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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 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.
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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 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.
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- Open a Study Details page.
In the Visualize and Select area, click one of the entities.
Info title Study Hierarchy The hierarchy of entities for studies according to the ISA-TAB Tab standard is as follows, from less granular to more granular:
Source > Protocol > Sample
For example, click Source. Metadata for that source appears.
Info Follow this same procedure if you want to filter on Protocol or Sample instead of Source.
- From the Source Name list, click the arrow to open the list of values. Each value is a Source Name from the study file, which in this case is s_mrna.txt.
- Click one or more values in the list to select them. Each value appears immediately below the Source Name box. To clear a selection, click the value again.
- Click Filter Results.
The Source Count reduces from the 40 original values in the unfiltered study file,s_mrna.txt, to the three selected in this procedure.
- Options you have at this point include continuing to explore this data set, downloading the metadata of the three values you selected, downloading the selected data of the three values you selected (which includes the metadata), or clicking Clear Filters to filter a different entity.
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- Open an Assay Details page.
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.
Info title Assay Hierarchy The hierarchy of entities for assays according to the ISA-TAB 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.
Info Follow this same procedure if you want to filter on protocol instead of sample.
- From the Sample Name list, click the arrow to open the list of values. Each value is a Sample Name from the assay file, which in this case is a_mrna_transcription_profiling_nucleotide_sequencing.txt.
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.
Info 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.
- Click Filter Results.
The Sample Count reduces from the 39 original values in the unfiltered assay file, a_mrna_transcription_profiling_nucleotide_sequencing.txt, to the 5 selected in this procedure.
- Options you have at this point include continuing to explore this data set, downloading the metadata of the 3 values you selected, downloading the selected data of the 3 values you selected (which includes the metadata), or clicking Clear Filters to filter a different entity.
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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-TABTab), which is based on the ISA-TAB Tab specification
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