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The Electrophysiology (EP) Ontology is part of Project 2 of the Cardiovascular Research Grid (CVRG), an NHLBI funded effort to develop a national infrastructure for managing, sharing, and analyzing a broad range of cardiac data. The EP Ontology will contain terms for describing single-channel electrophysiological experiments and data obtained using voltage-clamp, current clamp and fluorescence imaging techniques applied at the cell level and multi-channel fluorescence imaging techniques applied at the cell, tissue and whole heart levels.

Dr. Raimond L. Winslow, Stephen J. Granite

An open source ISA software suite and an extensible hierarchical data structure implemented by a growing number of international public resources. It caters to data as diverse as stem cell, toxicogenomics, environmental gene surveys, microbial diversity studies, and a variety of metabolomics and metagenomics-based studies. But it maintains cross-domain compatibility in the way the experimental context is described.

International collaborative effort

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

NEMO is developing ontologies for representation and integration of event-related brain potentials (ERPs). To support this work, we are developing an integrated tool environment for storage and management of ERP data, ontologies, and ontology-based markup and analysis of data.

NEMO core (Gwen Frishkoff, Robert Frank, Paea LePendu, Haishan Liu, Dejing Dou, Allen Malony, Jason Sydes, Nathan Dunn); NEMO ERP Consortium (Gwen Frishkoff, Tim Curran, Dennis Molfese, John Connolly, Kerry Kilborn, Chuck Perfetti)

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 BioAssay Ontology (BAO) is an NIH-funded project to develop standard terminologies and a formal, extensible, knowledge-based description of biological assays and assay data (the ontology). Biocuration is a component of the BAO project to systematically annotate biological assays such as those in PubChem with standardized terminology describing assay concepts defined in the ontology. The BAO project also develops software tools to query and explore data sets in the context of the ontology.

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