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

PID phenomer is a web-based integrated platform for collection, mapping, storage and visualization of observed phenotypic terms for primary immunodeficiency diseases (PIDs). It presents controlled vocabulary of ontology class structures and entities in downloadable formats such as Web Ontology Language (OWL) and Resource Description Framework (RDF) that facilitate global sharing and free exchange of PID data among other users' communities.

RCAI Immunoinformatics Research Unit

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

The International Fanconi Anemia Registry (IFAR) was started in 1982 at The Rockefeller University by Dr. Arleen Auerbach. The purpose of the IFAR is to study the nature, diagnosis, and treatment of individuals with Fanconi anemia (FA). The IFAR group is creating an ontology-driven application for data entry and analysis. This will enable more standardized and advanced genotyping and phenotyping which will also allow us to assess any correlations between the two.

Erica Sanborn, Agata Smogorzewska, Arleen Auerbach, Francis Lach, Edward Barbour, Shamim Mollah, Sajin Balakrishnan, Ummey Johra