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 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 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 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.

You can also search investigations, studies, and assays using any keyword. You can download selected files, the entire data archive, or only the metadata associated with a study.

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 or select Investigations > Browse.

The Browse Investigations page appears, showing pie charts at the top and a list of investigations below them. All 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 Pie Charts and Investigations List

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 8 investigations currently in the portal (as of January 2017). 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 1 investigation used genome sequencing, 6 used imaging assay, and 2 used transcription profiling. Note that there are 9 field values and only 8 investigations because 1 investigation listed 2 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 Investigations 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 fields in the Investigations list match the pie chart selections. The list includes only those 4 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.
If you add or remove fields from the pie charts, the Investigations list fields immediately reflect the same changes.

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.

You can add and remove fields

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 disappear from the page. When you reset all of the pie charts or select Browse > Investigations, however, they reappear.
Click any of the field values to select them. For example, select Study Protocol Type.
The pie charts immediately update to include one for Study Protocol Type.

Correspondingly, the Investigations list updates to show Study Protocol Type in the fields available for the investigation.

You could also opt to clear all of the check boxes except for Study Protocol Type. In this case, that is the only pie chart that would appear.

The field also disappears from the Investigations list.
When you have selected or cleared as many fields as you want from the pie charts, click .
The Select menu moves back to its original position.

Exploring Investigation Details

You can continue exploring investigation data by clicking a link to investigation, study, or assay details. Links to these details are on the Browse Investigations page or on the Search Investigations page, after you search on a keyword or phrase. These details include counts of studies, assays, samples, and files. The metadata available for an investigation determines if other entities, such as sources and collections, are available for counts. From these details pages, you can visualize the structure of the investigation and download selected study files, download the full archive, and download only the metadata.

To explore investigation details

Browse investigations or search investigations until you find an investigation, a study, or an assay in which you are interested.
The search results appear.
Click the link corresponding with the investigation, study, or assay you are interested in exploring.
The respective investigation details, study details, or assay details page appears.
You can do the following from the details pages:
- Explore the data at every level of the investigation.
- Filter the data so that you can download selected data.

Investigation Details Page

The investigation details page shows the investigation name at the top followed by a visualization of the investigation filename, study filename and number of samples in the study, and assay filename and number of files (and total file size) in the assay. Below the visualization are links to download all or part of the investigation, its identifier, and its description. All of the icons on the page are clickable links.

The currently selected entity has a green box behind its icon in the visualization. When the investigation is selected, its study/studies, and assay(s) are also selected. In the following screenshot, the investigation is selected.

Study Details Page

The study details page shows the investigation name at the top followed by a visualization of the investigation filename, study filename and number of samples in the study, and assay filename and number of files (and total file size) in the assay. Below the visualization are links to download all or part of the investigation, its identifier, and its description. All of the icons on the page are clickable links.

Assay Details Page

The assay details page shows the study name at the top followed by a visualization of the investigation filename, study filename and number of samples in the study, and assay filename and number of files (and total file size) in the assay. Below the visualization are links to download all or part of the assay, its file name, measurement type, and technology type. In the Processes and Filters section, the relationship of the study to its processes, and its processes to its files, are depicted in clickable icons. Click any icon to further filter the investigation data and download only a selected portion of it.

Visualizing and Filtering Data

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 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.

The following image depicts the hierarchy, without the samples and protocols.

Visualizing and Filtering Investigations

The investigation details page shows icons that represent the relationship of the investigation to its studies and assays. In the case of PSON Cell Line Genomic Characterization - mRNA, the investigation has one study and one assay.

You cannot filter data currently at the investigation level any further in the CSSI DCC Portal. You can only download the investigation's full data at this point, or start exploring its studies and assays.

Visualizing and Filtering Study Data

If you select the study in the PSON Cell Line Genomic Characterization - mRNA investigation or arrive at any other Study Details page through a search, you can visualize the study's file structure and filter on any field.

To visualize and select study data

Open a Study Details page.
In the Visualize and Select area, click one of the entities.
Study Hierarchy
The hierarchy of entities for studies according to the ISA-TAB standard is as follows, from less granular to more granular:
Source > Protocol > Sample
For example, click Source. Metadata for that source appears.
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. To select multiple values, click one, wait for it to appear on the Metadata for Source page, and then click the arrow again to select another value. To clear a selection, click that value again.
Click Filter Results.
The Source Count reduces from the 40 original values in the unfiltered study file, s_mrna.txt, to the 3 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.

Visualizing and Filtering Assay Data

If you select the assay in the PSON Cell Line Genomic Characterization - mRNA investigation or arrive at any other Assay Details page through a search, you can visualize the assay's file structure and filter on any field.

To visualize and select assay data

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.
Assay Hierarchy
The hierarchy of entities for assays according to the ISA-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.
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.
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.

Searching Investigation Data

You can search investigations, studies, or assays using any keyword.

To search investigation data

From the CSSI Data Portal home page, click the Search button select Investigations > Search.

The Search Investigations page appears.
In the search box, enter a keyword or phrase. Keywords are any word that appears in the fields belonging to any investigation, study, or assay in the CSSI DCC Portal. This includes all file columns, field definitions, and placeholders that describe the structure of the data collected in this study.

Search results appear immediately, using the context currently in the Search for box, which by default is Investigations. The time the CSSI DCC Portal took to first search for the keyword or phrase and then render the results on the page also appear.
In the Search for box, change the context for your search if desired. Select Investigations, Studies, or Assays. Examples of each search result follow.

In the following example, the keyword is "genomic" and the context is Investigations. Three investigations appear in the search results, along with information about each one that includes the investigation name, number of studies, number of assays, number of files, and description.

In the following example, the keyword is "genomic" and the context is Studies. Three studies appear in the search results, along with information about each one that includes the study name, name of the investigation the study is associated with, number of assays, number of files, and description. In these cases, the investigation name and study names are identical.

In the following example, the keyword is "genomic" and the context is Assays. Three assays appear in the search results, along with information about each one that includes the assay filename, name of the study that the assay is associated with, name of the investigation the assay is associated with, number of files (such as image files), and description.
Click any investigation name, study name, or assay filename to explore the data further.

Downloading Investigation Data

After reaching an investigation entity (such as investigation, study, assay, source, protocol, sample, or data file), you can download the full data, selected metadata, or selected data associated with that entity. The full data is always associated with the investigation as a whole. All of the data currently in the portal is public.

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-TAB), which is based on the ISA-TAB specification .

The data files often contain image files and spreadsheets and can be a large file size.

Each download option has a button on the Investigation Details, Study Details, and Assay Details pages.

Download Full Data downloads metadata and data files for the entire investigation. Since this can be a large file size, the file size appears on the button.
Download Selected Metadata downloads only the metadata of a selection you make after filtering a study an assay.
Download Selected Data downloads both the metadata and the data files of a selection you make after filtering a study or an assay.

To download full data

Open the investigation you want to download.
The Investigation Details page appears.
Click the Download Full Data button.
Your browser prompts you to open or save full_archive.zip.
It may be useful to rename the .zip file as you save it to include the name of the investigation so that you can identify it more easily. For example, miRNA_full.zip.

While it is compressed as a .zip file, this file may still be very large. Consider its size before downloading.
Follow your browser's instructions to open or save the file.

To download selected metadata

Filter a study or an assay until you reach a selection of investigation data you are interested in downloading. You may be interested in only the metadata so that you can see how that selection of entities was structured.
Click Download Selected Metadata.
Your browser prompts you to open or save the .zip file.
It may be useful to rename the .zip file as you save it to include the name of the investigation so that you can identify it more easily. For example, miRNA_metadata.zip.

Follow your browser's instructions to open or save the file.
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

To download selected data

Filter a study or an assay until you reach a selection of investigation data you are interested in downloading.
Click Download Selected Data.
If the data you want to download exceeds 30 GB, a message appears, instructing you to reduce the file size by further filtering the data.
If you are still interested in downloading your selection, enter your email address in the box and click the I'm not a robot box to request the data download.
Although an investigation's full data download usually results in a larger file than 30 GB, due to technical issues, a request is only required when you want to download selected data.

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