Changes for page Data Curation
Last modified by abonard on 2025/06/03 10:55
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... ... @@ -17,9 +17,9 @@ 17 17 {{/html}} 18 18 19 19 20 -== Publishing neuroscience data, models and software via EBRAINS == 20 +(% class="wikigeneratedid" id="HPublishingneurosciencedata2CmodelsandsoftwareviaEBRAINS" %) 21 +(% style="font-size:2em" %)**Publishing neuroscience data, models and software via EBRAINS** 21 21 22 - 23 23 (% class="wikigeneratedid" %) 24 24 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]]. 25 25 ... ... @@ -29,13 +29,15 @@ 29 29 30 30 == **Information to get started** == 31 31 32 -**[[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. **32 +**[[REQUEST CURATION>>https://nettskjema.no/a/386195]] to share data, simulations, computational models, and software, - or to add a new version of an existing one. ** 33 33 34 34 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. 35 35 36 36 37 -(% style="text-align: center;" %) 38 -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 +))) 39 39 40 40 41 41 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. ... ... @@ -65,7 +65,9 @@ 65 65 66 66 The curation of data, models and software is different. Thus, below we explain the process for sharing for each research product separately. 67 67 70 +**Before you get started, make sure you[[ sign up for a free EBRAINS account>>https://www.ebrains.eu/page/sign-up]]. This is needed to complete the data sharing process. ** 68 68 72 + 69 69 ---- 70 70 71 71 === Step by step - Data === ... ... @@ -80,7 +80,7 @@ 80 80 //with all you need to know// 81 81 //to share data on EBRAINS: // 82 82 // // 83 -[[[[image:image-20230324171114-2.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]] //87 +[[[[image:image-20230324171114-2.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]] 84 84 ))) 85 85 86 86 ... ... @@ -87,32 +87,38 @@ 87 87 ==== **1. Provide some general information about your dataset** ==== 88 88 89 89 90 -[[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#/]]. ** 91 91 92 - Thisform collectspreliminaryinformation aboutyour data, allowingtoassesswhetherdataset fitswithin thescope ofEBRAINS.The submission generates a curationID allowingusotrack thecase.95 +(% style="margin-right:10px" %)[[image:https://lh3.googleusercontent.com/zh7TvO6w04YGW9jIhfhmdT6CexdGs-AWOLfJXKRq7-tdHOu6ar1rOQx8o4rZevrjXqgPZ7-Ejv4b6X9XpgXuHpdUXi-mBTHIUnv5Vz-DktHt0sP-PZ3gE8XgZid3TV3swV1uTCBhHx11ge0pjP7RVxswGQ=s2048||height="85px;" width="91px;"]](%%)** Fill in the [[EBRAINS Curation Request Form>>https://nettskjema.no/a/386195]]. ** 93 93 97 +The form collects general 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 and follow up on incoming requests. 94 94 95 - [[image:https://lh6.googleusercontent.com/yw442oS6BwZOlY-_0BoVxyCW3DrdcJ5ogCes92iOD16_rgNEVk56aNMDaVWXFfBLYv24bHzmGgBF9wg0szjH70xzuRTqxoQAeuy3knNO7axCHoyZDXwtyTcMgFnYwbOYxOT29LK-zchrUKLW6Mle93kOkQ=s2048||height="94px;"width="94px;"]]**Fillin the[[Ethics andRegulatorycompliance form>>https://nettskjema.no/a/224765]]**.99 +You will also be asked to fill in information related to ethics and regulatory compliance, so that we can evaluate whether we can ethically and legally share the data via EBRAINS (earlier, this was recorded via a [[separate form>>https://nettskjema.no/a/224765]]). See below for information about the ethical and legal aspects concerning sharing of human subject data. 96 96 97 -This form collects the necessary information needed for us to evaluate whether we can ethically and legally share the data via EBRAINS. 98 98 99 -See below for information about the ethical and legal aspects concerning sharing of human subject data. 100 - 101 - 102 102 ==== **2. Upload data ** ==== 103 103 104 +(% class="box floatinginfobox" id="share-data-infographic" %) 105 +((( 106 +(% style="text-align:center" %) 107 +//Download our infographic// 108 +//with guidelines 109 +on data organization: // 104 104 105 -[[image:https://lh5.googleusercontent.com/sieKO-kW8O18iPaUyonwyo4UfHBmtc2E9BDnjbx52j6J_uGmm-OzGAo7sloMk3sYwKa6QW3hYQsOA9N4H7uGQpca088Wrk0Nurpt_J3B0-NSbcaPNdZIh21otQcG6jnAxLGiKoEvkTyaDGTMk3fu7me8mQ=s2048||height="94px;" width="94px;"]]**Ensure data is structured consistently prior to upload. ** 111 +(% style="text-align:center" %) 112 +[[[[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/]] 113 +))) 106 106 107 - Welook fororganizeddata, notrganized accordingto our standard.Thiss tosupportthebroadest degreeofsharingpossible. Wedohowever require that the data isorganizedin aconsistentandprecise manner. Please seeour////[[collectionof guidelineson data organization>>https://drive.ebrains.eu/smart-link/25299f04-c4e5-4028-8f5f-3b8208f9a532/]] forfurther guidance.115 +(% 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. ** 108 108 109 - [[image:https://lh5.googleusercontent.com/EWtYwfVlbeC-jqPasgmzidqc50GrkKIEgwXeUeql8aaMHIukmFdWEy0nufVWWATbxDDK3XwwZEDmASrbpCsBk1u0HpAd8x4ZgAMsMPRcWyrb9etlV6FgKE_QN2e6SqKxHE0rzkR8uI1rRW_5z21TFGYVnw=s2048||height="91px;"width="91px;"]]**UploaddatatoEBRAINS Storage,eitherusingag-and-dropsolution(opt.1)orctivepythonscript(opt.2).**117 +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. 110 110 111 - //Opt.1. //Forsmallerdatasets witha reasonableamountfiles,werecommendng the Collab-Bucketsolution(drag-and-drop).A Collab Bucketmustfirstbeassignedtoadataset, which happenswhena datasets is acceptedforsharing.119 +(% 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).** 112 112 113 - //Opt.2.//Forlarger datasetsor datasetswith alarge amount of files, we recommend usinga programmaticapproach. The[[pythonscript>>https://github.com/eapapp/ebrains-data-storage/tree/main/data-proxy]] isinteractive anddoesnotrequireanyadditionalprogramming.121 +**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. 114 114 123 +**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. 115 115 125 + 116 116 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. 117 117 118 118 If a data collection is already uploaded elsewhere, we may link to the already existing repository. ... ... @@ -121,23 +121,25 @@ 121 121 ==== **3. Submit metadata** ==== 122 122 123 123 124 -[[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 throughdirect interactionwiththe Knowledge Graph (opt. 2) **134 +(% 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) ** 125 125 126 - //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 automatically136 +**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 127 127 128 - //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:138 +**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: 129 129 130 130 * 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. 131 131 * [[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. 132 132 * [[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. 133 133 134 -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.144 +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/f/3e226ad165054b35b456/||rel="noopener noreferrer" target="_blank"]] on EBRAINS. 135 135 136 136 137 -==== **4. Write a Data Descriptor 147 +==== **4. Write a Data Descriptor** ==== 138 138 139 -[[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]]** . ** 140 140 150 + 151 +(% 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]]**.** 152 + 141 141 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. 142 142 143 143 See our infographic about the data descriptor for inspiration or guidance. ... ... @@ -146,270 +146,344 @@ 146 146 147 147 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. 148 148 149 -==== [[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]//The EBRAINS Data descriptor at-a-glance// ==== 150 150 162 +(% class="box floatinginfobox" id="data-descriptor-infographic" %) 163 +((( 164 +(% style="text-align:center" %) 165 +//Download our infographic 166 +about the EBRAINS Data// 167 +//Descriptor// 168 +// // 169 +[[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]] 170 +))) 151 151 152 -==== **5. Preview and publish 172 +==== **5. Preview and publish** ==== 153 153 154 154 155 -[[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.175 +(% 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. ** 156 156 177 +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. 157 157 179 + 180 + 181 + 158 158 ---- 159 159 160 -=== =**Sharinghuman subjectdata**====184 +=== Step by Step - Models === 161 161 162 -(% class="box floatinginfobox" %) 163 -((( 164 -**Human subject data that can be shared on EBRAINS:** 165 165 166 -- Post-mortem data 167 -- Aggregated data 168 -- Strongly pseudonymized or de-identified subject data with a legal basis for sharing (e.g. Informed Consent) 187 +==== 1. Start early ==== 169 169 170 -(% 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. // 171 -))) 189 +It is not necessary to wait until you are ready to publish to register your model with EBRAINS. 172 172 173 -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]]. 191 +By registering a model early in your project, you can take advantage of EBRAINS tools 192 +to keep track of simulations and to share them with your collaborators. 174 174 175 - Post-mortemandaggregated human datacan be sharedopenly, given direct identifiersin themetadataareremoved. Strongly pseudonymizedand de-identified datacan beshared via the Human Data Gateway (HDG).194 +==== 2. Create/choose a Collab workspace ==== 176 176 177 - TheHuman Data Gateway (HDG) wasintroducedinFebruary2021asaresponse totheneeds of multipledata providers who are bringing humansubject data to EBRAINS. HDG coversthesharing of strongly pseudonymizedorde-identified data, alimitedrange human subject data without directdentifiersand with very few indirect identifiers.196 +We use EBRAINS Collaboratory "collab" workspaces to help manage the model curation process. 178 178 179 - The HDG adds an an authenticationlayeron top of thedata. This means that **datausers**must request access tothe data (via their EBRAINS account) and willreceiveaccessprovided they actively accept the [[EBRAINS Access Policy>>https://ebrains.eu/terms#access-policy]],the[[EBRAINS GeneralTermsof Use>>https://ebrains.eu/terms#general-terms-of-use]],and the [[EBRAINS Data Use Agreement>>https://ebrains.eu/terms#data-use-agreement]]. The accountholderalsohave toaccept that informationabout their requestand access tospecificdata under HDGis beingtrackedand stored. **Dataowners**must beawarethat sharing under the HDGaffects the legalresponsibilities forthe data. They must agree to joint controlofthe data (see the [[Data ProvisionProtocol 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.198 +In particular, we use collab membership (the "Team") to control who can view or edit your model metadata prior to publication. 180 180 181 -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. 200 +It is up to you whether you create a new collab for each model, or reuse an existing collab 201 +(it is no problem to have multiple models associated with a single collab). 182 182 203 +Collabs are also useful for storing simulation results, adding documentation for your model, 204 +and/or providing tutorials in Jupyter notebooks. 183 183 184 - ----206 +==== 3. Upload code ==== 185 185 186 -=== Step by Step - Models === 208 +We recommend storing model code and/or configuration files in an online Git repository, for example on GitHub. 209 +This repository should be public when you publish the model, but a private repository can be used for model development. 187 187 211 +Alternatively, you can upload code to the Collab Drive or Bucket storage. 188 188 189 - ~1.Request curation usingthe[[Curation request form>>https://nettskjema.no/a/277393#/]]. You will be contactedbyacurator with more information.213 +==== 4. Submit metadata ==== 190 190 215 +We recommend submitting metadata using the Model Catalog app, installed in your collab. 191 191 192 - //Additionalinformation willbe added soon.//217 +To install it: 193 193 194 ----- 219 +1. click the "+ Create" button 220 +1. in the "Create Page" form, add a title, such as "Model Catalog", and select "Community App", then click "Create" 221 +1. scroll down until you find the "Model Catalog" app, click "Select", then "Save & View" 195 195 196 -=== Step by Step - Software === 223 +You will then see a table of all the models and validation tests associated with this collab. 224 +If this is your first time using the app, the table will probably be empty. 225 +To add your model, click "+", fill in the form, then click "Add model". 197 197 198 -[[[[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"]] 227 +As development of your model proceeds, you can easily register new versions of the code, 228 +and new parameterizations, by clicking "Add new version". 199 199 200 -~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. 230 +If you prefer not to use the app, you can instead fill in the [[EBRAINS Curation Request Form>>https://nettskjema.no/a/386195]]., 231 +and you will be contacted by e-mail with further instructions. 201 201 202 - 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 providethe metadataforyour softwareas complete as possible. This makes it easierfor users to find and useyour software. If you have questions feel free tocontact thecuration support. After you have finishedediting your entries, please letthe curatorsknow by replyingtoyour ticket. We curate your metadata and get back to you, if necessary.233 +==== 5. Provide a reference dataset ==== 203 203 204 -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. 235 +Once you're ready to publish your model entry in the EBRAINS Knowledge Graph, 236 +we encourage you to provide a dataset containing the simulation results produced by your model, 237 +following the process under "Step by step - Data" above. 205 205 206 -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]]. 239 +These reference data will be linked to the model, and will be helpful to anyone trying to 240 +reuse your model. 207 207 208 -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. 242 +We will soon introduce a "Reproducible" badge for all models that include a reference dataset, 243 +and whose simulation results can be reproduced by an EBRAINS curator. 209 209 210 -(% style="text-align: right;" %) 211 -==== //Software curation at a glance //[[[[image:Thumb2.png||alt="EBRAINS-Share-Software.pdf" height="287" width="197"]]>>attach:EBRAINS-Share-Software-4.pdf]] ==== 245 +==== 6. Request publication, preview and publish ==== 212 212 213 ----- 247 +Until you request your model entry to be published in the EBRAINS Knowledge Graph, 248 +only members of the collab will be able to view the model entry, in the Model Catalog app 249 +or using the Model Validation Python client. 214 214 215 - ==**The openMINDSmetadata framework**==251 +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. 216 216 217 -o penMINDS(open MetadataInitiative for Neuroscience Data Structures)is a community-driven, open-source metadata framework for graph database systems, such astheEBRAINSKnowledge Graph. Itis composed of linked metadata models, libraries of serviceable metadata instances, and supportivetooling ([[openMINDSPython>>url:https://pypi.org/project/openMINDS/]], openMINDS Matlab). Forxploringthe openMINDS schemas,go to the[[HTML documentation>>url:https://humanbrainproject.github.io/openMINDS/]].Fora fulloverview of the framework,goto [[theopenMINDScollab>>url:https://wiki.ebrains.eu/bin/view/Collabs/openminds/]] orthe[[GitHub repository>>https://github.com/HumanBrainProject/openMINDS]].253 +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. 218 218 219 -For feedback, requests, or contributions, please get in touch with the openMINDS development team via 220 220 221 -* the support-email: [[openminds@ebrains.eu>>path:mailto:openminds@ebrains.eu]] 222 -* the [[GitHub issue tracker>>url:https://github.com/HumanBrainProject/openMINDS/issues]] 223 -* the INCF NeuroStars [[openMINDS Community Forum>>url:https://neurostars.org/t/openminds-community-forum-virtual/20156]] 256 +Curators will then perform a number of checks: 224 224 225 ----- 258 +1. Does the model description provide sufficient context to understand the purpose and use of the model? 259 +1. Does the code repository contain a licence file, explaining the conditions for reusing the code? 260 +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. 226 226 227 - == **The curationteam:meetthecurators**==262 +The curators will also take a snapshot of your model code. 228 228 229 -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. 264 +* 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"]]. 265 +* 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. 230 230 231 - Thecurators inEBRAINSarelocated inOslo,Jülich,TrierandParis.232 - 267 +Once this is done, you will be invited to review a preview of how the model entry will appear in the KG Search, 268 +and will have the opportunity to request modifications prior to approval and publication. 233 233 234 - **Located in Norway:**270 +---- 235 235 236 -|(% style="width:303px" %)((( 237 -[[image:My project2.jpg||height="209" width="167"]] 272 +=== Step by Step - Software === 238 238 239 -**Archana Golla** 274 +1. Fill in the [[EBRAINS Curation 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. 275 +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. 276 +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. 240 240 241 -(% class="small" %)Curation Scientist 242 -Neuroscience (PhD)(%%) 243 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Behavioral neuroscience and microscopy** 244 -)))|(% style="width:303px" %)((( 245 -[[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]] 278 +If you want to add a new version to an already curated software, please request this via the [[EBRAINS Curation Request Form>>https://www.ebrains.eu/tools/ebrains-curation-request-form]]. 246 246 247 - **CamillaH.Blixhavn**280 +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. 248 248 249 -(% class="small" %)Curation Scientist, 250 -Phd Student 251 -Neuroscience (M. Sc.)(%%) 252 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and data integration** 253 -)))|(% style="width:303px" %)((( 254 -[[image:My project (1).jpg||height="209" width="167"]] 255 255 256 - **Ingrid Reiten**283 +---- 257 257 258 -(% class="small" %)Curation Scientist, 259 -Phd Student 260 -Neuroscience (M. Sc.)(%%) 261 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and structural connectivity** 262 -)))|(% style="width:303px" %)((( 263 -[[image:My project1.jpg||height="209" width="167"]] 285 +=== Sharing human subject data === 264 264 265 -**Sophia Pieschnik** 287 +(% class="box floatinginfobox" %) 288 +((( 289 +**Human subject data that can be shared on EBRAINS:** 290 +// // 291 +// - Post-mortem data// 292 +// - Aggregated data// 293 +// - Strongly pseudonymized or de-identified subject data// 294 +// with a legal basis for sharing (e.g. Informed Consent)// 295 +// // 266 266 267 -(% class="small" %) Curation Scientist268 - NeurocognitivePsychology(M.Sc.)(%%)269 - (% class="small"style="--darkreader-inline-color:#d3cbbf;color:#4a5568" %)**Neuroimaging **297 +(% class="small" %) 298 +//If you have human data that does not qualify as any of the above,// 299 +//please [[get in touch>>https://www.ebrains.eu/contact/]] and we will clarify the available options.// 270 270 ))) 271 271 272 -|(% style="width:303px" %)((( 273 -[[image:My project.jpg||height="209" width="167"]] 274 274 275 - **HeidiKleven**303 +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]]. 276 276 277 -(% class="small" %)Curation Scientist, 278 -Phd Student 279 -Neuroscience (M. Sc.)(%%) 280 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and brain atlases** 281 -)))| | | 305 +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). 282 282 283 - 284 -\\**Located in Germany:** 307 +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. 285 285 286 -|(% style="width:303px" %)((( 287 -[[image:My project (2).jpg||height="209" width="167"]] 309 +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. 288 288 289 - **JanGündling**311 +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. 290 290 291 -(% class="small" %)Curation Scientist, 292 -Phd Student 293 -Sensors and Cognitive Psychology (M. Sc.)(%%) 294 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Human-Computer Interaction** 295 -)))|(% style="width:303px" %)((( 296 - 313 +---- 297 297 315 +== **The openMINDS metadata framework** == 298 298 317 +(% class="box floatinginfobox" %) 318 +((( 319 +[[[[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]] 320 +))) 299 299 322 +openMINDS is a community-driven, open-source metadata framework for linked data, as used in graph database systems, such as the EBRAINS Knowledge Graph. It is composed of multiple metadata models with interlinked schemas, libraries of serviceable metadata instances, and supportive tooling (e.g., [[openMINDS Python>>https://github.com/openMetadataInitiative/openMINDS_Python]] or [[openMINDS Matlab>>https://github.com/openMetadataInitiative/openMINDS_MATLAB]]). A full documentation (for users and contributors) of the openMINDS framework can be found on [[ReadTheDocs>>https://openminds-documentation.readthedocs.io||rel="noopener noreferrer" target="_blank"]]. 300 300 324 +For feedback, requests, or contributions, please get in touch with the openMINDS development team via 301 301 326 +* [[support@openmetadatainitiative.org>>mailto:mailto:support@openmetadatainitiative.org]] 327 +* [[GitHub Issues>>https://github.com/openMetadataInitiative/openMINDS/issues]] (for metadata schemas) 328 +* [[GitHub Issues>>https://github.com/openMetadataInitiative/openMINDS_instances/issues]] (for metadata instances) 329 +* [[openMINDS Community Forum>>https://neurostars.org/t/openminds-community-forum-virtual]] 302 302 331 +---- 303 303 333 +== **Add practical value to your shared data, model or software** == 304 304 305 305 336 +=== **Showcase shared data, models or software in other services** === 306 306 338 +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. 307 307 308 -**Lyuba Zehl** 309 309 310 -(% class="small" %)Knowledge Systems Engineer 311 -Dr. rer. nat. (Systems Neuroscience)(%%) 312 -(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis** 313 -)))|(% style="width:303px" %) | 341 +|(% colspan="2" %)**Viewer for 2D images** 342 +|[[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]]. 343 +|(% colspan="2" %)**Viewer for sequential atlas-registered 2D images with annotation options** 344 +|[[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]]. 345 +|(% colspan="2" %)**Interactive 3D atlas viewer with options for data visualization** 346 +|[[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]]. 347 +|(% colspan="2" %)**Use your research product in an interactive publication** 348 +|[[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]]. 314 314 315 315 ---- 316 316 317 -== **Add practicalvalue toyourshared data, model or software** ==352 +==== **Add a tutorial or learning resource ** ==== 318 318 354 +(% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %) 355 +(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow// 319 319 357 + 358 +==== **Create a workflow** ==== 359 + 360 +(% class="wikigeneratedid" id="H-Workflows5Binformation5D" %) 361 +(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow// 362 + 320 320 ---- 321 321 322 -== =**Showcaseshared data, modelsor softwareinotherservices** ===365 +== **EBRAINS commits to the FAIR principles** == 323 323 324 - Belowis alistofadditional services thatdata,modelsorsoftwaresharedviaEBRAINScan benefit from.EBRAINSiscontinuously looking toincrease the number ofinteroperable services.367 +In 2016, the 'FAIR Guiding Principles for the management and guardianship of scientific data'{{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}} were introduced to the scientific community. The objective of the authors was to provide a set of general recommendations aimed at enhancing the Findability, Accessibility, Interoperability, and Reusability of digital resources (data). They emphasize the importance of making data more open, discoverable, and usable, ultimately facilitating collaboration and knowledge sharing within the scientific community. Today, the FAIR principles are widely recognized and adopted as best practices in data management and stewardship across scientific fields. 325 325 326 - **Viewer for2D images**369 +In EBRAINS, all datasets, models and software shared go through a streamlined curation process that ensures relevant annotation of the data using the [[openMINDS>>url:https://github.com/HumanBrainProject/openMINDS]] metadata framework and integration into the [[EBRAINS Knowledge Graph>>url:https://docs.kg.ebrains.eu/]] metadata management system. The research products are Findable and Accessible through the [[Knowledge Graph Search>>url:https://search.kg.ebrains.eu/?category=Dataset]] as dataset/model/software cards that display further information regarding the dataset's Interoperability and Reusability. 327 327 328 - *Integrateimagedata with//the Mioviewer//:EBRAINSMulti-Image OpenSeadragonviewer providesan intuitivewayof navigating high-resolution2Dimage series.Itasbrowser-based classicpan and zoomcapabilities. A collectioncan be displayedas a filmstrip(FilmstripMode)orsa table (Collection Mode)with adjustablenumber of row andcolumns.See[[Mio viewerlinksavailable for this dataset>>https://search.kg.ebrains.eu/?category=Dataset&q=nr2f1#9677359c-73fa-4425-b8fa-3de794e9017a]] as anexample. MioViewerusermanual isfound[[here>>https://multi-image-osd.readthedocs.io/en/latest/index.html]].371 +To further specify how EBRAINS aligns with the FAIR principles, we have assessed the FAIRness of datasets shared in the EBRAINS Knowledge Graph following the [[FAIRsFAIR Data Object Assessment Metrics>>https://zenodo.org/record/6461229||style="background-color: rgb(255, 255, 255); --darkreader-inline-bgcolor: #1c1e1f;"]]: see our **[[FAIR assessment of EBRAINS datasets>>doc:.FAIR assessment of EBRAINS datasets.WebHome]]. ** 329 329 330 -**Viewer for sequential atlas-registered 2D images with annotation options** 331 331 332 - * 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]].374 +---- 333 333 334 -** Useyourresearchproductin an interactivepublication**376 +== **General benefits of sharing data ** == 335 335 336 - *Addyour data,models or software to a// Live paper.//Readmore about[[Livepapers onebrains.eu>>https://www.ebrains.eu/data/live-papers/live-papers]].378 +By sharing your data via EBRAINS, you gain access to the following benefits: 337 337 338 - **Interactive 3Datlas viewer with options for data visualization**380 +[[image:image-20230324170841-3.png]] 339 339 340 -* 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]]. 341 341 383 + 384 +We support you to better follow the [[FAIR^^ ^^guiding principles>>https://www.nature.com/articles/sdata201618]] for data management and stewardship. 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. 385 + 342 342 ---- 343 343 344 -== ==**Add a tutorialor learningresource** ====388 +== **Frequently asked questions ** == 345 345 346 -(% class="wikigeneratedid" id="H-LearningresourceA05Binformation5D" %) 347 -(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow// 390 +>Is the curation process time consuming and difficult? 348 348 392 +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. 349 349 350 - ====**Createaworkflow**====394 +>Is sharing my data also beneficial for me or only for others? 351 351 352 -(% class="wikigeneratedid" id="H-Workflows5Binformation5D" %) 353 -(% style="--darkreader-inline-color:#ffffff; color:#000000" %)//More information will follow// 396 +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. 354 354 355 - ----398 +>Can my data be too insignificant to share? 356 356 357 - ===**Thebenefits of sharingdata**===400 +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. 358 358 359 - By sharingyourdataviaEBRAINS, you gainaccesstothefollowing benefits:402 +>Can my data be easily misused if I share it? 360 360 361 - [[image:image-20230324170841-3.png]]404 +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. 362 362 406 +>Can I share my data before my paper is published? 363 363 408 +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. 364 364 365 - Wesupportyou to better follow the[[FAIR^^^^guiding principles>>https://www.nature.com/articles/sdata201618]] for data management and stewardship{{footnote}}Wilkinson, M., Dumontier,M., Aalbersberg, I. et al. The FAIR GuidingPrinciplesfor scientificdatamanagement andstewardship. Sci Data 3, 160018 (2016). https://doi.org/10.1038/sdata.2016.18 {{/footnote}}.Publishingdata,modelsorcodevia EBRAINSwillprovide youwitha citeable[[DataCite DOI>>https://www.doi.org/the-identifier/resources/handbook/]] foryour researchproduct.410 +>Can I lose my competitive edge if I share my data before I publish the associated paper? 366 366 412 +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. 413 + 414 + 367 367 ---- 368 368 369 -== =**Frequentlyaskedquestions** ===417 +== (% style="--darkreader-inline-color:#f1ede6; color:#1a202c; font-family:inherit; font-size:29px" %)**The curation team: meet the curators**(%%) == 370 370 371 -((( 372 -==== ==== 419 +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. 373 373 374 -((( 375 ->The curation process is time consuming and difficult 376 -))) 377 -))) 421 +The curators in EBRAINS are located in Oslo, Jülich, Trier and Paris. 422 + 378 378 379 -(% class="wikigeneratedid" id="HHowcanIshareA0models3F" %) 380 -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. 424 +**Located in Norway** 381 381 382 ->Sharing my data is not beneficial for me - only for others 426 +|(% style="width:303px" %)((( 427 +[[image:My project2.jpg||height="209" width="167"]] 383 383 429 +**Archana Golla** 384 384 385 -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. 431 +(% class="small" %)Curation Scientist 432 +Neuroscience (PhD)(%%) 433 +(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Behavioral neuroscience and microscopy** 434 +)))|(% style="width:303px" %)((( 435 +[[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]] 386 386 387 - >My datais too insignificanttoshare437 +**Camilla H. Blixhavn** 388 388 439 +(% class="small" %)Curation Scientist, 440 +Phd Student 441 +Neuroscience (M. Sc.)(%%) 442 +(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and data integration** 443 +)))|(% style="width:303px" %)((( 444 +[[image:My project (1).jpg||height="209" width="167"]] 389 389 390 - There isno such thingas insignificant data. Data that is consideredinsignificant for a given topic, may have great significance for another. By making “insignificant”datapublicly available, other researchers may find something interestingthat was off-topic for your own purposes.446 +**Ingrid Reiten** 391 391 392 ->My data can easily be misused if I share it with the world 448 +(% class="small" %)Curation Scientist, 449 +Phd Student 450 +Neuroscience (M. Sc.)(%%) 451 +(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and structural connectivity** 452 +)))|(% style="width:303px" %)((( 453 +[[image:My project1.jpg||height="209" width="167"]] 393 393 455 +**Sophia Pieschnik** 394 394 395 -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. 457 +(% class="small" %)Curation Scientist 458 +Neurocognitive Psychology (M. Sc.)(%%) 459 +(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroimaging ** 460 +))) 396 396 397 ->I don't think I'm allowed to share my data 462 +|(% style="width:303px" %)((( 463 +[[image:My project.jpg||height="209" width="167"]] 398 398 465 +**Heidi Kleven** 399 399 400 -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. 467 +(% class="small" %)Curation Scientist, 468 +Phd Student 469 +Neuroscience (M. Sc.)(%%) 470 +(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Neuroanatomy and brain atlases** 471 +)))| | | 401 401 402 ->I can't share my data before my paper is published 473 + 474 +\\**Located in Germany** 403 403 476 +|(% style="width:303px" %)((( 477 +[[image:My project (2).jpg||height="209" width="167"]] 404 404 405 - If you do not wantto share your data before publishing the results in an article, you can publish yourdataset with an embargo status. This will makeit possible to find information about the data without makingthe data itself available, and give you a citeable DOI.479 +**Jan Gündling** 406 406 407 ->If I share my data before I publish the associated paper, I will lose my competitive edge 481 +(% class="small" %)Curation Scientist, 482 +Phd Student 483 +Sensors and Cognitive Psychology (M. Sc.)(%%) 484 +(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Human-Computer Interaction** 485 +)))|(% style="width:303px" %)((( 486 +[[image:Lyuba.jpg||height="209" width="167"]] 408 408 488 +**Lyuba Zehl** 409 409 410 -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. 490 +(% class="small" %)Knowledge Systems Engineer 491 +Dr. rer. nat. (Systems Neuroscience)(%%) 492 +(% class="small" style="--darkreader-inline-color:#cac2b7; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis** 493 +)))|(% style="width:303px" %) |(% style="width:303px" %) 411 411 495 +---- 412 412 497 + 498 + 413 413 ---- 414 414 415 415 == Contact == ... ... @@ -416,9 +416,16 @@ 416 416 417 417 [[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]] 418 418 505 +---- 419 419 507 +== Affiliated laboratories == 508 + 509 +//Institute of Basic Medical Sciences,** **University of Oslo, Norway (PI: Jan G. Bjaalie, Trygve B. Leergaard)// 510 + 511 +//Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Germany (PI: Timo Dicksheid)// 512 + 513 +---- 514 + 515 +== References == 516 + 420 420 {{putFootnotes/}} 421 -~)~)~)~)~)~) 422 -~)~)~) 423 -~)~)~)~)~)~)~)~)~) 424 -~)~)~)~)~)~)
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