Title: Ontological%20Model%20for%20Colon%20Carcinoma:%20A%20Case%20Study%20for%20Knowledge%20Representation%20in%20Clinical%20Bioinformatics
1Ontological Model for Colon Carcinoma A Case
Study for Knowledge Representation in Clinical
Bioinformatics
O N C O L O G Y O N T O L O G Y
- Kumar A1,2, Yip L3, Jaremek M2, Scheib H3
- 1IFOMIS, University of Saarland, Germany
- 2Ludwig-Maximilians Universität, München, Germany
- 3Swiss Institute for Bioinformatics, Geneva,
Switzerland
2How the two worlds meet?
O N C O L O G Y O N T O L O G Y
Clinical
Specific disease topics E-Health, Health support
system Patient Management Patient health education
?
Molecular Biology
Biomedical Information on the Web Swiss-Prot,
Swiss-Prot Variant pages Proteins, mutations,
functions and structures
3How the two worlds meet?
O N C O L O G Y O N T O L O G Y
- Diseases
- Pathological Processes
- Body site for diseases
- Diseases by staging
- Risk factors
SNOMED
- Anatomy
- Is-a, part-of
- Granular relationship
FMA
- Biological Processes
- Ontology
- Classification
GO
- Swiss-Prot proteins
- Annotation function, structure, mutation
4How the two worlds meet?
O N C O L O G Y O N T O L O G Y
Disease schema
Protein 3D models
Swiss-Prot entries
ModSNP database
5What is Protégé?
O N C O L O G Y O N T O L O G Y
- Frame based system Allows formation of
class-subclass relations, provides support for
other relations between classes, compatible with
OWL, XML, database standards - Support for various types of visualizations
Graphical, Web-based - Support for import/export
- Support for reasoning Description Logic based
- Can give outputs in various formats
- Difficulties with input
6Disease Representation
O N C O L O G Y O N T O L O G Y
- Disease classification based on Snomed CT
- Various aspects considered for classification
(currently present in the form of multiple
inheritance) - Added from textbooks (deVita Principles of
Oncology and Harrison Principles of Internal
medicine) - Staging of diseases (TNM, Dukes, Modified
Asler-Coller) - Screening (Patients screened based on their level
of risk) - Risk factors
- Localization
- Pathology
- To be added Pharmacotherapeutics, Symptoms and
Signs
7Anatomical and Histological Representation
O N C O L O G Y O N T O L O G Y
- Anatomy of colon represented at Organ system,
Organ, Tissue, Cell and Subcellular levels of
granularity (Foundational Model of Anatomy) - Gene Ontologys Cellular Component axis situated
within the FMA axis - Gross pathology mapped to the Carcinoma location
- Information regarding Clinical procedures,
Carcinoma extent, Vascular invasion, Histological
pathology being added - Extensions being done to add relations like
is-located-in, is-surrounded-by, etc. to make the
anatomical representation deducible
8Interlink between disease, LocusLink, Swiss-Prot,
GO annotations
O N C O L O G Y O N T O L O G Y
Colon cancer/Colon carcinoma
LocusLink
SwissProt
Gene Ontology
9Gene Ontology
O N C O L O G Y O N T O L O G Y
- Association rules found considering the Gene
Ontology annotations of SWISSPROT proteins - Gene Ontology consists of three axes
- Cellular Component
- Molecular Function
- Biological Processes
- Association between GO terms were established on
the basis of these annotations - Database-based approach
- Apriori-algorithm based approach
- Dependency relations based on POS tagger
10Levels of granularity
O N C O L O G Y O N T O L O G Y
- Levels of granularity in human body
- Organism
- Organ system
- Cardinal body parts
- Organ
- Organ part
- Tissues
- Cells
- Subcellular organelles
- Molecules
- Atoms
- Fundamentals behind the levels of granularity
- Grains, Structure, Origin
11Results
O N C O L O G Y O N T O L O G Y
12Results (Apriori)
O N C O L O G Y O N T O L O G Y
- Support and Confidence are defined
- ribosome lt- ribosome biogenesis protein
biosynthesis (0.2, 93.2) - This rule says that there are 0.2 of the total
annotations, put together ribosome biogenesis and
protein biosynthesis, of which 93.2 (i.e. 82)
are also annotated with the term ribosome. - Formal ontological relationsapplied between the
entities, which would help to have deductions
has spatial projection, processual part of,
facilitates, mediates, perpetrates
13Relations to biological pathways
O N C O L O G Y O N T O L O G Y
- Pathway resources KEGG, PATH, GenePath
- Protein interaction database resources DIP,
BIND, PiP, IntAct - Links to these databases possible through
Swissprot and GO annotations - Associations found within GO annotations parallel
the pathways and protein interactions (under
verification) - Text mining resources being considered
14Ontological Model for Colon Carcinoma A Case
Study for Knowledge Representation in Clinical
Bioinformatics
O N C O L O G Y O N T O L O G Y
- Kumar A1,2, Yip L3, Jaremek M2, Scheib H3
- 1IFOMIS, University of Saarland, Germany
- 2Ludwig-Maximilians Universität, München, Germany
- 3Swiss Institute for Bioinformatics, Geneva,
Switzerland