Use Advanced Search (Tutorial)
| Abbreviations Key | |
| HISE | Human Immune System Explorer |
| IDE | integrated development environment |
| CBC | complete blood count |
Your project might have hundreds of subjects, and thousands of unique samples, making it difficult to find the results, subjects, or samples that correspond to a specific set of criteria. To address this issue, HISE has a powerful advanced search feature that lets you define the subjects, file types, or studies you want to find. You can quickly create a query and save it so that you can return to it later or share it with your colleagues. The advanced search functionality is the gateway to finding and accessing all your research data, including data files and human metadata.
Find Data Files and Reports
The various assay data analysis pipelines configured for your project produce specific output files and reports. To inspect the output of an analysis for a number of samples at the same time, use advanced search. If your project is configured with a project folder instead or in addition, you can also use advanced search to locate specific files within the project folder.
Advanced search lets you create queries and filter result files by metadata related to the subject, the sample, CBC results, or pipeline characteristics. The selected search results can be visualized or sent to an IDE for further inspection. You can also run multiple queries side by side, group the results of each query, and send them to a visualization tool for comparison.
| Type of Query Output | Description |
| Data files and reports | Automated pipelines outputs (results files) or derived results from another colleague working in the same project. The code snippets users retrieve have unique file IDs. |
| Sample metadata, survey data, and lab data | Sample metadata and any associated survey and lab data for each sample a user searches for. The code snippets users retrieve have unique sample IDs. |
| Subject metadata and EMR | Demographic data (subject metadata) and patient history information, if any. The code snippets users retrieve have unique subject IDs. |
Select Query Output
To select query output, choose a type of output from the accompanying table.
Choose File Groups
To narrow down the file types a user can select, filter by file group.
Set Privacy
You can set your query to be private or public. By default, the query is set to private, so that it is visible only to the user who created the query. If the query is set to public, you can share it with specific collaborators.
Instructions
Open Advanced Search
1. To open advanced search, navigate to Research > Advanced Search.
Create a Query
In the advanced search page, users have the option to create a new query or open an existing one.
1. To create a new query, in the upper-right corner of your screen, click New Query.
2. In the dialog box, choose Data files and reports.
3. Name your query and select the project(s) being worked on, the type of output, the file groups, and the file types. Only projects you have access to are shown, and you can't create a query for multiple projects that are in separate accounts. For details, see Understand and View Accounts and Projects.
4. Make the required selections, and then click Submit.
Use the Query Builder
In the Query Builder page, users can specify field names to filter their data.
Select a metadata group to filter by and one of the field names from the dropdown; a query block will appear with the chosen field name. Using the block, you can choose the logical conditions* and value/s to filter for any given field name. Continue to create additional blocks until you have a desired query.
*By default, the query will look for values that are equal to the one specified in the query block. Users can set the comparison operator to any of "equals", “does not equal”, “is one of”, “is none of”, or “contains term”.
Change the Clause
Multiple query blocks are combined with the “and” clause by default. Users can change this to an “or” clause by clicking and holding the waffle icon and dragging it to another query block.
Clone a Query
Users can clone their queries in order to quickly create an identical, duplicate query by selecting the copy icon next to the edit and delete icons. A cloned query's values can be adjusted.
Once a query is finalized, users can click “View Results” at the bottom right of the screen.
Use Search Results
In the “Search Results” page, users can select entries to produce a code snippet, save a file set, or view visualizations of their queried data.
Get IDE scripts
Clicking “Get IDE Scripts” will show a modal containing a method for reading data in digital notebooks, depending on the output specified in the query. The files selected in the Search Results page are listed by file ID.
Save files
Through Advanced Search, users can create a file set and bundle several result files together. Once a user has selected one or more result files, clicking “Save files” opens a prompt asking which Study to save the file set to. Users can share the saved file set with collaborators so that they can begin their analysis using the same input files.
For more information on file sets, please refer to this support page .
Visualize
Also through Advanced Search, users can visualize certain file types within the HISE UI. After selecting one or more result files, clicking “Visualize” directs the user to a new page with Visualizations.
For more information on visualizations, please refer to this support page .