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) data sets. These data sets are in ISA-TAB format, which organizes investigation, study, and assay data according to the rules in the ISA-TAB specification.
Each data set contains three files--investigation, study, and assay--that conform to the ISA-TAB structure and naming conventions. Within this structure are field names 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 a hierarchical 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. This chapter provides detailed instructions on how to browse, search, and download data.
You can browse and explore investigation data from the investigation, study, and assay files.
To browse investigations
On the Browse Investigations page, you can explore investigation data in the following ways:
By filtering the investigations in the portal so that only those matching the fields you select appear in the pie charts and the list. If you do not filter the investigations, you see a pie chart analysis of the three default filters: Study Protocol Name, Study Assay Measurement Type, and Study Assay Technology Type. All of the investigations appear in the list.
Note that not all investigations in the portal have a value for each field. For example, in the Characterization of Circulating Tumor Cells (CTCs) study in the screenshot above, there is no value for Study Assay Technology Type. This is reflected in second pie chart for Study Assay Technology Type at the top of the screen. In that pie chart, five investigations have no value for this field while the remaining three have the value of "nucleotide sequencing." |
You can filter the investigation data on the Browse Investigations page in the following ways:
Filter the list to see fewer results that match your interests. To filter the list, click the checkbox next to one or more categories in the Current Investigations list. For example, click the Biomedical Investigations 9909 category to see the current investigations that match that category.
View the buttons under the study title, which show the number of studies, assays, and files associated with this investigation.
While the Search Result page includes summaries of all of the studies meeting your filters or search criteria, additional details are available about each study. Click the study title to view the study's measurement types, experimental factors, study description, protocols, and files.
You can then download the full archive, only the metadata, or selected study files. You can also modify your search.
The data archive is a compressed (.zip) file that combines the assay, investigation, and study text files, and associated study data files. The study text files contain the metadata. Downloading the data archive means that you do not need to also download the metadata and files for that investigation.
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 .
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.
Your role determines which studies you can view in the CSSI DCC Portal. |
To view study details
Click a study title, for example, "Muscle Satellite Cells: MyoD and p53 genes".
The study details page appears.
Click Expand All to view the investigation's associated protocols and files.
The Protocols section is a table showing Protocol Name, Protocol Type, and Description.
The Files section lists File Name, Size, Type, and Submission Date. Enter any keyword from these column names into the search box to search this list. You can also download selected files.
Clicking Modify Search returns you to the Search Result page where you can change how you filter the current investigations. |
An alternative to filtering by investigation is to narrow down a long list of search results by searching within those results.
To search within results
You can search investigations by keywords and filter the results. You do not need to log in to CSSI DCC Portal to search investigations.
To search experiments
You can download selected files, the entire data archive, or only the metadata associated with a study. All of the data currently in the Portal is public.
To download study files
To download a single file
To download multiple files
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
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 .
To download metadata
Open the file or save it for later analysis.
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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