Automatic annotation of bioinformatics workflows with biomedical ontologies

TL;DR

This paper introduces an automated method for annotating bioinformatics workflows with biomedical ontologies, enhancing their discoverability and reusability despite limited textual descriptions.

Contribution

It presents a novel automated annotation approach that successfully annotates workflows with ontological terms, improving data structuring in bioinformatics.

Findings

Annotated 530 workflows with over 2600 services

Annotation quality comparable to manual curation

Effective despite scarce textual descriptions

Abstract

Legacy scientific workflows, and the services within them, often present scarce and unstructured (i.e. textual) descriptions. This makes it difficult to find, share and reuse them, thus dramatically reducing their value to the community. This paper presents an approach to annotating workflows and their subcomponents with ontology terms, in an attempt to describe these artifacts in a structured way. Despite a dearth of even textual descriptions, we automatically annotated 530 myExperiment bioinformatics-related workflows, including more than 2600 workflow-associated services, with relevant ontological terms. Quantitative evaluation of the Information Content of these terms suggests that, in cases where annotation was possible at all, the annotation quality was comparable to manually curated bioinformatics resources.