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

SEEK is the SysMO Assets Catalogue. It contains information about who holds what data, models, protocols and expertise, and where those assets are held. The SEEK is the main web-based access point to the system and provides an access control layer to enable researchers to restrict access to collaborators, colleagues or other individuals until they are ready to share with the whole consortium or the wider community.

Stuart Owen, Katy Wolstencroft, Olga Krebbs, Quyen Nguyen, Franco du Preeze, Jacky Snoep, Carole Goble

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

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

XEML Lab has been created to assist plant biologists in designing and documenting simple or sophisticated experiments in a machine readable format, to link this metadata with any type of data generated in the corresponding experiments, and ultimately, to make both metadata and data available for data mining.

Chemical biology resource providing biological activities of small molecules and substances.

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.