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Exploring Investigation Details
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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.
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Investigation Details Page
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Study Details Page
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Assay Details Page
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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
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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.
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Visualizing and Filtering Investigations
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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
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In the Visualize and Select area, click one of the entities.
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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.
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Follow this same procedure if you want to filter on Protocol or Sample instead of Source. |
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Selecting Multiple Objects
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Visualizing and Filtering Study Data
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Visualizing and Filtering Assay Data
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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
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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.
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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.
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Follow this same procedure if you want to filter on protocol instead of sample. |
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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.
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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. |
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Searching Investigation Data
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