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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 Physical Sciences Oncology Network (PSON) data sets. As of January 2017, there are 8 PSON data sets in the portal. These data sets are in ISA-TAB access data generated through CSSI funded projects and other user uploaded data sets. This data is in ISA-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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If you add or remove fields from the pie charts, the Investigations list fields immediately reflect the same changes. |
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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.
You can add and remove fields
To add or remove fields
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Expand fields by clicking the plus signs. Note that in the STUDY PROTOCOLS and Study Assays section, the field values of Study Protocol Name, Study Assay Technology Type, and Study Assay Measurement Type are already selected. These field values are the ones that appear in the three default pie charts on the Browse Investigations page. If you clear these check boxes, those pie charts disappear from the page. When you reset all of the pie charts or select Browse > Investigations, however, they reappear.
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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
Browse investigations or search investigations until you find an investigation, a study, or an assay in which you are interested.
The search results appear.Click the link corresponding with the investigation, study, or assay you are interested in exploring.
The respective investigation details, study details, or assay details page appears.- You can do the following from the details pages:
- Explore the data at every level of the investigation.
- Filter the data so that you can download selected data.
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.
Visualizing and Filtering Data
Once you browse or search the CSSI DCC data sets and reach a selected investigation details, study details, or assay details page, you can continue exploring the data. The ISA-TAB format is hierarchical, with investigation components becoming more granular as you proceed down the hierarchy. The largest organizing entity is the investigation, which holds one or more studies. Each study includes one or more assays. Assays are composed of samples, which in turn are composed of protocols. Data files are often associated with a protocol.
The following image depicts the hierarchy, without the samples and protocols.
Visualizing and Filtering Investigations
The investigation details page shows icons that represent the relationship of the investigation to its studies and assays. In the case of PSON Cell Line Genomic Characterization - mRNA, the investigation has one study and one assay.
You cannot filter data currently at the investigation level any further in the CSSI DCC Portal. You can only download the investigation's full data at this point, or start exploring its studies and assays.
Visualizing and Filtering Study Data
If you select the study in the PSON Cell Line Genomic Characterization - mRNA investigation or arrive at any other Study Details page through a search, you can visualize the study's file structure and filter on any field.
To visualize and select study data
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In the Visualize and Select area, click one of the entities.
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The hierarchy of entities for studies according to the ISA-TAB standard is as follows, from less granular to more granular: Source > Protocol > Sample |
For example, click Source. Metadata for that source appears.
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Follow this same procedure if you want to filter on Protocol or Sample instead of Source. |
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Visualizing and Filtering Assay Data
If you select the assay in the PSON Cell Line Genomic Characterization - mRNA investigation or arrive at any other Assay Details page through a search, you can visualize the assay's file structure and filter on any field.
To visualize and select assay data
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In the Visualize and Select area, click one of the entities. Note that the width of some visualizations require you to scroll by clicking the arrows at the bottom of the page.
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The hierarchy of entities for assays according to the ISA-TAB standard is as follows, from less granular to more granular: Sample > Protocol > Data File |
For example, click the sample. Metadata for the sample appears.
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Follow this same procedure if you want to filter on protocol instead of sample. |
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Click one or more values in the list to select them. To select multiple values, click one, wait for it to appear on the Metadata for Sample page, and then click the arrow again to select another value. To clear a selection, click that value again.
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Some entities do not have associated metadata fields on which you can filter the study or assay. In that case, when you click the icon for that entity, you see a message letting you know that no metadata fields are available. |
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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Searching Investigation Data
You can search investigations, studies, or assays using any keyword.
To search investigation data
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Downloading Investigation Data
After reaching an investigation entity (such as investigation, study, assay, source, protocol, sample, or data file), you can download the full data, selected metadata, or selected data associated with that entity. The full data is always associated with the investigation as a whole. All of the data currently in the portal is public.
Metadata describes the structure of the data collected in an investigation and translates to the file columns, field definitions, and placeholders that appear in a spreadsheet. It is in Investigation-Study-Assay tab-delimited format (ISA-TAB), which is based on the ISA-TAB specification
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The data files often contain image files and spreadsheets and can be a large file size.
Each download option has a button on the Investigation Details, Study Details, and Assay Details pages.
- Download Full Data downloads metadata and data files for the entire investigation. Since this can be a large file size, the file size appears on the button.
- Download Selected Metadata downloads only the metadata of a selection you make after filtering a study an assay.
- Download Selected Data downloads both the metadata and the data files of a selection you make after filtering a study or an assay.
To download full data
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Click the Download Full Data button.
Your browser prompts you to open or save full_archive.zip.
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It may be useful to rename the .zip file as you save it to include the name of the investigation so that you can identify it more easily. For example, miRNA_full.zip. |
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While it is compressed as a .zip file, this file may still be very large. Consider its size before downloading. |
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To download selected metadata
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Click Download Selected Metadata.
Your browser prompts you to open or save the .zip file.
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It may be useful to rename the .zip file as you save it to include the name of the investigation so that you can identify it more easily. For example, miRNA_metadata.zip. |
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The metadata file is in compressed format. It contains one folder called
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To download selected data
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If you are still interested in downloading your selection, enter your email address in the box and click the I'm not a robot box to request the data download.
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