The UCSF Mouse Inventory Database Application, an Open Source Web App for Sharing Mutant Mice Within a Research Community

Abstract

The UCSF Mouse Inventory Database Application is an open-source Web App that provides information about the mutant alleles, transgenes, and inbred strains maintained by investigators at the university and facilitates sharing of these resources within the university community. The Application is designed to promote collaboration, decrease the costs associated with obtaining genetically-modified mice, and increase access to mouse lines that are difficult to obtain. An inventory of the genetically-modified mice on campus and the investigators who maintain them is compiled from records of purchases from external sources, transfers from researchers within and outside the university, and from data provided by users. These data are verified and augmented with relevant information harvested from public databases, and stored in a succinct, searchable database secured on the university network. Here we describe this resource and provide information about how to implement and maintain such a mouse inventory database application at other institutions.

Keywords: inbred strain; mouse; mutant allele; transgene; web application.

Figure 1

Sample mouse records table. A view of the Mouse Record page in the Database Web App shows examples of records for each of the three categories in which entries are classified: mutant allele, transgene, inbred strain. A full description of the information in each column is provided in the section of the text entitled “Information included in a Database Record”; here attention is drawn to the hyperlinks in the records (shown in blue): In the “Name” column, every record has a link to a change request form that can be completed online. The “Category” column in the records for mutant alleles (records #1 and #2) contains links to the page on MGI that describes the gene that is altered in the mutant allele. In record #4 there is a link to the supplier’s catalog page for the inbred strain listed. The “Details” column provides links to the MGI and PubMed accession pages for the mutant alleles and transgenes. The “Comments” column provides some information about modifications with additional relevant URL links. The “Files” column contains links to downloadable files for genotyping protocols and oligonucleotide sequences. The “Holders” column has a link to the E-mail address for each Holder in order to facilitate communication with the holder about the entry. The following are examples of the URLs for the hyperlinks. MGI:96556, http://www.informatics.jax.org/marker/MGI:96556, MGI:2176574, http://www.informatics.jax.org/allele/MGI:2176574, PubMed: 11520464, https://www.ncbi.nlm.nih.gov/pubmed/11520464?dopt=Abstract, www.gudmap.org specimen, https://www.gudmap.org/chaise/record/#2/Gene_Expression:Specimen/RID=N-GZ5G.

Figure 2

The Mouse Database Web App Homepage. The Navigation Bar across the top has links (in white lettering) to specific pages (see Figure 3). The three large boxes provide links to (left) the database search engine, (middle) a form for requesting the creation of a new record, and (right) a detailed description of all the features of the Database Application and a list of Frequently Asked Questions (FAQs). The “Quick Search” field (top right) routes to the search results page (see Figure 3A). The yellow boxes provide resources for education about mouse mutants and means of getting help in using the Application.

Figure 3

The navigation bar. A demo database was created with 5 mouse records, 4 holders, and 3 facilities for the purpose of displaying the various features of the mouse database application. (A) Clicking on the Search button brings up a search field page and when a search term is entered (in this case ‘actin’) redirects to a search results page like the one shown here. It includes the search field at the top with the search term that was entered followed by sample queries (“Search examples”). Below that, all of the records that contain the search term are displayed. (B) Gene List enables users to sort the genes that are modified in mutant alleles and includes links to the mouse record table for those mutations. (C) Holder List is a searchable table of principal investigators with contact details and links to their mouse records and when records were audited (last review date). (D) Facility List describes all the vivaria, each of which has a link to a display of the mouse records table for all the mice housed in that facility. The names of individuals who use that facility and are willing to provide help in using the Web App are provided. Clicking on Submit Mice brings up the online form for requesting the creation of a new record. Clicking on Admin use only (extreme right of the navigation bar) provides access to the password-protected administrator portal (see Figure 4).

Figure 5

System overview of the Mouse Inventory Database Application. Users and admin access the Database Web App via a Web Browser (e.g., Safari, Chrome, Firefox, etc.). The Web Browser contacts the Web Server, which runs on an Elastic Compute Cloud (EC2) instance hosted in Amazon Web Services (AWS). The Web Server functions to ensure the security of the web connections. The Web Server proxies the request to a Tomcat Application Server, which routes the request to the “Mouse Inventory Database” Application, which is coded in Java, using JSP, JDBC, and additional custom logic. Data processed by the Application is stored in a MySQL database. The Application also makes requests to 3^rd Party Application Programming Interfaces (APIs) such as Mouse Genome Informatics (MGI) and PubMed. Such requests enable the database to automatically look up and include important information about the mutant alleles and transgenes: their accession number in the MGI database and the PubMed ID for the first publication describing how each was produced.

Figure 4

Administrator Navigation Portal. The navigation bar for the Admin Portal is shown at the top with a view of the Admin Home Page below. This page provides the Administrator with a to-do list for keeping the database up-to-date. The red box contains a list of action items generated by the semi-automated system that reports purchases and transfers from the animal care facility: 1 purchase and 3 internal transfers are in process for mice already in the database and these “pending requests” need to be pursued to determine if changes to the existing records need to be made (e.g., adding new holders); purchases of 7 mice and 1 import from another university are in process for mice not in the database. These “new submissions” need to be pursued to determine if new records need to be added. In addition, requests submitted by users online for changes to 2 existing records and a new submission are in the queue to be edited. Other buttons in the navigation bar enable the Administrator to access pages that contain information on Change requests or Submissions, or to Edit Records, Edit Holders. The Admin Search item button enables the Administrator to view all mouse records including records that are screened from view by users (e.g., records that have been deleted from the database). The Data Upload and Reports buttons provide access to features of the semi-automated system. The Notes button provides access to a page where the Administrator can create and edit panels for admin view only. Options gives access to pages for editing the content panels on the Main Home Page and for storing templates for emails sent to holders by the Administrator.