ICBO_2018_32: Ontolobridge – A Semi-Automated Ontology Update Request System for Better FAIR-ifying BioAssay Ontology, Drug Target Ontology, and LINCS Ontology

TitleICBO_2018_32: Ontolobridge – A Semi-Automated Ontology Update Request System for Better FAIR-ifying BioAssay Ontology, Drug Target Ontology, and LINCS Ontology
Publication TypeConference Paper
Year of Publication2018
AuthorsKüçük-Mcginty, H, Clark, A, Graybeal, J, Cooper, D, Turner, J, Dorf, M, Musen, M, Bunin, B, Schurer, S
Conference NameInternational Conference on Biomedical Ontology (ICBO 2018)
Date Published08/06/2018
PublisherInternational Conference on Biological Ontology
Keywordsannotation, big data, BioAssay Express, BioAssay Ontology, CEDAR, FAIR, FAIR data, life sciences big data, ontology term request, semi-automated ontology updates
Abstract

Ontologies are products that are becoming more relevant for data science as the need for standardized vocabulary and meta-data is increasing. However, if they want to stay relevant, ontologies have a constant need for evolving, especially in domains that involve dynamic data, like life-sciences data. Based on the need pointed out by domain experts for updating and/or requesting ontology terms while annotating BioAssay Protocols, we are developing a semi-automated technology that will allow users to request new terms and update existing ones easier. This need was pointed out by domain experts who are using CDD’s new tool BioAssay Express (BAE). BAE allows users to annotate their bioassays in a semi-automated and standardized fashion using the highly-accessed ontologies (BioAssay Ontology (BAO), Gene Ontology (GO), Disease Ontology (DOID), and Drug Target Ontology (DTO) among others) in the background. Our goal in the Ontolobridge project is to help various users of BAE (researchers performing curation, dedicated curators, IT specialists, ontology owners, and librarians/repositories) request and update the existing vocabulary provided by BAO in a semi-automated way, with a user-friendly interface. Furthermore, APIs and tools including templates from CEDAR will be created in order to would allow users to request new ontology terms or changes to existing terms easily during the annotation process. In this way, we’re aiming to increase the Findability, Interoperability, Accessibility, and Reproducibility (FAIR) of above mentioned ontologies and BioAssay Protocols better.

URLhttp://icbo2018.cgrb.oregonstate.edu/