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. 2011 Jun 15;27(12):1684-90.
doi: 10.1093/bioinformatics/btr256. Epub 2011 May 5.

PLIO: an ontology for formal description of protein-ligand interactions

Olga Ivchenko  1 , Erfan Younesi, Mohammad Shahid, Antje Wolf, Bernd Müller, Martin Hofmann-Apitius
Affiliations

PLIO: an ontology for formal description of protein-ligand interactions

Olga Ivchenko et al. Bioinformatics. .

Abstract

Motivation: Biomedical ontologies have proved to be valuable tools for data analysis and data interoperability. Protein-ligand interactions are key players in drug discovery and development; however, existing public ontologies that describe the knowledge space of biomolecular interactions do not cover all aspects relevant to pharmaceutical modelling and simulation.

Results: The protein--ligand interaction ontology (PLIO) was developed around three main concepts, namely target, ligand and interaction, and was enriched by adding synonyms, useful annotations and references. The quality of the ontology was assessed based on structural, functional and usability features. Validation of the lexicalized ontology by means of natural language processing (NLP)-based methods showed a satisfactory performance (F-score = 81%). Through integration into our information retrieval environment we can demonstrate that PLIO supports lexical search in PubMed abstracts. The usefulness of PLIO is demonstrated by two use-case scenarios and it is shown that PLIO is able to capture both confirmatory and new knowledge from simulation and empirical studies.

Availability: The PLIO ontology is made freely available to the public at http://www.scai.fraunhofer.de/bioinformatics/downloads.html.

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Figures

Fig. 1.
Fig. 1.
Top-level classes of PLIO. Root classes and the type of their relations are depicted.
Fig. 2.
Fig. 2.
The concept ‘binding activity’ was included in PLIO to characterise the features that are important for ligand activity against a certain biological target.
Fig. 3.
Fig. 3.
The ontology concept ‘Ki’ (equilibrium dissociation constant) annotated with its mathematical formula and web services.
See this image and copyright information in PMC

References

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