Development of an Ontology specific to Computational Chemistry

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The presentation from 2015 Spring ACS meeting in Denver

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Mirek Sopek, Stuart J. Chalk, Bing Wang, Louis Nardozi, Neil S. Ostlund:

Mirek Sopek, Stuart J. Chalk, Bing Wang, Louis Nardozi, Neil S. Ostlund Development of an Ontology specific to Computational Chemistry

The presentation plan:

The presentation plan The mission of Chemical Semantics, Inc. The Chemical Semantics Portal The Chemical Semantics Data Path: Structured Data – CSX Data with explicit meaning – RDF graphs Gainesville Core Ontology

The mission of Chemical Semantics:

The mission of Chemical Semantics 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 to a limited class of users. In parallel to portal creation, the company created the CSX file format (Common Standard of eXchange) which enables traditional software packages to publish data on the Semantic Web, and the GC ontology ( Gainesville Core ) that captures knowledge related to computational chemistry data. The ultimate goal is to build a data publishing platform that is applicable to all of various branches of chemistry.

Chemical Semantics Portals’ targets :

Chemical Semantics Portals ’ targets Interoperable PUBLISHING of Computational Chemistry calculations Semantic REPRESENTATION OF DATA for both humans and machines FEDERATION of published data with existing web-based chemical datasets Cloud-like ARCHIVING of Computational Chemistry calculations results, input/output files etc. http://chemsem.com

Publishing on the portal:

Publishing on the portal Automated publication directly from Modelling Software ( via Web API) Supported packages (as for today): Gamess , PSI4, NWCHEM, Hyperchem Manual publication (upload ) http://chemsem.com

Chemical Semantics Portal:

Chemical Semantics Portal Works like cloud data storage for computational chemistry publications Has basic “chemical” visualization features http://chemsem.com

SPARQL queries on 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   ? graph WHERE   {      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"   .      } }   } SPARQL queries on CS Portal Number of molecular systems with halogen atoms the CS Portal http://chemsem.com

URI naming scheme:

URI naming scheme 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/molSys http:// purl.org/chem/pub/2013-08-05-betacyanin/molSys/m1 http:// purl.org/chem/pub/2013-08-05-betacyanin/molSys/m1/a1a12 Publication Molecular Calculations Molecular System A Molecule of the system Bonds between atoms in the molecule CS Portal is a semantic DATA portal

CS Portal is a semantic DATA portal:

CS Portal is a semantic DATA portal http://chemsem.com http://chemsem.com/pub/mirek-20150322152506 Controlled by portal instance owner Generated by Chemical Semantics, Inc. f or the user. Owned by the user. http:// chemsem.com/pub/mirek-20150322152506 Unique URI – display for Humans http:// chemsem.com/pub/mirek-20150322152506 Unique URI – display for Machines

Chemical Semantics Data Publishing Path:

Chemical Semantics Data Publishing Path CSX Common Standard of eXchange RDF G raph on the Semantic Web Computational Chemistry Packages Gainesville Core Ontology http://chemsem.com

Gainesville Core Ontology:

Gainesville Core Ontology

Gainesville Core Ontology – short history:

Gainesville Core Ontology – short history First version (0.2.0) was built in 2012 –published at http://purl.org/gc Second version (0.3.0) was built in 2013 Work on the c urrent version ( in progress ) (0. 5 .0) has started at the end of 2014

Why are we building Gainesville Core Ontology?:

Why are we building Gainesville Core Ontology? To provide VOCABULARY of terms for RDF GRAPHS that represent chemical objects . To encode KNOWLEDGE about computational chemistry through expression of its terminology. To define FORMAL semantics of concepts used by (computational) chemists To link MACHINE (i.e. algorithmic) understanding of concepts with their meaning for HUMANS .

Problems with ontologies …:

Problems with ontologies … From the very beginning of the discipline of ontological studies in computer science it was not quite clear: W hat do the ontologies really represent ? What is their main goal ? Who should be in charge of their creation ? How are the communities going to use them? Martin Hepp in "Ontology Management" Springer Science 2008

We follow pragmatic approach to ontological research…:

We follow pragmatic approach to ontological research… Our vision of ontologies: They represent shared knowledge of the community Their main goal is to encode the domain knowledge into machine interpretable information The domain experts and ontologists should be in charge of their creation Communit i es will use the m for easier access and integration of data. Dieter Fensel in "Ontology Management" Springer Science 2008

CSX and GC – Relations between XML schemas and ontologies:

CSX and GC – Relations between XML schemas and ontologies XML Schemas Ontologies Define representation syntax for a domain Define semantics of domain elements Define sequence and ordering of fields in XML documents Define explicit semantics of ordering and conceptual hierarchies They define types of elements and their hierarchies in a context-dependent way They define context-independent reusable categories of things Inspired by " Ontology Management" Springer Science 2008

GC Ontology main concept classes:

GC Ontology main concept classes

GC Ontology „Molecular” concept classes:

GC Ontology „Molecular” concept classes

GC Ontology „Molecular Calculation” concept classes:

GC Ontology „Molecular Calculation” concept classes

GC Ontology „Calculation Result” concept classes:

GC Ontology „Calculation Result” concept classes

GC Ontology „Quantum Mechanics” concept classes:

GC Ontology „Quantum Mechanics” concept classes

GC Ontology uses/extends …:

GC Ontology uses / extends … BFO Ontology ( http:// purl.obolibrary.org/obo/bfo.owl ) Units Ontology ( http:// sweet.jpl.nasa.gov/ ontology / units.owl ) Periodic Table Ontology ( http://www.daml.org/2003/01/ periodictable / PeriodicTable # ) Dublin Core Ontology ( http://purl.org/dc/ elements /1.1 / , http://purl.org/dc/terms / )

GC creation process: manual coding using advanced text editors in Turtle syntax. Source managed with help of BitBucket. QA with help of Protégé Ontology tool.:

GC creation process: manual coding using advanced text editors in Turtle syntax. Source managed with help of BitBucket . QA with help of Protégé Ontology tool.

Exploring new visualization methods for the RDF graphs and for the Ontology:

Exploring new visualization methods for the RDF graphs and for the O ntology

Chemical Semantics reception (with drinks & food) Common Standard of eXchange March 25 Room 608 5-8 PM :

Chemical Semantics reception (with drinks & food) C ommon S tandard of e X change March 25 Room 608 5-8 PM

Thank you!:

Thank you ! Mirek Sopek , PhD Chemical Semantics , Inc. 1115 NW 4th Street 32601 Gainesville , Florida cell : + 1 917 3467500 w eb: www.chemicalsemantics.com e m ail : sopek@ chemicalsemantics.com

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