NanoParticle Ontology for cancer nanotechnology research

Abstract

Data generated from cancer nanotechnology research are so diverse and large in volume that it is difficult to share and efficiently use them without informatics tools. In particular, ontologies that provide a unifying knowledge framework for annotating the data are required to facilitate the semantic integration, knowledge-based searching, unambiguous interpretation, mining and inferencing of the data using informatics methods. In this paper, we discuss the design and development of NanoParticle Ontology (NPO), which is developed within the framework of the Basic Formal Ontology (BFO), and implemented in the Ontology Web Language (OWL) using well-defined ontology design principles. The NPO was developed to represent knowledge underlying the preparation, chemical composition, and characterization of nanomaterials involved in cancer research. Public releases of the NPO are available through BioPortal website, maintained by the National Center for Biomedical Ontology. Mechanisms for editorial and governance processes are being developed for the maintenance, review, and growth of the NPO.

Fig. 1

OWL object properties and the number of times they are used for asserting class-level associations in the NPO.

Fig. 2

Asserted OWL hierarchy showing the BFO-based upper-level classification of domain terms in NPO with selected examples.

Fig. 3

Asserted OWL hierarchy of a subset of NPO classes. (A) Subclasses of Nanomaterial. (B) Subclasses of Molecular Entity, and other classes representing atoms, elements, and isotopes. (C) Subclasses of Instrument. (D) Subclasses of Material Site. (E) Subclasses of Material Boundary.

Fig. 4

(A) Asserted OWL hierarchy of a subset of classes under Material Fiat Part. (B) Asserted OWL hierarchy of subclasses of Linkage. (C) An example showing how an amide linkage formed between a primary amine and a carboxylic acid are associated to the respective functional groups in the NPO.

Fig. 5

Asserted OWL hierarchy of a subset of NPO classes. (A) Subclasses of Quality. (B) Subclasses of Role, Function, and Disposition. (C) Subclasses of Unit Of Measurement. (D) Subclasses of Chemical Interaction.

Fig. 6

Asserted OWL hierarchy of a subset of NPO classes. (A) Subclasses of Antineoplastic Activity and Molecular Function. (B) Subclasses of Biological Process.

Fig. 7

Asserted OWL hierarchy of a subset of NPO classes. (A) Subclasses of Stimulus For Nanoparticle Function, Nanoparticle Response To Stimulus, and Tumor Targeting. (B) Subclasses of Study, Characterization, and Procedure.

Fig. 8

Single and multiple inheritances of subclasses of Nanotube, as shown in the asserted and inferred hierarchies, respectively.

Fig. 9

Example showing how an OWL reasoner infers parent-child relationships among Polymer-Coated Nanoparticle, Biopolymer-Coated Nanoparticle, and Dextran-Coated Nanoparticle based on their asserted associations to and based on the asserted hierarchy of Polymer, Biopolymer, and Dextran respectively.