The NCBO Resource Web service is a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to enable users to locate biomedical data resources related to particular ontology concepts. The annotations are generated using the NCBO Annotator and presented through integration with BioPortal, enabling researchers to search for biomedical resources associated (annotated) with specific ontology terms. The NCBO Resources web service uses a concept recognizer (currently provided by the National Center for Integrative Biomedical Informatics, University of Michigan) to produce a set of annotations and expand these using ontology is_a relations in the ontology. The system's indexing workflow processes the text metadata of diverse resource elements such as gene expression data sets, descriptions of radiology images, clinical trial reports, and PubMed article abstracts to annotate and index them with concepts from appropriate ontologies. Researchers can then search biomedical data sources using ontology concepts.

NCBO

High level abstraction API (Java/REST/R) for interacting with ontology resources including local ontology files in standard OWL and OBO formats (via OWL API) and public ontology repositories: EBI Ontology Lookup Service (OLS) and NCBO BioPortal.

Tomasz Adamusiak, Helen Parkinson, Natalja Kurbatova, Misha Kapushesky, Morris Swertz

It is a healthcare analysis system

OntoMaton is a google spreadsheet application allowing for ontology search and tagging directly within google spreadsheets. More information can be found here: https://github.com/ISA-tools/OntoMaton

ISA team

Integration of high-dimensional genomic and phenomic data is challenged with scalability and semantic robustness for intuitive querying. To address these needs, we develop a hybrid ontology and graph database into a seamless datastore that we have named an ontolograph. The ontolograph leverages the best features of ontologies and graph databases.

James Chen, Arka Pattanayak, Chaitanya Shivade