The Influenza Ontology is an application ontology covering the numerous aspects if influenza virus basic research, and surveillance. The influenza ontology extends the Infectious Disease Ontology (IDO).

Burke Squires, Lynn Schriml, Joanne Luciano

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

The Blood Ontology is a set of co-related ontologies being created to gather and represent data about blood according to well-founded ontological principles.

HTLV Interdisciplinar Research Group

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

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

A Web service that tags free text with ontology concepts. NCBO uses these Web services to annotate resources in the NCBO Resource Index to create an ontology index of these resources. This Web service can be accessed through BioPortal or used directly in your software. Currently, the annotation workflow is based on syntactic concept recognition (using concept names and synonyms) and on a set of semantic expansion algorithms that leverage the semantics in ontologies (e.g., is_a relations). Our service methodology leverages ontologies to create annotations of raw text and returns them using semantic web standards.

NCBO

The Epidemic Marketplace is a data integration platform where epidemiological data and related resources are stored, managed and made available, fostering collaboration.

Database and analysis resource for human pathogenic viruses, including sequence, surveillance and host response data.

Richard H. Scheuermann, et al.

The mission of the Influenza Research Database (IRD) is to provide a resource for the influenza virus research community that will facilitate an understanding of the influenza virus and how it interacts with the host organism, leading to new treatments and preventive actions. This resource will contain avian and non-human mammalian influenza surveillance data, human clinical data associated with virus extracts, phenotypic characteristics of viruses isolated from extracts, and all genomic and proteomic data available in public repositories for influenza viruses. The resource will link host surveillance and clinical data to sequence and phenotypic data for all well characterized influenza virus strains. Data obtained from public data sources for well characterized virus strains will be supplemented with IRD generated data. The IRD will provide a suite of tools for analysis of all types of influenza data and a personal work bench on which each scientist can store lists of important data selected from that available on IRD.

Richard H. Scheuermann, et al.