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Page History
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- 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
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Pie Charts and Investigations
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List
The Browse Investigation page has two interactive components:
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- On the Browse Investigations page, click
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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.
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 have selected or cleared as many fields as you want to use to filter the investigation data, click
The Select menu moves back to its original position.
Exploring Investigation Data
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 and Search Investigations (search results) pages. These details include counts of studies, assays, samples, and files. The metadata available for an investigation determines if other entities are available for counts such as sources and collections. From these detail details pages you can visualize the structure of the investigation and download selected study files, download the entire archive, and download only the metadata.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.
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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
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To view study details
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| Info |
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Clicking Modify Search returns you to the Search Result page where you can change how you filter the current investigations. |
Searching
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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 Investigation Data
You can search investigations, studies, or assays using any keyword.
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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.
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
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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 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.
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