To DAG or not to DAG?
Almost all biomedical ontologies are either simple tree structures that represent hierarchical classifications or directed acyclic graphs (DAGs). The difference is that the latter allows a term to be related to multiple broader tems (green arrows) whereas the former does not. Directed cyclic graphs are very rarely used for ontologies; the reason is that cycles (red arrows) can only arise in ontologies that make use of other relationships than is-a and part-of are used [28]. We illustrate each structure with simplified examples, namely an ontology of vertebrates, an ontology of cellular components, and an ontology of cell-cycle regulation that shows the mutual regulation of cyclin-dependent kinase (CDK) and anaphase-promoting complex/cyclosome (APC/C).
doi:10.1371/journal.pbio.1000374.g001
Taken from Figure 1 of Ontologies in Quantitative Biology by Lars Juhl Jensen and Peer Bork
To DAG or not to DAG?
Almost all biomedical ontologies are either simple tree structures that represent hierarchical classifications or directed acyclic graphs (DAGs). The difference is that the latter allows a term to be related to multiple broader tems (green arrows) whereas the former does not. Directed cyclic graphs are very rarely used for ontologies; the reason is that cycles (red arrows) can only arise in ontologies that make use of other relationships than is-a and part-of are used [28]. We illustrate each structure with simplified examples, namely an ontology of vertebrates, an ontology of cellular components, and an ontology of cell-cycle regulation that shows the mutual regulation of cyclin-dependent kinase (CDK) and anaphase-promoting complex/cyclosome (APC/C).
doi:10.1371/journal.pbio.1000374.g001
Taken from Figure 1 of Ontologies in Quantitative Biology by Lars Juhl Jensen and Peer Bork