The Neuroscience Information Framework (NIF; http://nif.nih.gov) is a dynamic inventory of Web-based neuroscience resources, data, and tools accessible via any computer connected to the Internet. An initiative of the NIH Blueprint for Neuroscience Research, NIF advances neuroscience research by enabling discovery and access to public research data and tools worldwide through an open source, networked environment. The NIF project is designed to serve the biomedical research community. The more participation from the community, the better the NIF. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through the NIF. We offer a variety of methods for making resources searchable through the NIF. For more information or to recommend a resource, follow the link to Register Your Resource, or send us an e-mail at curation@neuinfo.org. Collaborating institutions working on the current version of NIF include University of California, San Diego, California Institute of Technology, George Mason University, Yale University Medical College, and Washington University.

Maryann Martone, Jeffrey Grethe, Amarnath Gupta, Gordon Shepherd, Giorgio Ascoli, Paul Sternberg, David Van Essen

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 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