links to your software and software version entries in the Knowledge Graph.
	289	+1. Enter the metadata of your software in your private space of the [[Knowledge Graph Editor>>url:https://editor.kg.ebrains.eu/]] by using the links provided by the curator. Please provide the metadata for your software as complete as possible. This makes it easier for users to find and use your software. If you have questions feel free to contact the curation support. After you have finished editing your entries, please let the curators know by replying to your ticket. We curate your metadata and get back to you, if necessary.
	290	+1. After a quality check, we integrate and publish the information to the Knowledge Graph. Your software is then searchable and usable for the neuroscience community.
179	179
180	180	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]].
181	181
182		-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 below.
	294	+For more information, visit our [[Guide to Software Curation in the EBRAINS Knowledge Graph>>url:https://wiki.ebrains.eu/bin/view/Collabs/swc-guide]] or see our infographic on the right.
183	183
184		-(% style="text-align: right;" %)
185		-==== //Software curation at a glance //[[[[image:Thumb2.png||alt="EBRAINS-Share-Software.pdf" height="287" width="197"]]>>attach:EBRAINS-Share-Software-4.pdf]] ====
186	186
187	187	----
188	188
	299	+=== Sharing human subject data ===
	300	+
	301	+(% class="box floatinginfobox" %)
	302	+(((
	303	+**Human subject data that can be shared on EBRAINS:**
	304	+// //
	305	+// - Post-mortem data//
	306	+// - Aggregated data//
	307	+// - Strongly pseudonymized or de-identified subject data//
	308	+// with a legal basis for sharing (e.g. Informed Consent)//
	309	+// //
	310	+
	311	+(% class="small" %)
	312	+//If you have human data that does not qualify as any of the above,//
	313	+//please [[get in touch>>https://www.ebrains.eu/contact/]] and we will clarify the available options.//
	314	+)))
	315	+
	316	+
	317	+Human subject data shared on EBRAINS must comply with [[GDPR >>https://gdpr-info.eu/]]and [[EU directives>>https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=celex%3A32010L0063]]. The information we need to assess this is collected via our [[Ethics and Regulatory Compliance Survey>>https://nettskjema.no/a/224765]].
	318	+
	319	+Post-mortem and aggregated human data can be shared openly, given direct identifiers in the metadata are removed. Strongly pseudonymized and de-identified data can be shared via the Human Data Gateway (HDG).
	320	+
	321	+The Human Data Gateway (HDG) was introduced in February 2021 as a response to the needs of multiple data providers who are bringing human subject data to EBRAINS. HDG covers the sharing of strongly pseudonymized or de-identified data, a limited range human subject data without direct identifiers and with very few indirect identifiers.
	322	+
	323	+The HDG adds an an authentication layer on top of the data. This means that **data users **must request access to the data (via their EBRAINS account) and will receive access provided they actively accept the [[EBRAINS Access Policy>>https://ebrains.eu/terms#access-policy]], the [[EBRAINS General Terms of Use>>https://ebrains.eu/terms#general-terms-of-use]], and the [[EBRAINS Data Use Agreement>>https://ebrains.eu/terms#data-use-agreement]]. The account holder also have to accept that information about their request and access to specific data under HDG is being tracked and stored. **Data owners** must be aware that sharing under the HDG affects the legal responsibilities for the data. They must agree to joint control of the data (see the [[Data Provision Protocol v1>>url:https://strapi-prod.sos-ch-dk-2.exo.io/EBRAINS_Data_Provision_Protocol_dfe0dcb104.pdf]], section 1.4 - 1.5) and the Data Protection Officers of the responsible institutions must have accepted that the data can be shared under HDG.
	324	+
	325	+The HDG is an extension of the existing services and does not replace the future EBRAINS Service for sensitive data (planned for 2024) which is outside the domain of the current EBRAINS Data and Knowledge services.
	326	+
	327	+----
	328	+
189	189	== **The openMINDS metadata framework** ==
190	190
	331	+(% class="box floatinginfobox" %)
	332	+(((
	333	+[[[[image:https://github.com/HumanBrainProject/openMINDS/raw/main/img/light_openMINDS-logo.png||alt="openMINDS logo" height="87" width="164"]]>>https://github.com/HumanBrainProject/openMINDS]]
	334	+)))
	335	+
191	191	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]].
192	192
193	193	For feedback, requests, or contributions, please get in touch with the openMINDS development team via
...	...	@@ -205,8 +205,10 @@
205	205	The curators in EBRAINS are located in Oslo, Jülich, Trier and Paris.
206	206
207	207
208		-**Located in Norway:**
	353	+**Located in Norway**
209	209
	355	+//Institute of Basic Medical Sciences,** **University of Oslo, Norway (PI: Jan G. Bjaalie, Trygve B. Leergaard)//
	356	+
210	210	|(% style="width:303px" %)(((
211	211	[[image:My project2.jpg||height="209" width="167"]]
212	212
...	...	@@ -214,7 +214,7 @@
214	214
215	215	(% class="small" %)Curation Scientist
216	216	Neuroscience (PhD)(%%)
217		-(% class="small" style="color:#4a5568" %)**Behavioral neuroscience and microscopy**
	364	+(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Behavioral neuroscience and microscopy**
218	218	)))|(% style="width:303px" %)(((
219	219	[[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
220	220
...	...	@@ -223,7 +223,7 @@
223	223	(% class="small" %)Curation Scientist,
224	224	Phd Student
225	225	Neuroscience (M. Sc.)(%%)
226		-(% class="small" style="color:#4a5568" %)**Neuroanatomy and data integration**
	373	+(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and data integration**
227	227	)))|(% style="width:303px" %)(((
228	228	[[image:My project (1).jpg||height="209" width="167"]]
229	229
...	...	@@ -232,7 +232,7 @@
232	232	(% class="small" %)Curation Scientist,
233	233	Phd Student
234	234	Neuroscience (M. Sc.)(%%)
235		-(% class="small" style="color:#4a5568" %)**Neuroanatomy and structural connectivity**
	382	+(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and structural connectivity**
236	236	)))|(% style="width:303px" %)(((
237	237	[[image:My project1.jpg||height="209" width="167"]]
238	238
...	...	@@ -240,7 +240,7 @@
240	240
241	241	(% class="small" %)Curation Scientist
242	242	Neurocognitive Psychology (M. Sc.)(%%)
243		-(% class="small" style="color:#4a5568" %)**Neuroimaging **
	390	+(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroimaging **
244	244	)))
245	245
246	246	|(% style="width:303px" %)(((
...	...	@@ -251,12 +251,16 @@
251	251	(% class="small" %)Curation Scientist,
252	252	Phd Student
253	253	Neuroscience (M. Sc.)(%%)
254		-(% class="small" style="color:#4a5568" %)**Neuroanatomy and brain atlases**
	401	+(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and brain atlases**
255	255	)))| | |
256	256
257	257
258		-\\**Located in Germany:**
	405	+\\**Located in Germany**
259	259
	407	+//Human-Computer Interaction, University of Trier, Germany  //
	408	+
	409	+//Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Germany (PI: Timo Dicksheid)//
	410	+
260	260	|(% style="width:303px" %)(((
261	261	[[image:My project (2).jpg||height="209" width="167"]]
262	262
...	...	@@ -265,26 +265,16 @@
265	265	(% class="small" %)Curation Scientist,
266	266	Phd Student
267	267	Sensors and Cognitive Psychology (M. Sc.)(%%)
268		-(% class="small" style="color:#4a5568" %)**Human-Computer Interaction**
	419	+(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Human-Computer Interaction**
269	269	)))|(% style="width:303px" %)(((
270		-
	421	+[[image:Lyuba.jpg||height="209" width="167"]]
271	271
272		-
273		-
274		-
275		-
276		-
277		-
278		-
279		-
280		-
281		-
282	282	**Lyuba Zehl**
283	283
284	284	(% class="small" %)Knowledge Systems Engineer
285	285	Dr. rer. nat. (Systems Neuroscience)(%%)
286		-(% class="small" style="color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
287		-)))|(% style="width:303px" %) |
	427	+(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
	428	+)))|(% style="width:303px" %) |(% style="width:303px" %)
288	288
289	289	----
290	290
...	...	@@ -295,36 +295,30 @@
295	295
296	296	=== **Showcase shared data, models or software in other services** ===
297	297
298		-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.
	439	+Below is a list of additional services that data, models or software shared via EBRAINS can benefit from. EBRAINS is continuously looking to increase the number of interoperable services.
299	299
300		-**Viewer for 2D images **
301	301
302		-* 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]].
	442	+|(% colspan="2" %)**Viewer for 2D images**
	443	+|[[image:MIO_screenshot.PNG]]|Integrate image data with //the Mio viewer//: EBRAINS Multi-Image OpenSeadragon viewer provides an intuitive way of navigating high-resolution 2D image series. It has browser-based classic pan and zoom capabilities. A collection can be displayed as a filmstrip (Filmstrip Mode) or as a table (Collection Mode) with adjustable number of row and columns. See [[Mio viewer links available for this dataset>>https://search.kg.ebrains.eu/?category=Dataset&q=nr2f1#9677359c-73fa-4425-b8fa-3de794e9017a]] as an example. MioViewer user manual is found [[here>>https://multi-image-osd.readthedocs.io/en/latest/index.html]].
	444	+|(% colspan="2" %)**Viewer for sequential atlas-registered 2D images with annotation options**
	445	+|[[image:LZ_screenshot.PNG]]|Integrate atlas-registered 2D image data with //the LocaliZoom viewer//: The EBRAINS LocaliZoom serial section viewer displays series of registered 2D section images with atlas overlay, allowing the users to zoom into high-resolution images and have information about the brain regions. See the [[LocaliZoom links available for this dataset>>https://doi.org/10.25493/T686-7BX]] as an example. LocaliZoom user manual is found [[here>>https://localizoom.readthedocs.io/en/latest/index.html]].
	446	+|(% colspan="2" %)**Interactive 3D atlas viewer with options for data visualization**
	447	+|[[image:3Datlas_screenshot.PNG]]|Upload your data to the //Siibra-explorer//: The siibra-explorer is used for visualizing volumetric brain data in all the brain atlases provided by EBRAINS (Human, Monkey, Rat and Mouse). The siibra-explorer viewer uses siibra-api to enable navigation of brain region hierarchies, maps in different coordinate spaces, and linked regional data features. Furthermore, it is connected with the siibra toolsuite providing several analytical workflows. To learn more about how to register your data to atlases, read about the [[Atlas services on ebrains.eu>>https://ebrains.eu/services/atlases#Integratedatatoanatlas]].
	448	+|(% colspan="2" %)**Use your research product in an interactive publication**
	449	+|[[image:LivePaper_screenshot.PNG]]|Add your data, models or software to a// Live paper. //Read more about [[Live papers on ebrains.eu>>https://www.ebrains.eu/data/live-papers/live-papers]].
303	303
304		-**Viewer for sequential atlas-registered 2D images with annotation options**
305		-
306		-* 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]].
307		-
308		-**Use your research product in an interactive publication **
309		-
310		-* 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]].
311		-
312		-**Interactive 3D atlas viewer with options for data visualization**
313		-
314		-* 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]].
315		-
316	316	----
317	317
318	318	==== **Add a tutorial or learning resource ** ====
319	319
320	320	(% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %)
321		-(% style="color:#000000" %)//More information will follow//
	456	+(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
322	322
323	323
324	324	==== **Create a workflow** ====
325	325
326	326	(% class="wikigeneratedid" id="H-Workflows5Binformation5D" %)
327		-(% style="color:#000000" %)//More information will follow//
	462	+(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow//
328	328
329	329	----
330	330
...	...	@@ -343,47 +343,36 @@
343	343	=== **Frequently asked questions ** ===
344	344
345	345	(((
346		-==== ====
	481	+==== ====
347	347
348	348	(((
349		->The curation process is time consuming and difficult
	484	+>Is the curation process time consuming and difficult?
350	350	)))
351	351	)))
352	352
353		-(% class="wikigeneratedid" id="HHowcanIshareA0models3F" %)
354		-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.
	488	+No, if communication is on a regular basis, we are able to finish curation within two weeks. Publishing your data naturally takes some effort but we will support you as much as possible.
355	355
356		->Sharing my data is not beneficial for me - only for others
	490	+>Is sharing my data also beneficial for me or only for others?
357	357
358		-
359	359	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.
360	360
361		->My data is too insignificant to share
	494	+>Can my data be too insignificant to share?
362	362
	496	+No, there is no such thing as insignificant data. Data that is considered insignificant for a given topic, may have great significance for another. By making “insignificant” data publicly available, other researchers may find something interesting that was off-topic for your own purposes.
363	363
364		-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.
	498	+>Can my data be easily misused if I share it?
365	365
366		->My data can easily be misused if I share it with the world
	500	+No, your data will be covered by a Creative Commons license of your choice. There are a variety of licenses available, enabling you to prevent use for specific purposes, e.g. commercial use.
367	367
	502	+>Can I share my data before my paper is published?
368	368
369		-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.
	504	+Yes, if you do not want to share your data before publishing the results in an article, you can publish your dataset with an embargo status. This will make it possible to find information about the data without making the data itself available, and give you a citeable DOI.
370	370
371		->I don't think I'm allowed to share my data
	506	+>Can I lose my competitive edge if I share my data before I publish the associated paper?
372	372
	508	+No, publishing your data does not mean that others can use it however they want. Use of your data will require citation, and by choosing an appropriate Creative Commons licence you decide what others are allowed to do with it. If you still feel worried, you can publish your data under embargo, and in this way delay the date of data release, but still make it possible for others to find the information about the data.
373	373
374		-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.
375	375
376		->I can't share my data before my paper is published
377		-
378		-
379		-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.
380		-
381		->If I share my data before I publish the associated paper, I will lose my competitive edge
382		-
383		-
384		-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.
385		-
386		-
387	387	----
388	388
389	389	== Contact ==
...	...	@@ -391,8 +391,6 @@
391	391	[[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
392	392
393	393
	518	+== References ==
	519	+
394	394	{{putFootnotes/}}
395		-~)~)~)~)~)~)
396		-~)~)~)
397		-~)~)~)~)~)~)~)~)~)
398		-~)~)~)~)~)~)

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