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 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.
You can browse and explore investigation data contained in investigation, study, and assay files.
To browse investigations
The Browse Investigation page has two interactive components:
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. |
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
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.
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.
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.
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.
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.
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.
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
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. |
s_mrna.txt
, to the three selected in this procedure.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
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. |
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. |
You can search for investigations, studies, or assays in the CSSI DCC Portal by:
You can search all investigations, studies, and assays in the CSSI DCC Portal by keyword or phrase. Search words fewer than 4 characters are treated as full words. Search words greater than 4 characters are treated as both full words and partial words, if applicable. A search looks for matches in all file columns, field definitions, and placeholders in those investigations, studies, and assays.
To search investigation data by keyword or phrase
In the Search for box, select the context of the search. Options include Investigations, Studies, or Assays. Your search will be restricted to the context you select.
Search results appear below the search criteria area.
In the following example of search results, the keyword for the search is cell and the context is Investigations. All investigations that include the word cell anywhere in the investigation metadata appear in these search results.
If the context were Studies or Assays, the results would include information specific to these components, as follows
Search results from a search with a context of Studies display 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.
Search results from a search with a context of Assays display 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.
To further narrow your results, you can filter by Investigation Public Release Date. Click Filters to show the From and To date selection boxes. Click Search. Note that if you do not enter a search term but select dates in this filter that the CSSI DCC Portal searches all investigations that match the dates you selected.
Investigations matching your search appear on the page.
You can search all investigations, studies, and assays in the CSSI DCC Portal by terms found in related ontologies, for example, the Ontology for Biomedical Investigations and NCI Thesaurus (NCIt). A search looks for synonyms and subclasses of the keyword you entered in the ontology(ies) you selected and matches them to investigations, studies, and assays in the CSSI DCC Portal. The matching ontological terms can exist in file columns, field definitions, and placeholders of the investigations, studies, or assays.
To search investigation data by related terms
If any ontological synonyms or subclasses of the keyword you selected exist in the CSSI DCC Portal, those terms appear in the Synonyms or Subclasses box, respectively.
In the following example, the keyword is neoplasm and its synonym found in one or both of the selected ontologies is tumor. The subclasses of tumor that appear in the search results appear in the Subclasses box. You can click any of those terms and refresh the search results to show only those investigations, studies, or assays that contain those terms. In the following example, only cc is selected. Note that the selected term has a solid black outline while terms that are not selected have a dotted line.
To expand your ontological search to include all synonyms and subclasses, even if they do not appear in the search results, click the click here link.
The page refreshes and shows all synonyms and subclasses, even if they're not in the search results. You can return to the view of synonyms and subclasses only in the search results by clicking click here again.
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.
An investigation's full data file is always available for download. However, due to the processing resources required, Selected Data downloads are currently limited to 30GB. |
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
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. A link to the archive will be emailed to you.
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.
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
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.
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. |
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
Click the Transfer with Globus checkbox.
Click Request Download.
The Globus Upload window appears, asking you to confirm your Globus ID.