Talk at Web Science Montpellier Meetup - 13th May 2011

1. EnCOrE
Chemistry, Education, Knowledge.
From the Real to the Virtual.
Needs, Perceptions, Tools, Concepts
Montpellier, 05/12/2011

2. For organic chemists by organic chemists
http://www-fleming.ch.cam.ac.uk/http://www.fundp.ac.be/facultes/sciences/departements/chimie/recherche/centres/cos/
We plan to create a freely available, net-
based, encyclopaedia of organic chemistry.
It will remain up-to-date to assist education,
and provide information and knowledge in
organic chemistry at all levels from
university students to practitioners in
research.
(I. Fleming, A. Krief, 28.08. 1999)

3. "In a time of turbulence and
change, it is more true today than
ever that knowledge is power."
John Fitzgerald Kennedy
State of the Union: Knowledge, 1963; White House Dinner Reception, April 1962;
http://www.socialstudieshelp.com/Lesson_104_GreatQuotes.htm)

4. Turnover 2009
€ 1,900 billion (Basic)
€ 550 billion (Pharma) Chemistry ?
Chemistry is the science of substances: their structure, their
properties, and the reactions that change them into other substances
(Pauling, Linus, 1947, General Chemistry. Dover Publications, Inc.. ISBN 0486656225.
composition, structure, properties, matter, changes, reactions, atomic, molecular, supra-
molecular, art.

5. WebScience for what purpose ?
Learning, Teaching & Chemical Encyclopedia
Formal learning requires to take into account:
• the past (what is known by the learner)
• the future (what we want to achieve and to what
purpose)
Encyclopedia should be
• inspiration for teachers to which they can link their
presentations
• an help to learner to access more detailed information
• a standardization of secure source of chemical
knowledge and data

6. Distant Learning Course in
Organic Chemistry
1. University of Mexico & IOCD (http://organica1.org)
2. Visits: 1,400 000 (2009); 1,850 000 (45,000 000 clicks, 2010);
>2,200 000 (2011)
3. Visited by students & Professors Universities of Mexico, Colombia,
Chile, Venezuela,
4. Reasons
1. Continuous update of the information for nearly 13 years (Since
1998)
2. Visitors are not required to register;
3. Material is free to use and in different versions, PDF, Power
Point, Flash, Text, HTML, etc
4. The programs are very visual and interactive in order to help
students to understand and learn difficult concepts.
5. Future
1. Developing applications for mobile, iphone and ipad (light
version: free of charge;
2. Full version nominal cost of US$5-10, to generate resources to
expand the program, and give more visibility to IOCD.

7. From Guttemberg to HTML
7
http://www.nwlink.com/~donclark/history_knowledge/printpress.html http://www.greatsite.com/facsimile-reproductions/gutenberg-1455.html

8. WebSicence = Tools?
E-learning = Series of tools?
Do we a need it?
For what purpose ?
Wranch Screw drivers
Bolts
Screws

9. WebSicence = Database?
E-learning = Series of Databases?
Concepts, Tools, Databases, Infrastructures

10. Teacher/learners interactions
Computer / Human interactions Teacher/learner interactions (Human/Human)
Strategy
1. Understand how the Chemists behave
2. Understand how the Computer works
3. Describe protocols to transfer the message from Human to Computer
4. Use the proper language & psychology to train a Computer

11. Chemical Information
ChemDic
Describing Chemical terms
in context
Name of chemists
Abbreviations
Entry to the Encyclopedia
Description of
structures is related Chemical dictionary
to Ontological dictionary
Visual perceptions Etymological dictionary
Grammatical dictionary
Encyclopedic dictionary
ChemEd Visual dictionary
Translator
Describing chemical structures
in text
in context
Describing numbers related to
chemical structures in text
ChemGroup
ChemOrg ©◊

12. Visual perceptions:
Photography of a painter painting
Camera, Film
Eye, Brain
Perceive
Process
Hodler peignant « Le Faucheur » sur le toit de son atelier, rue du Rhône à Genève Express
Photographie anonyme 1910 Winterthour SSP © Fotostiftung Schweiz, Winterthur
Shared Vision
"All our knowledge has its origins in our perceptions" (Leonardo da Vinci)

13. Mimesis & Perception of painters
Gericault
Galopping horse photograph by E. Muybridge (1878)
Gericault Miro

14. Photos and Retouching
M. Minoret
Martial Caillebotte
Martial Caillebotte rowing Gustave Caillebotte
Soins naturels NIVEAwww.nivea.be/pure&natural
Soins enrichis en huile d'argan
BIO Pour une belle peau, naturellement
Caillebotte
Martial Caillebotte Gustave Caillebotte
portrait
http://www.creabar.com/tutoriaux,poupee.html

15. Mimesis & contextual perception in chemistry
Context Name and Formula
7,7-dimethylbicyclo[2.2.1]heptan-2-one
O
C9H14O
Context Framework, Groups and Functional Groups
O O
Context Spectroscopy (NMR)
H H 1H NMR 0.99 0.99 21.1 45.2 21.1 13CNMR
H H
HH H 2.03 58.1
H O 1.88;1.62 O 25.0 O
H 218.5
H H
H H 1.59;1.34 1.99 2.15;1.90 27.6 43.3 44.1
H 3 2 1 0 240 220 200 180 160 140 120
PPM
100 80 60 40 20 0
PPM

16. Mimesis & contextual perception in chemistry
Contexte of reactivity
H H
H
H OLi OLi
OO
O LDA
H N Li
H
H HH H
H
H
Me
MeLi Me OLi
CH2 Ph3P CH2 H O
O
O
LiBr OLi Me
H
Context of synthesis
RO CN OR O
O O
+ H
+ H
CN
H H

17. ChemEd : Graphical User Interface (GUI)
Ontology Ontology Ontology Ontology Ontology
1 2 3 4 5
Query H
O
O
O
HO
H
Zzadcf gjdbn Ccbnxw sssss azerty
sxnkv;f,n;xw bn wnwxn,n;wx uiopqsdfghjklmù
cccccc wx, cvbn bn
cccccc wnwxn,n;wx
sssssssss
VVVVVVVVV
<?xml version="1.0"?> cccccc
<structure id="s1" title="acetaldehyde.xml">
<fragment fNo="0" id="0carbon" title="carbon" type="base" linkHead1="" linkHeadId1=“” linkHead2="" linkHeadId2=""
x1="" y1=""/>
<fragment fNo="1" id="1carbonyl" title="carbonyl" type="singleLink" linkHead1="0”linkHeadId1="carbon-a1-o1"
linkHead2="" linkHeadId2="" x1="" y1=""/>
<fragment fNo="2" id="2hydrogen" title="hydrogen" type="singleLink" linkHead1="1” linkHeadId1="carbonyl-a1-o4"
linkHead2="" linkHeadId2="" x1="" y1=""/>
</structure>

18. “In a time of turbulence and change, it is more true today than ever that knowledge is power" (John Fitzgerald Kennedy, State of the Union, 1963;
White House Dinner Reception, April 1962). "In the new economy, information, education, and motivation are everything" (William J. Clinton).
"Dreams are often most profound when they seem the most crazy" (Sigmund Freud). "Il est établit que nous ne pensons qu'avec le secours des
mots; que les langues sont de véritables méthodes analytiques; que l'algèbre la plus simple, la plus exacte et la mieux adaptée à son objet de
toutes les manières de s'énoncer, est à la fois une langue et une méthode analytique; enfin, que l'art de raisonner se réduit en une langue bien
"In the new economy, information, education, and
faite. Et en effet, tandis que je croyais ne m'occuper que de nomenclature, tandis que je n'avais pour objet que de perfectionner le langage de la
chimie, mon ouvrage s'est transformé insensiblement entre mes mains, sans qu'il m'ait été possible de m'en défendre, en un traité élémentaire
de chimie. L'impossibilité d'isoler la nomenclature de la science et la science de la nomenclature tient à ce que toute science physique est
motivation are everything” (William J. Clinton).
nécessairement formée de trois choses : la série des faits qui constituent. la science ; les idées qui les rappellent ; les mots qui les expriment. Le
mot doit faire naître l'idée; l'idée doit peindre le fait : ce sont trois empreintes d'un même cachet ; et, comme ce sont les mots qui conservent les
idées et qui les transmettent, il en résulte qu'on ne peut perfectionner le langage sans perfectionner la science, ni la science sans le langage, et
que, quelque certains que fussent les faits, quelque justes que fussent les idées qu'ils auraient fait naître, ils ne transmettraient encore que des
impressions fausses, si nous n'avions pas des expressions exactes pour les rendre" (A. Lavoisier, Traité élémentaire de Chimie, 1789). "La
chimie crée son objet " (Marcelin Berthelot, 1860). "A scientific truth does not triumph by convincing its opponents and making them see the light,
"..dove la natura finisce di produrre le sue specie, l'uomo
but rather because its opponents eventually die and a new generation grows up that is familiar with it" (Max Plank). Research is what I'm doing
when I don't know what I'm doing (Wernher von Braun). "..dove la natura finisce di produrre le sue specie, l'uomo quivi comincia con le cose
naturali, con l'aiutorio di essa natura a creare infinite spezie" (Leonardo da Vinci, Designi Anatomici). "Le langage est une législation, la langue
quivi comincia con le cose naturali, con l'aiutorio di essa
en est un code" (Roland Barthes, Leçon inaugurale, Collége de France, 1977). "Tout comme il existe un domaine de la chimie moléculaire
caractérisée par la molécule covalente, il existe un domaine de la chimie supramoléculaire qui est la chime des assemblages moléculaires et de
natura a creare infinite spezie" (Leonardo da Vinci,
la liaison intermoleculaire" (Jean-Marie Lehn,1978). "A man should look for what he thinks should be" (Albert Einstein). "Do not quench your
inspiration and your imagination; do not become the slave of your model" (Vincent Van Gogh). "Education is what remains after one has forgotten
what one has learned in school" (Albert Einstein). "Education is the most powerful weapon which you can use to change the world" (Nelson
Designi Anatomici)
Mandela). “Never doubt that small group of dedicated individuals can change the world. In fact it is the only thing that ever has" (Magaret Mead).
“Facts are the air of scientists. Without them you can never fly" (Linus Pauling). "Give me a lever long enough and a fulcrum on which to place it,
and I shall move the world" (Archimede). "All our knowledge has its origins in our perceptions" (Leonardo da Vinci). Iron rusts from disuse; water
loses its purity from stagnation even so does inaction sap the vigor of the mind (Leonardo da Vinci). "Man is the best computer we can put
aboard a spacecraft, and the only one that can be mass produced with unskilled labor" (Wernher von Braun). Analogies, it is true, decide nothing,
but they can make one feel more at home" (Sigmund Freud). "Conscience is a man's compass" (Vincent Van Gogh). "Eppur si muove" (Galileo
“Never doubt that small group of dedicated individuals
Galile, 1633). "If you will it, it is no dream" (Theodor Herzl. "Le meilleur travail n'est pas celui qui te coûtera le plus ; c'est celui que tu réussiras le
mieux " (Jean-Paul Sartre, 1948). Lorsqu'un nouveau domaine de science apparait, grandit et murit, il élabore des concepts fondamentaux et
génère une terminologie pour nommer les concepts qui le définissent et les objets qui le constituent. Le fait de conceptualiser et de nommer joue
can change the world. In fact it is the only thing that ever
un rôle très important non seulement pour donner forme au domaine mais aussi parce qu'il offre un projet à l'imagination créatrice-tant il est vrai
que l'imagination peut se laisser emporter par la magie des mots et entrainer par le pouvoir évocateur et stimulant des concepts (Jean-Marie
has" (Magaret Mead)
Lehn, 1995). "After climbing a great hill, one only finds that there are many more hills to climb" (Nelson Mandela). Age is whatever you think it is.
You are as old as you think you are" (Muhammad Ali). "Silence is the ultimate weapon of power" (Charles de Gaulle). "A man who views the
world the same at fifty as he did at twenty has wasted thirty years of his life"(Muhammad Ali). ). "J'ai entendu vos points de vue. Ils ne rencontrent
pas les miens. La décision est prise à l'unanimité" (Charles de Gaulle). "Time destroys everything" (Monica Bellucci). "In today's knowledge-
based economy, what you earn depends on what you learn" (William J. Clinton). "Always bear in mind that your own resolution to succeed is
more important than any other" (Abraham Lincoln). "We all need illusions. That's why we love movies" (Monica Bellucci). Ugliness is in a way
superior to beauty because it lasts (Serge Gainsbourg). ). "Better to die standing, than to live on your knees (Ernesto "Che" Guevara)

19. EnCOrE Organization from Matter to Substance
matter
material Chemical Physical Energy
properties properties
mixture of chemical
chemical substance Chemical Physical Exothermic Radiative
substances
changes changes Change energy
solid/liquid/gaz Kinetic
Chemical Changes Endothermic energy
changes of state Change
pure chemical Potential
substance energy
methane, graphite Conformationnal Chemical Chemical
changes reaction Transformation
pure chemical substance Inorganic Organic Oxidation Transformation
pure chemical substance reaction reaction status type
isotopically
isotopically heterogeneous
homogeneous
Named Oxidation Addition
reactions
Reduction Substitution
hysoipsic Elimination
chemical substance isotopically enriched
isComposedOf natural abundance Rearrangement
13CH , C2H4
chemical substance
4

20. EnCOrE Organization from Matter to Substance
matter
material Chemical Physical Energy
properties properties
mixture of chemical
chemical substance
substances
solid/liquid/gaz
pure chemical
homogeneous interface heterogeneous
substance
methane, graphite
single phase colloid
pure chemical substance solution composite
pure chemical substance
isotopically
isotopically heterogeneous
homogeneous multiphase
solvent solute composition molarity
chemical substance isotopically enriched
isComposedOf natural abundance
13CH , C2H4
chemical substance
4

21. Pure chemical substance
EnCOrE Organization from Matter to Substance
isotopically
homogeneous
Metallic Molecular Supramolecular
compounds compounds compounds
Metal Molecule Supramolecule Ionic compounds
Helium, chlore, methane
Interaction
Species
Week
Strong interaction
interaction
Atom
Ion mechanical Hydrogen
Element covalent bond bond bonding
Like H, C, O
Radical- Ion/dipole Dipole/dipole
isAKindOf ion interaction interaction
isACollectionOf
metallic bond Cation-Pi Pi-Pi interaction
Radical interaction
Isotope
Like 1H, 2H, 3H Hydrophobic Van der Walls
Intermediate
interaction interaction
s

22. From Atom to AtomGroup
BeCl2
A A
VSEPR Theorie
Linear0
BF3 O3 Linear
CH3+ trigonal planar
Bent
A A A Tetrahedral
Trigonal pyramidal
Trigonal bipyramide
Seesaw
CH4 NH3 H2O HCl T-shaped
NH4+ Octahedral
A A A A Square pyramidal
SO42-
Square
A A A A A
SF6
Fe(CN)63-
Fe(CN)64-
Ni(NH3)62+
A A A A A A

23. From Atom to Functional Group
Hydrogen Hydrogen
Isotopes Element
Hydrogen
H H H H
Atom
Hydrogen Hydronium Hydride Hydrogen
AtomGroup ion ion Radical
Deuterium
Atom
Tritium
Atom

24. From Atom to Functional Group
Carbon Carbon
Isotopes Element
C C C
11-Carbon
Carbonium Carbon Aromatic Carbenium Carbanion Carbon
ion AtomGroup carbon ion Radical
12-Carbon
C C C C
C C
13-Carbon
C
C C C C C C
Di-carbenium Radical-cation Carbene
14-Carbon C Di-carbanion Radical-anion
C
C C

25. Knowledge?
Knowledge differs from data or information in that new knowledge
may be created from existing knowledge using logical inference. If
information is data plus meaning then knowledge is information plus
processing (http://www.thefreedictionary.com/knowledge)
Kowledge can include facts and information, as well as understanding
that is gained through experience, education or reason. It can be:
implicit (as with practical skill or expertise) or explicit (as with the
theoretical understanding of a subject), more or less formal or
systematic (http://en.wikipedia.org/wiki/Knowledge)
Knowledge is human faculty resulting from interpreted information;
understanding that germinates from combination of data, information,
experience, and individual interpretation.
http://www.businessdictionary.com/definition/knowledge.html
Knowledge has come to be recognized as a factor of production in its
own right, and distinct from labor.

26. Learning ?
Learning is acquiring new or modifying existing knowledge, behaviors,
skills, values, or preferences and may involve synthesizing different
types of information.
The ability to learn is possessed by humans, animals and some machines
Human learning may occur as part of education, personal development,
or training. It may be goal-oriented and may be aided by motivation.
The study of how learning occurs is part of neuropsychology,
educational psychology, learning theory, and pedagogy.
Learning may occur as a result of habituation or classical conditioning,
(seen in many animal species, or as a result of more complex activities
such as play, seen only in relatively intelligent animals). Learning may
occur consciously or without conscious awareness.
Play has been approached by several theorists as the first form of
learning. (Lev Vygotsky, Social constructivism)

27. Learning?
Learning is the act, process, or experience of gaining knowledge
or skill (The free dictionary)
Learning is knowledge or skill gained through schooling or study
(The free dictionary)
Learning is behavioral modification especially through experience
or conditioning (The free dictionary)
Learning is measurable and relatively permanent change in behavior
through experience,
Learning is "detection and correction of error" where an error
means "any mismatch between our intentions and what actually
happens" (Harvard Business School psychologist Chris Argyris)
(Business dictionary

28. E-Learning?
E-Learning
E-learning is essentially the computer and network-enabled transfer of
skills and knowledge. E-learning applications and processes include
Web-based learning, computer-based learning, virtual classroom
opportunities and digital collaboration. Content is delivered via the
Internet, intranet/extranet, audio or video tape, satellite TV, and CD-
ROM. It can be self-paced or instructor-led and includes media in the
form of text, image, animation, streaming video and audio (Wikipedia).
E-learning that is supported by information and communication
technologies (ICT). E-learning is, therefore, not limited to ‘digital
literacy’ (the acquisition of IT competence) but may encompass
multiple formats and hybrid methodologies, in particular, the use of
software, Internet, CD-ROM, online learning or any other electronic or
interactive media (European Commission).

29. Chemistry ?
Chemistry is the science of matter
Chemistry is the branch of the natural sciences dealing with the
composition of substances and their properties and reactions.
(wordnetweb.princeton.edu/perl/webwn)
Chemistry is the science of the composition, structure, properties, and
reactions of matter, especially of atomic and molecular systems.
http://www.thefreedictionary.com/chemistry
Chemistry is the art of resolving mixt, compound, or aggregate bodies
into their principles; and of composing such bodies from those
principles (Stahl, 1730, Philosophical Principles of Universal Chemistry. London.)
Chemistry is the science of substances: their structure, their
properties, and the reactions that change them into other substances
(Pauling, Linus, 1947, General Chemistry. Dover Publications, Inc.. ISBN 0486656225.
Chemistry is the study of matter and the changes it undergoes
(Chang,1998, Chemistry, 6th Ed.. New York: McGraw Hill. ISBN 0-07-115221-0)