Use Advanced Search (Tutorial)–DRAFT

	Abbreviations Key
HISE	Human Immune System Explorer
IDE	integrated development environment
CBC	complete blood count
CMV	cytomegalovirus

At a Glance

The powerful advanced search feature in HISE lets you define the subjects, file types, or studies you want to find. 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 then 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. This document explains how to create, save, and share queries, as well as how to use the results. If you have questions, contact Support.

Description

The advanced search functionality is the gateway to finding and accessing all your research output, including data files and human metadata. 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), use advanced search to locate specific files within the folder. 

Instructions

 Open Advanced Search and sign in

1. Navigate to HISE, and use your organizational email address to sign in.

2. In the top navigation menu, click RESEARCH.

3. From the drop-down menu, choose Advanced Search.

4. Alternatively, you can open Advanced Search directly from a Saved & Shared Queries link: 

A. Open Advanced Search as described in the preceding steps. 

B. In the upper-right corner, click Saved & Shared Queries. 

C. [More once I have access to this area]

 Choose a filter

In the left sidebar, choose FILES, SAMPLES, or SUBJECTS as your search type. Each type of search has different subfilters that branch into context-specific options as you make selections. Follow the instructions outline here for your selected search type. 

 FILES filter

1. To choose files, stay on the default FILES tab. To use this filter, you must choose at least one project and file type. 

A. In the Projects field, click the arrow at right. Then, from the drop-down list, choose one or more projects whose files you want to include in the search. To select all available projects, click Add all. 

If you select multiple projects, you might see duplicate results in the results window. This can happen, for example, when multiple surveys contain the same question.

B. In the File Type field, click the arrow at right. Then, from the drop-down list, choose one or more file types whose files you want to include in the search. To select all available file types, click Add all. 

C. (Optional) In the Advanced Filters field, choose additional filters. For details, see Use Advanced Search Filters (Tutorial).

C. Your search results populate the results window.

i. To select all results, click SELECT ALL ITEMS.

ii. To choose specific results, click the checkbox next to each row you want to select.

iii. In the modal, choose an action: 

a. ADD TO FILE SET

b. CREATE FILE SET

c. COPY FILE IDS

d. VISUALIZE

B.

C. To choose subjects, click the SUBJECTS tab. 

Choose file types (required for files)

Open the file type dropdown and:

Pick one or more file types.

Use type-ahead search to find a specific file type.​

Explanation that projects and file types must be set before you can run a file search.

SAMPLES filter

1. To choose samples, click the SAMPLES tab.

SUBJECTS filter

To choose samples, click the SUBJECTS tab.

Use simple vs advanced filters

Simple filters in the header vs advanced filters in the sidebar.​

When to rely on simple filters alone (quick narrowing) vs opening advanced filters for detailed criteria.

Use advanced filters

Open an advanced filter

Browse the advanced filter list (for example, Batch ID) and click to configure it.​

How the configuration UI appears (inline or in a modal) and what fields you see.

Select values and apply

If suggested values are available, how to:

Open the suggestions list.

Select one or multiple suggested values.​

If no suggestions exist, how to type free-text values into an input field.​

Use the Apply action to add the filter to your search, and when to remove or clear it.

Combine with other filters

Add multiple advanced filters and how they are combined (AND/OR behavior as implemented).​

Tips for building up complex searches without over‑filtering.

Run the search and interpret feedback

How the run/“See results” control behaves once required filters are filled.​

Reading the result count and understanding empty or low-result states, including suggestions to broaden or adjust filters.​

Set up sample and subject searches

Switch the search type from files to samples or subjects.​

Note that for samples and subjects:

Projects are required.

File type is not required and may not appear.​

How the list of available advanced filters and table columns changes by search type.

Work with results

Understand the results table

Column layout for each search type (files, samples, subjects) and common columns such as identifiers and key metadata.​

Hover-only controls (such as column menus or overflow actions) to keep the table from feeling cluttered.

Navigate and select items

Scroll or paging behavior in the results grid.​

Selecting individual rows, multi-select, and any “select all” options.

Take actions on selected results

Save selected items to a study or file set, with link to that tutorial.​

Visualize from selected results, with link to visualization documentation.​

Copy IDs (file IDs, subject IDs, sample IDs) from selected results for use in scripts and SDK methods.

Save, reuse, and share your query

Turn a temporary search into a saved query (steps to save and name it).​

Reopen a saved query from the Saved & Shared page and run it again.​

Share a query with collaborators or at the account level, and what they can do with it.

Manage saved queries

Use the Saved & Shared Queries page to:

Locate, sort, and filter saved queries.

Edit, clone, rename, or delete a query, and how that affects shared users.​

Use Advanced Search with SDKs and IDEs

Copy IDs from Advanced Search and paste them into R/Python SDK workflows.​

Note that query ID parameters in SDK methods are deprecated; new notebooks should use IDs or explicit filters instead.​

Link to “Use HISE SDK Methods and Get Help in the IDE” and other SDK tutorials.​

Troubleshooting

Required filters not filled (for file searches, missing projects or file types).​

No results or fewer results than expected; how to relax or adjust filters.​

Losing work when the page refreshes (unsaved queries) and how to avoid it.​

 Create a query

1. On the Advanced Search screen, you can create a new query or open an existing one.

A. To create a new query, click +New Query.

B. Enter or select each field in the dialog box:

i. In the Name field, enter a name for your query.

ii. In the Projects field, click the arrow at right, and select one or more projects from the drop-down list. Only projects to which you have access are shown, and the projects you select must be in the same account. For details, see the Accounts and Projects section in Get Started with HISE.

iii. In the Query Output field, choose Data files and reports or Sample metadata, survey and lab data. For help choosing one of the query output types, see the accompanying table.

iv. In the Result File Types field, choose the file types you want to see.

v. Use the Set privacy field to indicate the visibility of your query.

a. By default, the query is set to PRIVATE, so it's visible only to you.

b. To give others permission to see and use the query, choose SHARED.

c. To share the query only with specific collaborators, choose SELECT USERS, and enter the names of those with permission to view and access the query.

C. Click Submit. 

Use the query builder 

1. On the Query Builder page, filter your data. 

A. From the FILE METADATA menu, filter by FILE NAME or VERSION.

B. From the SAMPLE METADATA menu, filter by name or ID, such as BATCH ID or SAMPLE GUID.

C. From the SUBJECT METADATA menu, filter according to the metadata you want to find.

D. From the USER TAGS menu, filter by tag.

E. From the SELECT LAB RESULT GROUP menu, add and then select the field you want to use as a filter. 

F. From the SELECT SURVEY QUESTIONNAIRE menu, add and then select the field to use as a filter.

 Clone a query (Optional) 

1. To create an identical, duplicate query, select the Copy icon to the left of the Edit and Delete icons.

2.To create a new query, adjust the values as needed.

3. In the lower-left corner of the screen, click View Results.

 Use search results

1. On the Search Results screen, select the checkbox to the left of each entry you want to see. To see all results, click SELECT ALL ITEMS, or select the checkbox to the left of the Result Type column heading.

2. In the bottom-right corner of the screen, choose what you want to do with your results:

A. Save the files to study. You can share the saved file set with collaborators so that they can begin their analysis using the same input files.

i. On the Search Results page, select one or more results.

ii. Click SAVE FILES TO STUDY.

iii. In the Save file set dialog box, enter the title and (optional) a description of your file set.

iv. In the Select study to save these files to field, click the arrow to select a study from the drop-down list. For details, see Work with File Sets (Tutorial).

B. Get IDE scripts. You can generate a script to read data in digital notebooks.

i. On the Search Results page, select one or more results.

ii. In the Query IDE Scripts dialog box, click Copy Script. (The files you selected are listed by file ID in the script.)

C. Visualize. You can visualize certain file types within the HISE UI.

i. On the Search Results page, select one or more results.

ii. Cick Visualize.

iii. Click Visualize using this abstraction. For details, see Visualize Your Data.

Related Resources

Visualize Your Data

Configure a Pipeline (Tutorial)

Track Your IDE Billing Expenses (Tutorial)