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EnCOrE: Chemistry, Education, Knowledge From the Real to the Virtual Needs, Perceptions, Tools, Concepts - P. Sankar
 

EnCOrE: Chemistry, Education, Knowledge From the Real to the Virtual Needs, Perceptions, Tools, Concepts - P. Sankar

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Talk at Web Science Montpellier Meetup - 13th May 2011

Talk at Web Science Montpellier Meetup - 13th May 2011

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    EnCOrE: Chemistry, Education, Knowledge From the Real to the Virtual Needs, Perceptions, Tools, Concepts - P. Sankar EnCOrE: Chemistry, Education, Knowledge From the Real to the Virtual Needs, Perceptions, Tools, Concepts - P. Sankar Presentation Transcript

    • EnCOrE: Chemistry, Education, Knowledge From the Real to the Virtual Needs, Perceptions, Tools, Concepts Encoding of Chemical Knowledge in the Context of Evolving Semantic WebConsolidating networks of excellence - WebScience Montpellier Meetup International Workshop on Web Science 13th May, 2011 Montpellier, France Dr. P. Sankar Associate Professor & Head Department of Chemistry Pondicherry Engineering College, Puducherry – 605 014 INDIA
    • Simple Text Special Text Images Special Text Simple Texthttp://en.wikipedia.org/wiki/Acetaldehyde
    • Structure databases Structure representation formats Other structure related datahttp://en.wikipedia.org/wiki/Acetaldehyde
    • http://en.wikipedia.org/wiki/Acetaldehyde
    • Conceptual Name Formula Structure Properties Reactions Making the chemistryChemical structure is central domain different from otherfor all chemical information domains in the context ofand related activities storage, retrieval and communication in web media Real substance / material Real time reactions
    • Where we are ? CAS Chemical Abstract 50 million organic and inorganic substances, and Services more than 60 million protein and DNA sequences PubChem NCBI 31 million compounds and 75 substances free eMolecules Commercial Suppliers 7.0 million molecules free ChEMBL EBI 2.97 million bioassay measurements covering free 636,269 compounds ChemSpider Royal Chemical Society 25 million molecules free ChemACX CambridgeSoft 2.5 million products and 727,161 substances At present chemical information is almost fully Structure handled with the support of databases using Database Structure various structure encoding formats Reaction Encoding Database Formats Unfortunately none of these are efficient enough to be interoperable with the web language Property Database There is a serious need for linking the structural information with the text or image or any other appropriate part of the contents in a Web page containing the chemical information
    • Recent predictions on chemical information …the conventional resources of chemical information become incompatible with the requirements of the evolving Web 2.0 Murray-Rust, P. Chemistry for All. Nature. 2008, 451, 648-651 …huge capacity storage device and the revolutionary computer-human interface, will bring a new revolution to the entire human society. For example, the paper notebooks used for centuries by chemists will eventually be replaced with the electronic notebooks armed with the truly advanced technologies of hand-writing recognition and voice recognition. Chemists will become more and more computer dependent, Internet dependent, and chemoinformatics dependent. William Lingran Chen* Chemoinformatics: Past, Present, and Future J. Chem. Inf. Model., Vol. 46, No. 6, 2006
    • Web ScenarioThe chemical domain has to adopt with the changing scenario of web by considering thefollowings: encoding of chemical knowledge in semantically rich format development of knowledge based tools and techniques shift from database to knowledge base support making the computer intelligent enough to report like an experience chemist
    • EnCOrE project the only initiative taken to achieve new generation chemical informatics EnCOrE (Web-Based, free access Electronic Encyclopedia of Organic Chemistry) (a multinational collaborative project) Prof. Alain Krief Director (Chief Coordinator cum Advisor) Emeritus Professor FUNDP (Faculté N.-D de la Paix) Chemistry department Laboratoire de Chimie des Matériaux Organiques Supramoléculaires (CMOS) & Laboratoire de Chimie des Matériaux Inorganiques (CMI) 61 rue de Bruxelles, B-5000, Namur, Belgium Director of IOCD (International Organization for Chemical Sciences in Development) Advisory Board Prof. Stefano Cerri University of Montpellier, Laboratoire d’Informatique; de Robotique et de Microelectronique de Montpellier, Montpellier, France Prof, Ian Fleming Cambridge University, Cambridge, United Kingdom Prof. Alain Krief Département de Chimie, Facultés N.-D. de la Paix, Namur, Belgium and Executive Director IOCD (International Organization for Chemical Sciences in Development) Prof. Jean-Marie Lehn Nobel, Strasbourg University, Strasbourg, France and Président of IOCD (International Organization for Chemical Sciences in Development) Prof. Goverdhan Mehta FNA, FRS, CSIR Bhatnagar Fellow, Department of Organic Chemistry, Indian Institute of Science, Bangalore-560 012, India Prof. Ryoji Noyori Nobel, Rikken Institute, Tokyo, Japan EnCOrE attempts to frame an Intelligent Chemical Web for the future
    • A possible attempt to achieve Intelligent Chemical Web ontology supported, text based, semantically rich structure description system Human and Machine understandable Chemist’s Knowledge APIs to encode chemical knowledge through Internet Efficient algorithms Chemical domain ontologies Intelligent inference and reasoning capabilities (in-silico basis) chemical hyper-linking !?
    • ChemEd Model Tool to Describe Chemical Structures in XML Format Utilizing Structural Fragments and Chemical Ontology Developed by Punnaivanam Sankar * Krief Alain and Gnanasekaran Aghila Published in J. Chem. Inf. Model. 2010, 50, 755–770
    • Achieving Human and Machine understandable Chemist’s Knowledge oxygen atom Carbonyl carbon has two lone bonded to Hydrogen pair electrons atom through sigma Carbonyl Group bond Sp2 carbon atom bonded with sp2 oxygen atom through a double bond composed of a sigma bond and a pi bond Carbonyl carbon bonded to a carbon atom This is an alpha The functional group carbon atom and is is aldehyde part of some skeleton Chemical Reactiivity
    • information and knowledge needed Electron acid-catalysed hemiacetal formation movements H H O OH OH O CH3 HO O CH3 H H H3C H H3C H CH3OH hemiacetalMaterial / Substance acid-catalysed acetal formation from hemiacetal intermediate H H HO O CH3 H2O O CH3 O CH3 H3CO O CH3 H3CO OCH3 species H H H H H H3C H3C H3C H3C H3C hemiacetal CH3OH acetal Structural information Reaction Specific information Chemist knowledge Group Formation of hemiacetal Functional groupHybridization Protonation at carbonyl oxygen atom Alpha carbongeometry Addition of methanol to carbonyl carbon Ring skeleton (bridged, fused, spiro)Charge status Elimination of proton Linear skeletonElectronic environment Bridgehead positionBonding details Formation of acetal Exo / endo orientation of groupsLocation of the atom on Axial / equatorial orientation of groupsspecific skeleton structure Protonation of hydroxyl group Reaction sitesPresence of lone pair electrons Loss of water by elemination Heatisotope label Addition of methanol to oxonium ion PressureIsomerism (optical, Breaking of pi bond Lightgeometrical, etc) Loss of proton Timeetc. etc Action, equipments, observation
    • Chemist Computer Structural Reaction Structural Reactioninformation information information information Chemist Chemist knowledge knowledge Through a proper structure description system rich in semanticsOut of experience and expertise gained overthe period of years a chemist is capable of Integration of external knowledge resourcescorrelating the structural features with reaction through chemical ontologiesspecific details Tools to integrate reaction knowledge with structural features
    • An approach available to achieve encoding of chemical knowledge ontology XML SemanticsChemical Ontologies implemented in OWL Java based programsOntology Editors - Protege XML description to support software agents
    • ChemGp – A Knowledge Editor for Groups, Functional Groups and Chemical Reactivity or transformations To be communicated
    • We believe strongly that we can provide challenging tasks in the following areas to build an Intelligent Chemical Web of Trust Knowledge Representation Visualization Web Technology Techniques Cloud / distributed APIs Computing Robotics Linguistics / Theme Education / AcademicsWe are interested to associate with people / group to achieve our proposed objectives
    • Thank you AcknowledgementThe authors acknowledge the support of:The Department of Science and Technology (DST), New Delhi, India for a funding supportThe Belgian Science Foundation (FNRS) especially for the creation of Fragment Library(A. Krief) and FUNDP (Namur, Belgium).Prof. Mark A. Musen, and Dr. Tania Tudorache, Biomedical Informatic Research Center(BMIR), Stanford University for their support in learning Protégé and developing OWLontologies in Protégé.
    • Development of a Semantically Rich Structure Representation SystemModel Tool to Describe Chemical Structures in XML Format Utilizing Structural Fragments and Chemical Ontology Punnaivanam Sankar*, Krief Alain, and Gnanasekaran Aghila J. Chem. Inf. Model. 2010, 50, 755–770
    • Development of Semantically Rich Structure Representation on conceptual basis O O H C Structure H C H H H H C H C O Fragment O Atom H C O H C O H C O H C O Electron
    • Development of Semantically Rich Structure Representation on conceptual basis Structure Fragment has isA Fragment Fragment Fragment has isA Fragment Fragment Atom Fragment has Electron
    • Development of Semantically Rich Structure Representation on conceptual basis O H C Structure C H H H Chemical Ontology H C Fragment O Atom H C O Electron H C O XML
    • Fragment Ontology
    • Fragment Ontology
    • Fragment Ontology
    • Fragment Ontology
    • Fragment Ontology
    • Composition of Fragment Fragment has Atom has Atom ElectronLink ElectronLink ElectronLink has ElectronLink ElectronLink ElectronLink Atom has ElectronLink ElectronLink ElectronLink Atom has ElectronLink ElectronLink ElectronLink
    • Composition of Structure in tree view Structure Fragment Atom XML Format ElectronLink <structure > <fragment > ElectronLink <atom > <electronLink /> <electronLink /> Atom </atom> <atom > ElectronLink <electronLink /> <electronLink /> ElectronLink </atom> </fragment> Fragment <fragment > <atom > <electronLink /> Atom <electronLink /> </atom> ElectronLink <atom > <electronLink /> ElectronLink <electronLink /> </atom> Atom </fragment> ElectronLink </structure> ElectronLink
    • Composition of Structure in XML representation <structure id="" title="" type="" formula="" X="" Y="" caption="" captionX="" captionY=""> <fragment id="" title="" type="" symbol="" linkType="" orientation="" projection=“” x1="" y1="" x2="" y2=""> <atom id="" title="" hybridization="" symbol="" position="" isotopeLabel=“” x="" y=""> <electronLink id="" title="" electronStatus="" charge="" chargeCount="" affinity="" bond=“” order="" linkStatus="" target="" orientation="" projection="" x1="" y1="" x2="" y2=""/> </atom> </fragment> </structure>
    • structure construction based on conceptual description advantages the conceptual description of structural components based on fragments, atoms and the electronLinks allows: the structure construction through the selection of fragments represented by text the validation of bonding during the structure construction on screen instantaneously to make the computer to behave intelligently to infer the type of skeleton from the combination of fragments the generation of semantically rich XML representation of chemical structure the computer to understand the meaning of the components of the chemical structure the processing of the structural features in XML document of structure to arrive at useful inference the computer to mimic the Chemist’s view on the chemical structure We need a tool
    • EnCOrE - ChemEd – the Structure Editor developed by us ChemEd Model Tool to Describe Chemical Structures in XML Format Utilizing Structural Fragments and Chemical Ontology Developed by Punnaivanam Sankar *1 jointly with Krief Alain2 and Gnanasekaran Aghila3 1Department of Chemistry, Pondicherry Engineering College, Puducherry - 605 014, India 2Department of Chemistry, Facultés N.–D. de la Paix, Namur, B 5000, Belgium 3Department of Computer Science, Pondicherry University, Puducherry - 605 014, India ChemEd is the first of a series of tools designed in the context of EnCOrE, a project aimed to create a Web-based Encyclopedia of Organic Chemistry built collaboratively but under a strict editorial board policy. We have identified several tools with original features to achieve this objective and have ranked first the design of a tool able to interoperate between structure, and the perception of chemist, which allows among others creativity through chemical synthesis and organization of chemical data ChemEd is an ontology supported Structure Editor to draw/edit and to describe chemical structures
    • About EnCOrE project EnCOrE (Web-Based, free access Electronic Encyclopedia of Organic Chemistry) (a multinational collaborative project) Prof. Alain Krief Director (Chief Coordinator cum Advisor) Emeritus Professor FUNDP (Faculté N.-D de la Paix) Chemistry department Laboratoire de Chimie des Matériaux Organiques Supramoléculaires (CMOS) & Laboratoire de Chimie des Matériaux Inorganiques (CMI) 61 rue de Bruxelles, B-5000, Namur, Belgium Director of IOCD (International Organization for Chemical Sciences in Development) Advisory Board Prof. Stefano Cerri University of Montpellier, Laboratoire d’Informatique; de Robotique et de Microelectronique de Montpellier, Montpellier, France Prof, Ian Fleming Cambridge University, Cambridge, United Kingdom Prof. Alain Krief Département de Chimie, Facultés N.-D. de la Paix, Namur, Belgium and Executive Director IOCD (International Organization for Chemical Sciences in Development) Prof. Jean-Marie Lehn Nobel, Strasbourg University, Strasbourg, France and Président of IOCD (International Organization for Chemical Sciences in Development) Prof. Goverdhan Mehta FNA, FRS, CSIR Bhatnagar Fellow, Department of Organic Chemistry, Indian Institute of Science, Bangalore-560 012, India Prof. Ryoji Noyori Nobel, Rikken Institute, Tokyo, Japan
    • Tool barChemEd – Graphical User Interface Contains the icons to modify or to manipulate the structures on screen Fragment Icons bar Menu bar Functional Group Commonly needed Display Panel structural fragments to build structure Reactivity Panel Drawing Panel ChemLib To draw structures Fragment Group Display Instances from Panel Ontology ChemFul display panel Shows the full XML description of structure drawn on the screen
    • tool bar: consists of icons to manipulate the structure drawn on screen and to process the structure description Cursor tool – used to select and create structures on screen Eraser Eraser tool – erase drawings representing a structure Show/Hide Grid tool – used to show or hide the grid guide lines toCursor align the structures on screen Show/Hide Grid Move Structure Move Atom Group Move Structure Moving the drawings on the screen can be done using these icons. Move Structure Group – moves the whole drawings on the screen Move Structure – to move structures representing individual structures on the screen Move Structure Group – to relocate atoms or points representing atoms on the screen
    • tool bar: consists of icons to manipulate the structure drawn on screen and to process the structure description Projection Labeling Atom Position Change Atom Labeling Coordinates Change Add/Remove Orientation Isotope Electron Labeling Atom Position Labelling : Atom labelling allows official numbering in a skeleton Isotope Labelling : provides the facility to label a selected atom with appropriate isotope label guided by external ontology Projection Labelling : The bonds can be labelled to indicate the three projections, in plane, above plane, and below plane relative to the plane of screen using the “Projection Labeling” icons Add/Remove Electron : ChemEd has the facility to (i) create charge on an atom by adding or removing electron on the “electronLink” of the atom using this tool Change Atom Coordinates : can be used to relocate the atom positions so as to reflect this change in the ChemFil and ChemFul. This facility is particularly needed to create templates like “CyclohexaneChairRing” from a “SixMemberRing” Change Orientation : provides the possibility to edit the orientation of fragment if needed
    • tool bar: consists of icons to manipulate the structure drawn on screen and to process the structure description to display a brief report on the group, functional group and skeleton related information for the Electron Status structure drawn on the Display screen show / hide the lone pair, unpaired and empty electron status of “electronLink” to allow the display of more details Functional group of the atoms on the screen when needed Report Atom Draw Supra- Descriptor Molecular Interaction Display the atom descriptors such asdraw and encode supra-molecular interactions such as symbol; name; isotope label;ion-ion, ion-dipole, dipole-dipole, metal-pi, hydrogen hybridization, charge, and electron status,bonding and multi-centre bonding bonding details of any selected atom on the screen
    • Structure drawing The structure drawing in ChemEd starts by bringing with cursor an appropriate fragment available as icons on the Fragment Icons bars or from ChemLib into the screen. The drawing can be pursued and completed by joining other fragments to the existing one through a click or drag event
    • ChemLib: Provides the basic structural fragments organized in Fragment ontology for structure drawing AtomFragment: represents single atom fragment classified as NeutralAtomFragment such as C, H, O, N, Cl, Br, I, S, P, etc. AnionicAtomFragment like C-, H-, F-, Cl-, Br-, I- and CationicAtomFragment such as C+, H+, Cl+, Br+, I+, Na+, K+, Mg2+, Fe2+, Fe3+, etc
    • ChemLib: Provides the basic structural fragments organized in Fragment ontology for structure drawing The “AtomGroupFragment” represents a group of atoms to describe meaningful chemical groups such as carbonyl, formyl, hydroxyl, etc. It is also classified as anionic, cationic, neutral atom groups to represent condensed structures of atom groups such as OH-, COO-, NH2-, CN-; NH4+, OH3+; OH, CHO, CO, COOH, CH3, C2H5, C3H7, etc which can include molecular “AtomGroupFragment” such as BH3, NH3, CH3OH, (C2H5)2O, CH3COCH3 particularly useful for describing complexes.
    • ChemLib: Provides the basic structural fragments organized in Fragment ontology for structure drawing The “SkeletonFragment” represent the structural fragments with more than one atom connected with bonds. The default atom in the SkeletonFragment is carbon and the skeleton includes both acyclic and cyclic systems like single bond, double bond, three member ring, six member ring etc. There are five classes of skeleton fragments identified viz. BondSkeletonFragment RingSkeletonFragment BridgeSkeletonFragment FuseSkeletonFragment SpiroSkeletonFragment
    • ChemLib: Provides the basic structural fragments organized in Fragment ontology for structure drawing The “TemplateFragment” is to describe fragments derived from the first three fragment types. For example, a bicyclic template fragment like “Bicyclo221HeptaneRing” can be constructed with a suitable “RingSkeletonFragment” and one of the “BridgeSkeletonFragment” fragments. Similarly a polyclyclic template fragment representing a steroid skeleton can be constructed by fusing the ring skeleton fragments appropriately. Different conformations of same cyclic structures like chair and boat forms of Cyclohexane ring systems can be created and added into the ChemLib in the “TemplateSkeletonFragment” category for structure construction
    • Fragment Icon bar: To draw single / double / triple bond fragments Provides the frequently needed structural fragments for structure drawingTo create one / two / three To draw skeleton systemsmember bridge fragments representing 3-8 member ring skeletons To create BenzeneRing and Bicyclo221HeptaneRing templates To create Neutral atom fragment / to introduce atoms in the skeleton
    • ChemEd – Shows the structure drawn on draw panel. It also detects the functional group andDisplays in the Functional Group Panel
    • ChemEd – Shows the functional group specific information along with the chemical groups and theReactivity information associated with the functional group
    • ChemEd – outlines the chemical group selected
    • ChemEd – Shows a reactive site
    • XML markup generated by ChemEd for the full description of benzaldehyde structure ChemFul <?xml version="1.0"?> <structureGroup id="" title="C:ChemFilbenzaldehyde.xml" type=""> <structure id="s1" title="structure1" type="" formula="" X="0" Y="0" caption="" captionX="0" captionY="0"> <fragment id="s1-0" title="SixMemberRing" type="SkeletonFragment" template="" symbol="C6" linkType="" orientation="270" projection="" x1="329" y1="121" x2="329" y2="121"> <atom id="s1-0-a1" title="Carbon" hybridization="sp3" symbol="C" position="1" isotopeLabel="" x="329" y="121"> <electronLink id="s1-0-a1e1" title="2sp3" electronStatus="bPair" charge="0" chargeCount="0" affinity="" bond="sigma" order="single" linkStatus="link" target="s1-0-a2e1" orientation="330" projection="" x1="329" y1="121" x2="355" y2="136"/> <electronLink id="s1-0-a1e2" title="2sp3" electronStatus="bPair" charge="0" chargeCount="0" affinity="" bond="sigma" order="single" linkStatus="link" target="s1-0-a6e2" orientation="210" projection="" x1="329" y1="121" x2="303" y2="136"/> <electronLink id="s1-0-a1e3" title="2sp3" electronStatus="bPair" charge="0" chargeCount="0" affinity="" bond="sigma" order="single" linkStatus="linkTarget" target="s1-4-a1e1" orientation="" projection="" x1="329" y1="121" x2="329" y2="121"/> 12.4 KB <electronLink id="s1-0-a1e4" title="2sp3" electronStatus="bPair" charge="0" chargeCount="0" affinity="" bond="sigma" order="single" linkStatus="linkTarget" target="s1-5-a1e1" orientation="" projection="" x1="329" y1="121" x2="329" y2="121"/> </atom> <atom id="s1-0-a2" title="Carbon" hybridization="sp3" symbol="C" position="2" isotopeLabel="" x="355" y="136"> <electronLink id="s1-0-a2e1" title="2sp3" electronStatus="bPair" charge="0" chargeCount="0" affinity="" bond="sigma" order="single" linkStatus="link" target="s1-0-a1e1" orientation="150" projection="" x1="355" y1="136" x2="329" y2="121"/> <electronLink id="s1-0-a2e2" title="2sp3" electronStatus="bPair" charge="0" chargeCount="0" affinity="" bond="sigma" order="single" linkStatus="link" target="s1-0-a3e1" orientation="270" projection="" x1="355" y1="136" x2="355" y2="166"/> <electronLink id="s1-0-a2e3" title="2sp3" electronStatus="bPair" charge="0" chargeCount="0" affinity="" bond="sigma" order="single" linkStatus="linkTarget" target="s1-1-a1e1" orientation="30" projection="" x1="355" y1="136" x2="381" y2="121"/>
    • XML markup generated by ChemED for the construction of benzaldehyde structure ChemFil<?xml version="1.0"?><structureGroup id="" title="C:ChemFilbenzaldehyde" type=""> <structure id="s1" title="structure1" type="" formula="" X="0" Y="0" caption="" captionX="0”captionY="0"> <fragment id="s1-0" title="BenzeneRing" type="TemplateFragment" template="BenzeneRing” link="" orientation="270" target1="" target2="" bgX1="" bgY1="" bgX2="" bgY2=""/> <fragment id="s1-1" title="Carbon" type="AtomFragment" template="BenzeneRing" link="direct“orientation="30" t arget1="s1-0-a2e3" target2="" bgX1="" bgY1="" bgX2="" bgY2=""/> <fragment id="s1-2" title="DoubleBond" type="SkeletonFragment" template="BenzeneRing“link="direct" orientation="90“ target1="s1-1-a1e2" target2="" bgX1="" bgY1="" bgX2=“”bgY2=""/> <fragment id="s1-3" title="Hydrogen" type="AtomFragment" template="BenzeneRing”link="direct" orientation="330“ target1="s1-1-a1e4" target2="" bgX1="" bgY1="" bgX2=“”bgY2=""/> <modification title="Atom" sourceObject="Oxygen" targetObject="Carbon" targetId1="s1-2-a1” targetId2="" x1="0" y1="0"/> </structure></structureGroup> 2 KB
    • Markup for Benzaldehyde construction<?xml version="1.0"?><structureGroup id="" title="C:ChemFilbenzaldehyde" type=""> <structure id="s1" title="structure1" type="" formula="" X="0" Y="0" caption="" captionX="0”captionY="0"> <fragment id="s1-0" title="BenzeneRing" type="TemplateFragment" template="BenzeneRing” link="" orientation="270" target1="" target2="" bgX1="" bgY1="" bgX2="" bgY2=""/> <fragment id="s1-1" title="Carbon" type="AtomFragment" template="BenzeneRing" link="direct“orientation="30" t arget1="s1-0-a2e3" target2="" bgX1="" bgY1="" bgX2="" bgY2=""/> <fragment id="s1-2" title="DoubleBond" type="SkeletonFragment" template="BenzeneRing“link="direct" orientation="90“ target1="s1-1-a1e2" target2="" bgX1="" bgY1="" bgX2=“”bgY2=""/> <fragment id="s1-3" title="Hydrogen" type="AtomFragment" template="BenzeneRing”link="direct" orientation="330“ target1="s1-1-a1e4" target2="" bgX1="" bgY1="" bgX2=“”bgY2=""/> <modification title="Atom" sourceObject="Oxygen" targetObject="Carbon" targetId1="s1-2-a1” targetId2="" x1="0" y1="0"/> </structure></structureGroup>
    • Markup for Benzaldehyde construction<?xml version="1.0"?><structureGroup id="" title="C:ChemFilbenzaldehyde" type=""> <structure id="s1" title="structure1" type="" formula="" X="0" Y="0" caption="" captionX="0”captionY="0"> <fragment id="s1-0" title="BenzeneRing" type="TemplateFragment" template="BenzeneRing” link="" orientation="270" target1="" target2="" bgX1="" bgY1="" bgX2="" bgY2=""/> <fragment id="s1-1" title="Carbon" type="AtomFragment" template="BenzeneRing" link="direct“orientation="30" t arget1="s1-0-a2e3" target2="" bgX1="" bgY1="" bgX2="" bgY2=""/> <fragment id="s1-2" title="DoubleBond" type="SkeletonFragment" template="BenzeneRing“link="direct" orientation="90“ target1="s1-1-a1e2" target2="" bgX1="" bgY1="" bgX2=“”bgY2=""/> <fragment id="s1-3" title="Hydrogen" type="AtomFragment" template="BenzeneRing”link="direct" orientation="330“ target1="s1-1-a1e4" target2="" bgX1="" bgY1="" bgX2=“”bgY2=""/> <modification title="Atom" sourceObject="Oxygen" targetObject="Carbon" targetId1="s1-2-a1” targetId2="" x1="0" y1="0"/> </structure></structureGroup>
    • Markup for Benzaldehyde construction<?xml version="1.0"?><structureGroup id="" title="C:ChemFilbenzaldehyde" type=""> <structure id="s1" title="structure1" type="" formula="" X="0" Y="0" caption="" captionX="0”captionY="0"> <fragment id="s1-0" title="BenzeneRing" type="TemplateFragment" template="BenzeneRing” link="" orientation="270" target1="" target2="" bgX1="" bgY1="" bgX2="" bgY2=""/> <fragment id="s1-1" title="Carbon" type="AtomFragment" template="BenzeneRing" link="direct“orientation="30" t arget1="s1-0-a2e3" target2="" bgX1="" bgY1="" bgX2="" bgY2=""/> <fragment id="s1-2" title="DoubleBond" type="SkeletonFragment" template="BenzeneRing“link="direct" orientation="90“ target1="s1-1-a1e2" target2="" bgX1="" bgY1="" bgX2=“”bgY2=""/> <fragment id="s1-3" title="Hydrogen" type="AtomFragment" template="BenzeneRing”link="direct" orientation="330“ target1="s1-1-a1e4" target2="" bgX1="" bgY1="" bgX2=“”bgY2=""/> <modification title="Atom" sourceObject="Oxygen" targetObject="Carbon" targetId1="s1-2-a1” targetId2="" x1="0" y1="0"/> </structure></structureGroup>
    • Markup for Benzaldehyde construction<?xml version="1.0"?><structureGroup id="" title="C:ChemFilbenzaldehyde" type=""> <structure id="s1" title="structure1" type="" formula="" X="0" Y="0" caption="" captionX="0”captionY="0"> <fragment id="s1-0" title="BenzeneRing" type="TemplateFragment" template="BenzeneRing” link="" orientation="270" target1="" target2="" bgX1="" bgY1="" bgX2="" bgY2=""/> <fragment id="s1-1" title="Carbon" type="AtomFragment" template="BenzeneRing" link="direct“orientation="30" t arget1="s1-0-a2e3" target2="" bgX1="" bgY1="" bgX2="" bgY2=""/> <fragment id="s1-2" title="DoubleBond" type="SkeletonFragment" template="BenzeneRing“link="direct" orientation="90“ target1="s1-1-a1e2" target2="" bgX1="" bgY1="" bgX2=“”bgY2=""/> <fragment id="s1-3" title="Hydrogen" type="AtomFragment" template="BenzeneRing”link="direct" orientation="330“ target1="s1-1-a1e4" target2="" bgX1="" bgY1="" bgX2=“”bgY2=""/> <modification title="Atom" sourceObject="Oxygen" targetObject="Carbon" targetId1="s1-2-a1” targetId2="" x1="0" y1="0"/> </structure></structureGroup>
    • Markup for Benzaldehyde construction<?xml version="1.0"?><structureGroup id="" title="C:ChemFilbenzaldehyde" type=""> <structure id="s1" title="structure1" type="" formula="" X="0" Y="0" caption="" captionX="0”captionY="0"> <fragment id="s1-0" title="BenzeneRing" type="TemplateFragment" template="BenzeneRing” link="" orientation="270" target1="" target2="" bgX1="" bgY1="" bgX2="" bgY2=""/> <fragment id="s1-1" title="Carbon" type="AtomFragment" template="BenzeneRing" link="direct“orientation="30" t arget1="s1-0-a2e3" target2="" bgX1="" bgY1="" bgX2="" bgY2=""/> <fragment id="s1-2" title="DoubleBond" type="SkeletonFragment" template="BenzeneRing“link="direct" orientation="90“ target1="s1-1-a1e2" target2="" bgX1="" bgY1="" bgX2=“”bgY2=""/> <fragment id="s1-3" title="Hydrogen" type="AtomFragment" template="BenzeneRing”link="direct" orientation="330“ target1="s1-1-a1e4" target2="" bgX1="" bgY1="" bgX2=“”bgY2=""/> <modification title="Atom" sourceObject="Oxygen" targetObject="Carbon" targetId1="s1-2-a1” targetId2="" x1="0" y1="0"/> </structure></structureGroup>
    • Fragment markup – semantics at fragment level <fragment id="s1-1" title="Carbon" type="AtomFragment" template="" symbol="C" linkType="direct" orientation="30" projection="" x1="355" y1="136" x2="381" y2="121"> <atom id="s1-1-a1" title="Carbon" hybridization="sp2" symbol="C" position="" isotopeLabel="" x="381" y="121"> <electronLink id="s1-1-a1e1" title="2sp2" electronStatus="bPair" charge="0" chargeCount="0" affinity="" bond="sigma" order="single" linkStatus="linkSource" target="s1-0-a2e3" orientation="30" projection="" x1="381" y1="121" x2="355" y2="136"/> C <electronLink id="s1-1-a1e2" title="2sp2" electronStatus="bPair" charge="0" chargeCount="0" affinity="" bond="sigma" order="double" linkStatus="linkTarget" target="s1-2-a1e1" orientation="90" projection="" x1="381" y1="121" x2="381" y2="91"/>Fragment <electronLink id="s1-1-a1e3" title="2pz" electronStatus="bPair" charge="0" chargeCount="0" affinity="" bond="pi" order="double" linkStatus="link" target="s1-2-a1e2" orientation="90" projection="" x1="376" y1="121" x2="376" y2="91"/> <electronLink id="s1-1-a1e4" title="2sp2" electronStatus="bPair" charge="0" chargeCount="0" affinity="" bond="sigma" order="single" linkStatus="linkTarget" target="s1-3-a1e1" orientation="330" projection="" x1="381" y1="121" x2="407" y2="136"/> </atom> </fragment>
    • Fragment markup – semantics at atom level <fragment id="s1-1" title="Carbon" type="AtomFragment" template="" symbol="C" linkType="direct" orientation="30" projection="" x1="355" y1="136" x2="381" y2="121"> <atom id="s1-1-a1" title="Carbon" hybridization="sp2" symbol="C" position="" isotopeLabel="" x="381" y="121"> <electronLink id="s1-1-a1e1" title="2sp2" electronStatus="bPair" charge="0" chargeCount="0" affinity="" bond="sigma" order="single" linkStatus="linkSource" target="s1-0-a2e3" orientation="30" projection="" x1="381" y1="121" x2="355" y2="136"/> C <electronLink id="s1-1-a1e2" title="2sp2" electronStatus="bPair" charge="0" chargeCount="0" affinity="" bond="sigma" order="double" linkStatus="linkTarget" target="s1-2-a1e1" orientation="90" projection="" x1="381" y1="121" x2="381" y2="91"/>Atom <electronLink id="s1-1-a1e3" title="2pz" electronStatus="bPair" charge="0" chargeCount="0" affinity="" bond="pi" order="double" linkStatus="link" target="s1-2-a1e2" orientation="90" projection="" x1="376" y1="121" x2="376" y2="91"/> <electronLink id="s1-1-a1e4" title="2sp2" electronStatus="bPair" charge="0" chargeCount="0" affinity="" bond="sigma" order="single" linkStatus="linkTarget" target="s1-3-a1e1" orientation="330" projection="" x1="381" y1="121" x2="407" y2="136"/> </atom> </fragment>
    • Fragment markup – semantics at electronLink level <fragment id="s1-1" title="Carbon" type="AtomFragment" template="" symbol="C" linkType="direct" orientation="30" projection="" x1="355" y1="136" x2="381" y2="121"> <atom id="s1-1-a1" title="Carbon" hybridization="sp2" symbol="C" position="" isotopeLabel="" x="381" y="121"> <electronLink id="s1-1-a1e1" title="2sp2" electronStatus="bPair" charge="0" chargeCount="0" affinity="" bond="sigma" order="single" linkStatus="linkSource" target="s1-0-a2e3" orientation="30" projection="" x1="381" y1="121" x2="355" C y2="136"/> <electronLink id="s1-1-a1e2" title="2sp2" electronStatus="bPair" charge="0" chargeCount="0" affinity="" bond="sigma" order="double" linkStatus="linkTarget" target="s1-2-a1e1" orientation="90" projection="" x1="381" y1="121" x2="381" y2="91"/>electronLink <electronLink id="s1-1-a1e3" title="2pz" electronStatus="bPair" charge="0" chargeCount="0" affinity="" bond="pi" order="double" linkStatus="link" target="s1-2-a1e2" orientation="90" projection="" x1="376" y1="121" x2="376" y2="91"/> <electronLink id="s1-1-a1e4" title="2sp2" electronStatus="bPair" charge="0" chargeCount="0" affinity="" bond="sigma" order="single" linkStatus="linkTarget" target="s1-3-a1e1" orientation="330" projection="" x1="381" y1="121" x2="407" y2="136"/> </atom> </fragment>
    • The basic Semantic Levels in Structure description Structure structure Fragment fragment atom Atom electronLink Electron
    • The Semantics at electronLink level Descriptor Presentational attributes attributes id title Specifies the electronStatus unique charge chargeCount identification orientation X1 affinity value Y1 bond X2 order y2 linkStatus id="s1-1-a1e1" Target projection
    • The Semantics at electronLink level Descriptor Presentational attributes attributes id Presents the title name of the electronStatus orbital / charge orientation chargeCount hybridization X1 affinity Y1 bond X2 order s, p, sp3, sp2, y2 linkStatus Target sp, dsp2 projection
    • The Semantics at electronLink level Descriptor Presentational attributes attributes id electronic status title electronStatus of the charge electronLink orientation chargeCount X1 affinity lone pair Y1 bond bond pair X2 order unpaired y2 linkStatus ion pair Target empty projection
    • The Semantics at electronLink level Descriptor Presentational attributes attributes id title electronStatus Charge as charge 0 / + / - / δ+ and orientation chargeCount affinity δ- X1 Y1 bond X2 order linkStatus chargeCount as y2 Target 0,1,2,3… projectionMeaningful inferences can be obtained by combining the values of ‘electronStatus’, ‘charge’ and ‘chargeCount’attributes. For example a value of “empty” for ‘electronStatus’ followed by a “+” in the ‘charge’ and “1” in the‘charge’ attribute can be inferred as the positive charge is due to the loss of an unpaired electron. Similarly thevalues “lPair”, “-” and “1” for ‘electronStatus’, ‘charge’ and ‘chargeCount’ attributes respectively provides themeaning of acquired negative charge due to the gain of one electron.
    • The Semantics at electronLink level Descriptor Presentational attributes attributes id title electronStatus charge chargeCount provides the orientation affinity semantics of X1 Y1 bond order chemical bonding X2 y2 linkStatus Target projection
    • The Semantics at electronLink level Descriptor Presentational attributes attributes id title electronStatus Affinity charge indicating the normal tendency of orientation chargeCount the “electronLink” towards chemical affinity X1 bonding using the values such as Y1 bond “covalent / ionic / coordinate” quoting for covalent-, ionic- or X2 order dative-bond y2 linkStatus Target projection
    • The Semantics at electronLink level Descriptor Presentational attributes attributes id title Bond electronStatus charge type of bond is denoted with values like “sigma / pi-y / pi-z” to separately orientation chargeCount encode the sigma and pi systems affinity X1 Y1 bond Order X2 order indicates bond order with values y2 linkStatus “single / double / triple” Target projection
    • The Semantics at electronLink level Descriptor Presentational attributes attributes id Target title electronStatus Target attribute of the source charge “electronLink” is used to hold the unique id-value of the “electronLink” orientation chargeCount of the targeted atom to represent a affinity X1 chemical bond. Y1 bond At the same time the ‘target’ X2 order attribute of the target “electronLink” y2 linkStatus is filled with the id-value of the Target “electronLink” of the source atom projection
    • The Semantics at electronLink level Descriptor Presentational attributes attributes linkStatus id specifies whether the link is between two title “electronLink” belong to same fragment or different fragments. In case of a link electronStatus within the fragment, the linkStatus holds charge the value as “link”. If the link is between Orientation chargeCount two different fragments, then the X1 “electronLink” belong to the target affinity fragment takes up the value as Y1 bond “linkTarget” and that of source fragment is X2 order filled with the value as “linkSource”. The y2 same attribute is used to hold the bridge linkStatus head positions in bridged structures with Target the values of “bridgeTarget” and “bridgeSource”
    • The Semantics Descriptor presentational attributes imaginary attributes id orientation of orientation title eStatus orbitals X1 Y1 link linkType restricted to two X2 y2 bondType charge dimensional chargeCount linkTarget plane linkTargetIdThe ‘orientation’ attribute provides the description of imaginary orientation of bond links in a twodimensional plane. A value from 0 to 360 in anticlockwise direction is suggested as the possibleorientations along which the atoms are oriented with respect to the mapped atom
    • The Semantics at electronLink level Descriptor Presentational attributes attributes coordinates in pixels id The exact coordinates in pixel values at which the fragments are placed on the title screen are provided using ‘x1’, ‘y1’, ‘x2’, electronStatus and ‘y2’ for rendering the chemical charge structures on the computer screen as 2D Orientation graphics. These attributes renders the chargeCount “electronLink” as points with x1 = x2 and x1 affinity y1 = y2 indicating unmapped free links or y1 bond as the mapped bond link to show the x2 order chemical bond with the values as x1 ≠ x2 y2 and y1 ≠ y2. Accordingly a point at an linkStatus atom indicates the presence of an open Target “electronLink”. A line connecting between two atoms represents a chemical bond
    • The Semantics at atom level descriptor attributes Id Title Hybridization Title and symbol of atom Symbol Position isotopeLabel Carbon, hydrogen, nitrogen … presentational C, H, N … attributes x y
    • The Semantics at atom level descriptor attributes Id Title Hybridization Hybridization Symbol Position isotopeLabel specifies the hybridization status of the atom if any presentational Like sp, sp2, sp3, dsp2 etc attributes x y
    • The Semantics at atom level 7 10 2 8 9 descriptor 1 3 attributes 4 6 5 Id Position Title allows the numbering of atoms in a skeleton Hybridization Symbol Position isotopeLabel IsotopeLabel brings the possibility to label the atoms at any stage presentational of structure construction guided by external attributes ontology x y
    • The Semantics at Fragment level Descriptor attributes Title specifies the fragment name Id Type is used to indicate the class to which the Title Type fragment belongs as defined in the fragment ontology Symbol linkType Symbol denotes the symbol of the fragment like “C / H / N / OH / CHO / COOH / etc” Presentational attributes linkType to hold values such as “direct” or “bridge” or Orientation “fuse” or “spiro” to represent the nature of link when the Projection fragment is joined with other fragment during structure x1 y1 construction x2 y2
    • Additional Semantics The semantic level can be expanded further to accommodate “material” level to markup the substance or material material structure fragment atom The XML format of ChemFul includes the description of individual fragments inside a electronLink “structure” element and then all the “structure” elements into a “material” element. So, the ChemEd generates the ChemFul with an additional layer of semantics in terms of “structure” and “material” along with the details of fragments.
    • Our attempt on encoding Chemical Knowledge Conceptual Basis of Encoding Organic Groups and Functional Groups Punnaivanam Sankar*, Krief Alain, and Gnanasekaran Aghila To be communicatedChemical Knowledge Editor for Encoding Organic Groups and Functional Groups and Chemical Reactivity Punnaivanam Sankar*, Krief Alain, and Gnanasekaran Aghila To be communicated
    • ChemGp – Knowledge Editor for Groups, Functional Groups and Chemical Reactivity To be communicated
    • ChemEd captures and shows the information defined in ChemGp
    • Challenges to be solvedA common Vocabulary System EnCorE – ChemDic - online free access chemical dictionary to collect chemical terms from any part of the world to evaluate the terms by expert group online to publish in the InternetKnowledge Integration Computer Chemist ScientistFunding EnCorE Cheminformatician
    • conclusion The generation of reports meaningful for chemists will allow the development of interactive applications allowing chemists to encode and process his perceptions about the structure in a collaborative manner The semantic markup is suitable to develop algorithms for functional group interchange, functional group modifications etc. required for a meaningful reaction description The semantics at various levels will allow the possibility to create JAVA objects associated with suitable properties representing virtual substances and virtual materials to simulate reactions virtually The markup code is suitable for the conversion into the existing formats such as the Connection Table, Molfile, CML, SMILES, InChI etc. with suitable algorithms ChemEd can be suitably integrated with other applications to build open and shared applications working on common and approved vocabulary making use of chemical ontologies The markup system is suitable for the evolving Semantic Web
    • Thank you AcknowledgementThe authors acknowledge the support of:The Department of Science and Technology (DST), New Delhi, India for a funding supportThe Belgian Science Foundation (FNRS) especially for the creation of Fragment Library(A. Krief) and FUNDP (Namur, Belgium).Prof. Mark A. Musen, and Dr. Tania Tudorache, Biomedical Informatic Research Center(BMIR), Stanford University for their support in learning Protégé and developing OWLontologies in Protégé.
    • BicyclicTemplateFragment hasFragment hasFragment hasRingBridgeNumber hasBridgeSize hasRingSize valueRingSkeletonFragment BridgeSkeletonFragment value value The relationships in a bridged bicyclic ring system “Bicyclo221HeptaneRing” associated with “hasRingBridgeNumber” relations <DataPropertyAssertion> <DataProperty URI="&Fragment ontology;hasRingBridgeNumber"/> <Individual URI="&Fragment ontology;Bicyclo221HeptaneRing"/> <Constant datatypeURI="&xsd;string">6-1</Constant> </DataPropertyAssertion> <DataPropertyAssertion> <DataProperty URI="&Fragment ontology;hasRingBridgeNumber"/> <Individual URI="&Fragment ontology;Bicyclo221HeptaneRing"/> <Constant datatypeURI="&xsd;string">5-2</Constant> </DataPropertyAssertion>
    • source electronLink ionic covalent dative hydrogen <axiom • • • • • •¨ ¨ ¨ ¨ bondId="covalent" anion • • • • neutral • • cation δ+ • • • • • • sEStatus="uPair"¨ ¨ ¨ ¨ • • • • • • sChargeType="0" sBondType="covalent" tEStatus="uPair"• • • • • • • • tChargeType="0" tBondType="covalent" rsEStatus="bPair"• ¨ • • • • • • ¨ ¨ • rsChargeType="0"•anion • • • neutral • cation • δ+ rtEStatus="bPair"• • • • • • ¨ • • ¨ ¨ rtChargeType="0"/>• • • • • • ionic covalent dative hydrogen target electronLink
    • The functionalities of ChemEd is described in the following movies Movie 1 : draw Cyclohexane carboxaldehyde Movie 2 : draw Norbornanone Movie 3 : draw structures with ion-ion interaction Movie 4 : draw structures with ion-dipole interaction Movie 5 : draw structures showing metal-pi interaction Movie 6 : creation and use of steroid template Movie 7 : detection of isomerism (R/S) (E/Z) Movie 8 : isotope labeling, projection labeling
    • Reaction components + Equipment Actions Substances Substances ObservationsMethylation of norbornanone Bridgehead H H H O O O H Exo (i) 2 eq. NaNH2, ether, 20 °C, 1h, reflux, 1h + H Me H (ii) 3 eq. MeI, ether, 20°C, 2h Me H 80 % 20 % EndoBicyclo[2.2.1]heptan-2-one 3-methylbicyclo[2.2.1]heptan-2-oneNorbornan-2-one 3-methyl-norbornanone