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

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 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

The goal of DDI project is to develop an ontology for the description of drug discovery investigations. DDI aims to follow to the OBO (Open Biomedical Ontologies) Foundry principles, uses relations laid down in the OBO Relation Ontology, and be compliant with Ontology for biomedical investigations (OBI).

Da Qi, Larisa Soldatova, Ross King, Andrew Hopkins, Richard Bickerton

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 Integrative Tools for Protozoan Parasite Research project is using OBI to develop forms to capture structured meta-data about studies (e.g., genotyped isolates of parasites, phenotypes of transgenic parasites) for EuPathDB and to provide terms for annotating bioinformatics web services available through Galaxy.

Christian Stoeckert

The Functional Genomics Data (FGED) Society has incorporated the MGED Ontology (MO) into OBI for use in annotating functional genomics studies especially with the MAGE-TAB format.

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

ImmPort, the Immunology Database and Analysis Portal, is a one stop shop to access reference and experiment data for immunologists. ImmPort provides advanced information technology support in the production, analysis, archiving, and exchange of scientific data for the diverse community of life science researchers supported by NIAID/DAIT.

Richard H. Scheuermann, et al.

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

MeRy-B is a plant metabolomics platform allowing the storage and visualisation of Nuclear Magnetic Resonance (NMR) metabolic profiles from plants. This database is involved in the ISA commons project (isacommons.org).

Daniel Jacob, Catherine Deborde, Annick Moing

The eagle-i project is building a searchable network of research resources at research institutions nationwide. We are developing an application ontology for indexing and querying, and this effort is being guided by discussions within the ontology community aimed at promoting interoperability. We will be inventorying laboratories, services, instruments, services, reagents, organisms, persons, protocols, human studies (metadata), tissue/biological sample repositories and training opportunities. The eagle-i application ontology is being used to drive our data tool and search applications, and is available in beta form from google code: http://code.google.com/p/eagle-i/

Melissa Haendel, Carlo Torniai

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)

The Bioinformatics Web Services ontology (OBIws) is an ontology that extends the Ontology for Biomedical Investigations (OBI) to build an Ontology that supports consistent annotation of Bioinformatics Web services.

Jie Zheng, Alok Dhamanaskar

Gemma is a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles. Gemma contains data from thousands of public studies, referencing thousands of published papers. Users can search, access and visualize coexpression and differential expression results.

Dr. Paul Pavlidis

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 IEDB contains data related to antibody and T cell epitopes for humans, non-human primates, rodents, and other animal species.

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

OntoDM is a general-purpose ontology for the domain of data mining. The ontology includes the information processing processes that occur in the domain of data mining, participants in the processes and their specifications. OntoDM is highly transferable and extendable due to its adherence to accepted standards, and compliance with existing ontology resources. The generality in scope allows wide number of applications of the ontology, such as semantic annotation of data mining scenarios, ontology based support for QSARs, etc.

Pance Panov, Saso Dzeroski, Larisa Soldatova

This project will provide a public space for reviewing and commenting on the ontologies related to biodiversity information standards such as TDWG Ontology, Darwin-SW, TaxonConcept, and the Biological Collections Ontology (BCO).

Ramona Walls, John Deck

The Adverse Event Reporting Ontology (AERO) is an ontology aimed at providing logical representation of adverse events guidelines, increasing quality and accuracy of reported events.

Melanie Courtot

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.