This document outlines a method for modeling structured domains like molecules and chemical entities using description graphs and logic programming. It discusses limitations of representing cyclic structures like chemical rings in OWL and proposes an extension called Description Graph Logic Programs (DGLPs) that uses description graphs and logic programming semantics. DGLPs provide an expressive yet decidable logic-based formalism that can represent all cycles using a closed-world assumption, addressing issues in modeling domains with complex interconnected structures in OWL.
Classifying Chemicals with Description Graphs and Logic ProgrammingDespoina Magka
OWL 2 is widely used to describe complex objects such as chemical molecules; however, OWL 2 axioms cannot represent `structural' features of chemical entities such as having a ring. A combination of OWL 2, rules and \emph{description graphs} (DGs) has been suggested as a possible solution, but an attempt to apply this formalism in a chemical Semantic Web application has revealed several drawbacks. Based on this experience, we present a radically different approach to modelling complex objects via a novel formalism that we call Description Graph Logic Programs. At the syntactic level, our approach combines DGs, rules, and OWL 2 RL axioms, but we give semantics to our formalism via a translation into logic programs interpreted under stable model semantics. The result is an expressive formalism that is well suited for modelling objects with complex structure, that captures the OWL 2 RL profile, and that thus fits naturally into the Semantic Web landscape. Additionally, we test the practical feasibility of our approach by means of a prototypical implementation which provides encouraging results.
Ontology-Based Classification of Molecules: a Logic Programming ApproachDespoina Magka
We describe a prototype that performs structure-based classification of molecular structures. The software we present implements a sound and com- plete reasoning procedure of a formalism that extends logic programming and builds upon the DLV deductive databases system. We capture a wide range of chemical classes that are not expressible with OWL-based formalisms such as cyclic molecules, saturated molecules and alkanes. In terms of performance, a no- ticeable improvement is observed in comparison with previous approaches. Our evaluation has discovered subsumptions that are missing from the the manually curated ChEBI ontology as well as discrepancies with respect to existing subclass relations. We illustrate thus the potential of an ontology language which is suit- able for the Life Sciences domain and exhibits an encouraging balance between expressive power and practical feasibility.
This document discusses various methods for dating fossils and archaeological samples, including relative dating techniques that rely on the position of artifacts in stratigraphic layers, as well as absolute dating using radioactive isotopes. It describes how radioactive dating works by measuring the decay of isotopes with known half-lives, like carbon-14, in organic materials. Examples are given of formulas to calculate ages from radioactive dating. Limitations are noted, such as applicability only to certain materials and accuracy of instruments. Lists of human evolution fossils and radioactive isotopes are also included.
Carbon is the basis of life and is constantly recycled through various processes. It can take many forms, including diamond and graphite, and is the fourth most abundant element in the universe. Carbon dioxide emissions contribute to global warming, so industries aim to reduce their carbon footprint by decreasing food miles, the distance food travels from farm to plate. The carbon cycle describes how carbon is exchanged between the atmosphere, ocean, living things and non-living things through various natural processes.
This document provides an overview of organic chemistry. It begins by discussing how organic chemistry emerged as a field after Friedrich Wöhler synthesized urea in 1828, disproving the vitalist theory that organic compounds could only be produced in living organisms. The document then outlines the key topics in organic chemistry, including hydrocarbons, hydrocarbon derivatives, and important organic compounds found in living things like proteins, carbohydrates, and fats. It provides examples of simple hydrocarbon molecules like methane and ethene to illustrate carbon-carbon single, double and triple bonds. The summary discusses the four main classes of hydrocarbons - alkanes, alkenes, alkynes, and aromatic hydrocarbons - and how alkane names
This document provides an overview of photosynthesis. It begins by outlining the learning objectives, which include understanding that energy can change forms, defining photosynthesis, and explaining the processes that occur in the chloroplast. The document then defines photosynthesis as a process where plants use sunlight, water and carbon dioxide to produce glucose. It explains that photosynthesis is important as it produces organic molecules and oxygen, and forms the basis of food chains. The document provides details on the light-dependent and light-independent reactions, and describes the structures involved like chloroplasts, thylakoids and pigments. It outlines the absorption of light by chlorophyll and movement of electrons, and explains how ATP and NADPH are produced to ultimately fix carbon
This document discusses various methods for dating fossils and rocks, including carbon-14 dating and radioisotope dating. It explains how these methods work, such as by measuring the ratio of carbon-12 to carbon-14 in a sample. However, it notes that all of these dating methods rely on assumptions, like the starting conditions and decay rates having always remained constant, that are difficult to prove and have been shown to be inaccurate at times by experiments. Therefore, the ages provided by these dating methods are not completely reliable and should be interpreted with caution.
Mike Riddle has put together a brilliant slideshow examining the truths and misnomers of dating methods currently used by scientists eager to propogate their evolutionary agenda. I hope you enjoy Mr. Riddle's slidshow as much as I have.
Classifying Chemicals with Description Graphs and Logic ProgrammingDespoina Magka
OWL 2 is widely used to describe complex objects such as chemical molecules; however, OWL 2 axioms cannot represent `structural' features of chemical entities such as having a ring. A combination of OWL 2, rules and \emph{description graphs} (DGs) has been suggested as a possible solution, but an attempt to apply this formalism in a chemical Semantic Web application has revealed several drawbacks. Based on this experience, we present a radically different approach to modelling complex objects via a novel formalism that we call Description Graph Logic Programs. At the syntactic level, our approach combines DGs, rules, and OWL 2 RL axioms, but we give semantics to our formalism via a translation into logic programs interpreted under stable model semantics. The result is an expressive formalism that is well suited for modelling objects with complex structure, that captures the OWL 2 RL profile, and that thus fits naturally into the Semantic Web landscape. Additionally, we test the practical feasibility of our approach by means of a prototypical implementation which provides encouraging results.
Ontology-Based Classification of Molecules: a Logic Programming ApproachDespoina Magka
We describe a prototype that performs structure-based classification of molecular structures. The software we present implements a sound and com- plete reasoning procedure of a formalism that extends logic programming and builds upon the DLV deductive databases system. We capture a wide range of chemical classes that are not expressible with OWL-based formalisms such as cyclic molecules, saturated molecules and alkanes. In terms of performance, a no- ticeable improvement is observed in comparison with previous approaches. Our evaluation has discovered subsumptions that are missing from the the manually curated ChEBI ontology as well as discrepancies with respect to existing subclass relations. We illustrate thus the potential of an ontology language which is suit- able for the Life Sciences domain and exhibits an encouraging balance between expressive power and practical feasibility.
This document discusses various methods for dating fossils and archaeological samples, including relative dating techniques that rely on the position of artifacts in stratigraphic layers, as well as absolute dating using radioactive isotopes. It describes how radioactive dating works by measuring the decay of isotopes with known half-lives, like carbon-14, in organic materials. Examples are given of formulas to calculate ages from radioactive dating. Limitations are noted, such as applicability only to certain materials and accuracy of instruments. Lists of human evolution fossils and radioactive isotopes are also included.
Carbon is the basis of life and is constantly recycled through various processes. It can take many forms, including diamond and graphite, and is the fourth most abundant element in the universe. Carbon dioxide emissions contribute to global warming, so industries aim to reduce their carbon footprint by decreasing food miles, the distance food travels from farm to plate. The carbon cycle describes how carbon is exchanged between the atmosphere, ocean, living things and non-living things through various natural processes.
This document provides an overview of organic chemistry. It begins by discussing how organic chemistry emerged as a field after Friedrich Wöhler synthesized urea in 1828, disproving the vitalist theory that organic compounds could only be produced in living organisms. The document then outlines the key topics in organic chemistry, including hydrocarbons, hydrocarbon derivatives, and important organic compounds found in living things like proteins, carbohydrates, and fats. It provides examples of simple hydrocarbon molecules like methane and ethene to illustrate carbon-carbon single, double and triple bonds. The summary discusses the four main classes of hydrocarbons - alkanes, alkenes, alkynes, and aromatic hydrocarbons - and how alkane names
This document provides an overview of photosynthesis. It begins by outlining the learning objectives, which include understanding that energy can change forms, defining photosynthesis, and explaining the processes that occur in the chloroplast. The document then defines photosynthesis as a process where plants use sunlight, water and carbon dioxide to produce glucose. It explains that photosynthesis is important as it produces organic molecules and oxygen, and forms the basis of food chains. The document provides details on the light-dependent and light-independent reactions, and describes the structures involved like chloroplasts, thylakoids and pigments. It outlines the absorption of light by chlorophyll and movement of electrons, and explains how ATP and NADPH are produced to ultimately fix carbon
This document discusses various methods for dating fossils and rocks, including carbon-14 dating and radioisotope dating. It explains how these methods work, such as by measuring the ratio of carbon-12 to carbon-14 in a sample. However, it notes that all of these dating methods rely on assumptions, like the starting conditions and decay rates having always remained constant, that are difficult to prove and have been shown to be inaccurate at times by experiments. Therefore, the ages provided by these dating methods are not completely reliable and should be interpreted with caution.
Mike Riddle has put together a brilliant slideshow examining the truths and misnomers of dating methods currently used by scientists eager to propogate their evolutionary agenda. I hope you enjoy Mr. Riddle's slidshow as much as I have.
1. The reaction between manganese dioxide (MnO2) and hydrochloric acid (HCl) is represented by the equation: MnO2 + 4HCl → MnCl2 + 2H2O + Cl2.
2. In the reaction, hydrochloric acid (HCl) is oxidized while manganese dioxide (MnO2) is reduced.
3. Manganese dioxide (MnO2) acts as the oxidizing agent by accepting electrons, while hydrochloric acid (HCl) acts as the reducing agent by donating electrons.
This document provides an overview of different chapters of fundamentals of chemistry. It defines key terms like biochemistry, industrial chemistry, nuclear chemistry and organic chemistry. It also discusses classification of substances as elements, compounds and mixtures. Examples are provided to differentiate between homogeneous and heterogeneous mixtures. Concepts like empirical formula, molecular formula, atomic mass unit and mole are explained. Mass to mole conversions are demonstrated through examples.
This document discusses the physical states of matter and properties of gases, liquids and solids. It addresses questions about diffusion rates, gas compressibility, pressure units and conversions, gas laws, phase changes, and properties of different states of matter. Key points covered include that gases diffuse more rapidly than liquids due to lower density and weaker intermolecular forces, gases are compressible due to empty spaces between molecules, and the definitions of various pressure units.
This document is an assessment schedule for a 2011 NCEA Level 1 Science test covering aspects of acids and bases. It provides the evidence statements and scoring criteria for four multi-part questions on the test. For each question, it describes the key points of information required for a response to be scored at the Achievement, Merit, or Excellence levels. Correct explanations relating subatomic particle arrangements and charges to ion formations are needed for top scores. The document also provides example answers and equations for acid-base reactions.
This document discusses periodic trends in atomic and ionic properties, including:
- Atomic and ionic radii decrease across a period as effective nuclear charge increases. Radii increase down a group as principal quantum number increases.
- Ionization energies generally increase across a period as it becomes more difficult to remove electrons. Exceptions include group 2A and 5A having higher energies than 3A and 6A respectively within periods.
- Cations have smaller radii than their parent atoms as electrons are removed. Anions have larger radii as more electrons are gained. Isotectronic ions with more protons have smaller radii.
Introduction of University Chemistry Syllabus B. Sc.-III (Sem-VI) Session 202...pramod padole
This PowerPoint presentation introduces the B.Sc. Sem-VI chemistry syllabus at Shri Shivaji Science College in Amravati, India. It covers 6 units: inorganic chemistry, organic chemistry, physical chemistry, and elementary quantum mechanics. The inorganic chemistry units cover topics like kinetics of metal complexes, analytical chemistry techniques like spectroscopy and chromatography. The organic chemistry units cover spectroscopy techniques like electronic, infrared, and NMR spectroscopy and mass spectrometry. The physical chemistry units cover elementary quantum mechanics, electrochemistry, and nuclear chemistry.
This module discusses exponential functions and their applications to problems involving population growth, radioactive decay, and compound interest. It provides examples of solving problems involving exponential growth and decay. Students are expected to learn how to model situations exhibiting constant growth or decay rates using exponential functions and use the half-life formula to determine the amount of radioactive substance remaining after a given number of half-lives. The module contains practice problems for students to solve involving exponential growth, decay, and half-lives.
Introduction of University Chemistry Syllabus of B. Sc.-Part-I (Sem-II) by Dr...pramod padole
This document provides an overview of the B.Sc. Part I Semester II chemistry syllabus taught by Dr. Pramod R. Padole at Shri Shivaji Science College in Amravati, India. The syllabus covers inorganic chemistry, organic chemistry, and physical chemistry units. For inorganic chemistry, the units cover topics like polarization, covalent bonding, acids and bases, p-block elements, noble gases, and non-aqueous solvents. The organic chemistry units discuss alkenyl halides, aryl halides, alcohols, phenols, ethers, and epoxides. Finally, the physical chemistry units focus on physical properties and molecular structure, and chemical kinetics.
Carbon 14 and archeological ages, Christian and Intelligent Design discussion of source, measurement, results, interpretation, and errors in Carbon-14 dating.
Organic chemistry is a chemistry subdiscipline involving the scientific study of the structure, properties, and reactions of organic compounds and organic materials, i.e., matter in its various forms that contain carbon atoms.
Organic compounds can be classified based on their functional groups. Members of the same homologous series have similar chemical properties and their physical properties change gradually with increasing carbon chain length. Key factors that affect the physical properties of organic compounds include the structure of the functional group, length of carbon chains, and ability to form hydrogen bonds or dipole-dipole interactions. Non-polar compounds have lower boiling points than polar compounds due to weaker intermolecular forces.
This document provides an introduction to organic chemistry. It discusses that organic chemistry is the study of carbon compounds and their structures and reactions. Over 16 million carbon compounds are known. Carbon can form stable chains and rings due to its strong single and double bonds. Functional groups are atoms or groups that are involved in characteristic chemical reactions. Hydrocarbons only contain carbon and hydrogen, and homologous series differ by CH2 units. Isomers have the same molecular formula but different structures. The document also discusses alkenes, alkynes and alkyl halides.
The document provides an introduction to organic chemistry. It begins by discussing the history of organic chemistry and how vitalism led early scientists to distinguish between organic and inorganic compounds. It then outlines some key objectives of the lesson, including recognizing important scientists in the development of organic chemistry, understanding organic chemical compounds, and differentiating between organic compound types and isomers. The document proceeds to define organic chemistry as the study of carbon compounds and explains why carbon is uniquely suited to form complex molecules through covalent bonding.
Chemistry is important in biology because the structure and function of living things are governed by chemical laws. All living things are composed of six main elements: carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur. Atoms of these elements form bonds and combine to create molecules and compounds through chemical reactions. Carbon is unique in that it can form four bonds, allowing it to make complex molecules with different shapes that are essential for life.
This document provides an introduction to organic chemistry, including:
- Definitions of organic and inorganic compounds
- Empirical, molecular, and structural formulas and how to determine them
- Functional groups and homologous series that classify organic molecules
- Primary, secondary, tertiary classifications of carbon atoms and related groups
- Types of isomerism including structural, stereoisomerism, and examples of each
Organic chemistry is the study of carbon compounds. Carbon forms strong covalent bonds and can form long chains and rings, resulting in a vast number of possible structures. Organic molecules are classified based on their functional groups, such as alkanes (no functional group), alkenes (C=C double bond), and haloalkanes (halogen atom attached to carbon). Isomers are compounds with the same molecular formula but different structures, including positional isomers (functional group in a different position), chain isomers (different carbon skeleton arrangement), and functional isomers (different functional groups). Nomenclature involves naming compounds based on the parent chain, functional groups, and location of any branches.
Organic chemistry is the study of carbon-containing compounds. It was originally thought that compounds found in living things were fundamentally different than non-living compounds, but we now know this is not true. Organic structures can be represented using condensed or skeletal structures, assuming carbons and hydrogens are present. Common organic reactions include substitution, elimination, and addition reactions. Substitution reactions involve replacing one group with another. The SN2 substitution reaction proceeds in one step with simultaneous attack of the nucleophile and departure of the leaving group. This results in inversion of configuration at any chiral centers.
Organic chemistry is the study of carbon compounds. The document introduces organic chemistry, discussing the history and key figures in the field. It describes the properties of carbon that allow it to form many different compounds and categorizes the main types and sources of organic compounds, including naturally occurring, synthetic, and invented compounds. Organic compounds have applications in areas like medicine, pesticides, dyes, plastics, and more.
This document provides an introduction to organic chemistry, including definitions of organic compounds, differences between organic and inorganic compounds, and key concepts. It discusses the early history when vitalism prevented the synthesis of organic compounds. Friedrich Wöhler was the first to synthesize an organic compound in a laboratory. The document also outlines types of organic compounds like hydrocarbons, and how they are named according to IUPAC rules. Carbon properties and different hybridizations that allow multiple bonds are covered.
This document provides an introduction to organic chemistry, including definitions of key terms and concepts. It discusses:
- The early history of organic chemistry and the discovery that organic compounds could be synthesized in the lab.
- The main differences between organic and inorganic compounds in terms of their properties and bonding.
- The central role of carbon atoms in organic compounds and their ability to form chains and complex structures through catenation.
- The different classes of hydrocarbons including alkanes, alkenes, alkynes, aromatics, and their IUPAC naming conventions.
- Important organic functional groups derived from hydrocarbons like alkyl halides, alcohols, ethers, al
Organic chemistry is the study of carbon-containing compounds that are extremely important to life. Our bodies, medicines, fuels, plastics and many other materials are made of organic compounds. Carbon can form diverse compounds because it can form various bonds to itself and other elements. The structure and bonding of organic molecules determines their properties. Key groups like alcohols, ethers, carboxylic acids and esters impact a molecule's chemistry. There are several families of hydrocarbons including alkanes, alkenes and aromatics whose formulas vary based on saturation.
1. The reaction between manganese dioxide (MnO2) and hydrochloric acid (HCl) is represented by the equation: MnO2 + 4HCl → MnCl2 + 2H2O + Cl2.
2. In the reaction, hydrochloric acid (HCl) is oxidized while manganese dioxide (MnO2) is reduced.
3. Manganese dioxide (MnO2) acts as the oxidizing agent by accepting electrons, while hydrochloric acid (HCl) acts as the reducing agent by donating electrons.
This document provides an overview of different chapters of fundamentals of chemistry. It defines key terms like biochemistry, industrial chemistry, nuclear chemistry and organic chemistry. It also discusses classification of substances as elements, compounds and mixtures. Examples are provided to differentiate between homogeneous and heterogeneous mixtures. Concepts like empirical formula, molecular formula, atomic mass unit and mole are explained. Mass to mole conversions are demonstrated through examples.
This document discusses the physical states of matter and properties of gases, liquids and solids. It addresses questions about diffusion rates, gas compressibility, pressure units and conversions, gas laws, phase changes, and properties of different states of matter. Key points covered include that gases diffuse more rapidly than liquids due to lower density and weaker intermolecular forces, gases are compressible due to empty spaces between molecules, and the definitions of various pressure units.
This document is an assessment schedule for a 2011 NCEA Level 1 Science test covering aspects of acids and bases. It provides the evidence statements and scoring criteria for four multi-part questions on the test. For each question, it describes the key points of information required for a response to be scored at the Achievement, Merit, or Excellence levels. Correct explanations relating subatomic particle arrangements and charges to ion formations are needed for top scores. The document also provides example answers and equations for acid-base reactions.
This document discusses periodic trends in atomic and ionic properties, including:
- Atomic and ionic radii decrease across a period as effective nuclear charge increases. Radii increase down a group as principal quantum number increases.
- Ionization energies generally increase across a period as it becomes more difficult to remove electrons. Exceptions include group 2A and 5A having higher energies than 3A and 6A respectively within periods.
- Cations have smaller radii than their parent atoms as electrons are removed. Anions have larger radii as more electrons are gained. Isotectronic ions with more protons have smaller radii.
Introduction of University Chemistry Syllabus B. Sc.-III (Sem-VI) Session 202...pramod padole
This PowerPoint presentation introduces the B.Sc. Sem-VI chemistry syllabus at Shri Shivaji Science College in Amravati, India. It covers 6 units: inorganic chemistry, organic chemistry, physical chemistry, and elementary quantum mechanics. The inorganic chemistry units cover topics like kinetics of metal complexes, analytical chemistry techniques like spectroscopy and chromatography. The organic chemistry units cover spectroscopy techniques like electronic, infrared, and NMR spectroscopy and mass spectrometry. The physical chemistry units cover elementary quantum mechanics, electrochemistry, and nuclear chemistry.
This module discusses exponential functions and their applications to problems involving population growth, radioactive decay, and compound interest. It provides examples of solving problems involving exponential growth and decay. Students are expected to learn how to model situations exhibiting constant growth or decay rates using exponential functions and use the half-life formula to determine the amount of radioactive substance remaining after a given number of half-lives. The module contains practice problems for students to solve involving exponential growth, decay, and half-lives.
Introduction of University Chemistry Syllabus of B. Sc.-Part-I (Sem-II) by Dr...pramod padole
This document provides an overview of the B.Sc. Part I Semester II chemistry syllabus taught by Dr. Pramod R. Padole at Shri Shivaji Science College in Amravati, India. The syllabus covers inorganic chemistry, organic chemistry, and physical chemistry units. For inorganic chemistry, the units cover topics like polarization, covalent bonding, acids and bases, p-block elements, noble gases, and non-aqueous solvents. The organic chemistry units discuss alkenyl halides, aryl halides, alcohols, phenols, ethers, and epoxides. Finally, the physical chemistry units focus on physical properties and molecular structure, and chemical kinetics.
Carbon 14 and archeological ages, Christian and Intelligent Design discussion of source, measurement, results, interpretation, and errors in Carbon-14 dating.
Organic chemistry is a chemistry subdiscipline involving the scientific study of the structure, properties, and reactions of organic compounds and organic materials, i.e., matter in its various forms that contain carbon atoms.
Organic compounds can be classified based on their functional groups. Members of the same homologous series have similar chemical properties and their physical properties change gradually with increasing carbon chain length. Key factors that affect the physical properties of organic compounds include the structure of the functional group, length of carbon chains, and ability to form hydrogen bonds or dipole-dipole interactions. Non-polar compounds have lower boiling points than polar compounds due to weaker intermolecular forces.
This document provides an introduction to organic chemistry. It discusses that organic chemistry is the study of carbon compounds and their structures and reactions. Over 16 million carbon compounds are known. Carbon can form stable chains and rings due to its strong single and double bonds. Functional groups are atoms or groups that are involved in characteristic chemical reactions. Hydrocarbons only contain carbon and hydrogen, and homologous series differ by CH2 units. Isomers have the same molecular formula but different structures. The document also discusses alkenes, alkynes and alkyl halides.
The document provides an introduction to organic chemistry. It begins by discussing the history of organic chemistry and how vitalism led early scientists to distinguish between organic and inorganic compounds. It then outlines some key objectives of the lesson, including recognizing important scientists in the development of organic chemistry, understanding organic chemical compounds, and differentiating between organic compound types and isomers. The document proceeds to define organic chemistry as the study of carbon compounds and explains why carbon is uniquely suited to form complex molecules through covalent bonding.
Chemistry is important in biology because the structure and function of living things are governed by chemical laws. All living things are composed of six main elements: carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur. Atoms of these elements form bonds and combine to create molecules and compounds through chemical reactions. Carbon is unique in that it can form four bonds, allowing it to make complex molecules with different shapes that are essential for life.
This document provides an introduction to organic chemistry, including:
- Definitions of organic and inorganic compounds
- Empirical, molecular, and structural formulas and how to determine them
- Functional groups and homologous series that classify organic molecules
- Primary, secondary, tertiary classifications of carbon atoms and related groups
- Types of isomerism including structural, stereoisomerism, and examples of each
Organic chemistry is the study of carbon compounds. Carbon forms strong covalent bonds and can form long chains and rings, resulting in a vast number of possible structures. Organic molecules are classified based on their functional groups, such as alkanes (no functional group), alkenes (C=C double bond), and haloalkanes (halogen atom attached to carbon). Isomers are compounds with the same molecular formula but different structures, including positional isomers (functional group in a different position), chain isomers (different carbon skeleton arrangement), and functional isomers (different functional groups). Nomenclature involves naming compounds based on the parent chain, functional groups, and location of any branches.
Organic chemistry is the study of carbon-containing compounds. It was originally thought that compounds found in living things were fundamentally different than non-living compounds, but we now know this is not true. Organic structures can be represented using condensed or skeletal structures, assuming carbons and hydrogens are present. Common organic reactions include substitution, elimination, and addition reactions. Substitution reactions involve replacing one group with another. The SN2 substitution reaction proceeds in one step with simultaneous attack of the nucleophile and departure of the leaving group. This results in inversion of configuration at any chiral centers.
Organic chemistry is the study of carbon compounds. The document introduces organic chemistry, discussing the history and key figures in the field. It describes the properties of carbon that allow it to form many different compounds and categorizes the main types and sources of organic compounds, including naturally occurring, synthetic, and invented compounds. Organic compounds have applications in areas like medicine, pesticides, dyes, plastics, and more.
This document provides an introduction to organic chemistry, including definitions of organic compounds, differences between organic and inorganic compounds, and key concepts. It discusses the early history when vitalism prevented the synthesis of organic compounds. Friedrich Wöhler was the first to synthesize an organic compound in a laboratory. The document also outlines types of organic compounds like hydrocarbons, and how they are named according to IUPAC rules. Carbon properties and different hybridizations that allow multiple bonds are covered.
This document provides an introduction to organic chemistry, including definitions of key terms and concepts. It discusses:
- The early history of organic chemistry and the discovery that organic compounds could be synthesized in the lab.
- The main differences between organic and inorganic compounds in terms of their properties and bonding.
- The central role of carbon atoms in organic compounds and their ability to form chains and complex structures through catenation.
- The different classes of hydrocarbons including alkanes, alkenes, alkynes, aromatics, and their IUPAC naming conventions.
- Important organic functional groups derived from hydrocarbons like alkyl halides, alcohols, ethers, al
Organic chemistry is the study of carbon-containing compounds that are extremely important to life. Our bodies, medicines, fuels, plastics and many other materials are made of organic compounds. Carbon can form diverse compounds because it can form various bonds to itself and other elements. The structure and bonding of organic molecules determines their properties. Key groups like alcohols, ethers, carboxylic acids and esters impact a molecule's chemistry. There are several families of hydrocarbons including alkanes, alkenes and aromatics whose formulas vary based on saturation.
Stereochemistry is the study of the three-dimensional structure of molecules. Stereoisomers differ in their spatial arrangement but have the same connectivity and functional groups. The two main classes of isomers are constitutional isomers and stereoisomers. Stereochemistry plays an important role in determining the properties and reactions of organic compounds. Many drugs exhibit different biological effects based on their stereochemistry. Enzymes can also distinguish between stereoisomers.
This document provides an introduction to organic chemistry for A-level students. It begins with an overview of organic chemistry and the special properties of carbon that allow for the vast number of carbon compounds. It then discusses specific topics like functional groups, isomers, naming conventions (IUPAC), and more. The document is intended to help students understand key concepts in organic chemistry.
This document discusses the nomenclature of organic compounds, specifically alkanes. It begins by explaining that organic compounds are named systematically using IUPAC nomenclature rules. It then discusses naming conventions for acyclic and cyclic alkanes, including classifying carbon and hydrogen atoms. The document outlines the steps for naming alkanes, which include identifying the parent hydrocarbon chain, numbering the carbons, and assigning locants to substituents. Examples are provided to illustrate carbon and hydrogen classification and alkane naming.
1) Organic chemistry is the study of carbon compounds and their properties. It is a separate discipline due to the vast number and variety of organic compounds, many of which are essential to life.
2) Carbon can form chains and rings by bonding to itself and other elements like hydrogen, oxygen, nitrogen and halogens. Functional groups like alcohols, aldehydes, ketones and carboxylic acids determine the properties and reactivity of organic molecules.
3) Chiral molecules are non-superimposable mirror images called enantiomers that can have different biological effects. The R/S system is used to distinguish these two forms.
Carbon plays a central role in organic compounds that make up living organisms. It can form four strong covalent bonds with other elements like hydrogen, oxygen, nitrogen and phosphorus to create a diverse array of molecules. The document outlines several important functional groups that are commonly found attached to carbon skeletons in organic molecules, including hydroxyl, carbonyl, carboxyl, amino, sulfhydryl and phosphate groups. These functional groups give organic molecules their distinctive properties and allow them to participate in important biological reactions.
Carbon is the backbone of biological molecules due to its ability to form diverse and complex structures through covalent bonding. Organic chemistry studies carbon compounds, from simple to enormous molecules. Key aspects include carbon's tetravalent bonding, allowing varied arrangements and lengths of carbon chains, and functional groups that confer unique properties and participate in reactions. Isomers have identical formulas but different structures or arrangements. Carbon's versatility enables myriads of organic molecules that underlie life's diversity.
KEY CONCEPTS
4.1 Organic chemistry is the study of carbon compounds
4.2 Carbon atoms can form diverse molecules by bonding to four other atoms
4.3 A few chemical groups are key to molecular function
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• How can it help today’s business and the benefits
• Phases in Communication Mining
• Demo on Platform overview
• Q/A
Communications Mining Series - Zero to Hero - Session 1
Modelling Structured Domains with Description Graphs and Logic Programming
1. M ODELLING S TRUCTURED D OMAINS U SING
D ESCRIPTION G RAPHS AND L OGIC
P ROGRAMMING
Despoina Magka, Boris Motik and Ian Horrocks
Department of Computer Science, University of Oxford
May 29, 2012
2. O UTLINE
1 M OTIVATION
2 DGLP S , I MPLEMENTATION AND OVERVIEW
1
3. M ODELLING S TRUCTURED D OMAINS WITH OWL
OWL used for the representation of complex structures:
2
4. M ODELLING S TRUCTURED D OMAINS WITH OWL
OWL used for the representation of complex structures:
Aerospace
2
5. M ODELLING S TRUCTURED D OMAINS WITH OWL
OWL used for the representation of complex structures:
Aerospace
Cellular biology
2
6. M ODELLING S TRUCTURED D OMAINS WITH OWL
OWL used for the representation of complex structures:
Aerospace
Cellular biology
Human anatomy
2
7. M ODELLING S TRUCTURED D OMAINS WITH OWL
OWL used for the representation of complex structures:
Aerospace
Cellular biology
Human anatomy
Molecules
2
8. T HE C H EBI O NTOLOGY
OWL ontology Chemical Entities of Biological Interest
3
9. T HE C H EBI O NTOLOGY
OWL ontology Chemical Entities of Biological Interest
Freely accessible dictionary of ‘small’ molecular entities
3
10. T HE C H EBI O NTOLOGY
OWL ontology Chemical Entities of Biological Interest
Freely accessible dictionary of ‘small’ molecular entities
High quality annotation and taxonomy of chemicals
3
11. T HE C H EBI O NTOLOGY
OWL ontology Chemical Entities of Biological Interest
Freely accessible dictionary of ‘small’ molecular entities
High quality annotation and taxonomy of chemicals
Interoperability between researchers
3
12. T HE C H EBI O NTOLOGY
OWL ontology Chemical Entities of Biological Interest
Freely accessible dictionary of ‘small’ molecular entities
High quality annotation and taxonomy of chemicals
Interoperability between researchers
Drug discovery and elucidation of metabolic pathways
3
14. AUTOMATE C HEMICAL C LASSIFICATION
ChEBI is manually incremented
Currently contains approx. 28,000 fully annotated entities
4
15. AUTOMATE C HEMICAL C LASSIFICATION
ChEBI is manually incremented
Currently contains approx. 28,000 fully annotated entities
Grows at a rate of ~1,500 entities per curator per year
4
16. AUTOMATE C HEMICAL C LASSIFICATION
ChEBI is manually incremented
Currently contains approx. 28,000 fully annotated entities
Grows at a rate of ~1,500 entities per curator per year
Biologically interesting entities possibly > 1,000,000
4
17. AUTOMATE C HEMICAL C LASSIFICATION
ChEBI is manually incremented
Currently contains approx. 28,000 fully annotated entities
Grows at a rate of ~1,500 entities per curator per year
Biologically interesting entities possibly > 1,000,000
Each new molecule is subsumed by several chemical
classes
4
18. AUTOMATE C HEMICAL C LASSIFICATION
ChEBI is manually incremented
Currently contains approx. 28,000 fully annotated entities
Grows at a rate of ~1,500 entities per curator per year
Biologically interesting entities possibly > 1,000,000
Each new molecule is subsumed by several chemical
classes
Is dinitrogen inorganic?
4
19. AUTOMATE C HEMICAL C LASSIFICATION
ChEBI is manually incremented
Currently contains approx. 28,000 fully annotated entities
Grows at a rate of ~1,500 entities per curator per year
Biologically interesting entities possibly > 1,000,000
Each new molecule is subsumed by several chemical
classes
Is dinitrogen inorganic?
Does cyclobutane contain a four-membered ring?
4
20. AUTOMATE C HEMICAL C LASSIFICATION
ChEBI is manually incremented
Currently contains approx. 28,000 fully annotated entities
Grows at a rate of ~1,500 entities per curator per year
Biologically interesting entities possibly > 1,000,000
Each new molecule is subsumed by several chemical
classes
Is dinitrogen inorganic?
Does cyclobutane contain a four-membered ring?
Is acetylene a hydrocarbon?
4
21. AUTOMATE C HEMICAL C LASSIFICATION
ChEBI is manually incremented
Currently contains approx. 28,000 fully annotated entities
Grows at a rate of ~1,500 entities per curator per year
Biologically interesting entities possibly > 1,000,000
Each new molecule is subsumed by several chemical
classes
Is dinitrogen inorganic?
Does cyclobutane contain a four-membered ring?
Is acetylene a hydrocarbon?
Does benzaldehyde contain a benzene ring?
4
22. AUTOMATE C HEMICAL C LASSIFICATION
ChEBI is manually incremented
Currently contains approx. 28,000 fully annotated entities
Grows at a rate of ~1,500 entities per curator per year
Biologically interesting entities possibly > 1,000,000
Each new molecule is subsumed by several chemical
classes
Is dinitrogen inorganic?
Does cyclobutane contain a four-membered ring?
Is acetylene a hydrocarbon?
Does benzaldehyde contain a benzene ring?
Speed up curating tasks with automated reasoning tools
4
23. AUTOMATE C HEMICAL C LASSIFICATION
ChEBI is manually incremented
Currently contains approx. 28,000 fully annotated entities
Grows at a rate of ~1,500 entities per curator per year
Biologically interesting entities possibly > 1,000,000
Each new molecule is subsumed by several chemical
classes
Is dinitrogen inorganic? Yes
Does cyclobutane contain a four-membered ring? Yes
Is acetylene a hydrocarbon? Yes
Does benzaldehyde contain a benzene ring? Yes
Speed up curating tasks with automated reasoning tools
4
24. (M IS )R EPRESENTING R INGS WITH OWL
Chemical compounds with rings are highly frequent
5
25. (M IS )R EPRESENTING R INGS WITH OWL
Chemical compounds with rings are highly frequent
Fundamental inability of OWL to represent cycles
5
26. (M IS )R EPRESENTING R INGS WITH OWL
Chemical compounds with rings are highly frequent
Fundamental inability of OWL to represent cycles
At least one tree-shaped model for each consistent OWL
knowledge base
5
27. (M IS )R EPRESENTING R INGS WITH OWL
Chemical compounds with rings are highly frequent
Fundamental inability of OWL to represent cycles
At least one tree-shaped model for each consistent OWL
knowledge base
E XAMPLE
Cyclobutane ∃(= 4)hasAtom.(Carbon ∃(= 2)hasBond.Carbon)
C C
C C
5
28. (M IS )R EPRESENTING R INGS WITH OWL
Chemical compounds with rings are highly frequent
Fundamental inability of OWL to represent cycles
At least one tree-shaped model for each consistent OWL
knowledge base
E XAMPLE
Cyclobutane ∃(= 4)hasAtom.(Carbon ∃(= 2)hasBond.Carbon)
C C
C C
5
29. (M IS )R EPRESENTING R INGS WITH OWL
Chemical compounds with rings are highly frequent
Fundamental inability of OWL to represent cycles
At least one tree-shaped model for each consistent OWL
knowledge base
E XAMPLE
Cyclobutane ∃(= 4)hasAtom.(Carbon ∃(= 2)hasBond.Carbon)
C C
C C
5
30. (M IS )R EPRESENTING R INGS WITH OWL
Chemical compounds with rings are highly frequent
Fundamental inability of OWL to represent cycles
At least one tree-shaped model for each consistent OWL
knowledge base
E XAMPLE
Cyclobutane ∃(= 4)hasAtom.(Carbon ∃(= 2)hasBond.Carbon)
C C
C C
OWL-based reasoning support
5
31. (M IS )R EPRESENTING R INGS WITH OWL
Chemical compounds with rings are highly frequent
Fundamental inability of OWL to represent cycles
At least one tree-shaped model for each consistent OWL
knowledge base
E XAMPLE
Cyclobutane ∃(= 4)hasAtom.(Carbon ∃(= 2)hasBond.Carbon)
C C
C C
OWL-based reasoning support
Does cyclobutane contain a four-membered ring?
Does benzaldehyde contain a benzene ring?
5
32. OWL E XTENSIONS
Limitation of OWL to represent cycles (partially) remedied
by extension of OWL with Description Graphs and rules
[Motik et al., 2009]
6
33. OWL E XTENSIONS
Limitation of OWL to represent cycles (partially) remedied
by extension of OWL with Description Graphs and rules
[Motik et al., 2009]
A Description Graph represents structures by means of a
directed labeled graph
6
34. OWL E XTENSIONS
Limitation of OWL to represent cycles (partially) remedied
by extension of OWL with Description Graphs and rules
[Motik et al., 2009]
A Description Graph represents structures by means of a
directed labeled graph
E XAMPLE
Cyclobutadiene 1
C C Carbon 2 3 Carbon
C C Carbon 5 4 Carbon
6
35. OWL E XTENSIONS
Limitation of OWL to represent cycles (partially) remedied
by extension of OWL with Description Graphs and rules
[Motik et al., 2009]
A Description Graph represents structures by means of a
directed labeled graph
E XAMPLE
Cyclobutadiene 1
C C Carbon 2 3 Carbon
C C Carbon 5 4 Carbon
6
36. OWL E XTENSIONS
Limitation of OWL to represent cycles (partially) remedied
by extension of OWL with Description Graphs and rules
[Motik et al., 2009]
A Description Graph represents structures by means of a
directed labeled graph
E XAMPLE
Cyclobutadiene 1
C C Carbon 2 3 Carbon
C C Carbon 5 4 Carbon
Does cyclobutadiene have a conjugated four-membered
ring?
6
37. OWL E XTENSIONS
Limitation of OWL to represent cycles (partially) remedied
by extension of OWL with Description Graphs and rules
[Motik et al., 2009]
A Description Graph represents structures by means of a
directed labeled graph
E XAMPLE
Cyclobutadiene 1
C C Carbon 2 3 Carbon
C C Carbon 5 4 Carbon
Does cyclobutadiene have a conjugated four-membered
ring?
6
38. OWL E XTENSIONS
Limitation of OWL to represent cycles (partially) remedied
by extension of OWL with Description Graphs and rules
[Motik et al., 2009]
A Description Graph represents structures by means of a
directed labeled graph
E XAMPLE
Cyclobutadiene 1
Oxygen
C C Carbon 2 3 Carbon
C C Carbon 5 4 Carbon
6
39. OWL E XTENSIONS
Limitation of OWL to represent cycles (partially) remedied
by extension of OWL with Description Graphs and rules
[Motik et al., 2009]
A Description Graph represents structures by means of a
directed labeled graph
E XAMPLE
Cyclobutadiene 1
Oxygen
C C Carbon 2 3 Carbon
C C Carbon 5 4 Carbon
∀hasAtom.(Carbon Hydrogen) Hydrocarbon
6
40. OWL E XTENSIONS
Limitation of OWL to represent cycles (partially) remedied
by extension of OWL with Description Graphs and rules
[Motik et al., 2009]
A Description Graph represents structures by means of a
directed labeled graph
E XAMPLE
Cyclobutadiene 1
Oxygen
C C Carbon 2 3 Carbon
C C Carbon 5 4 Carbon
∀hasAtom.(Carbon Hydrogen) Hydrocarbon
Is cyclobutadiene a hydrocarbon?
6
41. OWL E XTENSIONS
Limitation of OWL to represent cycles (partially) remedied
by extension of OWL with Description Graphs and rules
[Motik et al., 2009]
A Description Graph represents structures by means of a
directed labeled graph
E XAMPLE
Cyclobutadiene 1
Oxygen
C C Carbon 2 3 Carbon
C C Carbon 5 4 Carbon
∀hasAtom.(Carbon Hydrogen) Hydrocarbon
Is cyclobutadiene a hydrocarbon?
6
43. R ESULTS OVERVIEW
Key idea:
Switch from first-order logic to logic programming semantics
7
44. R ESULTS OVERVIEW
Key idea:
Switch from first-order logic to logic programming semantics
Use negation-as-failure to derive non-monotonic inferences
7
45. R ESULTS OVERVIEW
Key idea:
Switch from first-order logic to logic programming semantics
Use negation-as-failure to derive non-monotonic inferences
Expressive decidable logic-based formalism for modelling
structured entities: Description Graph Logic Programs
(DGLPs)
7
46. R ESULTS OVERVIEW
Key idea:
Switch from first-order logic to logic programming semantics
Use negation-as-failure to derive non-monotonic inferences
Expressive decidable logic-based formalism for modelling
structured entities: Description Graph Logic Programs
(DGLPs)
DGLP S all cycles CWA
OWL+DG S + RULES some cycles OWA
OWL no cycles OWA
7
47. R ESULTS OVERVIEW
Key idea:
Switch from first-order logic to logic programming semantics
Use negation-as-failure to derive non-monotonic inferences
Expressive decidable logic-based formalism for modelling
structured entities: Description Graph Logic Programs
(DGLPs)
DGLP S all cycles CWA
OWL+DG S + RULES some cycles OWA
OWL no cycles OWA
Negation-as-failure ↔ Closed-world assumption ↔ Missing
information treated as false
7
48. R ESULTS OVERVIEW
Key idea:
Switch from first-order logic to logic programming semantics
Use negation-as-failure to derive non-monotonic inferences
Expressive decidable logic-based formalism for modelling
structured entities: Description Graph Logic Programs
(DGLPs)
DGLP S all cycles CWA
OWL+DG S + RULES some cycles OWA
OWL no cycles OWA
Negation-as-failure ↔ Closed-world assumption ↔ Missing
information treated as false
Classical negation ↔ Open-world assumption ↔ Missing
information treated as not known
7
49. R ESULTS OVERVIEW
Key idea:
Switch from first-order logic to logic programming semantics
Use negation-as-failure to derive non-monotonic inferences
Expressive decidable logic-based formalism for modelling
structured entities: Description Graph Logic Programs
(DGLPs)
DGLP S all cycles CWA
OWL+DG S + RULES some cycles OWA
OWL no cycles OWA
Prototypical implementation of DGLPs with application in
structure-based chemical classification
7
50. R ESULTS OVERVIEW
Key idea:
Switch from first-order logic to logic programming semantics
Use negation-as-failure to derive non-monotonic inferences
Expressive decidable logic-based formalism for modelling
structured entities: Description Graph Logic Programs
(DGLPs)
DGLP S all cycles CWA
OWL+DG S + RULES some cycles OWA
OWL no cycles OWA
Prototypical implementation of DGLPs with application in
structure-based chemical classification
7
51. O UTLINE
1 M OTIVATION
2 DGLP S , I MPLEMENTATION AND OVERVIEW
8
52. W HAT IS A DGLP O NTOLOGY ?
The syntactic objects of a DGLP ontology:
9
53. W HAT IS A DGLP O NTOLOGY ?
The syntactic objects of a DGLP ontology:
Description graphs
9
54. W HAT IS A DGLP O NTOLOGY ?
The syntactic objects of a DGLP ontology:
Description graphs
E XAMPLE
Cyclobutane 1
O O
Dioxygen 1
C C Carbon 2 3 Carbon
C C Carbon 5 4 Carbon Oxygen 2 3 Oxygen
9
55. W HAT IS A DGLP O NTOLOGY ?
The syntactic objects of a DGLP ontology:
Description graphs
Function-free FOL Horn rules
9
56. W HAT IS A DGLP O NTOLOGY ?
The syntactic objects of a DGLP ontology:
Description graphs
Function-free FOL Horn rules
E XAMPLE
Bond(x, y) → Bond(y, x)
SingleBond(x, y) → Bond(x, y)
9
57. W HAT IS A DGLP O NTOLOGY ?
The syntactic objects of a DGLP ontology:
Description graphs
Function-free FOL Horn rules
E XAMPLE
Bond(x, y) → Bond(y, x)
SingleBond(x, y) → Bond(x, y)
Rules with negation-as-failure
9
58. W HAT IS A DGLP O NTOLOGY ?
The syntactic objects of a DGLP ontology:
Description graphs
Function-free FOL Horn rules
E XAMPLE
Bond(x, y) → Bond(y, x)
SingleBond(x, y) → Bond(x, y)
Rules with negation-as-failure
E XAMPLE
HasAtom(x, y) ∧ Carbon(y) → HasCarbon(x)
Molecule(x)∧ not HasCarbon(x) → Inorganic(x)
9
59. W HAT IS A DGLP O NTOLOGY ?
The syntactic objects of a DGLP ontology:
Description graphs
Function-free FOL Horn rules
E XAMPLE
Bond(x, y) → Bond(y, x)
SingleBond(x, y) → Bond(x, y)
Rules with negation-as-failure
E XAMPLE
HasAtom(x, y) ∧ Carbon(y) → HasCarbon(x)
Molecule(x)∧ not HasCarbon(x) → Inorganic(x)
Facts
9
60. W HAT IS A DGLP O NTOLOGY ?
The syntactic objects of a DGLP ontology:
Description graphs
Function-free FOL Horn rules
E XAMPLE
Bond(x, y) → Bond(y, x)
SingleBond(x, y) → Bond(x, y)
Rules with negation-as-failure
E XAMPLE
HasAtom(x, y) ∧ Carbon(y) → HasCarbon(x)
Molecule(x)∧ not HasCarbon(x) → Inorganic(x)
Facts
E XAMPLE
Cyclobutane(c1 ), Dinitrogen(c2 ), . . .
9
61. E NCODING D ESCRIPTION G RAPHS
Translate DGs into logic programs with function symbols
10
62. E NCODING D ESCRIPTION G RAPHS
Translate DGs into logic programs with function symbols
E XAMPLE
10
64. C LASSIFYING O BJECTS
E XAMPLE
Molecule(x) ∧ HasAtom(x, y) ∧ not Carbon(y) ∧ not Hydrogen(y)
→ NotHydroCarbon(x)
Molecule(x) ∧ not NotHydroCarbon(x) → HydroCarbon(x)
11
65. C LASSIFYING O BJECTS
E XAMPLE
Molecule(x) ∧ HasAtom(x, y) ∧ not Carbon(y) ∧ not Hydrogen(y)
→ NotHydroCarbon(x)
Molecule(x) ∧ not NotHydroCarbon(x) → HydroCarbon(x)
C C
C C
11
66. C LASSIFYING O BJECTS
E XAMPLE
Molecule(x) ∧ HasAtom(x, y) ∧ not Carbon(y) ∧ not Hydrogen(y)
→ NotHydroCarbon(x)
Molecule(x) ∧ not NotHydroCarbon(x) → HydroCarbon(x)
Is cyclobutane a
C C hydrocarbon?
C C
11
67. C LASSIFYING O BJECTS
E XAMPLE
Molecule(x) ∧ HasAtom(x, yi ) ∧ Bond(yi , yi+1 ) ∧
1≤i≤4 1≤i≤3
Bond(y4 , y1 ) not yi = yj
1≤ij≤4
→ MoleculeWith4MemberedRing(x)
12
68. C LASSIFYING O BJECTS
E XAMPLE
Molecule(x) ∧ HasAtom(x, yi ) ∧ Bond(yi , yi+1 ) ∧
1≤i≤4 1≤i≤3
Bond(y4 , y1 ) not yi = yj
1≤ij≤4
→ MoleculeWith4MemberedRing(x)
C C
C C
12
69. C LASSIFYING O BJECTS
E XAMPLE
Molecule(x) ∧ HasAtom(x, yi ) ∧ Bond(yi , yi+1 ) ∧
1≤i≤4 1≤i≤3
Bond(y4 , y1 ) not yi = yj
1≤ij≤4
→ MoleculeWith4MemberedRing(x)
Does cyclobutane contain a
C C four-membered ring?
C C
12
70. U NDECIDABILITY
Logic programs with function symbols can axiomatise
infinitely large structures
13
71. U NDECIDABILITY
Logic programs with function symbols can axiomatise
infinitely large structures
Reasoning with DGLP ontologies is trivially undecidable
13
72. U NDECIDABILITY
Logic programs with function symbols can axiomatise
infinitely large structures
Reasoning with DGLP ontologies is trivially undecidable
We are only interested in finite structures
13
73. U NDECIDABILITY
Logic programs with function symbols can axiomatise
infinitely large structures
Reasoning with DGLP ontologies is trivially undecidable
We are only interested in finite structures
E XAMPLE
Carboxyl
O AceticAcid Carboxyl
Carbonyl 1 1
C
Methyl Hydroxyl
2 3 2 3
CH3 OH Methyl Carboxyl Carbonyl Hydroxyl
13
74. S YNTACTIC ACYCLICITY C ONDITIONS
Chase [Maier et al., 1979] termination is undecidable
14
75. S YNTACTIC ACYCLICITY C ONDITIONS
Chase [Maier et al., 1979] termination is undecidable
Problem extensively studied in theory of databases
14
76. S YNTACTIC ACYCLICITY C ONDITIONS
Chase [Maier et al., 1979] termination is undecidable
Problem extensively studied in theory of databases
Various syntax-based acyclicity conditions
14
77. S YNTACTIC ACYCLICITY C ONDITIONS
Chase [Maier et al., 1979] termination is undecidable
Problem extensively studied in theory of databases
Various syntax-based acyclicity conditions
weak acyclicity [Fagin et al., ICDT, 2002]
super-weak acyclicity [Marnette, PODS, 2009]
joint acyclicity [Krötzsch and Rudolph, IJCAI, 2011]
14
78. S YNTACTIC ACYCLICITY C ONDITIONS
Chase [Maier et al., 1979] termination is undecidable
Problem extensively studied in theory of databases
Various syntax-based acyclicity conditions
weak acyclicity [Fagin et al., ICDT, 2002]
super-weak acyclicity [Marnette, PODS, 2009]
joint acyclicity [Krötzsch and Rudolph, IJCAI, 2011]
rule out naturally-arising nested structures
14
79. S YNTACTIC ACYCLICITY C ONDITIONS
Chase [Maier et al., 1979] termination is undecidable
Problem extensively studied in theory of databases
Various syntax-based acyclicity conditions
weak acyclicity [Fagin et al., ICDT, 2002]
super-weak acyclicity [Marnette, PODS, 2009]
joint acyclicity [Krötzsch and Rudolph, IJCAI, 2011]
rule out naturally-arising nested structures
E XAMPLE
Carboxyl
O AceticAcid Carboxyl
Carbonyl 1 1
C
Methyl Hydroxyl
2 3 2 3
CH3 OH Methyl Carboxyl Carbonyl Hydroxyl
14
80. S EMANTIC ACYCLICITY
1 Transitive and irreflexive graph ordering which specifies
which graph instances may imply the existence of other
graph instances
15
81. S EMANTIC ACYCLICITY
1 Transitive and irreflexive graph ordering which specifies
which graph instances may imply the existence of other
graph instances
E XAMPLE
AceticAcid Carboxyl
1 1
AceticAcid Carboxyl
2 3 2 3
Methyl Carboxyl Carbonyl Hydroxyl
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82. S EMANTIC ACYCLICITY
1 Transitive and irreflexive graph ordering which specifies
which graph instances may imply the existence of other
graph instances
2 Extend the logic program with rules that detect violation of
the graph ordering
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83. S EMANTIC ACYCLICITY
1 Transitive and irreflexive graph ordering which specifies
which graph instances may imply the existence of other
graph instances
2 Extend the logic program with rules that detect violation of
the graph ordering
3 Repetitive construction of graph instances during reasoning
triggers derivation of Cycle
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84. S EMANTIC ACYCLICITY
1 Transitive and irreflexive graph ordering which specifies
which graph instances may imply the existence of other
graph instances
2 Extend the logic program with rules that detect violation of
the graph ordering
3 Repetitive construction of graph instances during reasoning
triggers derivation of Cycle
A DGLP ontology O is semantically acyclic if O |= Cycle
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85. S EMANTIC ACYCLICITY
1 Transitive and irreflexive graph ordering which specifies
which graph instances may imply the existence of other
graph instances
2 Extend the logic program with rules that detect violation of
the graph ordering
3 Repetitive construction of graph instances during reasoning
triggers derivation of Cycle
A DGLP ontology O is semantically acyclic if O |= Cycle
DGLP ontology with acetic acid is semantically acyclic
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86. S EMANTIC ACYCLICITY
1 Transitive and irreflexive graph ordering which specifies
which graph instances may imply the existence of other
graph instances
2 Extend the logic program with rules that detect violation of
the graph ordering
3 Repetitive construction of graph instances during reasoning
triggers derivation of Cycle
A DGLP ontology O is semantically acyclic if O |= Cycle
DGLP ontology with acetic acid is semantically acyclic
O
Carbonyl
C
Methyl Hydroxyl
CH3 OH
Carboxyl
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87. T ECHNICAL RESULTS
1 Termination guarantee for semantically acyclic ontologies
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88. T ECHNICAL RESULTS
1 Termination guarantee for semantically acyclic ontologies
2 Decidability of semantic acyclicity for negation-free DGLP
ontologies
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89. T ECHNICAL RESULTS
1 Termination guarantee for semantically acyclic ontologies
2 Decidability of semantic acyclicity for negation-free DGLP
ontologies
3 Decidability of semantic acyclicity for DGLP ontologies with
stratified negation
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90. T ECHNICAL RESULTS
1 Termination guarantee for semantically acyclic ontologies
2 Decidability of semantic acyclicity for negation-free DGLP
ontologies
3 Decidability of semantic acyclicity for DGLP ontologies with
stratified negation
Semantically acyclic DGLP ontologies with stratified
negation capture a wide range of chemical classes:
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91. T ECHNICAL RESULTS
1 Termination guarantee for semantically acyclic ontologies
2 Decidability of semantic acyclicity for negation-free DGLP
ontologies
3 Decidability of semantic acyclicity for DGLP ontologies with
stratified negation
Semantically acyclic DGLP ontologies with stratified
negation capture a wide range of chemical classes:
Is dinitrogen inorganic?
Does cyclobutane contain a four-membered ring?
Is acetylene a hydrocarbon?
Does benzaldehyde contain a benzene ring?
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92. T ECHNICAL RESULTS
1 Termination guarantee for semantically acyclic ontologies
2 Decidability of semantic acyclicity for negation-free DGLP
ontologies
3 Decidability of semantic acyclicity for DGLP ontologies with
stratified negation
Semantically acyclic DGLP ontologies with stratified
negation capture a wide range of chemical classes:
Is dinitrogen inorganic?
Does cyclobutane contain a four-membered ring?
Is acetylene a hydrocarbon?
Does benzaldehyde contain a benzene ring?
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93. E MPIRICAL E VALUATION
Data extracted from ChEBI in Molfile format
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94. E MPIRICAL E VALUATION
Data extracted from ChEBI in Molfile format
XSB logic programming engine
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95. E MPIRICAL E VALUATION
Data extracted from ChEBI in Molfile format
XSB logic programming engine
Chemical classes:
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96. E MPIRICAL E VALUATION
Data extracted from ChEBI in Molfile format
XSB logic programming engine
Chemical classes:
Hydrocarbons
Inorganic molecules
Molecules with exactly two carbons
Molecules with a four-membered ring
Molecules with a benzene
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97. E MPIRICAL E VALUATION
Data extracted from ChEBI in Molfile format
XSB logic programming engine
Chemical classes:
Hydrocarbons
Inorganic molecules
Molecules with exactly two carbons
Molecules with a four-membered ring
Molecules with a benzene
Preliminary evaluation ranging from 10 to 70 molecules
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98. E MPIRICAL E VALUATION
Data extracted from ChEBI in Molfile format
XSB logic programming engine
Chemical classes:
Hydrocarbons
Inorganic molecules
Molecules with exactly two carbons
Molecules with a four-membered ring
Molecules with a benzene
Preliminary evaluation ranging from 10 to 70 molecules
Results:
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99. E MPIRICAL E VALUATION
Data extracted from ChEBI in Molfile format
XSB logic programming engine
Chemical classes:
Hydrocarbons
Inorganic molecules
Molecules with exactly two carbons
Molecules with a four-membered ring
Molecules with a benzene
Preliminary evaluation ranging from 10 to 70 molecules
Results:
All DGLP ontologies were found acyclic
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100. E MPIRICAL E VALUATION
Data extracted from ChEBI in Molfile format
XSB logic programming engine
Chemical classes:
Hydrocarbons
Inorganic molecules
Molecules with exactly two carbons
Molecules with a four-membered ring
Molecules with a benzene
Preliminary evaluation ranging from 10 to 70 molecules
Results:
All DGLP ontologies were found acyclic
Molecules classified as expected
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101. E MPIRICAL E VALUATION
Data extracted from ChEBI in Molfile format
XSB logic programming engine
Chemical classes:
Hydrocarbons
Inorganic molecules
Molecules with exactly two carbons
Molecules with a four-membered ring
Molecules with a benzene
Preliminary evaluation ranging from 10 to 70 molecules
Results:
All DGLP ontologies were found acyclic
Molecules classified as expected
Suite of subsumption tests for largest ontology performed in
few minutes
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102. OVERVIEW AND F UTURE D IRECTIONS
1 Expressive and decidable formalism for representation of
structured objects
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103. OVERVIEW AND F UTURE D IRECTIONS
1 Expressive and decidable formalism for representation of
structured objects
2 Novel acyclicity condition for logic programs with restricted
use of function symbols
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104. OVERVIEW AND F UTURE D IRECTIONS
1 Expressive and decidable formalism for representation of
structured objects
2 Novel acyclicity condition for logic programs with restricted
use of function symbols
3 Prototype for the structure-based classification of complex
objects
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105. OVERVIEW AND F UTURE D IRECTIONS
1 Expressive and decidable formalism for representation of
structured objects
2 Novel acyclicity condition for logic programs with restricted
use of function symbols
3 Prototype for the structure-based classification of complex
objects
Future directions:
Generalise acyclicity condition for datalog rules with
existentials in the head
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106. OVERVIEW AND F UTURE D IRECTIONS
1 Expressive and decidable formalism for representation of
structured objects
2 Novel acyclicity condition for logic programs with restricted
use of function symbols
3 Prototype for the structure-based classification of complex
objects
Future directions:
Generalise acyclicity condition for datalog rules with
existentials in the head
Relax stratifiability criteria for negation
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107. OVERVIEW AND F UTURE D IRECTIONS
1 Expressive and decidable formalism for representation of
structured objects
2 Novel acyclicity condition for logic programs with restricted
use of function symbols
3 Prototype for the structure-based classification of complex
objects
Future directions:
Generalise acyclicity condition for datalog rules with
existentials in the head
Relax stratifiability criteria for negation
User-friendly surface syntax
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108. OVERVIEW AND F UTURE D IRECTIONS
1 Expressive and decidable formalism for representation of
structured objects
2 Novel acyclicity condition for logic programs with restricted
use of function symbols
3 Prototype for the structure-based classification of complex
objects
Future directions:
Generalise acyclicity condition for datalog rules with
existentials in the head
Relax stratifiability criteria for negation
User-friendly surface syntax
Fully-fledged classification system for graph-shaped objects
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109. OVERVIEW AND F UTURE D IRECTIONS
1 Expressive and decidable formalism for representation of
structured objects
2 Novel acyclicity condition for logic programs with restricted
use of function symbols
3 Prototype for the structure-based classification of complex
objects
Future directions:
Generalise acyclicity condition for datalog rules with
existentials in the head
Relax stratifiability criteria for negation
User-friendly surface syntax
Fully-fledged classification system for graph-shaped objects
Thank you for listening. Questions?
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