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The CSSI DCC Portal is a public repository of experiment-related information describing cancer research investigations. The current version of the Portal allows you to browse, search, and download the Physical Sciences Oncology Network (PSON) data sets.

You can browse and explore investigations using customizable dashboards. You can also search investigations, studies, and assays using any keyword. This chapter provides detailed instructions on how to browse and search.

Browsing Investigations

When you select Browse from the CSSI DCC home page, you can browse and explore investigations by organism, disease, cell type, or assays performed. You do not need to log in to the CSSI DCC Portal to browse investigations. You can also download selected files, the entire data archive, or only the metadata without logging in. All of the data currently in the Portal is public.

To browse investigations

  1. Navigate to the CSSI Data Portal.
  2. Click the Browse button.
    The Browse Investigations page appears, showing the three default filters of Study Protocol Name, Study Assay Measurement Type, and Study Assay Technology Type. Below the filters is a summary of each investigation available in the Portal. The following screenshot shows a subset of these investigations.
    Browse Investigations page showing filters and the CTCs and PSON Cell Line Genomic Characterization - Exome investigations
  3. On the Browse Investigations page, you can do the following:

 

Filtering Investigation Data

 

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.
No. of Studies (1), No. of Assays (1), No. of Files (2)

Viewing Study Details

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 Exit Disclaimer logo .

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

  1. Browse experiments.
    The Search Result page appears.
    Search Result page

  2. Click a study title, for example, "Muscle Satellite Cells: MyoD and p53 genes".
    The study details page appears.

  3. 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.
    Files list with a Search for files box, Download Selected button, and file information such as ks121202MGC3a.CEL 9 MB CEL 21 MAy 2015

    Clicking Modify Search returns you to the Search Result page where you can change how you filter the current investigations.

Searching Within Results

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

  1. Browse experiments.
    The Search Result page appears.
    Search Result page
  2. Locate the search box at the top of the page.
  3. In the search box, enter any keyword that may appear in the investigation metadata. This can include any keyword or part of a word. The number of results updates as you enter your keyword. In the following example, only the first two characters belonging to the word "cell" were entered, narrowing the number of search results from 18 to 15.

Downloading Study Files

You do not need to log in to CSSI DCC Portal to download files associated with a study.

To download study files

  1. Select an investigation and view its details.
    The study details page appears.
  2. In the Files area, click the down arrow to expand it.
    Files list with a Search for files box, Download Selected button, and file information such as ks121202MGC3a.CEL 9 MB CEL 21 MAy 2015

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.
    Firefox File Download Dialog Box

To download multiple files

  1. Click the box in the Select File column for any of the files in the list.
  2. ClickDownload Selected button.
    The Download window appears.
    Download link will be sent via email. Enter email address below to receive download instructions.
  3. Enter your email address and click OK.
    The Success window appears.
    Your request has been received. You'll receive an email with a link to download files once your download request is processed
  4. Click OK.
  5. Look for an email in your inbox with the subject line File Download.
  6. 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

  1. Select an investigation and view its details.
    The study details page appears.
  2. Click Download Archive Button.
    The Download window appears.
    Download link will be sent via email. Enter email address below to receive download instructions.
  3. Enter your email address and click OK.
    The Success window appears.
    Your request has been received. You'll receive an email with a link to download files once your download request is processed
  4. Click OK.
  5. Look for an email in your inbox with the subject line File Download.
  6. Save or open the file.

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 Exit Disclaimer logo .

To download metadata

  1. Select an investigation and view its details.
    The study details page appears.
  2. Click Download Metadata Button.
    Your browser opens a download dialog box with your download file in it.
    Opening Archive10290_metadata.zip dialog box

  3. Open the file or save it for later analysis.

    Metadata File Contents

    The metadata file is in compressed format. It contains one folder called metadata and a text file for each of the following: assay, investigation, and study.

    The contents of the archive folder look similar to the following (10290 is just an example of the file identifier):

    metadata/

       a_10290.txt

       i_10290.txt

       s_10290.txt

Searching Investigations

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

  1. Navigate to the CSSI Data Portal.
  2. Click the Search button.
    Search Search experiments by keywords and filter results or look up the activity of genes of interest.
    The Search Result page appears, displaying only a search box.
    Search Result page with Search keyword box
  3. In the search box, enter a keyword. Keywords are any word that appears in the investigation's metadata. This includes all file columns, field definitions, and placeholders that describe the structure of the data collected in this study.

    As you enter the characters in the keyword, the Search Result page immediately refreshes with the search results.

 

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