Formal ontology for natural language processing and the integration of biomedical databases

Abstract

Abstract:The central hypothesis of the collaboration between Language and Computing (L&C)

The Ecology of Ontologies in the Public Domain

“…After having identified an ontology with relevant and sufficient domain content, a user may consider applying this ontology for a specific task. For instance, in the area of natural language processing (NLP) ontologies are often used as hierarchically controlled vocabularies [4]. In such applications a series of metrics are commonly derived which seek to quantify the success of extraction of structured information content from corpora of unstructured text.…”

“…Categories of researchers interested in ontologies include philosophers, software developers, computational linguists, biologists and logicians, and their motives are varied. Much debate now focuses on the criteria by which ontologies should be evaluated [3] and this debate is often driven by the question regarding the usefulness of ontologies for applications such as support for natural language processing [4] text mining [5], annotation of genes for gene expression analysis [6], inference or knowledge discovery in general, the facilitation of data integration [7], providing cornerstones of the Semantic Web [8], and as educational resources [9] There is however general agreement that Ontologies can serve as portable and easily exploitable conceptualizations for use in a multitude of computational applications. This has lead to an increase in the creation of ontologies and the emergence of a new generation of computational ontologists.…”

The open source ISA software suite and its international user community: knowledge management of experimental data

“…Our methodology relies on the definition of mapping files, aligning the ISA terminology with existing domain ontologies. A noteworthy mapping is that between ISA and the Ontology of Biomedical Investigations (OBI) (Brinkman et al 2010), which in turn is built in the Basic Formal Ontology (BFO) framework (Simon et al, 2006). Given such mapping, ISA-Tab datasets are parsed to populate the ontology, following Linked Data best practices such as the five star scheme whereby data is made available on the web in a structured non-proprietary format using URIs for identifying elements and linking to other data to provide context (Heath and Bizer 2011).…”

Causality and the ontology of disease

“…Some widely used philosophical categories and distinctions, including the universal-particular distinction (Simon et al, 2006) are adopted. Similarity and generality have historically been distinguished from particularity, the former being described using the notion of universals (categories, kinds, types, classes), the latter with particulars (individuals, tokens, instances).…”