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The CSSI DCC Portal is a public repository of experiment-related information describing cancer research investigations. You can use the portal to browse, search, and download eight Physical Sciences Oncology Network (PSON) and access data generated through CSSI funded projects and other user uploaded data sets. These This data sets are is in ISA-TAB Tab format, which organizes investigation, study, and assay data according to the rules in the ISA-TAB Tab specification
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Each data set contains three files--investigation, study, and assay--that conform to the ISA-TAB Tab structure and naming conventions. Within this structure are fields that are standard for each type of file, though null values are allowed; that is, not every data set includes values for each field. The portal allows you to filter these fields in an interactive way so that you can visualize the data in a pie chart or list.
You can also search investigations, studies, and assays using any keyword. You can download selected files, the entire data archive, or only the metadata associated with a study.
This chapter provides detailed instructions on how to browse, search, and download data.
Browsing Investigations
You can browse and explore investigation data from the investigation, study, and assay files.
To browse investigations
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The
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Understanding the Pie Charts and Investigations List
The Browse Investigation page has two interactive components:
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CSSI DCC Portal allows you to perform various tasks:
- Search investigations, studies, and assays using any keyword.
- Download the data.
- Download the metadata.
- Download selected files, with the metadata.
- Upload your own investigation data to the portal and request open access for your uploaded data. (For more information, refer to Uploading Investigation Data and Requesting Open Access.)
The following page family describes how to browse, search, and download data.
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Adding and Removing Fields
You can customize which pie charts appear at the top of the page. Since the pie charts control how you filter the investigation data, you may prefer something other than, or in addition to, the three default fields of Study Protocol Name, Study Assay Technology Type, and Study Assay Measurement Type.
To add or remove fields
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Exploring Investigation Details
You can continue exploring investigation data by clicking a link to investigation, study, or assay details. Links to these details are on the Browse Investigations page or on the Search Investigations page, after you search on a keyword or phrase. These details include counts of studies, assays, samples, and files. The metadata available for an investigation determines if other entities, such as sources and collections, are available for counts. From these details pages, you can visualize the structure of the investigation and download selected study files, download the full archive, and download only the metadata.
To explore investigation details
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Investigation Details Page
The investigation details page shows the investigation name at the top followed by a visualization of the investigation filename, study filename and number of samples in the study, and assay filename and number of files (and total file size) in the assay. Below the visualization are links to download all or part of the investigation, its identifier, and its description. All of the icons on the page are clickable links.
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The currently selected entity has a green box behind its icon in the visualization. When the investigation is selected, its study/studies, and assay(s) are also selected. In the following screenshot, the investigation is selected. |
Study Details Page
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Assay Details Page
The assay details page shows the study name at the top followed by a visualization of the investigation filename, study filename and number of samples in the study, and assay filename and number of files (and total file size) in the assay. Below the visualization are links to download all or part of the assay, its file name, measurement type, and technology type. In the Processes and Filters section, the relationship of the study to its processes, and its processes to its files, are depicted in clickable icons. Click any icon to further filter the investigation data and download only a selected portion of it.
Exploring Processes and Filters
The Processes and Filters section of the investigation, study, or details page breaks down the entity to its smallest parts. Need to talk through this whole section of the application.
Searching Investigation Data
You can search investigations, studies, or assays using any keyword.
To search investigation data
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Downloading Investigation Data
You can download selected files, the entire data archive, or only the metadata associated with an investigation. All of the data currently in the portal is public.
The data archive is a compressed (.zip) file that combines the investigation, study, and assay text files, and associated data files. Each text file contains only metadata, which appear as column names when imported into a spreadsheet. The data files often contain images and can be a large file size.
If you only need the metadata, you can download it as a compressed file (.zip). The metadata includes only the assay, investigation, and study text files, which are the file columns, field definitions, and placeholders that describe the structure of the data collected in this study. They are in Investigation-Study-Assay tab-delimited format (ISA-TAB), which is based on the ISA-TAB specification
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While they are also included in the archive if you choose to download that, you can also download selected study files. These study files might be image files, spreadsheets, or any other data associated with the selected study that is not the metadata.
To download investigation files
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To download a single file
- To select only one file, click its File Name link.
Your browser's file download dialog box appears, which prompts you to open or save the file.
To download multiple files
- Click the box in the Select File column for any of the files in the list.
- Click
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The Download window appears. - Enter your email address and click OK.
The Success window appears. - Click OK.
- Look for an email in your inbox with the subject line File Download.
- Save or open the file.
Downloading Archives
Once you select an investigation and view its study details, you can choose to download the entire archive. An archive is a compressed file (.zip) that combines the assay, investigation, and study files with the metadata and data files.
You do not need to log in to CSSI DCC Portal to download an archive.
To download an archive
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Downloading Metadata
You do not need to log in to CSSI DCC Portal to download an investigation's metadata. The metadata includes only the assay, investigation, and study text files, which are the file columns, field definitions, and placeholders that describe the structure of the data collected in this study. They are in Investigation-Study-Assay tab-delimited format (ISA-TAB), which is based on the ISA-TAB specification 
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To download metadata
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Open the file or save it for later analysis.
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The metadata file is in compressed format. It contains one folder called The contents of the archive folder look similar to the following (
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