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

Encoding of Chemical Knowledge in the Context of Evolving Semantic Web

Consolidating 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 Text

http://en.wikipedia.org/wiki/Acetaldehyde

Structure databases

Structure representation formats

Other structure related data


Conceptual

Name Formula Structure Properties Reactions

Making the chemistry
Chemical structure is central domain different from other
for all chemical information domains in the context of
and 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 Scenario

The chemical domain has to adopt with the changing scenario of web by considering the
followings:

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 hemiacetal
Material / 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 group
Hybridization Protonation at carbonyl oxygen atom
Alpha carbon
geometry Addition of methanol to carbonyl carbon
Ring skeleton (bridged, fused, spiro)
Charge status Elimination of proton
Linear skeleton
Electronic environment
Bridgehead position
Bonding details Formation of acetal
Exo / endo orientation of groups
Location of the atom on
Axial / equatorial orientation of groups
specific skeleton structure Protonation of hydroxyl group
Reaction sites
Presence of lone pair electrons Loss of water by elemination
Heat
isotope label Addition of methanol to oxonium ion
Pressure
Isomerism (optical, Breaking of pi bond
Light
geometrical, etc) Loss of proton
Time
etc. etc
Action, equipments, observation

Chemist Computer

Structural Reaction Structural Reaction
information information information information

Chemist Chemist
knowledge knowledge

Through a proper structure description system
rich in semantics
Out of experience and expertise gained over
the period of years a chemist is capable of Integration of external knowledge resources
correlating the structural features with reaction through chemical ontologies
specific details
Tools to integrate reaction knowledge with
structural features

An approach available to achieve encoding of chemical knowledge

ontology XML

Semantics

Chemical Ontologies implemented in OWL Java based programs

Ontology 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 /
Academics

We are interested to associate with people / group to achieve our proposed objectives

Thank you

Acknowledgement

The authors acknowledge the support of:

The Department of Science and Technology (DST), New Delhi, India for a funding
support

The 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 OWL
ontologies in Protégé.

Development of a Semantically Rich
Structure Representation System

Model 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


Structure
Fragment
has

isA Fragment Fragment
Fragment

has isA
Fragment Fragment

Atom
Fragment
has

Electron


O

H C
Structure C H

H
H
Chemical
Ontology
H C
Fragment O

Atom
H C O

Electron H C O

XML

Composition of Fragment

Fragment

has
Atom

has
Atom

ElectronLink ElectronLink ElectronLink
has


Atom

has

Atom

has


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 bar
ChemEd – 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 to
Cursor 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


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


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 as
draw 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


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.


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


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
drawing

To create one / two / three To draw skeleton systems
member 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 and
Displays in the Functional Group Panel

ChemEd – Shows the functional group specific information along with the chemical groups and the
Reactivity 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"/>
y2="136"/>
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
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"
y2="121"/>
y2="166"/>
y2="121"/>

XML markup generated by ChemED for the construction of benzaldehyde structure

ChemFil

<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“
<modification title="Atom" sourceObject="Oxygen" targetObject="Carbon" targetId1="s1-2-a1” targetId2="" x1="0" y1="0"/>
</structure>
</structureGroup>

2 KB

Markup for Benzaldehyde construction


<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“

<fragment id="s1-3" title="Hydrogen" type="AtomFragment" template="BenzeneRing”link="direct" orientation="330“

<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=""

chargeCount="0" affinity="" bond="sigma" order="single" linkStatus="linkSource"
y2="136"/>
C
chargeCount="0" affinity="" bond="sigma" order="double" linkStatus="linkTarget"
y2="91"/>
Fragment
<electronLink id="s1-1-a1e3" title="2pz" electronStatus="bPair" charge="0"
chargeCount="0" affinity="" bond="pi" order="double" linkStatus="link"
y2="91"/>

y2="136"/>

</atom>

</fragment>

Fragment markup – semantics at atom level



y2="136"/>

C <electronLink id="s1-1-a1e2" title="2sp2" electronStatus="bPair" charge="0"
y2="91"/>
Atom
y2="91"/>

y2="136"/>

</atom>

</fragment>

Fragment markup – semantics at electronLink level




C y2="136"/>

y2="91"/>
electronLink
y2="91"/>

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



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



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


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…
projection

Meaningful 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 the
values “lPair”, “-” and “1” for ‘electronStatus’, ‘charge’ and ‘chargeCount’ attributes respectively provides the
meaning of acquired negative charge due to the gain of one electron.



id
title
electronStatus
charge
chargeCount
provides the orientation
affinity semantics of X1
Y1
bond
order chemical bonding X2
y2
linkStatus
Target
projection



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



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



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



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
linkTargetId

The ‘orientation’ attribute provides the description of imaginary orientation of bond links in a two
dimensional plane. A value from 0 to 360 in anticlockwise direction is suggested as the possible
orientations along which the atoms are oriented with respect to the mapped atom



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


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

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


To be communicated

Chemical Knowledge Editor for Encoding Organic Groups and Functional
Groups and Chemical Reactivity


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 solved
A 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 Internet

Knowledge Integration
Computer
Chemist
Scientist
Funding
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

BicyclicTemplateFragment

hasFragment hasFragment

hasRingBridgeNumber
hasBridgeSize
hasRingSize value
RingSkeletonFragment 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
Observations

Methylation 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 %
Endo

Bicyclo[2.2.1]heptan-2-one 3-methylbicyclo[2.2.1]heptan-2-one
Norbornan-2-one 3-methyl-norbornanone

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

Recommended

Recommended

More Related Content

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

Similar to EnCOrE: Chemistry, Education, Knowledge From the Real to the Virtual Needs, Perceptions, Tools, Concepts - P. Sankar (20)

More from webscience-montpellier

More from webscience-montpellier (11)

Recently uploaded

Recently uploaded (20)

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