Abstract
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 in support of bioelectronic medicine. As part of this effort, the SPARC program 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 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 autonomic nervous system 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.
Competing Interest Statement
M.E.M and J.S.G. have an equity interest in SciCrunch, Inc., a company that may potentially benefit from the research results. The terms of this arrangement have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies. S.T and M.H are employed by MBF Bioscience, the creator of software referenced in this paper. The remaining authors have no conflicts of interest to declare.
Footnotes
Email Addresses and ORCID: Troy Sincomb (tsincomb{at}ucsd.edu),
Thomas H. Gillespie (tgillesp{at}ucsd.edu),
Bernard de Bono (b.debono{at}auckland.ac.nz),
Jacqueline Bresnahan jacqueline.bresnahan{at}ucsf.edu),
Gary M. Mawe (gary.mawe{at}uvm.edu),
Jeffrey S. Grethe (jgrethe{at}ucsd.edu),
Susan Tappan (susan{at}mbfbioscience.com),
Maci Heal (maci{at}mbfbioscience.com),
Maryann E. Martone (mmartone{at}ucsd.edu)
This version of the manuscript has mainly been revised to change reference of the "SPARC project" to the "SPARC program".