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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) 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 specification.   Tab specification

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 field names 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 a hierarchical 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. 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 Browse Investigations Page

The Browse Investigation page has two interactive components:

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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

1. On the Browse Investigations page, click Image Removed.
   The Select menu appears to the left of the pie charts.
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2. 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 will disappear from the page. When you reset all of the pie charts or select Browse > Investigations, however, they will reappear.
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3. Click any of the field values to select them. For example, select Study Protocol Type.
   The pie charts immediately update to reflect the selection and a fourth pie chart appears on the Browse Investigations page.
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Exploring Investigation Data

On the Browse Investigations page, you can explore investigation data in the following ways:

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Filtering Investigation Data

You can filter the investigation data on the Browse Investigations page in the following ways:

• By adding and removing fields to and from the pie charts.
• By clicking one or more pie slices.

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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

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 view study details

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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.

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

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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

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Downloading Study Files

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

1. Select an investigation and view its details.
   The study details page appears.
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2. In the Files area, click the down arrow to expand it.
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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.
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To download multiple files

1. Click the box in the Select File column for any of the files in the list.
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2. ClickImage Removed.
   The Download window appears.
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3. Enter your email address and click OK.
   The Success window appears.
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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.
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2. Click Image Removed.
   The Download window appears.
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3. Enter your email address and click OK.
   The Success window appears.
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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 Image Removed .

To download metadata

1. Select an investigation and view its details.
   The study details page appears.
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2. Click Image Removed.
   Your browser opens a download dialog box with your download file in it.
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3. Open the file or save it for later analysis.

   Info
   title 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