data.md 6.06 KB
Newer Older
Cassandra Gould van Praag's avatar
Cassandra Gould van Praag committed
1
---
Cassandra Gould van Praag's avatar
Cassandra Gould van Praag committed
2
layout: default
Cassandra Gould van Praag's avatar
Cassandra Gould van Praag committed
3
4
5
6
7
8
9
10
11
12
13
14
title: Open Data
parent: Open WIN Tools
has_children: true
nav_order: 4
---

# Open Data
{: .fs-9 }

How to share your data responsibly
{: .fs-6 .fw-300 }

15
16
17
[Review current activity]((https://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree))
{: .label .label-red }

18

Cassandra Gould van Praag's avatar
Cassandra Gould van Praag committed
19
20
---

Cassandra Gould van Praag's avatar
Cassandra Gould van Praag committed
21
![open-data](../../img/img-open-data-flow.png)
Cassandra Gould van Praag's avatar
Cassandra Gould van Praag committed
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42

## Purpose

The Open Data Working Group has built a searchable, user friendly [XNAT](https://www.xnat.org) database to store MRI, EEG and MEG scan data directly from the scanners.  The database also has the capability to store other research data alongside the scans to create a research dataset.  Image conversion tools are be integrated into the database to convert raw image files to standard formats and the community standard [Brain Imaging Data Structure (BIDS)](https://bids.neuroimaging.io) file structures.

Data will only ever be shared when the participant has given explicit consent to open sharing. All access protocols have been developed to ensure the highest levels of security to protect against accidental or malicious data breaches.  

### General Data Protection Regulation (GDPR) compliant data sharing policy
The database has the capability to share data at between specified individuals, openly to all WIN members, or externally based on the requirements of the research lead.

#### De-identification
Before data is shared externally, it will be checked against a list of defined criteria to ensure the data are appropriately de-identified and any risk of identification of individual participants is negligible. The criteria for de-identification will include removal of identifying facial features (defacing), the removal of personal data from raw [dicom](https://en.wikipedia.org/wiki/DICOM) images, and the removal of any linkage with consent or experimental participant identification numbers.

#### Data usage Agreement
Individuals accessing shared data will additionally be required to agree to a Data Usage Policy, where they explicitly confirm that they will not attempt to re-identify participants, nor share the data with any third party who has not signed the same agreement.

The Data Usage Agreement and de-identification process is being developed with the support of Departmental and University level [Information Security and Compliance](https://www.infosec.ox.ac.uk) teams.

#### Quality control
WIN members will also be encouraged to run and share the results of predefined quality control algorithms, so anyone accessing the data can have a ready measure of image quality.

43
[![For WIN members](../../img/btn-win.png)](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/tools/data/#for-win-members)      [![For external researchers](../../img/btn-external.png)](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/tools/data/#for-external-researchers)
Cassandra Gould van Praag's avatar
Cassandra Gould van Praag committed
44
45
46
47
48
49
50
51
52

Coming soon
{: .label .label-yellow }

**THIS TOOL IS CURRENTLY IN DEVELOPMENT. PLEASE REFER TO THE INFORMATION BELOW TO UNDERSTAND THE AIM AND AMBITION OF THIS PROJECT. THE "HOW TO" GUIDE WILL BE BUILT BY THE COMMUNITY AND TOOL DEVELOPERS IN THE COMING MONTHS.**

<br>

## For WIN members
Cassandra Gould van Praag's avatar
Cassandra Gould van Praag committed
53
54
55
56
57

Note while the XNAT system is in development, we suggest you use the below wording in your data availability statement in journal submissions:

> "Data will be made available on the WIN Open Data server. This is currently in development. Register here to find out when materials are available for download: [https://web.maillist.ox.ac.uk/ox/subscribe/win-open-data](https://web.maillist.ox.ac.uk/ox/subscribe/win-open-data)"

58
### Benefits
Cassandra Gould van Praag's avatar
Cassandra Gould van Praag committed
59
#### Version control ![version-control](../../img/icon-version-control.png)
Cassandra Gould van Praag's avatar
Cassandra Gould van Praag committed
60
61
62
Coming soon
{: .label .label-yellow }

Cassandra Gould van Praag's avatar
Cassandra Gould van Praag committed
63
#### Citable research output ![doi](../../img/icon-doi.png)
Cassandra Gould van Praag's avatar
Cassandra Gould van Praag committed
64
65
66
Coming soon
{: .label .label-yellow }

Cassandra Gould van Praag's avatar
Cassandra Gould van Praag committed
67
#### Reproducible methods detail ![reproduce](../../img/icon-reproduce.png)
Cassandra Gould van Praag's avatar
Cassandra Gould van Praag committed
68
69
70
Coming soon
{: .label .label-yellow }

71
72
### How to use
[WIN XNAT](https://xnat.win.ox.ac.uk) (accessible from the university network or VPN) is currently being built and will be used to share imaging data internally within WIN.  
Cassandra Gould van Praag's avatar
Cassandra Gould van Praag committed
73

74
75
#### Access
You can log into [WIN XNAT](https://xnat.win.ox.ac.uk) using your WIN IT account (currently requires a connection to the university network or VPN).
Cassandra Gould van Praag's avatar
Cassandra Gould van Praag committed
76

77
#### Useful background
Cassandra Gould van Praag's avatar
Cassandra Gould van Praag committed
78
79
The [XNAT](https://xnat.org) website has useful background information about the XNAT platform.

80
#### BIDS in XNAT
81
For the current overview of how BIDS works in XNAT, see the [BIDS](./data/bids.md) page.
Cassandra Gould van Praag's avatar
Cassandra Gould van Praag committed
82

83
#### Python libraries
84
There are several python libraries](data/python.md) that can be used to write scripts against the XNAT API.  See [python libraries](data/python.md) for more info on pyxnat, xnatpy and dax.
Cassandra Gould van Praag's avatar
Cassandra Gould van Praag committed
85

86
#### Docker in XNAT
87
To see how Docker works in XNAT, see the [Docker](data/docker.md) page.
Cassandra Gould van Praag's avatar
Cassandra Gould van Praag committed
88

89
#### Case Studies
Cassandra Gould van Praag's avatar
Cassandra Gould van Praag committed
90

91
The [OPDC project](data/opdc.md) uploaded DICOM data from jalapeno using python and dcmtk.
Cassandra Gould van Praag's avatar
Cassandra Gould van Praag committed
92
93
94

TODO: More case studies!

95
96
97
98

## For external researchers
External users will be able to search the database for resources which individual teams have chosen to make openly available. These may be deposited to support publications as supplementary methods material, or they may form the main body of research in data papers.

99
[Sign up to the win-open-data mailing list](https://web.maillist.ox.ac.uk/ox/subscribe/win-open-data) to receive updates on new data shared to the WIN XNAT server or new features. This mailing list will be "broadcast only" with messages sent from WIN XNAT administrators. You can unsubscribe at any point. Enquiries about external access to WIN XNAT should be directed to cassandra.gouldvanpraag@psych.ox.ac.uk.
100
101
102



Cassandra Gould van Praag's avatar
Cassandra Gould van Praag committed
103
104
105
106
107
108
109
110
111
## Working group members (alphabetically)
We are grateful to the following WIN members for their contributions to developing the Open Data server.
- [Stuart Clare](https://www.win.ox.ac.uk/people/stuart-clare)
- [Dave Flitney](https://www.win.ox.ac.uk/people/david-flitney)
- [Clare Mackay](https://www.win.ox.ac.uk/people/clare-mackay)
- [Duncan Mortimer](https://www.win.ox.ac.uk/people/duncan-mortimer)
- Paul Semple
- Duncan Smith
- [Matt South](https://www.win.ox.ac.uk/people/matthew-south)