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1		-XWiki.ingrreit
	1	+XWiki.spieschnik

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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.
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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		-
7	7	{{box title="**Contents**"}}
8	8	{{toc depth="3" start="2"/}}
9	9	{{/box}}
10	10
11	11
12		-== **Information to get started** ==
13		-
14	14	(% style="text-align: center;" %)
15	15	**Get started! **
16	16
17	17	(% style="text-align: center;" %)
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. **
	14	+**[[REQUEST CURATION>>https://nettskjema.no/a/277393#/]] **
19	19
20	20	(% style="text-align: center;" %)
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.
	17	+ Search existing data, models and software in [[the EBRAINS Knowledge Graph Search>>https://kg.ebrains.eu/search/?facet_type[0]=Dataset]]
22	22
23	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]]
	20	+----
26	26
	22	+== **The EBRAINS curation process** ==
27	27
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		-
30		-
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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	36	(% class="box successmessage" %)
37	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
	26	+EBRAINS accepts **experimental data,** of all modalities and from all species, **models**, **software**, **web services **and **metadata models**. You'll find detailed information about each research product below.
39	39	)))
40	40
41		-----
42		-
43		-== **The EBRAINS curation process** ==
44		-
45	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.
46	46
47	47	>The EBRAINS curation process involves organising and annotating neuroscientific data to make the data discoverable and reusable.
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48	48
49	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.
50	50
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]].
	35	+Curated data, models and software are made available in the [[the EBRAINS Knowledge Graph>>https://kg.ebrains.eu/]]. This makes the data and metadata discoverable in the [[Knowledge Graph Search>>url:https://search.kg.ebrains.eu/]] and programmatically via the [[Knowledge Graph API>>url:https://docs.kg.ebrains.eu/8387ccd27a186dea3dd0b949dc528842/api_endpoints.html]]. The data, models and software are integrated in the EBRAINS Knowledge Graph by interoperable metadata schemas as defined in [[openMINDS>>url:https://github.com/HumanBrainProject/openMINDS/wiki]].Data and models are linked to and discoverable via the species-specific [[EBRAINS siibra atlas viewer>>url:https://ebrains.eu/services/atlases/brain-atlases]] by using interoperable metadata schemas as defined in [[SANDS>>url:https://github.com/HumanBrainProject/SANDS/wiki]].
52	52
53		-The curation of data, models and software is different. Thus, below we explain the process for sharing for each research product separately.
54	54
	38	+(% class="box infomessage" %)
	39	+(((
	40	+**We strongly recommend to start preparing for data sharing as early as possible.** With a structured data repository and adequate notes on how the data was acquired, you greatly minimize the effort required to publish your data. The time it takes to share data on EBRAINS heavily depends on on the engagement from the researcher and how well the data and metadata is prepared before-hand. **[[Contact us for personalised guidance on how to prepare for sharing>>mailto:curation-support@ebrains.eu]]. **
	41	+)))
55	55
	43	+(% class="box successmessage" %)
	44	+(((
	45	+**Particular needs? Contact us! **The workflows for sharing can be modified for researchers or research groups aiming to frequently publish larger numbers of their research products through EBRAINS. Please contact the curation service team in such cases.
	46	+)))
	47	+
56	56	----
57	57
58	58	=== Step by step - Experimental data ===
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107	107
108	108	==== **Sharing human data ** ====
109	109
	102	+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]].
	103	+
110	110	(% class="box floatinginfobox" %)
111	111	(((
112	112	For **Human subject data**, the data must be //either//
113	113
114	114	- Post-mortem data
	109	+
115	115	- Aggregated data
	111	+
116	116	- Pseudonymized subject data with a legal basis for sharing (e.g. Informed Consent)
117	117
118	118	(% 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. //
119	119	)))
120	120
121		-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]].
	117	+Pseudonymized data is shared via the Human Data Gateway (HDG) due to GDPR regulations. The HDG adds an authentication layer to the data.
122	122
123		-Post-mortem and aggregated human data can be shared openly. Pseudonymized data is shared via the Human Data Gateway (HDG) due to GDPR regulations. The HDG adds an authentication layer to the data.
124		-
125	125	**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.
126	126	\\**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.
127	127	\\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.
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131	131
132	132	=== Step by Step - Models ===
133	133
134		-(% style="color:#e74c3c" %){{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-1rb0hn"/}}
135		-
136	136	[place-holder-process-diagram]
137	137
138	138	==== **1. model step 1 ** ====
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149	149
150	150	=== Step by Step - Code ===
151	151
152		-[[[[image:swc-flow-no-header.png||alt="swc-flow.png"]]>>https://www.ebrains.eu/tools/ebrains-curation-request-form||rel="noopener noreferrer" target="_blank"]]
	144	+[place-holder-process-diagram]
153	153
154		-1. Fill in the [[request form>>https://www.ebrains.eu/tools/ebrains-curation-request-form]].[[[[image:Thumb.png||alt="EBRAINS-Share-Software.pdf" height="377" style="float:right" width="257"]]>>attach:EBRAINS-Share-Software.pdf]]
155		-1. One of our creators will then open a ticket and contact you with futher instructions. In these instructions you will find the links to your software and software version entries in the Knowledge Graph.
156		-1. In the next step you need to enter the metadata of your software in the [[Knowledge Graph Editor>>url:https://editor.kg.ebrains.eu/]] by using the links provided in the ticket. The links will lead you to the space in the KG, which was created especially for you. You can start directly with the editing of your software. Please provide the metadata for your software as complete as possible. This makes it easier for users to find and use your software. If you have questions feel free to contact the curation support.
157		-1. After you have finished editing your entries, please let the curators know by replying to your ticket. We curate your metadata and get back to you, if necessary.
158		-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.
	146	+==== **1. code step 1 ** ====
159	159
160		-If you want to add a new version to an already curated software, please write to [[curation-support@humanbrainproject.eu>>path:mailto:curation-support@humanbrainproject.eu]] or open a ticket at [[https:~~/~~/support.humanbrainproject.eu/.>>url:https://support.humanbrainproject.eu/]]
161		-For more information, visit our [[guide>>url:https://wiki.ebrains.eu/bin/view/Collabs/swc-guide]].
	148	+Text
162	162
	150	+
	151	+==== **2. code step 2** ====
	152	+
	153	+Text
	154	+
163	163	----
164	164
165	165	=== Webservices and metadata models ===
166	166
167	167	(% class="wikigeneratedid" id="HContact...." %)
168		-(% style="color:#e74c3c; font-size:16px" %){{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-np253c"/}}(% style="color:#4a5568; font-size:16px" %)
	160	+(% style="color:#e74c3c; font-size:16px" %)Contact....(% style="color:#4a5568; font-size:16px" %)
169	169
170	170	----
171	171
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182	182	Neuroscience (PhD)(%%)
183	183	(% class="small" style="color:#4a5568" %)**Behavioral neuroscience and microscopy**
184	184	)))|(% style="width:303px" %)(((
185		-[[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
	177	+[[image:My project.jpg||height="209" width="167"]]
186	186
187	187	**Camilla H. Blixhavn**
188	188
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190	190	Phd Student
191	191	Neuroscience (M. Sc.)(%%)
192	192	(% class="small" style="color:#4a5568" %)**Neuroanatomy and data integration**
193		-)))|(% style="width:303px" %)(((
	185	+)))|(% style="width:203px" %)
	186	+(((
194	194	[[image:My project (1).jpg||height="209" width="167"]]
195	195
196	196	**Ingrid Reiten**
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199	199	Phd Student
200	200	Neuroscience (M. Sc.)(%%)
201	201	(% class="small" style="color:#4a5568" %)**Neuroanatomy and structural connectivity**
202		-)))|(% style="width:303px" %)(((
	195	+)))|(% style="width:303px" %)
	196	+(((
203	203	[[image:My project1.jpg||height="209" width="167"]]
204	204
205	205	**Sophia Pieschnik**
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209	209	(% class="small" style="color:#4a5568" %)**Neuroimaging **
210	210	)))
211	211
212		-|(% style="width:303px" %)(((
213		-[[image:My project.jpg||height="209" width="167"]]
	206	+
	207	+
	208	+**Located in Germany:**
214	214
215		-**Heidi Kleven**
216		-
217		-(% class="small" %)Curation Scientist,
218		-Phd Student
219		-Neuroscience (M. Sc.)(%%)
220		-(% class="small" style="color:#4a5568" %)**Neuroanatomy and brain atlases**
221		-)))| | |
222		-
223		-
224		-\\**Located in Germany:**
225		-
226		-|(% style="width:303px" %)(((
227	227	[[image:My project (2).jpg||height="209" width="167"]]
228	228
229	229	**Jan Gündling**
230	230
231		-(% class="small" %)Curation Scientist,
232		-Phd Student
	214	+(% class="small" %)Curation Scientist
233	233	Sensors and Cognitive Psychology (M. Sc.)(%%)
234		-(% class="small" style="color:#4a5568" %)**Human-Computer Interaction**
235		-)))|(% style="width:303px" %)(((
236		-
	216	+(% class="small" style="color:#4a5568" %)**Human-Computer Interaction **
237	237
238		-
239		-
240		-
241		-
242		-
243		-
244		-
245		-
246		-
247		-
248		-**Lyuba Zehl**
249		-
250		-(% class="small" %)Knowledge Systems Engineer
251		-Dr. rer. nat. (Systems Neuroscience)(%%)
252		-(% class="small" style="color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
253		-)))|(% style="width:303px" %) |
254		-
255	255	----
256	256
257	257	== **Information and resources for researchers looking to share data** ==
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262	262
263	263	=== **Improve your research product ** ===
264	264
265		-(% class="wikigeneratedid" %)
266		-**{{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-fkdv6h"/}}**
267		-
268	268	==== **Add a tutorial or learning resource to your research product ** ====
269	269
270	270	==== (% style="color:#e74c3c" %)- Learning resource [information](%%) ====
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282	282
283	283	* 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]].
284	284	* 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]].
285		-* Add your data, models or software to a// Live paper//: (% style="color:#e74c3c" %)[description] {{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-62mbgl"/}}
	245	+* Add your data, models or software to a// Live paper//: (% style="color:#e74c3c" %)[description]
286	286	* Integrate your data to //the Siibra//-explorer: The siibra-explorer is used for visualizing volumetric brain data in all the brain atlases provided by EBRAINS (Human, Monkey, Rat and Mouse). The siibra-explorer viewer uses siibra-api to enable navigation of brain region hierarchies, maps in different coordinate spaces, and linked regional data features. Furthermore, it is connected with the siibra toolsuite providing several analytical workflows. To learn more about how to integrate your data to atlases, check out the [[Atlas services>>https://ebrains.eu/services/atlases#Integratedatatoanatlas]] on ebrains.eu.
287	287
288	288	----

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