The Open Biomedical Ontologies (OBO) Foundry is a community organized project that aims to facilitate the discovery, development, application, harmonization, interoperability and sharing of ontologies. OBO ontologies are widely used as a standard for knowledge representation in a broad range of domains relevant to the NIH basic, translational, and clinical research mission. They cover for example gene functions (Gene Ontology, GO), diseases and phenotypes (Disease Ontology, DO; Human Phenotype Ontology, HP; Uberon Anatomy Ontology), assay types (Ontology for Biomedical Investigations, OBI), and relationships connecting these entities, both within and across ontologies (Relationship Ontology, RO). For over a decade, OBO has provided a variety of widely used services to the community, including 1) the OBO registry, which collects standardized metadata for each member ontology such as domain, scope, license, point of contact, etc., thus enhancing findability of each ontology, 2) configurable Persistent URLs (PURLs), which provide an unchanging address for ontologies and ontology classes, enhancing accessibility and reuse, 3) optional content hosting for OBO ontologies that want to take advantage of centrally managed versioning, 4) standardized software tools that make it easy to follow best practices for ontology development, 5) OBO principles, guidelines and best practices, designed to enhance quality and interoperability, and 6) an outreach and coordination effort to mediate between different member ontologies with the goal to coordinate and reduce overlap, through a central email list and regular teleconferences. The present proposal will provide time-limited, catalytic support to increase robustness of existing services by upgrading critical infrastructure on which they are based, by defining and applying standards for metadata and PURL management, and by applying best practices from software engineering to increase maintainability of the codebase. Second, we will introduce new capabilities into our service infrastructure to add automated quality controls to ontologies (individually and in groups), enhance the integration between our services and standardized tools, and add monitoring and metrics. Third, we will perform outreach and training efforts to increase the ability of the community to participate in the OBO project. In accomplishing these aims we will continue to keep our operating costs extremely low, and to freely share the tools and resources we build.
/PUBLIC HEALTH RELEVANCE Ontologies provide a precise language to describe scientific findings, and have successfully been used by researchers to share and compare their results. Different ontologies describe different aspects of knowledge, sometimes in an incompatible way. Here we propose to implement a set of services that allows different ontology producers to develop ontologies in a standardized fashion that will make it easier to use them together.
|Vita, Randi; Overton, James A; Mungall, Christopher J et al. (2018) FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability. Database (Oxford) 2018:|