Biomedical ontologies are often very large and complex. Only a subset of the ontology may be needed for a specified application or community. For ontology end users, it is desirable to have community-based labels rather than the labels generated by ontology developers. Ontodog is a web-based system that can generate an ontology subset based on Excel input, and support generation of an ontology ...

Reference ontologies are often very large and complex. When applied to a specific application, generally a subset of one reference ontology is needed. Moreover, the labels of ontology terms that were given in the perspective of ontology developers might not be preferred labels to the end users. Therefore, it is desirable to have a community view of a reference ontology that is a subset of the o...

Progress in molecular investigations presents new data facilitating the recognition of pathogenic mechanisms of numerous nervous system diseases, among them amyotrophic lateral sclerosis (ALS). Molecular studies of ALS are mainly concentrated on genetic search, excitotoxicity and astrocytic participation, pathology of neurofilaments, apoptosis, trophic factors, and selective motoneurone degener...

seizure may occur after mild traumatic brain injury (tbi), and the severity of tbi can be considered the most crucial factor for an increased risk of recurring seizures as well as for the development of posttraumatic epilepsy. however, the effect of seizures in epileptogenesis after mild tbi cannot yet be accurately confirmed. this study was designed to determine whether mild tbi increases seiz...

The web-based Ontorat (http://ontorat.hegroup.org/) program has been developed to automatically generate and edit ontology terms from a spreadsheet format input (Excel or tab-delimited file) based on an ontology design pattern (ODP). The Ontorat web interface is intuitive and suitable for users with basic background in Manchester ontology format scripting, the same language used in the Protégé ...

There are numerous past and current examples of ontology-driven projects that provide auto-generated user interfaces for managing entities and relations, each presenting its own varied and complex data model. Our Datum Proof Sheet application aims to simplify the application development landscape by building community consensus about the way basic categorical, textual and numeric datum fields s...

We present a use case of the Ontology for Biomedical Investigations [1] (OBI) informing the software design of a suite of biobanking applications. We describe how OBI has influenced the design of the Penn Medicine BioBank applications that support the collection, processing, and storage of biobank specimens and our work in creating a robust search system over data produced by BioBank applicatio...

BACKGROUND Understanding the distinction between function and role is vexing and difficult. While it appears to be useful, in practice this distinction is hard to apply, particularly within biology. RESULTS I take an evolutionary approach, considering a series of examples, to develop and generate definitions for these concepts. I test them in practice against the Ontology for Biomedical Inves...