APE in the Wild: Automated Exploration of Proteomics Workflows in the bio.tools Registry

The bio.tools registry
is a main catalogue of computational tools
in the life sciences. More than 17 000 tools have been registered
by the international bioinformatics community. The bio.tools metadata
schema includes semantic annotations of tool functions, that is, formal
descriptions of tools’ data types, formats, and operations
with terms from the EDAM bioinformatics ontology. Such annotations
enable the automated composition of tools into multistep pipelines
or workflows. In this Technical Note, we revisit a previous case study
on the automated composition of proteomics workflows. We use the same
four workflow scenarios but instead of using a small set of tools
with carefully handcrafted annotations, we explore workflows directly
on bio.tools. We use the Automated Pipeline Explorer (APE), a reimplementation
and extension of the workflow composition method previously used.
Moving “into the wild” opens up an unprecedented wealth
of tools and a huge number of alternative workflows. Automated composition
tools can be used to explore this space of possibilities systematically.
Inevitably, the mixed quality of semantic annotations in bio.tools
leads to unintended or erroneous tool combinations. However, our results
also show that additional control mechanisms (tool filters, configuration
options, and workflow constraints) can effectively guide the exploration
toward smaller sets of more meaningful workflows.