Chemical Semantics at Sopron CC Conference

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ChemicalSemantics, Inc.

Publication and Retrieval of Computational Chemical-Physics Data via The Semantic Web

Applying the Semantic Web to Computational

Chemistry

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Chemical Semantics, September 20132

What is this all about ?

The principal objective of our enterprise is to create a testbed for comprehensive exploration of ideas behind the practical application of the Semantic Web in computational chemistry.

The aforementioned working testbed (Chemical Semantics Portal) is initially limited to computational chemistry and a limited class of users.

In addition, we will focus on the semi-empirical, ab-initio and density functional (DFT) calculations of quantum chemistry and their typical results.

The purpose of this talk is to present the ideas of the Semantic Web and their possible application in computational chemistry, and to present the working prototype of the Chemical Semantic Portal.

3Dr Mirek Sopek

INTRODUCTIONThe Basics of Semantic Web

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The evolution of the

Web

WEB 1.0 - Web of documents

WEB 2.0 - Social, Read/Write Web

WEB 3.0 - Semantic Web = Web of Data

? WEB 4.0 - Intelligent Web ?

* Assuming Christmas 1990 as its beggining

(http://en.wikipedia.org/wiki/History_of_the_World_Wide_Web)

The web is only 8287 days* (23 years) old !Print – 203,800 daysNewspapers – 142,800 daysRadio – 41,200 daysTV – 28,000 days

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Web 1.0 – Web of

documents1989-2000 - Web of Hyperlinked documents

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Web 2.0 – Social/Read-Write

Web2000-2010 - The Web of Social Networks and “Wisdom of the Crowds”

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Web 3.0 – Semantic Web

2010-2020(?) - Web of Data, Linked Data Web

Link

Link

Link

Link

Link

Link

Link

Link

LinkLink

Resource

Resource

Resource

Resource

Resource

Resource

Resource

Resource

hasPeople

humanResources

hasServices

hasProducts

hasPeople

hasPeople

hasProduct

hasProduct

colleague

colleague

Organization

HR

Services

Products

People

People

Product

Product

8Dr Mirek Sopek

What is wrong with today’s Web?

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The WEB is TOO BIG to know

Web 1.0 & 2.0 major

issuesThe WEB is TOO BIG to knowSocial Web dwells in isolated silos

Data Deluge - Scientific data stored in isolated silos

?

People look at the Web through Google’s Goggles

10Dr Mirek Sopek

THE SOLUTION:Semantic Web – Web 3.0

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What is Semantic Web ?

The Semantic Web is a Web of data. It is an extension of the current Web that provides an easier way to find, share, reuse and combine

information.

“The vision of the Semantic Web is to extend principles of the Web from documents to data.(...) This also means creation of a common framework that allows data to be shared and reused across application, enterprise, and community boundaries, to be processed automatically by tools as well as manually, including revealing possible new relationships among pieces of data.”http://www.w3.org/2001/sw/

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Foundations of Semantic

Web

“Semantic” in “Semantic Web” is about MEANING of data, not about the syntax it is expressed in. Semantic Web = Web Full of Meaning = Web of meaningful DataSemantic Web is about representation of THINGS (OBJECTS and CONCEPTS) and their properties on the Web, not just about documentsSemantic Web uses global NAMING scheme to identify THINGS, not just to address documentsSemantic Web links THINGS with TYPED LINKS, not with “blind” hyperlinksSemantic Web allows DISCOVERY of new FACTS about THINGS, not just browsing through pages

* Picture by Roger Sayle (http://pubs.acs.org/doi/abs/10.1021/ci800243w)

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Example

COC(=O)[C@H](C1=CC=CC=C1Cl)N2CCC3=C(C2)C=CS3InChI=1S/C16H16ClNO2S/c1-20-16(19)15(12-4-2-3-5-13(12)17)18-8-6-14-11(10-18)7-9-21-14/h2-5,7,9,15H,6,8,10H2,1H3/t15-/m0/s1

InchI (Key)=GKTWGGQPFAXNFI-HNNXBMFYSA-N

“Plavix” (Clopidogrel)

* Based on “Foreign Language Translation of Chemical Nomenclature by Computer” by Roger Sayle (DOI: 10.1021/ci800243w)

http://www.chemspider.com/InChIKey=GKTWGGQPFAXNFI-HNNXBMFYSA-N

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How do we represent THINGS on

SW

On the Semantic WEB we represent THINGS using elementary UNITS of data: TRIPLES.

We can create logical and structural relations between elements of the triple, build taxonomies, vocabularies and classes and finally “reason” on large sets of triples.

The file format we store the triples in — is called RDF.

:H2O gnvc:hasInChIString “1S/H2O/h1H2”

For example:

Subject Predicate Object

Thing Property Value

Resource Description Framework

:hasMolecularMass “18.0153”

“RDF is for THINGS as HTML is for DOCUMENTS”

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How do we Identify Things on the Semantic Web

For unambiguous identification of things (objects) on the Web and their properties, Semantic Web uses URIs — Universal Resource Identifiers, a generalization of URL i.e. Ordinary Web addresses:

WaterMolecular

Mass “18.0153”

http://www.chemicalsemantics.com/h2o

http://purl.org/chem/ns#MM A number

Chemical Semantics, September 201316 Hypercube

RDF/XML or

Turtle (Terse RDF Triple Language)1 @prefix cs: <http://ChemicalSemantics.com/chem/dictionary/ns#> .2 @prefix mol: <http://ChemicalSemantics.com/chem/molecules/simplewater.ttl#> .3 @prefix xs: <http://www.w3.org/2001/XMLSchema#> .4 mol:molecule_31 a cs:molecule ;5 cs:name “water" ;6 cs:atom _:atom31_1 ;7 cs:atom _:atom31_2 ;8 cs:atom _:atom31_3 ;9 cs:bond _:bond31_1 ;10 cs:bond _:bond31_2 .11 _:atom31_1 cs:atomType cs:O ;12 cs:x3 "-0.381950"^^xs:double;13 cs:y3 "0.243825"^^xs:double;14 cs:z3 "0.000000"^^xs:double.15 _:atom31_2 cs:atomType cs:H ;16 cs:x3 "-0.381950"^^xs:double;17 cs:y3 "1.203825"^^xs:double;18 cs:z3 "0.000000"^^xs:double.19 _:atom31_3 cs:atomType cs:H ;20 cs:x3 "0.523148"^^xs:double;(.....)

RDF Serialization – preliminary

example

http://ChemicalSemantics.com/chem/dictionary/ns

http://ChemicalSemantics.com/chem/molecules/smplewater.ttl



http://www.w3.org/2001/XMLSchema

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Semantic Web allows Discovery

Semantic Web tools for building “inteligent” vocabularies – RDFS (RDFS Schema) and OWL ontologies allow for simple logical INFERENCES and discovery of IMPLICIT facts.For example: When a user searches for a molecule with specific properties, it is possible to automatically provide him with other molecules that belong to the same “class” of molecules. .

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Semantic Web = GGG (Giant Global Graph)

Organization

HR

Services

Products

People

People

Product

Product

hasPeople

humanResources

hasServices

hasProducts

hasPeople

hasPeople

hasProduct

hasProduct

colleague

colleague

GGG – term coined by Tim Berners Lee in 2007

Ooops… sorry, but it’s BIG

Semantic Web = GGG (Giant Global Graph)

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Core Semantic Web Technologies

RDF — Resource Description Framework

RDFa — RDF “in attributes”

RDFS — Resource Description Framework Schema Language

OWL — Ontology Web Language

SPARQL — Semantic Protocol & RDF Query Language

RIF — Rule Interchange Format

RDF deals with THINGS

RDFa enables to embed RDF into ordinary HTML Web Pages

RDFS deals with SETS and CLASSES of THINGS

OWL deals with intelligent VOCABULARIES (with logical relations between concepts)

SPARQL allows for searching through graphs of triples stored in “triple stores”

RIF allows to express and interchange generalized IF...THEN constructs

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AAA — Anyone can say Anything about Any Topic.

... and one about Semantic Web Philosophy

OWA — Open World Assumption.We must assume that at any time a new piece of information may come so we can’t assume that we have ALL the information at the moment of information consumption. It also means that not knowing something does not necessarily imply falsity!

Hendler Hypothesis:“A Little Semantics Goes A Long Way”

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Link Data Four Principles:• Use WEB ADDRESES (URLs) as names for

things.

• Use ADDRESSES THAT WORK ON THE WEB - so that people can look up those names.

• When someone looks up a URL, PROVIDE USEFUL INFORMATION, USING THE STANDARDS (like RDF).

• Include LINKS TO OTHER URLs, so that they can discover more things.

Hendler Hypothesis in

action...

The Semantic Web isn't just about putting data on the web. It is about making links, so that a person or machine can explore the web of data. With linked data, when you have some of it, you can find other, related, data. (Tim-Berners Lee)

http://www.cafepress.com/w3c_shop

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Ontologies

“An ontology formally represents knowledge as a set of concepts within a domain, and the relationships between pairs of concepts. It can be used to model a domain and support reasoning about concepts.” (Wikipedia)

The fundamental goals of ontologies:

Define concepts used in Semantic graphs (like RDF)

Enable terminological standardisation

Provide tools for building intelligent dictionaries with synonyms and cross-references

Enable encoding of taxonomies (hierarchical definitions)

Enable reasoning and inferencing – discovering implicit knowledge

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

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


Antoine Lavoisier “Traité élémentaire de chimie”

Early ideas in ontology

"We think only through the medium of words. --Languages are true analytical methods. (…) The art of reasoning is nothing more than a language well arranged.

Thus, while I thought myself employed only in forming a Nomenclature, and while I proposed to myself nothing more than to improve the chemical language, my work transformed itself by degrees, without my being able to prevent it, into a treatise upon the Elements of Chemistry.


Nivaldo J. Tro “Chemistry. A Molecular Approach”

Example of Ontology “Hello world”

@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .@prefix chem: <http://purl.org/chem/simple_classification#> .@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .@prefix foo: <http://example.com/this/> .

## Classes

chem:Matter a rdfs:Class ; rdfs:label "Matter"@en ;

rdfs:label "Matière"@fr ; rdfs:label "Materia"@pl .

chem:PureSubstances a rdfs:Class ; rdfs:label "Pure Substances"@en ; rdfs:label "Substances Pures"@fr ; rdfs:label "Substancja"@pl ; rdfs:subClassOf chem:Matter .

chem:Mixture a rdfs:Class ;

rdfs:label "Mixture"@en ;rdfs:label "Mélange "@fr ;rdfs:label "Mieszanina"@pl ;

rdfs:subClassOf chem:Matter .

chem:Heterogeneous a rdfs:Class ;rdfs:label "Heterogeneous"@en ;rdfs:label "Hétérogène"@fr ;rdfs:label "Heterogeniczny"@pl ;rdfs:subClassOf chem:Mixture .

chem:Homogeneous a rdfs:Class ;rdfs:label "Homogeneous"@en ;rdfs:label "Homogène"@fr ;rdfs:label "Jednorodny"@pl ;rdfs:subClassOf chem:Mixture .

## Properties

chem:atomicNumber a rdf:Property ;rdfs:domain chem:Element; rdfs:range rdfs:Literal .

chem:moleculeName a rdf:Property ;rdfs:domain chem:Compound; rdfs:range rdfs:Literal .

chem:componentName a rdf:Property ;rdfs:domain chem:Mixture ;rdfs:range chem:Matter .


Non-Trivial Ontologies in Chemistry

ChEBI – Chemical Entities of Biological Interest

http://www.ebi.ac.uk/chebi/

Project of EMBL-EBI

European Bioinformatics Institute (Cambridge) of European Molecular Biology Lab (Heidelberg)

OBO Foundry Ontology (http://www.obofoundry.org/ )The Open Biological and Biomedical Ontologies

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The term ‘molecular entity’ refers to any constitutionally or isotopicaly distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.ChEBI incorporates an ontological classification, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified.



http://www.obofoundry.org/




Non-Trivial Ontologies in Chemistry

ChemINF – Chemical Information Ontology

https://code.google.com/p/semanticchemistry/Janna Hastings, Nico Adams, Christoph Steinbeck (EBI)Leonid Chepelev, Michel Dumontier,Egon Willighagen, Nico Adams

OBO Foundry Candidate

ChemINF descibes:

• Chemical graphs, and various formats for encoding them.• Chemical descriptors, with definitions and axioms describing what they

are specifically about.• Specifications for certain descriptors.• Algorithms and their software implementations and axioms describing

their inputs and outputs.• Chemical data representation formalisms and formats.

https://code.google.com/p/semanticchemistry/

https://code.google.com/p/semanticchemistry/

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Chemical Semantics Ontology

http://purl.org/gc/gc.owl

Gainesville Core (alpha edition)

Gainesville Core describes:• Molecular Publications• Molecular Systems• Molecular Calculations Molecular Systems contain Molecules• The Molecules may have Residues (for

biopolymers and polymers)• Molecular Calculations contain Initial

Data and Results• The Initial Data may have Methods,

Basis Sets, Functionals, etc.• The Results may have Energies, Wave

Functions and Spectra, etc.

GC aims at complete description of typical Computational Chemistry experiment





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Chemical Semantics Ontology

gc.owlwithProtege

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Related Ontologies ...

SIO – Semanticscience Integrated OntologyOPB – Ontology of Physics for BiologyRXNO – Name Reaction OntologyCMO – Chemical Methods OntologyMOP – Molecular Proocesses OntologySO – The Sequence Ontology Project

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Importance of Structural Data

Structures

CML – Chemical Markup Language

“CML is not 'just another file format'; it is capable of holding extremely complex information structures and so acting as an interchange mechanism or for archival. It interfaces easily with modern database architectures such as relational databases or object-oriented databases. Most importantly, it a large amount of generic XML software to process and transform it is already available from the community.”

P. Murray-Rust, H. S. Rzepa, 2001

CML “paved the road” to Semantics in Chemistry.Extremely useful as an interchange format between CC software and Semantic Web

Our position: Chemical Semantics will use CSX – similar structural format enriched by explicit description of molecular constituents, enriched description of computations inputs and results .

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A timeline of Semantic Web

RDF – 1999CML - Chemical Markup Language - 1999FOAF - 2000RDFa - 2004DBPedia – 2007ChEBI - Chemical Entities of Biological Interest - 2007GoodRelations (2008, Google adoption: November 2, 2010)Schema.org – June 2011Google’s Knowledge Graph – May 2012Facebook Graph Search - January 2013


An emerging successor to the web, the Semantic Web, will likely profoundly change the very nature of how scientific knowledge is produced and shared, in ways that we can now barely imagine.

Conclusion

33Dr Mirek Sopek

Chemical Semantics Portalhttp://portal.chemicalsemantics.com/cs

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CS Portal main targets

Interoperable PUBLISHING of Computational Chemistry calculationsFEDERATION of published data with existing web-based chemical datasetsCloud-like ARCHIVING of Computational Chemistry calulations results, input/output files etc.

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http://portal.chemicalsemantics.com/cs

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Manual publication (upload)Automated publication directly from Modelling Software - via Web API

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Automated generation of permanent URIs

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Permanent Chemical URIs

Automated generation of permanent URIs

http://purl.org/chem/pub/2013-08-04-quercetin

Owned & controlled by OCLC (Online Computer Library Center)Is claimed to be persistent and eternal.

Owned by OCLC controlled by Chemical Semantics, Inc.

Generated by Chemical Semantics, Inc. for the user. Owned by the user.



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URI naming scheme

Publicationhttp://purl.org/chem/pub/2013-08-05-betacyanin

http://purl.org/chem/pub/2013-08-05-betacyanin/mol-calc Molecular Calculations

http://purl.org/chem/pub/2013-08-05-betacyanin/molSys Molecular System

A Molecule of the system http://purl.org/chem/pub/2013-08-05-betacyanin/molSys/m1 Bonds between atoms in the molecule

http://purl.org/chem/pub/2013-08-05-betacyanin/molSys/m1/a1a12

http://purl.org/chem/pub/2013-08-05-betacyanin

http://purl.org/chem/pub/2013-08-05-betacyanin/mol-calc

http://purl.org/chem/pub/2013-08-05-betacyanin/mol-calc

http://purl.org/chem/pub/2013-08-05-betacyanin/molSys

http://purl.org/chem/pub/2013-08-05-betacyanin/molSys

http://purl.org/chem/pub/2013-08-05-betacyanin/molSys/m1

http://purl.org/chem/pub/2013-08-05-betacyanin/molSys/m1



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Dual nature of the URIs

Realizes Linked Data Principles

For Humans (i.e. as seen via web browser)http://purl.org/chem/pub/2013-08-02-pyridine_base

Returns:

http://purl.org/chem/pub/2013-08-02-pyridine_base


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Dual nature of the URIs

Realizes Linked Data Principles

For Machines (i.e. as seen via Semantic Tools (rdfEditor, Fidler))http://purl.org/chem/pub/2013-08-02-pyridine_base

Returns:

Content-negotiations: “One gets what one asks for”



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More on “Human-oriented” views

“Results” – a prototype for future publication “digest”

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“Molecules” – generic, webGL based molecular viewer

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“Wave function” – visualization of orbital energies

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“Graph” – explore the knowledge structure about your system

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“Data Federation” – explore Semantic Links to eternal resources

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“Data sets” – use CS Portal for archiving purposes

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SPARQL queries on CS Portal

Counting number of triples in the graphs of the CS Portal

SELECT ?graph (count(*) as ?count)

WHERE { GRAPH ?graph { ?s ?p ?o . }

}group by ?graph

order by DESC(?count)

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Counting number of elements in all molecular systems on the CS Portal

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>PREFIX gc: <http://purl.org/gc/>PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT ?element (count(*) as ?count)WHERE { ?atom gc:isElement ?element .}GROUP BY ?element ORDER BY DESC(?count)

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Number of different calculations in all molecular systems ofthe CS Portal

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>PREFIX gc: <http://purl.org/gc/>

SELECT ?resultType (count(*) as ?count)WHERE { GRAPH ?graph { ?calc rdf:type gc:Calculation ; gc:hasResult ?result . ?result rdf:type ?resultType . }}group by ?resultTypeorder by DESC(?count)

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Number of molecular systems with halogen atoms the CS PortalPREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>PREFIX gc: <http://purl.org/gc/>PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>SELECT ?graphWHERE { GRAPH ?graph { { ?something gc:hasAtom ?atom1 ; rdf:type ?somethingType ; rdfs:label ?somethingLabel . ?atom1 gc:isElement "F" . } UNION { ?something gc:hasAtom ?atom2 ; rdf:type ?somethingType ; rdfs:label ?somethingLabel . ?atom2 gc:isElement "Cl" . } UNION { ?something gc:hasAtom ?atom3 ; rdf:type ?somethingType ; rdfs:label ?somethingLabel . ?atom3 gc:isElement "Br" . } UNION { ?something gc:hasAtom ?atom4 ; rdf:type ?somethingType ; rdfs:label ?somethingLabel . ?atom4 gc:isElement "I" . } UNION { ?something gc:hasAtom ?atom4 ; rdf:type ?somethingType ; rdfs:label ?somethingLabel . ?atom4 gc:isElement "At" . }} }

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Number of inorganic molecular systems

## Show all molecules that contain atoms other than C,O,N,H

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>PREFIX gc: <http://purl.org/gc/>PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT DISTINCT ?graph WHERE { {GRAPH ?graph { ?mol gc:hasAtom ?atom}} MINUS {GRAPH ?graph { ?a gc:isElement "C" }} MINUS {GRAPH ?graph { ?b gc:isElement "O" }} MINUS {GRAPH ?graph { ?b gc:isElement "N" }} MINUS {GRAPH ?graph { ?b gc:isElement "H" }}}

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Energy values computed of all of molecular systems

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>PREFIX gc: <http://purl.org/gc/>

SELECT ?sysEnergy ?energyValue ?energyNameWHERE { GRAPH ?graph { ?molSys rdf:type gc:MolecularSystem ; gc:hasCalculationOn ?molCalc . ?molCalc rdf:type gc:Calculation ; gc:hasResult ?sysEnergy . ?sysEnerg rdf:type gc:SystemEnergies ; ?p ?o . ?o gc:hasFloatValue ?energyValue; rdfs:label ?energyName. }}ORDER BY ?energyName

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Stay tuned ...

If you want to work with us,or just share your opinions,Do not hesitate to notify us

at:[email protected]

mailto:[email protected]

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Thank you…

Neil Ostlund, Hypercube, Inc.

1115 NW 4th St. Gainesville, FL 32608, USA

Phone: (352) 371 7744Web: www.hyper.comeMail: [email protected]

Mirek SopekMakoLab SA

Demokratyczna 46, 93-430 Lodz, Poland

Phone: +48 600 814 537Web: www.makolab.comeMail: [email protected]

http://www.hyper.com/

http://www.makolab.com/

Technology

Chemical Semantics at Sopron CC Conference