Bio-medical Ontologies Maintenance and Change Management

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62 A.S. Sidhu and M. Bellgard Family and Super Family of the organism in which protein is present, are represented in FunctionalDomains by reference to the generic concept of Family. FunctionalDomains describes the Cellular and Organism Source of Protein using SourceCell sub-concept, Biological Functionality of Protein using BiologicalFunction sub-concept, and describes Active Binding Sites in Protein using ActiveBindingSites sub-concept. Active Binding Sites are represented in PO as a collection of various Site Groups, defined using SiteGroup generic concept. Derived Concepts for Chemical Bonds in Proteins Various chemical bonds used to bind various substructures in a complex protein structure are defined using ChemicalBonds concept in PO. Chemical Bonds are defined by their respective sub-concepts are: DisulphideBond, CISPeptide, HydrogenBond, ResidueLink, and SaltBridge. They are defined using generic concepts of Bind and Atomic Bind. Chemical Bonds that have Binding Residues (DisulphideBond, CISPeptide) reuse the generic concept of Bind. Similarly the Chemical Bonds that have Binding Atoms (HydrogenBond, ResidueLink, and SaltBridge) reuse the generic concept of AtomicBind. Derived Concepts for Constraints affecting the Protein Structural Conformation Various constraints that affect the final protein structural conformation are defined using the Constraints concept of PO. The constraints described in PO at the moment are: Monogenetic and Polygenetic defects present in genes that are present in molecules making proteins described using GeneticDefects sub-concept, Hydrophobic properties of proteins described using Hydrophobicity sub-concept, and Modification in Residue Sequences due to changes in chemical environment and mutations are described using in ModifiedResidue sub-concept. 3.3 Relationships Protein Ontology Semantics in protein data is normally not interpreted by annotating systems, since they are not aware of the specific structural, chemical and cellular interactions of protein complexes. A Protein Ontology Framework provides a specific set of rules to cover these application specific semantics. The rules use only the relationships whose semantics are predefined in PO to establish correspondence among terms. The set of relationships with predefined semantics is: {SubClassOf, PartOf, AttributeOf, InstanceOf, and ValueOf}. The PO conceptual modeling encourages the use of strictly typed relations with precisely defined semantics. Some of these relationships (like SubClassOf, InstanceOf) are somewhat similar to those in RDF Schema (W3C-RDFSchema 2004) but the set of relationships that have defined semantics in our conceptual PO model is too small to maintain the simplicity of the model. The following is a brief description of the set of pre-defined semantic relationships in our common PO conceptual model. SubClassOf relationship is used to indicate that one concept is a specialization of another concept. AttributeOf relationship indicates that a concept is an attribute of another concept. PartOf relationship indicates that a concept is a part of another concept. InstanceOf relationship indicates that an object is an instance of the concept. ValueOf
Fig. 3. Class Hierarchy of Protein Ontology Protein Data Integration Problem 63 relationship is used to indicate the value of an attribute of an object. By themselves, the relationships described above do not impose order among the children of the node. We defined a special relationship called Sequence(s) in PO to describe and impose order in complex concepts defining Structure, Structural Folds and Domains and Chemical Bonds of Proteins.
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Amandeep S. Sidhu and Tharam S. Dil
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Amandeep S. Sidhu and Tharam S. Dil
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Preface The molecular biology commu
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Preface VII biomedical systems, and
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X Contents Mining Clinical, Immunol
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2 A.S. Sidhu, M. Bellgard, and T.S.
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Page 19 and 20: Towards Bioinformatics Resourceomes
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Bio-medical Ontologies Maintenance
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TextToOnto (Maedche and Volz 2001)
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Extraction of Constraints from Biol
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Classifying Patterns in Bioinformat
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Mining Clinical, Immunological, and
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Substructure Analysis of Metabolic
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entry compound relation subtype com
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Running Time 4500 4000 3500 3000 25
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6 Conclusion Substructure Analysis
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Completing the Total Wellbeing Puzz
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Genetic Algorithm in Ab Initio Prot
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Author Index Apiletti, Daniele 169
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Bio-medical Ontologies Maintenance and Change Management

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