Constraint-Guided Workflow Composition Based on the EDAM Ontology

TL;DR

This paper explores how the EDAM ontology can aid in automatically composing bioinformatics workflows by providing domain knowledge and constraints, improving the search for suitable solutions.

Contribution

It demonstrates the use of EDAM as background knowledge and highlights the importance of flexible constraint formulation in workflow composition.

Findings

EDAM facilitates identifying possible workflows

Additional knowledge is needed for selecting adequate solutions

Flexible constraints support workflow development

Abstract

Methods for the automatic composition of services into executable workflows need detailed knowledge about the application domain,in particular about the available services and their behavior in terms of input/output data descriptions. In this paper we discuss how the EMBRACE data and methods ontology (EDAM) can be used as background knowledge for the composition of bioinformatics workflows. We show by means of a small example domain that the EDAM knowledge facilitates finding possible workflows, but that additional knowledge is required to guide the search towards actually adequate solutions. We illustrate how the ability to flexibly formulate domain-specific and problem-specific constraints supports the work ow development process.