Download ON nanotechnology, cancer research and ontologies - Maria

Faculty of Engineering in Foreign Languages
APPLICATION OF ONTOLOGIES
IN CANCER NANOTECHNOLOGY
RESEARCH
Student: Andreea Buga
Group: 1241E – FILS
Coordinating Teacher: Maria Iuliana Dascalu
1
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.
2
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.
3
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.
4
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 machineprocessible form and to integrate
experimental data that is annotated
with terms from these ontologies.”
5
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.
6
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.
7
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.
8
USE CASE
Chemist has
synthesized a
dextran-coated
nanoparticle
If the descriptor is type
of coating material, it
will help identify the
highly correlated
classes of
nanoparticles that are
either the sibling
classes or child classes
of dextran-coated
nanoparticles.
s/he plans to compare it
with nanoparticles from
data available in a
database such as
caNanoLab
These
descriptors can
be provided by
the ontology.
The researcher only
needs to look at
nanoparticle data
annotated with the
ontology classes,
The researcher must
identify that
nanoparticle that most
closely correlates with
the dextran-coated
nanoparticle
The researcher must
know what
descriptors to choose
for comparing the
nanoparticles
and compare results of
different nanoparticles
identified from the
classification in the
ontology.
9
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.
10
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.”
11
PROPOSED SOLUTION
12
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
13
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.
14
RESULT
• A powerful inference system has been developed:
15
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.
16
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.
17
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.
18
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
19
Questions
20
Thanks you for your
attention!
21