Difference between revisions of "Data Repository tools"
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# Use the data submission ticket from the previous step to upload the data submission package with the help of the [[#DataUpload| Data Upload]] module. | # Use the data submission ticket from the previous step to upload the data submission package with the help of the [[#DataUpload| Data Upload]] module. | ||
# Download the data using the means provided by the [[#DataDownload| Data Download]] module. | # Download the data using the means provided by the [[#DataDownload| Data Download]] module. | ||
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=== Data for uploading === | === Data for uploading === | ||
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| − | <div id=" | + | <div id="ImagingData"><div> |
| − | ==== | + | ==== Imaging data ==== |
| − | The following information is required for all image submissions and should be included in a CSV file: | + | Imaging data can be uploaded in the form of |
| + | |||
| + | * a brain image file | ||
| + | * and a corresponding [http://en.wikipedia.org/wiki/Comma-separated_values CSV] file that contains some additional patient/subject/visit information (not stored in the image header) as well as image related metadata. | ||
| + | |||
| + | The following information is required for all [[Image submission plug-in||image submissions]] and should be included in a CSV file: | ||
# The patient/subject information including - GUID, a patient/subject age, a study site name, and a visit date; | # The patient/subject information including - GUID, a patient/subject age, a study site name, and a visit date; | ||
# The image information including - imaging study date and time, imaging file name, imaging file itself, imaging file format and modality, image QA/QC information. | # The image information including - imaging study date and time, imaging file name, imaging file itself, imaging file format and modality, image QA/QC information. | ||
| − | ==== Image files ==== | + | ===== Image files ===== |
| − | The brain image file can be | + | The brain image file can be: |
* a single file in one of [[Supported Formats| supported formats]], | * a single file in one of [[Supported Formats| supported formats]], | ||
* a [[Other formats supported by MIPAV#DicomFormat|DICOM multifile]] or some other multifile in one of the supported formats, | * a [[Other formats supported by MIPAV#DicomFormat|DICOM multifile]] or some other multifile in one of the supported formats, | ||
* a ZIP archive that contains an image dataset (e.g. [[Other formats supported by MIPAV#DicomFormat|DICOM dataset]] with images of multiple slices stored in separate image files - [[Image _submission plug-in#Multifiles|a multifile]]). | * a ZIP archive that contains an image dataset (e.g. [[Other formats supported by MIPAV#DicomFormat|DICOM dataset]] with images of multiple slices stored in separate image files - [[Image _submission plug-in#Multifiles|a multifile]]). | ||
| + | For more information refer to: [[Image submission plug-in|Imaging data submission and validation module]]. | ||
<div id="ImagingSubmission"><div> | <div id="ImagingSubmission"><div> | ||
Revision as of 14:56, 26 July 2013
In order to help researches to upload and download data to the data repository, BRICS provides the Data Repository tool that includes the following modules (or sub-tools):
- Imaging data submission and validation module should be used for imaging data to create the image submission package.
- Data Validation module verifies that data conforms to the required format and range values defined in the data dictionary. It also creates a data submission package (XML) and submission ticket (XML) that can be uploaded to the data repository via Data Upload module.
- Data Upload module assists researches in uploading their data to the data repository (in the form of a submission package and submission ticket).
- Data Download module assists researches in downloading data from the data repository.
Contents
Steps in data preparation, validation, submission, and download
For imaging data:
- Create and pre-validate the image submission package using the Imaging data submission and validation module.
- Validate the the image submission package using the Data Validation module and create the data submission package/ticket using the same module.
- Use the data submission ticket from the previous step to upload the data submission package with the help of the Data Upload module.
- Download the data using the means provided by the Data Download module.
For non-imaging data:
- Create and validate the data submission package using the Data Validation module and create the submission ticket using the same module (creates automatically as soon as data pass validation).
- Use the data submission ticket from the previous step to upload the data submission package with the help of the Data Upload module.
- Download the data using the means provided by the Data Download module.
Data for uploading
Imaging data
Imaging data can be uploaded in the form of
- a brain image file
- and a corresponding CSV file that contains some additional patient/subject/visit information (not stored in the image header) as well as image related metadata.
The following information is required for all |image submissions and should be included in a CSV file:
- The patient/subject information including - GUID, a patient/subject age, a study site name, and a visit date;
- The image information including - imaging study date and time, imaging file name, imaging file itself, imaging file format and modality, image QA/QC information.
Image files
The brain image file can be:
- a single file in one of supported formats,
- a DICOM multifile or some other multifile in one of the supported formats,
- a ZIP archive that contains an image dataset (e.g. DICOM dataset with images of multiple slices stored in separate image files - a multifile).
For more information refer to: Imaging data submission and validation module.
Imaging data submission and validation module
The Imaging Data Submission and Validation module (also known as MIPAV Image Submission and Validation tool or MIPAV Image submission plug-in) is designed to help researches to validate and submit their data. Data validation is a necessary step that must be done prior data submission in order to ensure the quality of uploaded data and to make data queryable. The module runs as a Java Web Start application locally on a user's computer (Java runtime environment is required).
Read more...
Data Validation module
The Data Validation module assists researchers with the submission of both imaging and non-imaging data into the repository. The Data Validation module verifies that data conforms to the required format and range values defined in the data dictionary (note that for the imaging data this is going to be a second validation needed to ensure the quality of data). The Data Validation module validates the metadata associated with the data files identified by the user for submission against the data dictionary. If everything is OK, the Data Validation module creates a submission ticket and submission package. After that data are good for uploading. If errors are found, the module provides a detailed report of any data discrepancies, errors, and warnings. The module runs as a Java Web Start application locally on a user's computer (Java runtime environment is required).
Read more ...
Data Upload module
After the submission package has been created using either the Imaging Data Submission and Validation module (for imaging data) or by the Data Validation module (for non-imaging data), data can be submitted to the data repository. The Data Upload module facilitates this process. The module runs as a Java Web Start application locally on a user's computer (Java runtime environment is required).
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Data Download module
Data Download module helps users to select and download datasets from the data repository to their own systems. The module runs as a Java Web Start application locally on a user's computer (Java runtime environment are required).
Read more...