Ontology-based knowledge representation for bioinformatics

Abstract

Much of biology works by applying prior knowledge ('what is known') to an unknown entity, rather than the application of a set of axioms that will elicit knowledge. In addition, the complex biological data stored in bioinformatics databases often require the addition of knowledge to specify and constrain the values held in that database. One way of capturing knowledge within bioinformatics applications and databases is the use of ontologies. An ontology is the concrete form of a conceptualisation of a community's knowledge of a domain. This paper aims to introduce the reader to the use of ontologies within bioinformatics. A description of the type of knowledge held in an ontology will be given.The paper will be illustrated throughout with examples taken from bioinformatics and molecular biology, and a survey of current biological ontologies will be presented. From this it will be seen that the use to which the ontology is put largely determines the content of the ontology. Finally, the paper will describe the process of building an ontology, introducing the reader to the techniques and methods currently in use and the open research questions in ontology development.

Designing an Ontology Tool for the Unification of Biofilms Data

“…-BO is restricted to the biofilm knowledge domain and, therefore, it contains just model concepts and relations that are relevant to the representation of biofilm data; -BO should be used for annotating data in databases and for textual documentation as such, it should be understandable to people and unambiguously interpreted by software; -BO development should be pragmatic, that is as new devices, techniques or applications arise, it should be possible to integrate new branches without affecting the existent ontology structure; -any biofilm experiment should be comprehensively described by a combination of BO instances; -whenever possible, terms should have a synonyms list to avoid misinterpretations and to enable consistent data curation and repositories searching; Then, BO development followed the typical ontology life-cycle previously described [7]. The purpose and scope of the ontology were well identified and centred on the Biofilm domain, following MIABiE directives.…”

Ontology Update in the Cognitive Model of Ontology Learning

“…Ontology as an effective semantic modelling method has been widely used not only in the Semantic Web [1][2], Knowledge Base [3], E-commerce [4], Information Retrieval [5] and Digital Library [6], but also in many reasoning-based fields such as bio information and medicine information analysis [7][8] fields.…”

Reasoning on Dynamically Built Reasoning Space with Ontology Modules

“…The use of ontologies to formally describe a domain has been adopted by applications in various areas like bioinformatics [1,12,13], business [14,15], transportation [16,17] etc.. Such increasing interest on ontologies to support all kinds of web related and web agnostic applications do not, however, point to a future global and uniform ontology [18] but rather to a set of autonomously specified ones.…”