The HMBR Portal provides a summary of available data, as well as faceted and advanced search tools to identify data of interest.
The portal landing page is broken up into 3 section:
- The welcome box provides your entry to querying data, described in more detail immediately below.
- A bar graph breaks down number of samples per modality per study.
- The data portal summary bar at the bottom provides a high level summary of all data currently available through the HMBR portal.
Begin exploring data by study or through the faceted or advanced search options. The studies button takes users to a summary page listing available studies, with links to all samples or all files associated with the study.
The data button will take you to the faceted data search page, the heart of the portal's functionality, described below.
Below these are a set of pre-defined, commonly accessed queries. As an example, one can easily retreive all samples from male subjects in the PROTECT study.
The HMBR Data Portal provides a simple faceted search query interface to help identify data of interest. The faceted search page, accessible through the Data button in the landing page welcome box, is divided into 3 sections: the filter panel, the advanced search box and the summary results panel.
The filter panel on the left allows users to select one or more of the available facets to filter down the samples of interest (See #1 in figure). Selecting any facet automatically populates the advanced search box with the current query (See #2 in figure). The summary results panel provides dynamic pie charts summarizing data corresponding to the currently selected filters (See #3 in figure).
The filter panel contains two tabs of pre-configured facets associated with
- samples (study, assay prep, race, smoking history, gender, and age category), or
- files (format, category, matrix type)
The number next to each facet corresponds to the number of samples associated with this attribute across all projects in the portal. This number does not change dynamically as facets are selected or deselected. What does change is the summary results panel. As facets are selected, the file count, sample count and file size total will update to reflect the current filter(s). The pie charts will also update to reflect the current filter(s). Hovering over any of the pie charts will show a table of counts of files and total file size for each component of the pie chart. This table is also accessible by clicking on the table icon in the upper right corner of the pie chart to toggle between chart or table views.
In addition to filtering via the filter panel, users can click directly on a pie piece or table field to dig further into a specific component of the dataset. Once data has been refined to the dataset of interest, click on the Files tab of the summary results panel. From here, files can be added to the shopping cart, as described below.
Additional facets are available by Add a Filter in the upper right of the filter panel. The resulting pop-up lists all additional searchable facets available, which can be browsed or searched for using the search bar at the top. Clicking on any facet will add it to the top of the filter panel for incorporation into the current filter.
Doctor Ben wants is interested in sample data from male subjects enrolled in the PROTECT study. Starting at portal.microbiome-bioactives.org/, he takes the following steps:
- Click the
Databutton in the welcome box to access the faceted search page - In the Samples filter panel, select PROTECT in the Studies category AND Male in the Gender category. This narrows his results to male PROTECT data.
- He clicks on the Files tab and adds all files to his shopping cart using the cart icon at the top of the Files box.
The Advanced Search feature simulates querying a database directly. To begin an advanced search, click the "Advanced" button in the upper right corner of the advanced search box.
A query requires the following basic format:
(property) (comparison operator) (value)The property is what you're searching on, ie the facet. The comparison operator is how you want to relate your value to your property, ie equals, in. The value is what you're filtering the property on.
For example:
sample.assay_prep = "Metagenomics seq"
Clicking "Submit Query" will update the summary results panel in the same way as the faceted search.
Auto-complete helps in entering an advanced query. Auto-complete will pull all valid options directly from the database to ensure that a user's search contains a valid property, comparison operator, and value. If auto-complete suggests no results in your query, you know that you have entered nonexistent combinations of property+comparison operator+value. The auto-complete feature is also helpful in that it allows users to browse all current values in the database for that particular property.
Once data has been refined to the dataset of interest, click on the Files tab of the summary results panel. This will bring up the list of files matching the search criterion. The files list table provides some basic information about the file including access type, URL, data category, file format, and size.
Clicking on an individual file takes users to a summary page for the selected file, with the option to download via the Download button in the upper right.
To download multiple files, users can either click on the shopping cart icon to the left of all files of interest or select the shopping cart dropdown at the top left of the Files table and select Add all files to the Cart.
The cart icon on the top right of the page will display the number of items currently in the cart. At this point, users can continue to browse for additional files, combine results of multiple queries, or proceed to the cart page to download the selected files.