5.1 Bio-Ontologies 93
- Molecular function.The biochemical activity of a gene product. For ex-
ample, a gene product could be a transcription factor or a DNA helicase.
This classifies what kind of molecule the gene product is. - Biological process. The biological goal to which a gene product con-
tributes. For example, mitosis or purine metabolism. Such a process is
accomplished by an ordered assembly of molecular functions. This de-
scribes what a molecule does or is involved in doing. - Cellular component.The location in a cell in which the biological activity
of the gene product is performed. Examples include the nucleus, a telom-
ere, or an origin recognition complex. This is where the gene product is
located.
The terms within each of the three GO ontologies may be related to other
terms in two ways:
- is-a.This is the subclass relationship used by classic hierarchies such as
the taxonomy of living beings. For example,condensed chromosomeis-a
chromosome. - part-of.This is the containment relationship in which an entity is physi-
cally or conceptually contained within another entity. For example,nucle-
olusispart-ofnucleus.
An example of the GO hierarchy for the term “inositol lipid-mediated sig-
naling” is shown in figure 5.1. This shows the series of successively more
restrictive concepts to which this concept belongs.
GO:0003673 : Gene_Ontology (80972)
GO:0008150 : biological_process (56741)
GO:0009987 : cellular process (20309)
GO:0007154 : cell communication (6336)
GO:0007165 : signal transduction (4990)
GO:0007242 : intracellular signaling cascade (1394)
GO:0019932 : second-messenger-mediated signaling (219)
GO:0048015 : phosphoinositide-mediated signaling (3)
GO:0048017 : inositol lipid-mediated signaling (0)
Figure 5.1 The GO hierarchy for inositol lipid-mediated signaling. The parentheses
show the total number of terms in the category at that level.