An ontology to capture patients' and research participants' research permissions, consents and routine care permissions.

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

Terms associated with pediatrics, representing information related to child health and development from pre-birth through 21 years of age.

Ranjana Srivastava, Daniel Lyman, Ipsita Das

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

Logic-based and Scalable Ontology Matching. LogMap is a highly scalable ontology matching system with `built-in' reasoning and diagnosis capabilities. Currently, LogMap is the only matching system that can sucessfully deal with semantically rich ontologies containing tens (and even hundreds) of thousands of classes. Furthermore, LogMap is able to produce a `clean' set of output mappings in many cases. Our experiments with the ontologies NCI, FMA and SNOMED CT confirm that our system can efficiently match even the largest existing bio-medical ontologies.

Ernesto Jimenez Ruiz and Bernardo Cuenca Grau

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 Hypertrophic Cardiomyopathy (HCM) project is focused on the prognosis of HCM, i.e on the prediction of the possible outcome for individual patients. We have developed an ontology describing the clinical and genetic data elements necessary for the diagnosis and the prognosis of the disease, which is composed of three modules: Clinical Evaluation, containing concepts relative to the clinical evaluation of patients; Genotype Analysis, containing concepts relative to the genetic analysis of biological samples; and Medical Classifications, an auxiliary module containing standard clinical classifications. The HCM ontology is currently mapped to the following vocabularies: SNOMED CT, NCIt, Sequence Ontology and Gene Regulation Ontology.

Ontology alignment, the task of identifying mappings between ontologies, is a key task for knowledge sharing between applications that use different ontologies. Manual alignment is time-consuming and difficult when dealing with large ontologies, which are common in biomedical domain, while automatic alignment shows low coverage. We present a tool with user-friendly GUI for semi-automatic ontology alignment, called NViz. It helps human experts focus on pairs of ontology clusters that are likely to have missing mappings. NViz utilizes a state of-the-art system of ontology alignment, called BOAT, and a hierarchical clustering method.

Watson W.K. Chua, Jung-jae Kim, Bui Duc Hieu

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

This preliminary version of the eTMF content model ontology is designed to support clinical trial regulatory content management and eArchive exchange. Metadata terms are sourced from NCI thesaurus and from industry sources. CareLex is a non-profit organization formed to promote content interoperability for the BioPharma and Healthcare industry. For more info go to www.CareLex.Org.

Zachariah Schmidt

Adaptive EHR (AdaptEHR) is built upon a context-based framework, integrating data from different sources in the patient record and subsequently tailoring the presentation based on the contents of the patient’s clinical reports and the information needs of the user.

The International Fanconi Anemia Registry (IFAR) was started in 1982 at The Rockefeller University by Dr. Arleen Auerbach. The purpose of the IFAR is to study the nature, diagnosis, and treatment of individuals with Fanconi anemia (FA). The IFAR group is creating an ontology-driven application for data entry and analysis. This will enable more standardized and advanced genotyping and phenotyping which will also allow us to assess any correlations between the two.

Erica Sanborn, Agata Smogorzewska, Arleen Auerbach, Francis Lach, Edward Barbour, Shamim Mollah, Sajin Balakrishnan, Ummey Johra

SemGen is a software tool for automating the modular composition and decomposition of biosimulation models. It uses BioPortal web services to provide model annotators access to reference ontology terms.

Maxwell Neal, Daniel Cook, John Gennari

The Drug Interaction Knowledge Base (DIKB) is a clinically-oriented, evidence-based, knowledge base designed to support pharmacoepidemiology and clinical decision support. The DIKB contains quantitative and qualitative assertions about drug mechanisms and pharmacokinetic drug-drug interactions for over 90 drugs; primarily psychotropics and HMG-CoA reductase inhibitors (statins).

Richard D Boyce

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.