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- 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.Info If you add or remove fields from the pie charts, the Investigations list fields immediately reflect the same changes.
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- 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.
Info title 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.
Info 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.
Info 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.
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You can search for investigations, studies, or assays that exist in the CSSI DCC repository using any keyword, phrase, or related term.
To search investigation data
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database in the following ways:
Search by Keyword or Phrase
You can search all investigations, studies, and assays in the CSSI DCC database by keyword or phrase. A search looks for matches in all file columns, field definitions, and placeholders in those investigations, studies, and assays.
To search investigation data
- From the CSSI Data Portal home page, click the Search button or select Investigations > Search.
The Search Investigations page appears.
- In the Search box, enter a 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.
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In the following example, the keyword for the search is "cell" and the context is
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Investigations. All investigations that include the word "cell" anywhere in the investigation metadata appear in the
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search results.
Search by Related Terms
by a keyword or phrase or further . 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.
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- Click any investigation name, study name, or assay filename to explore the data further.
In the Search 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.
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Search by Related Terms
Keywords are any word that appears in the fields belonging to any investigation, study, or assay in the CSSI DCC Portal.
Downloading Investigation Data
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- 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.
