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Application of ontologies in Cancer nanotechnology research

Application of ontologies in Cancer nanotechnology research. Faculty of Engineering in Foreign Languages. Student: Andreea Buga Group: 1241E – FILS Coordinating Teacher: Maria Iuliana Dascalu. Introduction.

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Application of ontologies in Cancer nanotechnology research

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  1. Application of ontologies in Cancer nanotechnology research Faculty of Engineering in Foreign Languages Student: Andreea Buga Group: 1241E – FILS Coordinating Teacher: Maria IulianaDascalu

  2. Introduction • Scientific progress and the development of informatics systems has led to a large amount of data that has to be processed daily. • Life sciences are very important in the nowadays studies and latest discoveries are important steps to a better life in the future. • Data mining and analyzing is a very important tool in understanding life processes and establishing new theories and setting results.

  3. Problem Statement • One of the most important issues of our daily lives is finding a cure for the diseases that have started to spread and affect us more and more. • Cancer research is one the directions of study that gained importance due to the impact of the solutions proposed. • The large amount of data needed to be processed needs improved tools of classification, taxonomy and creating hierarchies.

  4. Looking deeper to ontologies • “An ontology may take a variety of forms, but necessarily it will include a vocabulary of terms, and some specification of their meaning. This includes definitions and an indication of how concepts are inter-related which collectively impose a structure on the domain and constrain the possible interpretations of terms." • Ontologies have been used in collaborative – research and working with databases in several ways.

  5. Ontologies and BioMedical Research • Biomedicine is an area containing a large vocabulary of specific terms related to diseases, symptoms, equipment, treatment, and diagnostics. • “In biomedical research, ontologies are used to represent the knowledge of a specific domain of interest in machine-processible form and to integrate experimental data that is annotated with terms from these ontologies.”

  6. More ON nanotechnology, cancer research and ontologies • Nanotechnology solutions have some advantages that may overcome the problems faced by the conventional engineering in cancer treatment and research. • The nanomaterials used in cancer research are called NP-CDTs and will be further on referred like this.

  7. More ON nanotechnology, cancer research and ontologies • Informatics methods are considered to be useful tools in the advancement of nanotechnology cancer research. • NP-CDT are very diverse and may have a wide large of applications, as studies revealed. The diversity is offered by the large number of interactions that may change the chemical composition. • Making a small change in the chemical properties of such a material will lead to generating new medicine data sets.

  8. State – of – the - art • caNanoLab Project stores, searches and shares data generated from characterization studies of nanomaterials used in cancer research. • This database needs a specific vocabulary that will allow the connection with other cancer related databases and data sharing. • Some existing vocabularies (from bioinformatics, genomics, cancer medicines) can be used to define terms needed for this area of expertise, but a specific vocabulary for cancer nanotechnologies does not exist.

  9. Use Case

  10. Proposed solution • We will analyze the solution proposed by NPO ontology • For the beginning, a specific list of terms used in nanotechnology to describe NP – CDTs is created. From this list of terms and their definition one can notice the complexity of the classes defined and related in the ontology.

  11. Proposed solution • “In general, a nanoparticle formulation consists of chemical components that can be enumerated as 1) nanoparticles, 2) active chemical constituents, which are part of the chemical makeup of the nanoparticle, and 3) active chemical components which functionalize the nanoparticle. • There can be one or more types of nanoparticle in a nanoparticle formulation, depending upon the nanoparticle structure, function or chemical composition. All of the chemical components can be described by their molecular structure, biochemical role, or function.”

  12. Proposed solution

  13. Proposed solution • The ontology has been built on the fundamentals of Basic Formal Ontology (BFO) framework and implemented in OWL using well-defined ontology principles from which we remember: • Principle of unbiased representation • Principle of asserted single “is a” inheritance • Principle of inferred multiple “is a” inheritances • Preferred name and textual definition: • Synonym • Code • Rdf ID and rdf:Label

  14. Result • The obtained results was an ontology having: • 1564 classes, • 45 object properties specifying class – level associations, • 5 OWL annotation properties (definition, synonym, code, preferred name, dBXreflId). • All the domain – specific entities are classified under the BFO classes, Entity being the top - most class.

  15. Result • A powerful inference system has been developed:

  16. Applications • It is clear that the ontology serves as an important tool in cancer nanotechnology research: diagnosis, treatments, analysis. • The application domain is wider than we can imagine. There are numerous publications and journals needed by researchers. Search results may be irrelevant and may lead to a time waste for the scientists. Such an ontology solves the search issues.

  17. Applications • NPO provides the needed terminology and enlarges the search possibilities (synonyms, search by topics, associations and relations based on the ontology). Therefore, the search can be done with knowing the details from the cancer nanotechnology area and increases inter-domains operability. • Data indexing, retrieval and integration can be done using NPO annotation. This part is an important step in data mining and knowledge discovery and will be essential in future research progress.

  18. Conclusions • NPO ontology is founded on the basis of BFO and is implemented in OWL. Knowledge embedded in this ontology is related to chemical proposition, properties, preparation of nanomaterial and it is also related to other cancer research databases. • This ontology brings new tools in establishing connections with other domains, making inferences and helping the scientists develop their current research. Knowledge-based search, logical connections, semantic integration and data mining are the first steps in future technology and they may be a key factor in the discovery of new treatments, predictions and studies related to cancer.

  19. Bibliography • M. Uschold, M. King, S. Moralee, and Y. Zorgios.  The Enterprise Ontology. ,The Knowledge Engineering Review, 13(1):31-89, 1998.  • http://www.w3.org/standards/semanticweb/inference, Inference, 09.05.2013 – 11:38 AM • Dennis G. Thomas, Rohit V. Pappu, Nathan A. Baker, Journal of Biomedical Informatics 44 (2011) 59–74,NanoParticle Ontology for cancer nanotechnology research, February 2011 • http://www.nano-ontology.org/; 09.05.2013 -1:37 PM • Data Mining in Cancer Research, Paulo J.G. Lisboa, Liverpool John Moores University, UK, IEEE COMPUTATIONAL INTELLIGENCE MAGAZINE, FEBRUARY 2010

  20. Questions

  21. Thanks you for your attention!

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