Imagine you’re organizing a massive music festival with different stages, genres, and artists. To keep everything running smoothly, you need a detailed map of the venue and clear communication among the staff. Similarly, the stimulating peripheral activity to relieve conditions (SPARC) program is creating a comprehensive vocabulary to navigate the complex world of bioelectronic medicine research. This vocabulary, called the SPARC Vocabulary, includes terms from various domains like anatomy, physiology, and experimental techniques. But sometimes, researchers encounter new terms that are not yet part of existing ontologies. That’s where the term management and review pipeline comes in. By extending the SPARC Vocabulary and collaborating with expert reviewers, the pipeline ensures that these new terms are incorporated into the vocabulary, enhancing our understanding of the autonomic nervous system (ANS) circuitry. This approach improves the findability, accessibility, interoperability, and reusability (FAIRness) of SPARC data and models. By exploring the underlying research, you can learn more about how this project is advancing bioelectronic medicine.

The stimulating peripheral activity to relieve conditions (SPARC) program is a US National Institutes of Health-funded effort to improve our understanding of the neural circuitry of the autonomic nervous system (ANS) in support of bioelectronic medicine. As part of this effort, the SPARC project is generating multi-species, multimodal data, models, simulations, and anatomical maps supported by a comprehensive knowledge base of autonomic circuitry. To facilitate the organization of and integration across multi-faceted SPARC data and models, SPARC is implementing the findable, accessible, interoperable, and reusable (FAIR) data principles to ensure that all SPARC products are findable, accessible, interoperable, and reusable. We are therefore annotating and describing all products with a common FAIR vocabulary. The SPARC Vocabulary is built from a set of community ontologies covering major domains relevant to SPARC, including anatomy, physiology, experimental techniques, and molecules. The SPARC Vocabulary is incorporated into tools researchers use to segment and annotate their data, facilitating the application of these ontologies for annotation of research data. However, since investigators perform deep annotations on experimental data, not all terms and relationships are available in community ontologies. We therefore implemented a term management and vocabulary extension pipeline where SPARC researchers may extend the SPARC Vocabulary using InterLex, an online vocabulary management system. To ensure the quality of contributed terms, we have set up a curated term request and review pipeline specifically for anatomical terms involving expert review. Accepted terms are added to the SPARC Vocabulary and, when appropriate, contributed back to community ontologies to enhance ANS coverage. Here, we provide an overview of the SPARC Vocabulary, the infrastructure and process for implementing the term management and review pipeline. In an analysis of >300 anatomical contributed terms, the majority represented composite terms that necessitated combining terms within and across existing ontologies. Although these terms are not good candidates for community ontologies, they can be linked to structures contained within these ontologies. We conclude that the term request pipeline serves as a useful adjunct to community ontologies for annotating experimental data and increases the FAIRness of SPARC data.

Read Full Article (External Site)