Gene Ontology annotations: what they mean and where they come from

Abstract

To address the challenges of information integration and retrieval, the computational genomics community increasingly has come to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). Here we address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations, in the hope that this will lead both to better representations of biological reality through annotation and ontology development and to more informed use of GO resources by experimental scientists.

Figure 1

Anatomy of an Annotation. Annotations are provided to the Gene Ontology Consortium as tab-delimited files with 15 fields. Four fields indicate the gene product being annotated, the ontology terms used in the association, the type of evidence supporting the annotation and the reference where the original evidence was presented. The three annotations described in this manuscript are shown.

Figure 2

Molecular Function Annotation Data. This graph is reproduced from Zhang et al [10]. The graph shows the concentration of retinoid used as substrate along the X axis and the retinol dehydrogenase activity along the Y axis. Open circles refer to all-trans-retinol as a substrate and closed circles refer to 9-cis-retinol as a substrate. The enzyme samples were taken from a crude extract of cells transfected with a cDNA encoding the Rdh1 gene. [Used by permission]

Figure 3

Biological Process Annotation Data. This figure is reproduced from Washington Smoak et al [11]. The figure shows micrographs of hearts in 16.5dpc mouse embryos. The figure on the left shows an animal with two functional copies of the Shh gene and the figure on the right shows an animal with no functional copies. Ao and Pa indicate the aorta and the pulmonary artery respectively. The ? indicates an aberrant outflow tract. Reprinted from Developmental Biology, 283, Washington Smoak et al, Sonic hedgehog is required for cardiac outflow tract and neural crest development, 357-72, Copyright 2005, with permission from Elsevier.

Figure 4

Cellular Component Annotation. This figure is reproduced from MacPhee et al [12]. The figure shows micrographs that are the results of an immunofluorescence localization of the ATP1A1 protein. The illuminated areas show the location of the protein along the plasma membrane. Reprinted from Developmental Biology, 222, MacPhee et al, Differential involvement of Na(+),K(+)-ATPase isozymes in preimplantation development of the mouse, 486-498, Copyright 2000, with permission from Elsevier.