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 access data generated through CSSI funded projects and other user uploaded data sets. This data is 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 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. You can also upload and publish your own investigation data to the portal.

The following sections provide detailed instructions on how to browse, search, and download data.

Accessing Investigation Data

Browsing Investigations

You can browse and explore investigation data contained in 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 a list of all investigations currently included in this release of the CSSI DCC Portal, and pie charts at the top showing fields from the investigations. Note that you can control how many investigations appear in the list by selecting a value from the Max Display box.
  
  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 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 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 Scaning in the Study Protocol Name chart, CNV analysis in the Study Assay Measurement Type chart, and Next Generation Sequencing in the Study Assay Technology 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.

To add or remove fields

1. On the Browse Investigations page, click Add/Remove fields. The Select menu appears to the left of the pie charts.
   

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 disappear from the page. When you reset all of the pie charts or select Investigations > Browse, however, they reappear.

   
   

3. 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.
   
   
   
   When you clear a field, it also disappears from the Investigations list.
   
   

4. When you have selected or cleared as many fields as you want from the pie charts, click Hide select menu. 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

1. Browse investigations or search investigations until you find an investigation, a study, or an assay in which you are interested.
   The search results appear.
   

2. 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.

3. 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

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 Visualize and Select 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 diagram 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.

Selecting Multiple Objects

If any investigation has more than one study and assay, you can select which ones you want to filter by clicking the Select Multiple Objects box.

For example, the following investigation has many studies and assays, so it displays horizontally with a slider on the side to move up and down. It also has zoom out and zoom in buttons to see more or fewer objects.

Select the boxes next to the objects you want to visualize and filter. If you download these objects, all of these objects will be included in the download.

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.

You can also select multiple objects to visualize and filter within a single investigation.

To visualize and select study data

1. Open a Study Details page.
   

   

2. In the Visualize and Select area, click one of the entities.

   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.

   
   

3. 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.
   
4. Click one or more values in the list to select them. Each value appears immediately below the Source Name box. To clear a selection, click the value again.
   
5. Click Filter Results.
   The Source Count reduces from the 40 original values in the unfiltered study file, s_mrna.txt, to the three selected in this procedure.
   
6. Options you have at this point include continuing to explore this data set, downloading the metadata of the three values you selected, downloading the selected data of the three 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.

You can also select multiple objects to visualize and filter within a single investigation.

To visualize and select assay data

1. Open an Assay Details page.
   

   

2. 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.

   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.

   
   

3. 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.
   

4. 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.

5. 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.
   
6. 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 for investigations, studies, or assays in the CSSI DCC Portal by:

• Keyword or phrase in all fields or specific fields 
• Related terms from ontologies

Performing a Basic Search

Searching by Keyword or Phrase

Searching ISA Tab Fields

Searching by Related Terms

Viewing Detailed Search Results

In the search results, click View next to a matching term to see where in the investigation this term occurs.

A detailed search results window appears. The matching term, cell, is highlighted in the metadata of each file in the ISA-Tab archive.

To close the window, click Ok at the bottom or the x in the upper-right corner of the window.

Saving Search Parameters

Managing Saved Search Parameters

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.

Also note that if you selected multiple objects to visualize and filter, a download includes all of those objects.

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.
• Add to Download downloads both the metadata and the data files of one or more selections you make after filtering a study or an assay.

Downloading Full Data

You do not have to log in before downloading the full data from an investigation. If you are not logged in, when you request the full data, you are prompted to provide your email address. You will receive a link at that address you can use to access and download the data. If you are logged in, you have the option of using Globus to download the file.

To download full data

1. Open the investigation you want to download.
   The Investigation Details page appears.
   

2. Click the Download Full Data button.
   The Request Data Files dialog appears. It offers different options depending on whether or not you are logged in to CSSI DCC.

   • If you are not logged in, enter your email address and then click Download. Your browser prompts you to save full_archive.zip.
     

   • If you are logged in, you have two options: 1) transfer the file with Globus, which is useful when the file is very large, or 2) download the file to your computer now.
     
     If you choose to transfer the file with Globus, click the checkbox and then click Download. The Transfer Files page in Globus opens. For more information about transferring files with Globus, see Uploading Files with Globus or Globus Support .
     
     If you choose to download the file now, just click Download.
     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.

     For example, the following dialog box appears in Google Chrome.
     
     
     Follow your browser's instructions to open or save the file.

Downloading Selected Metadata

An entity's metadata shows how that entity is structured. Metadata files are usually small text files, so you can download them directly to your computer. You do not need to log in before downloading metadata files.

To download selected metadata

1. Filter a study or an assay until you reach a selection of investigation data you are interested in downloading.

2. On the Investigation Details page, click Download Selected Metadata.
   Your browser prompts you to open or save the .zip file. Follow your browser's instructions to open or save the 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.

   The archive file is in compressed format. When you download it, it may be a single compressed folder or .zip file. When you open it, you see at minimum three text files at the root of the folder or file. An example of these follow.     a_10290.txt    i_10290.txt    s_10290.txt The text files describe the investigation, study or studies, and assay or assays. In this example, 10290 represents the file identifier but in practice, each file identifier may be named differently, even in the same investigation. Only the a, i, or s prefix is required. If you download full data or selected data, the archive may also contain other files or folders as appropriate for the investigation; for example, images. If you download metadata, the archive only includes the a, i, and s files.

Downloading Selected Data

Downloading Large Files with Globus

Globus is a service that enables large file transfers securely. You must have an account with Globus and install Globus Connect Personal to use it to download investigation files to CSSI DCC. If you do not already have an account, you are prompted to create one when you start the download process.

To download files using Globus

1. If you haven't already, start Globus Connect Personal.
2. Log in to the CSSI DCC portal. For instructions, refer to Logging In to the CSSI DCC Portal.
3. Start the download process as described in one of the following sections:
   • Downloading Full Data
   • Downloading Selected Data
4. The next step depends on whether you are downloading the investigation's full data or selected data:
   1. If you are downloading the investigation's full data, the Request Data Files page appears. Click the Transfer with Globus checkbox and then click Download.  
      
   2. If you are downloading selected data from the investigation, the Request Multiple Downloads dialog box appears. Enter your email address. Click the Transfer with Globus checkbox, click Request Download.
       

5. If you have not confirmed your Globus ID previously, the Globus Upload window appears, prompting you do to so.
   

6. If prompted to do so, enter your Globus ID (an email address) and click Confirm. The Download Requested window appears.

   

7. Click Ok. Check your email inbox for the link to the file on Globus. Click the link in the email. You are prompted to log into Globus.
8. On the Transfer Files page, one of the Endpoints you configured when you installed Globus Connect Personal is already populated, though you can change it.
   
9. Finish the download process as follows:
   1. Select the starting endpoint (on the right) where the file(s) you want to download reside(s). Narrow down to the path if necessary.
   2. Confirm or change the destination endpoint (on the left). 
   3. Click the left arrow button that points to the destination to begin the transfer request. 
      A message appears on the screen when the transfer request is submitted successfully.
      

      
      You will receive an email when the request is granted and the transfer succeeds.