Bgee is a database to compare expression patterns between animals. We create homology relationships between anatomical ontologies, and store this information in a multi-species ontology. On the download page of Bgee, you will find the Homologous Organ Group ontology, the developmental Stages ontology, and the Homolonto software for ontology alignment.

Robinson-Rechavi lab

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

A web-based environment that discovers ontological structure from empirical data.

Elissa Chesler, Erich Baker, Michael Langston, Jeremy Jay

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

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

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

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