DRAFT Chapter 2: Browsing and Searching Investigations

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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) 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.

Browsing Investigations

You can browse and explore investigation data from the investigation, study, and assay files.

To browse investigations

From the CSSI Data Portal home page, click the Browse button.

The Browse Investigations page appears, showing pie charts at the top and a list of investigations below them. All eight investigations currently included in this release of the CSSI DCC Portal appear in the list. A subset of the page appears in the following screenshot.

Understanding the Browse Investigations Page

The Browse Investigation page has two interactive components:

Pie charts that show fields from the investigations. When you first open the page or reset it to clear all selections, three pie charts appear at the top. These pie charts represent three of the fields, Study Protocol Name, Study Assay Technology Type, and Study Assay Measurement Type, that occur in the metadata of the eight investigations currently in the portal. The values for those fields, as well as a count for each value, appear in the pie charts. The count represents the number of times that field value occurs in all of the investigations currently in the portal.

For example, in the default pie charts represented in the above screenshot, the Study Assay Measurement Type pie chart shows that one investigation used genome sequencing, six used imaging assay, and two used transcription profiling. Note that there are nine field values and only eight investigations because one investigation listed two values for Study Assay Measurement Type. You can determine which investigation that was by clicking on each pie slice and reviewing the details in the list below.

Click one or more field values in the pie charts ("slices") to filter the data by that/those field value(s). The more field values you select, in one or more pie charts, the more narrowly you filter the investigation data and the fewer investigations match your selections. The investigation list refreshes each time you filter the data in this way. You can also customize which fields appear in the pie charts and how many pie charts appear by adding and removing fields.

In the following screenshot, a user has selected at least one field value in each pie chart. The selected values are sample collection and summarize trimmed reads in the Study Protocol Name chart, nucleotide sequencing in the Study Assay Technology Type chart, and genome sequencing in the Study Assay Measurement Type chart. Only one investigation matches all of these selections and appears in the list below. To reduce the amount of filtering, you can click Reset All to return to the default pie charts, or reset on an individual pie chart. You can also return to the default view by selecting Investigations > Browse.
A list of investigation details below the pie charts. The investigation list shows details associated with the investigations that match your pie chart selections. For example, in the following screenshot, a user has selected one field value in the Study Protocol Name pie chart: plate cells. The number 4 next to the label plate cells means that four investigations are associated with the Study Protocol Name field value of plate cells. Those four have a null value for Study Assay Technology Type, which is the second pie chart, and all use the same Study Assay Measurement Type of imaging assay.

The list below the pie charts match the pie chart selections. The list includes only those four investigations that have a Study Protocol Name field value of plate cells. Details for each investigation in the list includes the same fields represented by the pie charts: Study Protocol Name, Study Assay Technology Type, and Study Assay Measurement Type, plus the study name and description. The list also shows additional data about each investigation, such as the other keywords used in the Study Protocol Name field. You can return to the default (full) list at anytime by selecting Investigations > Browse.

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

On the Browse Investigations page, click .
The Select menu appears to the left of the pie charts.
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.
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.

Exploring Investigation Data

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.
- By clicking the study title to view and filter study details, download selected study files, download the entire archive, and download only the metadata.

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.

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.

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

Browse experiments.
The Search Result page appears.
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.

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

Browse experiments.
The Search Result page appears.
Locate the search box at the top of the page.
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.

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

Navigate to the CSSI Data Portal.
Click the Search button.

The Search Result page appears, displaying only a search box.
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.

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

Select an investigation and view its details.
The study details page appears.
In the Files area, click the down arrow to expand it.

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.

To download multiple files

Click the box in the Select File column for any of the files in the list.
Click.
The Download window appears.
Enter your email address and click OK.
The Success window appears.
Click OK.
Look for an email in your inbox with the subject line File Download.
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

Select an investigation and view its details.
The study details page appears.
Click .
The Download window appears.
Enter your email address and click OK.
The Success window appears.
Click OK.
Look for an email in your inbox with the subject line File Download.
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 .

To download metadata

Select an investigation and view its details.
The study details page appears.
Click .
Your browser opens a download dialog box with your download file in it.
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

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