Phylogenetic Analysis Workflows - User-Level Workflow Design: A Bioinformatics Perspective - page 76

Fig. 3.11 Part of the type taxonomy of the EMBOSS domain model
Figures 3.10 and 3.11 show excerpts from the service and type taxonomies,
respectively. The OWL class Thing is always the root of the taxonomies,
below which EDAM terms provide groups for concrete and abstract service
and type representations. Note that the taxonomies comprise 565 and 1425
terms, respectively, directly after being derived from EDAM. They are then
automatically cut down to those parts that are relevant for the services and
data that appear in the domain model in order to avoid overhead, still cov-
ering 236 and 207 terms, respectively. To facilitate presentation, the figures
again comprise only those parts of the taxonomies that are relevant for the
examples given in this section.
The (part of the) service taxonomy shown in Figure 3.10 comprises a num-
ber of service categories for different Operation s. The terms range from quite
general service classifications (such as Plotting and rendering or Analysis and
processing in the upper part of the figure) to rather specific service categories
like Phylogenetic tree construction (parsimony methods) or Multiple sequence
alignment (local) (lower part of the figure). The individual services in the
domain model are then associated with one or more of the available service
categories.
The (part of the) type taxonomy in Figure 3.11 contains various terms from
the Data branch of the EDAM ontology. The higher-level data type categories
comprise general terms like Metadata and annotations and Phylogenetic data ,
while the more specific categories at the lower levels allow for more precise