How Do I use ontologies in RGD?

Exploiting the power of ontologies and their knowledge bases relies on the ways that data is linked together and in the fact that fundamental principles underlie biological phenomena. The knowledge bases build upon ontologies can serve as links to various paths from which related biological information is pulled. The associations that are most important are:

• The ancestries, sibling and children of terms
• The annotations of various object to terms
• The profile of the object in terms of the terms that characterize it

Through these associations, an extensive network of related information can be accessed. As an illustration, the following paragraphs examine the information linked via the Gene Ontology and object reports to the gene Sgk (Figure 1) which codes for a serum/glucocorticoid regulated kinase in rats and is annotated to the term protein threonine/serine kinase activity. The quickest way to get to the terms data is to type in the accession number (Figure 2) for the gene ontology. This returns a single row for the formal term (Figure 3).

Figure 1: Gene Sgk reports page at rgd.mcw.edu.

Figure 2: Type in the accession number GO:0004674.

Figure 3

Clicking the accession number gets the user to the browser page (the term of interest is bolded) (Figure 4). This page presents suggestions as to how the study of, or data gathering on, other objects related to protein threonine/serine kinase activity can proceed. The parent term (protein kinase activity,GO:0004672) provides a larger context in which the research can proceed. The siblings (protein histidine kinase activity, GO:0004673; protein tyrosise kinase activity, GO:0004713; etc.) provide closely related concepts that can give leads to data on the evolution, physiology, kinetics, cell biology of enzymes annotated to the term. This is because biology tends to reuse and modify existing themes and rarely, if ever, invents things de novo. Thus data regarding objects annotated to a terms siblings can lead to information and insight regarding orthologs and paralogs, protein domain reuse, common enzyme mechanisms, gene expression variations, etc. A quick glace at sibling terms’ ontology reports turn-up growth factors, receptors and kinases. More related information can also be culled by accessing the information annotated to the term’s children.

Figure 4

On the other end of the spectrum, the context or contexts to which the term belongs can be seen via the paths to the terms in the ontology and to a good extent reflect the richness and complexity of biological phenomena.

Accessing the report on the objects annotated to the specific terms may also provide more avenues to related data. The details of object reports are available elsewhere in this help system, but regarding ontologies, there is a section in these pages that list the ontology terms to which the object is annotated (Figure 5). Accessing these terms ontology browser page and information as describe above can lead to more relevant information.

Figure 5: Ontology terms on gene Sgk reports page at rgd.mcw.edu.