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# WIN data sharing decision tree
This is the GitLab repository for the development (and possibly deployment) of the WIN data sharing decision tree - A guide for researchers to follow in designing their study with a view to sharing their data on the WIN XNAT Open Data server.
***"A guide for researchers to follow in designing their study with a view to sharing their data on the WIN XNAT Open Data server."***
This is the GitLab repository for the development (and possibly deployment) of the WIN data sharing decision tree.
---
## Welcome!
## The problem
*"Shared data should as open as possible and as closed as necessary"*.
Working out how to appropriately share data requires the navigation through various lines of guidance and legislation, notably GDPR. This is a complex process which is discipline and institutionally specific.
## The solution
We are developing a flow chart which researchers can walk through to address the question "Can I share my data on XNAT?".
These documents will guide you through the process of designing your study and preparing your data for sharing on the WIN XNAT Open Data server.
*Working through this flow chart will aid researchers in designing their projects and conducting the necessary stages of data preparation in order to share their data without compromising their ethical and legal obligations to participants and research funders.*
## What are we doing?
The Open WIN Steering Committee have been working to delineate the stages a researcher should (and in some cases *must*) go through in order to share their data in accordance with University of Oxford Best Practice and GDPR.
We are now opening this work up to the community to provide feedback on bottlenecks, missing guidance and further refinements. This will be started by inviting a small number of researchers (with a range of data types) to [add and comment on issues](https://git.fmrib.ox.ac.uk/open-science/data-sharing-decision-tree/-/issues) and update the diagram where appropriate.
We are now opening this work up to the community to provide feedback on bottlenecks, missing guidance and further refinements.
### The problem
This consultation will start by inviting a small number of researchers (with a range of data types) to [add and comment on issues with the proposed guidance](https://git.fmrib.ox.ac.uk/open-science/data-sharing-decision-tree/-/issues) and update the diagram where appropriate.
*"Shared data should as open as possible and as closed as necessary"*.
## What do we need
Working out how to appropriately share data requires the navigation through various lines of guidance and legislation, notably GDPR. This is a complex process which is discipline and institutionally specific.
We need researchers to walk through these documents with their existing or hypothetical research projects. Help us to identify gaps, issues and solutions!
Take a look at these documents:
- [Overview of the decision tree in its current state](./docs/overview/overview.md)
- [Appendices and notes](./docs/WIN-data-sharing-decision-tree-Appendicies.md)
- [Working diagrams of decision tree](./docs/decision-tree.md)
### The solution
We are developing a flow chart which researchers can walk through to address the question **"Can I share my data on XNAT"**.
If you'd like to comment on these documents, please submit an [issues](https://git.fmrib.ox.ac.uk/open-science/data-sharing-decision-tree/-/issues) describing your feedback. We'll be in touch to discuss your suggestions further.
**Working through this flow chart will aid researchers in designing their projects and conducting the necessary stages of data preparation in order to share their data without compromising our ethical and legal obligations to our participants and research funders.**
We will also be organising a group workshop, which you are invited to attend to review and provide feedback on these proposals. Stay tuned for details!
## Who are we
......@@ -34,16 +47,6 @@ Contributions to the development of this resource will be solicited from the [Op
The XNAT Open Data Server is being developed by the [Open Data Team](https://cassgvp.github.io/WIN-Open-Neuroimaging-Community/docs/tools/data.html#working-group-members-alphabetically)
## What do we need
We need researchers to walk through these documents with their existing or hypothetical research projects. Help us to identify gaps, issues and solutions!
Take a look at these documents:
- [Overview of the decision tree in its current state](./docs/overview/overview.md)
- [Appendices and notes](./docs/WIN-data-sharing-decision-tree-Appendicies.md)
- [Working diagrams of decision tree](./docs/decision-tree.md)
If you'd like to comment on these documents, please submit an [issues](https://git.fmrib.ox.ac.uk/open-science/data-sharing-decision-tree/-/issues) describing your feedback. We'll be in touch to discuss your suggestions further. We will also be organising a group workshop, which you are invited to attend. Stay tuned for details!
## Contact us
......
---
title: 'Open Data Process Diagram - Appendices'
---
# Contents
# 'Open Data Process Diagram - Appendices'
## Contents
- [Appendix 1 - DICOM Headers to be scrubbed](#dicom-scrub)
- [Appendix 2 - BIDS Compliance](#BIDS)
- [Appendix 3 - Scrubbing .json files](#json-scrub)
......@@ -18,28 +18,30 @@ title: 'Open Data Process Diagram - Appendices'
<a name="dicom-scrub"></a>
# Appendix 1 - DICOM Headers to be scrubbed
## Appendix 1 - DICOM Headers to be scrubbed
List of DICOM identifying fields that need to be scrubbed included in
McGill Centre for Integrative Neuroscience Open Science Guidance Open
Science Data Preparation Checklist.
[McGill Centre for Integrative Neuroscience Open Science Guidance Open
Science Data Preparation Checklist](http://loris.ca/MCINOpenScienceGuidance_DataPrepChecklist.pdf).
Fields to be scrubbed include anything which is identifiable as
participant information or unique to the scanning session or data
acquisition site. Fields identified by McGill have been checked against
acquisition site.
Fields identified by McGill have been checked against
DICOM fields appearing in data acquired on WIN 3T (OHBA) for human
participant.
participant (identifiable fields have been censored here using "x" placeholders).
|**Field name**|**In WIN dicom example (if field present)**|
|--------------|-------------------------------------------|
PatientAddress | n/a|
PatientAge | 042Y|
PatientBirthDate+D10 | 19751005|
PatientBirthDate+D10 | 1975xxxx|
PatientBirthName | n/a|
PatientID | W3T\_2016\_11\_090|
PatientID | W3T\_2016\_xx\_xxx|
PatientMotherBirthName | n/a|
PatientName | W3T\_2016\_11\_090|
PatientName | W3T\_2016\_xx\_xxx|
PatientReligiousPreference | n/a|
PatientSex | F|
PatientTelephoneNumbers | n/a|
......@@ -48,13 +50,13 @@ Patient Weight | 64|
OtherPatientIDs | n/a|
OtherPatientName | n/a|
OtherPatientNames | n/a|
AcquisitionDate | 20180515|
AcquisitionDate | 2018xxxx|
AcquisitionTime | 90931.46|
ContentDate | 20180515|
ContentDate | 2018xxxx|
ContentTime | 384 values: 091507.445000,| 091507.448000, 091507.450000, 091507.452000\...
DeviceSerialNumber | 66093|
FrameOfReferenceUID | 1.3.12.2.1107.5.2.43.66093.1.20180515090420048.0.0.0|
InstanceCreationDate | 20180515|
FrameOfReferenceUID | 1.3.12.2.1107.5.2.43.66093.1.2018xxxx090420048.0.0.0|
InstanceCreationDate | 2018xxxx|
InstanceCreationTime | 384 values: 091507.445000,| 091507.448000, 091507.450000, 091507.452000\...
InstitutionAddress | Warneford Lane| StreetNo,Oxford,District,GB,OX3 7JX
InstitutionalDepartmentName | BE3597|
......@@ -64,7 +66,7 @@ MediaStorageSOPInstanceUID | n/a|
OperatorsName | n/a|
PerformedProcedureStepDescription | n/a|
PerformedProcedureStepID | 0|
PerformedProcedureStepStartDate | 20180515|
PerformedProcedureStepStartDate | 2018xxxx|
PerformedProcedureStepStartTime | 85830.014|
PerformingPhysicianName | Blank|
PhysiciansOfRecord | n/a|
......@@ -72,18 +74,18 @@ ReferencedSOPInstanceUID | n/a|
ReferringPhysicianName | Blank|
RequestedProcedureDescription | n/a|
RequestingPhysician | Blank|
SeriesDate | 20180515|
SeriesInstanceUID | 2 values:| 1.3.12.2.1107.5.2.43.66093.2018051509150468746204326.0.0.0, 1.3.12.2.1107.5.2.43.66093.2018051509093178111004205.0.0.0
SeriesDate | 2018xxxx|
SeriesInstanceUID | 2 values:| 1.3.12.2.1107.5.2.43.66093.2018xxxx09150468746204326.0.0.0, 1.3.12.2.1107.5.2.43.66093.2018xxxx09093178111004205.0.0.0
SeriesTime | 2 values: 091507.443000, 091508.436000|
SOPInstanceUID | 384 values:| 1.3.12.2.1107.5.2.43.66093.2018051509150469069804346, ...
SOPInstanceUID | 384 values:| 1.3.12.2.1107.5.2.43.66093.2018xxxx09150469069804346, ...
StationName | AWP66093|
StudyDate | 20180515|
StudyDate | 2018xxxx|
StudyDescription | OHBA Projects\^2018\_108 RESTAND|
StudyInstanceUID | MR20180515085649|
StudyInstanceUID | MR2018xxxx085649|
StudyTime | 85829.922|
<a name="BIDS"></a>
# Appendix 2 - BIDS Compliance
## Appendix 2 - BIDS Compliance
Data should be confirmed as BIDS compliant using the BIDS-validator
......@@ -92,7 +94,7 @@ docker image available from
This could be installed on XNAT.
<a name="json-scrub"></a>
# Appendix 3 - Scrubbing .json files
## Appendix 3 - Scrubbing .json files
.json sidecar files are generated for each nifti image to conform with
......@@ -102,7 +104,7 @@ identifiable information relating to the participant which should not be
distributed openly.
<a name="qc"></a>
# Appendix 4 - Quality Control
## Appendix 4 - Quality Control
Quality control (QC) assessments should be completed as a matter of
......@@ -111,7 +113,7 @@ your data. QC can be performed on BIDS formatted data using mriqc. Mriqc
is available as a container on XNAT.
<a name="deface"></a>
# Appendix 5 - Defacing
## Appendix 5 - Defacing
Consider using fsl\_deface. Other defacing tools are available.
......@@ -120,7 +122,7 @@ Consider running QC on defaced images using
[https://github.com/raamana/visualqc/blob/master/docs/VisualQC\_TrainingManual\_v1p4.pdf](https://github.com/raamana/visualqc/blob/master/docs/VisualQC_TrainingManual_v1p4.pdf)
<a name="upload"></a>
# Appendix 6 - Upload to XNAT
## Appendix 6 - Upload to XNAT
TBD (not exhaustive)
......@@ -136,7 +138,7 @@ TBD (not exhaustive)
available.
<a name="data-freeze"></a>
# Appendix 7 - Data freeze
## Appendix 7 - Data freeze
The data freeze process as applied for the Dementias Platform UK (DPUK)
is computationally expensive -- multiple freeze generates duplicates of
......@@ -147,7 +149,7 @@ researchers the cost of snapshots carried by WIN. A cost model would
also be useful for project and infrastructure grant applications.
<a name="doi"></a>
# Appendix 8 - Digital object identifiers (DOI)
## Appendix 8 - Digital object identifiers (DOI)
A DOI is essential to ensure that the data shared can be effectively
......@@ -174,7 +176,7 @@ motivated to carry some of the burden, with their focus on effective
curation. Opened discussions with ORA on 10^th^ June 2021.
<a name="dua"></a>
# Appendix 9 - Data usage agreement (DUA)
## Appendix 9 - Data usage agreement (DUA)
Research Services (<research.services@admin.ox.ac.uk>.) can provide
......@@ -249,7 +251,7 @@ that I access these data under the following terms:
my privileges to access these data.
<a name="rdo"></a>
# Appendix 10 -- Advice from Research Data Oxford
## Appendix 10 -- Advice from Research Data Oxford
- Define what a breach looks like (how, why, impact) and demonstrate
......@@ -274,10 +276,10 @@ are interested in growing their experience of working directly with
specific examples.
<a name="policy"></a>
# Relevant policy and guidance
## Relevant policy and guidance
## University of Oxford Policy on the Management of Data Supporting Research Outputs
### University of Oxford Policy on the Management of Data Supporting Research Outputs
<https://researchdata.ox.ac.uk/university-of-oxford-policy-on-the-management-of-data-supporting-research-outputs/>
......@@ -309,7 +311,7 @@ for Data, or ORA-Data), a data record should also be created in ORA-Data
which describes and points to the data.
<a name="acknowledgements"></a>
# Acknowledgements
## Acknowledgements
Created using materials from: Das et al, 2019, \"MCIN Open Science
Guidance: Data Preparation Checklist\"
......
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