Wiki source code of test-ir2

Version 87.1 by spieschnik on 2023/05/03 10:31

version	line-number	content
47.2	1	== Publishing neuroscience data, models and software via EBRAINS ==
10.1	2
25.2	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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10.1	5	{{box title="Contents"}}
	6	{{toc depth="3" start="2"/}}
	7	{{/box}}
	8
	9
	10	(% style="text-align: center;" %)
	11	Get started!
	12
	13	(% style="text-align: center;" %)
	14	[[REQUEST CURATION>>https://nettskjema.no/a/277393#/]]
	15
	16	(% style="text-align: center;" %)
26.1	17	Search existing data, models and software in [[the EBRAINS Knowledge Graph Search>>https://kg.ebrains.eu/search/?facet_type[0]=Dataset]]
10.1	18
	19
	20	----
	21
30.1	22	== The EBRAINS curation process ==
10.1	23
55.1	24	(% class="box successmessage" %)
	25	(((
	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.
	27	)))
	28
29.1	29	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.
10.1	30
30.1	31	>The EBRAINS curation process involves organising and annotating neuroscientific data to make the data discoverable and reusable.
10.1	32
30.1	33	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.
10.1	34
61.1	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]].
34.1	36
47.3	37
61.1	38	(% class="box infomessage" %)
30.1	39	(((
35.1	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]].
30.1	41	)))
10.1	42
59.1	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	)))
10.1	47
34.1	48	----
	49
10.1	50	=== Step by step - Experimental data ===
	51
	52
23.2	53	[[image:image-20230326054341-1.png]]
10.1	54
36.1	55	==== ====
	56
10.1	57	==== 1. Provide some general information about your dataset ====
	58
	59	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.
	60
	61	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.
	62
	63
	64	==== 2. Upload data ====
	65
	66	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.
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35.1	68	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.
10.1	69
35.1	70	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.
10.1	71
	72
	73	If a data collection is already uploaded elsewhere, we may link to the already existing repository.
	74
	75
	76	==== 3. Submit metadata ====
	77
	78	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.
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68.1	80	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/]]. We have prepared [[a list of the metadata properties that are required>>https://drive.ebrains.eu/lib/47995dbc-f576-4008-a76c-eefbfd818529/file/ebrains-minimum-required-metadata.xlsx]] for publishing data on EBRAINS.
10.1	81
	82
	83	==== 4. Write a Data Descriptor ====
	84
	85	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.
	86
	87	[[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]]).
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	89
	90	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.
	91
	92
	93	==== 5. Preview and publish ====
	94
	95	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.
	96
	97
	98	----
	99
	100	==== Sharing human data ====
	101
	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
	104	(% class="box floatinginfobox" %)
1.1	105	(((
10.1	106	For Human subject data, the data must be //either//
1.1	107
10.1	108	- Post-mortem data
	109
	110	- Aggregated data
	111
	112	- Pseudonymized subject data with a legal basis for sharing (e.g. Informed Consent)
	113
	114	(% 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. //
1.1	115	)))
	116
10.1	117	Pseudonymized data is shared via the Human Data Gateway (HDG) due to GDPR regulations. The HDG adds an authentication layer to the data.
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10.1	119	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.
	120	\\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.
35.1	121	\\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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	123
10.1	124	----
	125
	126	=== Step by Step - Models ===
	127
	128	[place-holder-process-diagram]
	129
	130	==== 1. model step 1 ====
	131
	132	Text
	133
	134
	135	==== 2. model step 2 ====
	136
	137	Text
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	139
	140	----
	141
	142	=== Step by Step - Code ===
	143
	144	[place-holder-process-diagram]
	145
	146	==== 1. code step 1 ====
	147
	148	Text
	149
	150
	151	==== 2. code step 2 ====
	152
	153	Text
	154
	155	----
	156
56.1	157	=== Webservices and metadata models ===
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57.1	159	(% class="wikigeneratedid" id="HContact...." %)
	160	(% style="color:#e74c3c; font-size:16px" %)Contact....(% style="color:#4a5568; font-size:16px" %)
27.2	161
55.1	162	----
27.2	163
57.1	164	== The curation team: meet the curators ==
55.1	165
72.1	166	Located in Norway:
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	168
87.1	169	\|(% style="width:303px" %)[[image:69399800_399857187337623_8446982631391756288_n.jpg\|\|height="180" width="180"]] \|(% style="width:316px" %) [[image:fb6d6429-709e-4f4d-be3b-eab0a46695bd.JPG\|\|height="180" width="133"]] \|(% style="width:326px" %) [[image:ansattfoto2.jpg\|\|height="180" width="133"]] \|(% style="width:330px" %) [[image:Image-1.jpg\|\|height="180" width="180"]]
	170	\|(% style="width:303px" %)Archana Golla\|(% style="width:316px" %)Sophia Pieschnik\|(% style="width:326px" %)Ingrid Reiten \|(% style="width:330px" %)Camilla Hagen Blixhavn
	171	\|(% style="width:303px" %)Curation Scientist\|(% style="width:316px" %)Curation Scientist \|(% style="width:326px" %)Curation Scientist, Phd Student \|(% style="width:330px" %)Curation Scientist, Phd Student
	172	\|(% class="small" style="width:303px" %)Neuroscience (PhD) \|(% class="small" style="width:316px" %)Neurocognitive Psychology (M. Sc.) \|(% class="small" style="width:326px" %)Neuroscience (M. Sc.) \|(% class="small" style="width:330px" %)Neuroscience (M. Sc.)
	173	\|(% class="small" style="width:303px" %)Behavioral neuroscience and microscopy \|(% class="small" style="width:316px" %)Neuroimaging \|(% class="small" style="width:326px" %)Neuroanatomy and structural connectivity\|(% class="small" style="width:330px" %)Neuroanatomy and data integration
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	176
	177
72.1	178	Located in Germany:
	179
	180	[[image:csm_Jan_Gruendling_3_bf9567ebb1.jpg\|\|height="180" width="180"]]
	181
	182	Jan Gündling
	183
	184	Curation Scientist
81.1	185	(% class="small" %)Sensors and Cognitive Psychology (M. Sc.)
72.1	186	Human-Computer Interaction
	187
27.2	188	----
	189
37.1	190	== Information and resources for researchers looking to share data ==
10.1	191
	192	Below you can find some resources that can come in handy if you are looking to share data via EBRAINS, or in general.
	193
	194	----
	195
58.1	196	=== Improve your research product ===
55.1	197
58.1	198	==== Add a tutorial or learning resource to your research product ====
55.1	199
58.1	200	==== (% style="color:#e74c3c" %)- Learning resource [information](%%) ====
55.1	201
58.1	202
	203	==== Create a workflow for .... ? ====
	204
	205	==== (% style="color:#e74c3c" %)- Workflows [information](%%) ====
	206
55.1	207	----
	208
62.1	209	=== Integrate your data, models or software with other services ===
60.1	210
	211	EBRAINS supports further integration for a variety of data, and is continuously looking to increase the number of interoperable services.
	212
64.1	213	* 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]].
63.1	214	* 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]].
60.1	215	* Add your data, models or software to a// Live paper//: (% style="color:#e74c3c" %)[description]
63.1	216	* 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.
60.1	217
	218	----
	219
37.1	220	=== The benefits of sharing data ===
27.1	221
44.1	222	(% style="color:#000000" %)Sharing your data, models or code (research products) via EBRAINS makes it discoverable amongst other research products available in the (%%)[[(% style="color:#000000" %)EBRAINS Knowledge Graph>>https://kg.ebrains.eu/]](%%). This is made possible by the highly flexible metadata framework describing neuroscience data in detail.
33.1	223
43.1	224	(% style="color:#000000" %)EBRAINS is gradually implementing interconnected tools and analysis workflows developed in the Human Brain Project (HBP) to further enhance the output from adding your dataset to the database.
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	226
27.1	227	By sharing your data via EBRAINS, you gain access to the following benefits:
	228
	229	[[image:image-20230324170841-3.png]]
	230
	231
	232
30.1	233	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.
27.1	234
30.1	235
27.1	236	----
	237
40.1	238	=== At a glance: "Sharing experimental data on EBRAINS" ===
10.1	239
	240
46.1	241	\|(% style="width:439px" %)(((
47.1	242	[[[[image:image-20230324171114-2.png\|\|height="354" width="250"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
46.1	243	)))\|(% style="width:461px" %)(((
47.1	244	[[[[image:image-20230324171109-1.png\|\|height="352" width="250"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
	245	)))\|(% style="width:416px" %)[[[[image:image-20230330120354-1.png\|\|height="352" width="250"]]>>https://drive.ebrains.eu/f/707147a883b94fae8e69/]]
46.1	246	\|(% style="width:439px" %)//Collection of useful information for researchers looking to share experimental data on EBRAINS.//\|(% style="width:461px" %)//The EBRAINS data descriptor: a general overview //\|(% style="width:416px" %)//Introduction to data organization: A [[collection of guidelines>>https://drive.ebrains.eu/smart-link/25299f04-c4e5-4028-8f5f-3b8208f9a532/]] on how to organise files and folders to ensure consistency and reproducibility in the future. //
1.1	247
10.1	248	----
	249
	250	=== Common concerns - and answers ===
	251
1.1	252	(((
10.1	253	==== ====
1.1	254
23.2	255	(((
20.1	256	>The curation process is time consuming and difficult
1.1	257	)))
19.1	258	)))
10.1	259
	260	(% class="wikigeneratedid" id="HHowcanIshareA0models3F" %)
	261	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.
	262
	263	>Sharing my data is not beneficial for me - only for others
	264
	265
	266	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.
	267
	268	>My data is too insignificant to share
	269
	270
	271	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.
	272
	273	>My data can easily be misused if I share it with the world
	274
	275
	276	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.
	277
	278	>I don't think I'm allowed to share my data
	279
	280
	281	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.
	282
	283	>I can't share my data before my paper is published
	284
	285
	286	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.
	287
	288	>If I share my data before I publish the associated paper, I will lose my competitive edge
	289
	290
	291	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.
	292
	293
	294	----
	295
	296	== Contact ==
	297
	298	[[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
	299
	300
	301	{{putFootnotes/}}

Wiki source code of test-ir2

data-curation-copy