The Rat Genome Database curation tool suite: a set of optimized software tools enabling efficient acquisition, organization, and presentation of biological data

Abstract

The Rat Genome Database (RGD) is the premier repository of rat genomic and genetic data and currently houses over 40,000 rat gene records as well as human and mouse orthologs, 1771 rat and 1911 human quantitative trait loci (QTLs) and 2209 rat strains. Biological information curated for these data objects includes disease associations, phenotypes, pathways, molecular functions, biological processes and cellular components. A suite of tools has been developed to aid curators in acquiring and validating data objects, assigning nomenclature, attaching biological information to objects and making connections among data types. The software used to assign nomenclature, to create and edit objects and to make annotations to the data objects has been specifically designed to make the curation process as fast and efficient as possible. The user interfaces have been adapted to the work routines of the curators, creating a suite of tools that is intuitive and powerful. Database URL: http://rgd.mcw.edu.

Figure 1.

Homepage of the Gene Nomenclature Tool. Pre-loaded categories are displayed as hyperlinks. Individual genes or families of genes can be searched by the keyword search box. Genes that are scheduled to be reviewed in the future can be searched through the date search function.

Figure 2.

Editing page of the Gene Nomenclature Tool. All ortholog groups are listed in matched sets to simplify comparison of the rat nomenclature to the mouse and human nomenclature. The proposed change/editing text boxes and action selection radio buttons are at the bottom of every ortholog group. An ‘Accept All’ button is located at the top and bottom of every editing page so that all proposed changes on the page can be approved at once if the curator decides they are acceptable. ‘Submit Changes’ buttons are located next to the ‘Accept All’ buttons to send the changes to the database.

Figure 3.

The Object Creation and Editing Tool: QTL entry page. The QTL entry page consists of many text boxes specific for the different types of information collected by the curator to describe a QTL. Clicking the search icon to the side of the symbol box generates a pop-up window where current QTL symbols may be searched.

Figure 4.

(A) The Ontology Annotation Creation and Editing Tool homepage has ‘buckets’ for holding selected items. Each bucket (core objects, ontology terms and references) has its own search function, which appears in the right frame of the page when ‘Select Objects’, ‘Select Terms’ or ‘Select References’ is clicked. (B) Annotation frame. All the items from the buckets are repeated in the annotation frame to allow them to be selected for annotations. More information choices are available below the bucket items as drop-down text boxes for qualifier terms and evidence codes, radio buttons for ontology aspect and text boxes for free text information.

Figure 5.

This intermediate annotation page holds the currently constructed annotation for Ptgs1, all existing annotations for objects in the Core Objects bucket (PTGS1/Ptgs1 for human, mouse and rat), and options for editing. The current annotation can be edited by reselecting items above the annotation and re-clicking the ‘Generate List’ button. Any pre-existing annotation at the bottom of the frame can be edited by clicking the edit icon to the left of the annotation.

Figure 6.

A list of obsolete ontology terms with links to annotations containing those terms.