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

   will

   reappear.

   
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3. 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.
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   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.
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   Info
   If you add or remove a pie chart, the change is also reflected in the Investigation list fields.

4. 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.

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1. Open a Study Details page.
   

   

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

   Info
   title Study Hierarchy
   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 the Source. Metadata for that source appears.

   Info
   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. To select multiple values, click one, wait for it to appear on the Metadata for Source page, and then click the arrow again to select another value. To clear a selection, click that 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 3 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.

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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.

   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.

   
   
   
   

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.
   

   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.

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.

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1. From the CSSI Data Portal home page, click the Search button select Investigations > Search.
   
   
   The Search Investigations page appears.
   
   
   
2. In the search box, enter a keyword or phrase. 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.
   
   Search results appear immediately, using the context currently in the Search for box, which by default is Investigations. The time the CSSI DCC Portal took to first search for the keyword or phrase and then render the results on the page also appear.
   
   
3. In the Search for 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.
   
4. Click any investigation name, study name, or assay filename to explore the data further.

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

2. Click the Download Full Data button.
   Your browser prompts you to open or save full_archive.zip. If you save it, you may want to rename it to include the name of the investigation so that you can identify it more easily.
   

   Warning
   While it is compressed as a .zip file, this file may still be very large. Consider its size before downloading.

3. Follow your browser's instructions to open or save the file.

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1. Filter a study or an assay until you reach a selection of investigation data you are interested in downloading. You may be interested in only the metadata so that you can see how that selection of entities was structured.

2. 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.

   Info
   title Metadata File Contents
   The metadata file is in compressed format. It contains one folder called metadata and a text file for each of the following: assay, investigation, and study. The contents of the archive folder look similar to the following (10290 is just an example of the file identifier): metadata/    a_10290.txt    i_10290.txt    s_10290.txt

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