Ontology patterns for tabular representations of biomedical knowledge on neglected tropical diseases.
Bioinformatics
; 27(13): i349-56, 2011 Jul 01.
Article
em En
| MEDLINE
| ID: mdl-21685092
MOTIVATION: Ontology-like domain knowledge is frequently published in a tabular format embedded in scientific publications. We explore the re-use of such tabular content in the process of building NTDO, an ontology of neglected tropical diseases (NTDs), where the representation of the interdependencies between hosts, pathogens and vectors plays a crucial role. RESULTS: As a proof of concept we analyzed a tabular compilation of knowledge about pathogens, vectors and geographic locations involved in the transmission of NTDs. After a thorough ontological analysis of the domain of interest, we formulated a comprehensive design pattern, rooted in the biomedical domain upper level ontology BioTop. This pattern was implemented in a VBA script which takes cell contents of an Excel spreadsheet and transforms them into OWL-DL. After minor manual post-processing, the correctness and completeness of the ontology was tested using pre-formulated competence questions as description logics (DL) queries. The expected results could be reproduced by the ontology. The proposed approach is recommended for optimizing the acquisition of ontological domain knowledge from tabular representations. AVAILABILITY AND IMPLEMENTATION: Domain examples, source code and ontology are freely available on the web at http://www.cin.ufpe.br/~ntdo. CONTACT: fss3@cin.ufpe.br.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Doenças Parasitárias
/
Doenças Negligenciadas
/
Terminologia como Assunto
Limite:
Animals
/
Humans
Idioma:
En
Revista:
Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2011
Tipo de documento:
Article
País de afiliação:
Brasil
País de publicação:
Reino Unido