data-sharing-decision-tree issueshttps://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/issues2022-02-07T09:49:55+00:00https://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/issues/31cover FAIR principles2022-02-07T09:49:55+00:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.ukcover FAIR principlesDescribe FAIR and where it features in these plans.Describe FAIR and where it features in these plans.https://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/issues/29[task] Soft launch actions identified2022-01-13T12:00:20+00:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.uk[task] Soft launch actions identifiedIdentify actions from soft launch discussionsIdentify actions from soft launch discussionsMilestone 03: Soft Launch actions identifiedhttps://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/issues/28[task] first review of first draft of decision tree (soft launch meetings) co...2022-01-13T11:56:18+00:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.uk[task] first review of first draft of decision tree (soft launch meetings) completecomplete full review of all processes
- [x] Process 1
- [x] Process 2
- [x] Process 3
- [x] Process 4
- [ ] Process 5complete full review of all processes
- [x] Process 1
- [x] Process 2
- [x] Process 3
- [x] Process 4
- [ ] Process 5Milestone 02: Soft Launch meetings completehttps://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/issues/27[new supporting resource] DMP2022-01-13T11:52:47+00:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.uk[new supporting resource] DMPdraft sections for a funding body specific DMPsdraft sections for a funding body specific DMPsMilestone 09: New Data Management and Governance Resourceshttps://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/issues/26[governance infrastructure]2021-11-02T23:33:59+00:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.uk[governance infrastructure]Think about how we will regulate and monitor access of external users:
- [ ] How will accounts be verified (e.g. ORCID or institutional address?
- [ ] How long will accounts remain active?
- [ ] Can we give reviewer only access links?Think about how we will regulate and monitor access of external users:
- [ ] How will accounts be verified (e.g. ORCID or institutional address?
- [ ] How long will accounts remain active?
- [ ] Can we give reviewer only access links?Milestone 10: External user and reviewer access infrastructure agreedhttps://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/issues/25Use common language for researchers working at different levels2021-11-02T23:04:08+00:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.ukUse common language for researchers working at different levelsTalking about data in terms of "raw" or "preprocessed" is not useful when the document is intended for researchers in different fields ("raw" means a different thing to a clinician vs. a physicist). The most appropriate suggestion we cou...Talking about data in terms of "raw" or "preprocessed" is not useful when the document is intended for researchers in different fields ("raw" means a different thing to a clinician vs. a physicist). The most appropriate suggestion we could agree on would be to discuss things in terms of file types, e.g. "k-space", "dicom", "nifti".Milestone 07: Second Draft of decision treehttps://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/issues/24[diagram] Add route for when open sharing consent is not available2021-11-02T23:01:01+00:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.uk[diagram] Add route for when open sharing consent is not availableAdd a route in the diagram for when consent for (in vivio human) open data sharing was not given, e.g. for historical data. This may redirect to a letter to the editor, for example as below.
Below letter to the editor was prepared for ...Add a route in the diagram for when consent for (in vivio human) open data sharing was not given, e.g. for historical data. This may redirect to a letter to the editor, for example as below.
Below letter to the editor was prepared for a submission to [Wellcome Open Research](https://wellcomeopenresearch.org/for-authors/data-guidelines). Here data for which there is no consent for sharing falls under their “exceptions” description:
> "We recognise that there may be cases where openly sharing data may not be feasible (due to ethical or confidentiality considerations) […] If you think that you cannot provide the source data, please let the editorial team know, so we can advise further.”
-----
Dear [Editors]
We are pleased to submit our paper [...] for your consideration.
We are pleased to publish all anonymised behavioural data with the publication, along with the analysis code and stimulation presentation materials. We will also publish the code which generates the submitted figures (_Note: list the behavioural figures if they have been prepared_) exactly from the behavioural data. All code and behavioural data will be made available via the Open Science Framework.
The neuroimaging data were acquired in [anything predating CUREC AP17 version 6.3] and consent for open sharing was not established at that time. It is not possible to completely anonymise the raw MRI data, as each data set is unique to the individual participant. As the data cannot be anonymised we are required to control access inline with “biometric” data as defined by UK-GDPR. (_Note: once data are anonymised they no longer fall under UK-GDPR, but the argument here is that we cannot anonymise_)
We are pleased to share the aggregated clinical neuroimaging data once it has been transformed from identifiable participant space to a normalised space. These data will be made available as unthresholded participant level statistical maps of each of our conditions (_Note: You could just publish your contrasts of interest. The individual conditions would be more meaningful, I think, but potentially more work_) via Neurovault. We will also publish the code which generates neuroimaging figures (_Note: list figures if available_) via the Open Science Framework.
Sharing the aggregated data on Neurovault will make the data available for re-use in meta-analysis using this well established platform. For researchers interested in conducting more detailed re-analysis or re-use of this data, we would be pleased to facilitate closed or 1-to-1 sharing of the raw data with appropriate institutional contracts in place to protect the privacy of the participants. Such interested particles will be advised to contact the corresponding author.
We will align our shared materials with the FAIR principles. All shared materials will be issued with a DOI (via the Open Science Framework, Zenodo or the Oxford University Research Archive) and licensed for re-use with a CC-BY-4.0 license. All data will be shared using the appropriate discipline specific standards (for example the Brain Imaging Data Structure for neuroimaging data) and on repositories which have been assessed for persistence and sustainability. Behavioural data will be shared in open format machine readable .csv files, and supported by appropriate metadata including a data dictionary which describes all variables.
We have liaised with the WIN Open Neuroimaging Team for guidance in preparing these materials for sharing. We are confident that following the above procedure is appropriate for data of this type, such that it is “as open as possible, and as closed as necessary”. We feel this proposed level of sharing will maximise the openness of this publication within the legal and ethical constraints.
Please could you confirm that the above described procedure would be acceptable by the standards required for publication in your journal [...]
Please do not hesitate to contact me should you have any further questions [...]
Kind Regards,
[Corresponding Author]
-----Milestone 07: Second Draft of decision treehttps://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/issues/23[new supporting resource] Revise AP08 (MEG)2021-11-02T23:00:28+00:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.uk[new supporting resource] Revise AP08 (MEG)Milestone 04: new ethics documentation draftedhttps://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/issues/22[new supporting resource] Revise AP03 (EEG)2021-11-02T23:00:14+00:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.uk[new supporting resource] Revise AP03 (EEG)Milestone 04: new ethics documentation draftedhttps://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/issues/21[new supporting resource] Revise AP17 (MRI)2021-11-02T23:00:00+00:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.uk[new supporting resource] Revise AP17 (MRI)Revise CUREC approved procedure to extend the detail on open data sharing.
As per issue #14, current wording in AP17 is considered to be sufficient for sharing data on our open repository. We will, however, submit an amendment containin...Revise CUREC approved procedure to extend the detail on open data sharing.
As per issue #14, current wording in AP17 is considered to be sufficient for sharing data on our open repository. We will, however, submit an amendment containing further details, as best practice in transparency and courtesy to participants.
Amendments will be made in:
- [ap17-revised-PIS](https://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/blob/master/docs/new-supporting-resources/Revised_AP17-PIS.docx)
- [ap17-revised-consent](https://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/blob/master/docs/new-supporting-resources/Revised_AP17-consent.docx)
- [ap17-revised-procedure](https://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/blob/master/docs/new-supporting-resources/Revised_AP17-procedure.docx)Milestone 04: new ethics documentation draftedCassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.ukCassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.ukhttps://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/issues/20[diagram] Extend with new section about contracts2021-11-02T22:59:43+00:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.uk[diagram] Extend with new section about contractsFollowing request in [Soft Launch 1](https://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/blob/master/docs/CallNotes-SoftLanuch-process1-3.md) and in light of advice received from Dorota Pawlick in issue #15 , e...Following request in [Soft Launch 1](https://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/blob/master/docs/CallNotes-SoftLanuch-process1-3.md) and in light of advice received from Dorota Pawlick in issue #15 , extend the decision tree diagrams to cover what needs to be considered in identifying appropriate contract.Milestone 07: Second Draft of decision treehttps://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/issues/19[digram] Consider splitting the decision tree into levels relevant to each st...2021-11-02T23:31:23+00:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.uk[digram] Consider splitting the decision tree into levels relevant to each stakeholderPrompted by [Soft Launch 1](https://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/blob/master/docs/CallNotes-SoftLanuch-process1-3.md), researchers wanted to have it clearly identified which activities were their...Prompted by [Soft Launch 1](https://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/blob/master/docs/CallNotes-SoftLanuch-process1-3.md), researchers wanted to have it clearly identified which activities were their responsibility and which were the responsibility of the PI. Suggested by @msouth, this could also be extended into all levels of stakeholder interest (ethics IRB, InfoSec, contracts... etc.).
Consider a method for drawing or visualising the diagram which makes it easy for different stakeholders to identify the processes which are relevant for them. This could be adding a symbol to each box to indicate who it applies to, or perhaps making them extendable (for example, "extend this box for the full researcher process"). Could alternatively mean redrawing with the detail only for that group.
Currently favouring a top level summary, which links to sub-processes. Need to think about what level of granularity for top level.Milestone 07: Second Draft of decision treehttps://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/issues/18[new supporting resource] List data types with baseline and potential levels ...2021-11-02T22:58:57+00:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.uk[new supporting resource] List data types with baseline and potential levels of anonymityPrompted by [SoftLaunch request](https://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/blob/master/docs/CallNotes-SoftLanuch-process1-3.md), create a document which lists all the data types which are routinely co...Prompted by [SoftLaunch request](https://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/blob/master/docs/CallNotes-SoftLanuch-process1-3.md), create a document which lists all the data types which are routinely collected by WIN and describe their baseline anonymity alongside their maximal deidentification and route to achieve this.Milestone 07: Second Draft of decision treehttps://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/issues/17[new supporting resource] DPIA2021-11-02T22:58:23+00:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.uk[new supporting resource] DPIAThe DPIA will be the governance review of our processes. Is this required and what should it describe?
Suggestion form Karen Melham in issue #14 that the open repository should not be the place where de-identification takes place. De-id...The DPIA will be the governance review of our processes. Is this required and what should it describe?
Suggestion form Karen Melham in issue #14 that the open repository should not be the place where de-identification takes place. De-identification should be managed by the researcher (and their ethics) and handed over to the open repository for curation once already de-identified. Note however that XNAT is a very useful tool for the deidentification services we want to run (e.g. dicom strip). This makes a strong case for two XNATs (names TBC!): One as a researcher resource ("Research XNAT") and one as a public facing portal ("Public XNAT").
Q:
1. What DPIA etc. does Jalapeño have in place? This will be equivalent to what we need for Research XNAT. Probably includes DMP.
2. Do we need to have a secondary DPIA for Public XNAT? For the purposes of the DPIA screening, we can consider that this repository contains no identifiable information in most cases (as suggested by Karen Melham). "Edge cases" (e.g. where identifiable disease group) will still be protected under our DUA.Milestone 09: New Data Management and Governance Resourceshttps://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/issues/16[new supporting resource] Technical Development SOP update?2021-11-02T22:56:32+00:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.uk[new supporting resource] Technical Development SOP update?[WIN Technical Development SOP](https://sharepoint.nexus.ox.ac.uk/sites/NDCN/FMRIB/Shared%20Documents/SOP_Technical_Development_Scanning.pdf#search=technical%20development) is used for scanning on physics projects.
SOP Number: OHBA_009_...[WIN Technical Development SOP](https://sharepoint.nexus.ox.ac.uk/sites/NDCN/FMRIB/Shared%20Documents/SOP_Technical_Development_Scanning.pdf#search=technical%20development) is used for scanning on physics projects.
SOP Number: OHBA_009_V1; 004-V4 (FMRIB)
SOP Title: Ethical Considerations for Technical Development Scans
> [This SOP] describe circumstances in which MR scanning of human volunteers is permissible for technical development purposes, without the need for explicit NRES/CUREC ethical approval, and to describe the procedures that should be followed in these cases.
Does this need to be updated to allow data sharing via XNAT? Relevant wording around data sharing:
> 4.1 Technical Development Scans
> Examples of technical developments, where it has been advised that ethics committee approval is not required include:
> **1. Evaluating, testing or fixing a sequence whose use will be for other studies running under their own ethics approval.**
> - **Data collected will not be published**.
> 2. Acquiring a few data sets for demonstration of an image analysis methodology or optimising sequence parameters.
> - Data may be published as proof of method.
> 3. Developing and validating a new imaging sequence.
> - Validation data may be published.
> 4. Testing a device for use in the MRI scanner, including radiofrequency coils and stimulus delivery equipment.
> - Data may be published.
> 4.2 Training scans
> A training scan is one performed for the purposes of training other researchers or scanner operators in imaging techniques, and should be logged accordingly. Individual subject log sheets should still include these scans, which count towards the total.
> - **Data will not be published**
> 6.5 Data storage and protection
> Data storage will be on a password-protected computer. **Any data that is shared outside the University of Oxford must be completely anonymised and no information about the subject disclosed.**
Actions / suggested update options:
- [ ] 6.5 replace "completely anonymised" with "de-identified"
- [ ] Add a section on open data sharing, copying the proposed amended wording to the AP17 (see issue #14)
- [ ] System for identifying which basis (from the above) data were collected so this can be audited when preparing the data for sharing.Milestone 04: new ethics documentation draftedhttps://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/issues/15[new supporting resource] Data usage agreement2021-11-02T22:56:13+00:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.uk[new supporting resource] Data usage agreementWe will need to create +1 data usage agreements (DUA) which a researcher can select and apply to their data before it is made available for reuse. This issue documents the conversations, meetings and decisions contributing to the creatio...We will need to create +1 data usage agreements (DUA) which a researcher can select and apply to their data before it is made available for reuse. This issue documents the conversations, meetings and decisions contributing to the creation of this document.Milestone 05: Data usage agreements draftedhttps://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/issues/14[task] Do we need separate ethics for this repository? - Stakeholder feedback2021-11-02T22:55:55+00:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.uk[task] Do we need separate ethics for this repository? - Stakeholder feedback## Clare O'Donoghue + @cassag (19/08/21)
CUREC MRI [approved procedure](https://researchsupport.admin.ox.ac.uk/governance/ethics/resources/ap) (AP17)
- Consent form: "I agree for research data collected in this study to be **given to re...## Clare O'Donoghue + @cassag (19/08/21)
CUREC MRI [approved procedure](https://researchsupport.admin.ox.ac.uk/governance/ethics/resources/ap) (AP17)
- Consent form: "I agree for research data collected in this study to be **given to researchers**, including those working outside of the UK and the EU, to be used in other research studies. I give permission for data from this study to be used in publication. I understand that any data and/or brain images of me that leave the Centre will be de-identified."
- PIS: "If applicable: I/We would like your permission to use de-identified data in future studies, and to **share data with other researchers (e.g. in online databases). All personal information that could identify you will be removed or changed before information is shared with other researchers** or results are made public."
- **Is the wording above sufficient?**
[Ethics decision tree](https://researchsupport.admin.ox.ac.uk/governance/ethics/apply)
- Data will not be anonymous
- Some participants will be recruited into WIN studies via NHS, however they will be recruited into the database via the study, not directly via NHS.
WIN Ethics check list will need updating
How will we confirm consent is in place before making data public? Easiest if it is machine readable, but then easier to link to WIN Scan ID.Milestone 04: new ethics documentation draftedCassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.ukCassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.ukhttps://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/issues/11[New supporting resource] Create WIN template participant information sheets ...2021-11-02T22:55:34+00:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.uk[New supporting resource] Create WIN template participant information sheets and consent forms for data sharing[Incorporate Open Brain Consent suggestions](https://open-brain-consent.readthedocs.io/en/stable/gdpr/ultimate_gdpr.html#english) into WIN data sharing participant information sheets and consent forms.[Incorporate Open Brain Consent suggestions](https://open-brain-consent.readthedocs.io/en/stable/gdpr/ultimate_gdpr.html#english) into WIN data sharing participant information sheets and consent forms.Milestone 04: new ethics documentation draftedCassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.ukCassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.ukhttps://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/issues/5Add community standard data structure for physics projects2021-11-02T22:55:12+00:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.ukAdd community standard data structure for physics projectsISMRM Reproducibility study groups have been working to define data standards for raw MRI data. Investigate and incorporate these into physics-type paths.ISMRM Reproducibility study groups have been working to define data standards for raw MRI data. Investigate and incorporate these into physics-type paths.Milestone 07: Second Draft of decision treehttps://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree/-/issues/4Add community standard data structure for electrophysiology: NWB:N2021-11-02T22:54:42+00:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.ukAdd community standard data structure for electrophysiology: NWB:N"[Neurodata Without Borders: Neurophysiology (NWB:N)](https://www.nwb.org) is a data standard for neurophysiology, providing neuroscientists with a common standard to share, archive, use, and build analysis tools for neurophysiology data..."[Neurodata Without Borders: Neurophysiology (NWB:N)](https://www.nwb.org) is a data standard for neurophysiology, providing neuroscientists with a common standard to share, archive, use, and build analysis tools for neurophysiology data."
Incorporate into electrophysiology paths.Milestone 07: Second Draft of decision tree