Quick Start Guide

Welcome to BioConnect!

In this short guide, you will see how to search for studies and data, how to download a custom data package, and how to view all metadata and files for your package.

For instructions on curation and system administration, see creating and editing a study in BioConnect.

All you need to get started is to login with JAX single sign-on. Chrome is the recommended browser for BioConnect.

How to search

Navigate to the search app by selecting from the menu item on the left or the quick link in the applications section on the homepage.

Figure 1: Two ways to navigate to search.

On the search page there is a list of studies available in BioConnect and two ways to filter the study list. The search bar allows for free text search of study titles, descriptions, and contacts. Entering a study ID, e.g., JAXST000001, will return that specific study (see Figure 2a). The search filters, on the left, filter the study list based on controlled vocabulary terms (see Figure 2b).

Figure 2a: Use keywords and filters to search various studies, assays, investigations, and any other relevant information. Use the "What can I search?" button for suggestions. Each listed study will display basic information on the study including the description and investigation name. You may select on the numbers succeeding the words assays and files to preview the corresponding data.

To the left of the search results are search filters. These filter tools support search based on controlled vocabulary terms. This avoids the pitfalls of fuzzy matching on complex biological terms.

Filtering groups include organism, tissue, strain, assay measurement type, and study factors.

The filter section includes a listing of the applied filters at the top. The "clear all" button applies to all the filter groups below. Each of the filter groups includes a term search box. Start typing and the list of filter terms will themselves be filtered.

Multiple filter choices may be selected, along with the text search. Each search is disjunction among group members and a conjunction across groups. That is, terms in each group are connected with an OR operator, but the groups are ANDed. In the example to the right, the search looks for all studies where the organism is "Mus Musculus" AND (tissue is "Heart" OR "Lung"). The filter terms are further ANDed with the search box term from above.

A new search returns whenever a term is added, removed, or changed.

Figure 2b: Filtering groups include organism, tissue, strain, assay measurement type, and study factors. Each group can be expanded to show the list of controlled terms. A text search is included within the group to help find terms. Contacts (e.g. investigators) are not among the filter terms, but can be entered in the search box above the filters.

If you would like to view the entire study and all associated data, click the study link.

Figure 3: Selecting the Study link will redirect you to a page with all relevant information on the study, including the assays. Select the button on the far right of the card to open the page in a new window. You may also select the investigation link to view which studies are related to that investigation.

Once you select the study link, you are able to view the details pertaining to that study, including the assay(s). Select the back chevron (<) on the upper left of the page to return to the study list.

Figure 4: The read-only view of all relevant study and assay data. You are able to download this data using the "Generate Study Data Package" button on the top right of the study screen. If you only want data from one of the assays, open the assay and select the "Generate Assay Data Package" button on the top right of the screen. This data will be available from the User Space.

How to create a data package

Once you know which studies to download, you can create a data package.

If you desire to quickly make a data package without viewing all details, you may select the download button listed on the right of the individual study on the study list.

Figure 5: Create a data package using the download button on the study card.

Once you select a generate data package button, a dialog will appear. This dialog allows you to preview the files in the package, make updates to the package name, or customize which files will be included in the download.

Figure 6: Using the generate package dialog, you may update the name of the package or customize which files to include in the download. If you don't wish to customize the package, you may continue by selecting the button to generate the data package.

How to download your data package

Select your personal User Space from the menu item on the left. Here you will be able to view and manage your generated packages.

You can review your package details including file information or you may download your package in the actions section.

Figure 7: Your personal user space where you may view and download your data packages. You may also delete a package that was previously generated, this will not delete the studies included but will remove the package from your list. This view is not seen by any other user.

Once your data package is downloaded, you will receive a zip file locally on your machine. Included in the zip file should be a README file describing the package, ro-crate-preview.html, and ro-crate-preview.json. You should also see any files you chose to download locally.

Select the ro-crate-preview html file and open it on a browser.

The ro-crate-preview should look similar to the screenshot below. In this view you will be able to access all relevant files and details for your package.

Figure 8: After you have downloaded your data package, you will have access to the ro-crate-preview html file that you may open on a browser. This gives a detailed overview of the study and associated metadata. If any files are located in an external location such as google cloud, you may select the links to view and manage on that platform.

Links to data files are at the top of the data package preview page. If the files are accessible in the BioConnect system, then clicking the link should begin file download. Also see the documentation on JBQ for a quick way to extract metadata from the data package and convert it for use in analyses.

Thank you for using BioConnect!

Reach out to bioconnect_support@jax.org with any questions or concerns.