Name
Title | ||
|---|---|---|
Ontology patterns for tabular representations of biomedical knowledge on neglected tropical diseases. |
Abstract | ||
|---|---|---|
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.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.Domain examples, source code and ontology are freely available on the web at http://www.cin.ufpe.br/~ntdo.fss3@cin.ufpe.br. |
Year | DOI | Venue |
|---|---|---|
2011 | 10.1093/bioinformatics/btr226 | Bioinformatics [ISMB/ECCB] |
Keywords | Field | DocType |
tabular format,biomedical domain,comprehensive design pattern,ontology-like domain knowledge,ontology pattern,neglected tropical disease,domain example,tabular content,upper level ontology,ontological domain knowledge,tabular compilation,tabular representation,biomedical knowledge,internet,programming languages,disease vectors,knowledge | Ontology (information science),Ontology,Data mining,Domain knowledge,Process ontology,Computer science,Description logic,Suggested Upper Merged Ontology,Bioinformatics,Upper ontology,Design pattern | Journal |
Volume | Issue | ISSN |
27 | 13 | 1367-4811 |
Citations | PageRank | References |
4 | 0.45 | 13 |
Authors | ||
5 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Filipe Santana | 1 | 16 | 2.10 |
| Daniel Schober | 2 | 34 | 4.56 |
| Zulma Medeiros | 3 | 6 | 0.82 |
| Fred Freitas | 4 | 165 | 26.83 |
| Stefan Schulz | 5 | 1092 | 127.03 |