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M. Brändle, Physical Chemical Properties Ontology, 11.12.2006 1

Physical Chemical Properties Ontology

Martin BrändleChemistry Biology Pharmacy Information CenterETH Zürich, HCI G 5.38093 Zü[email protected]


Competences

• Physical Chemistry, Univ. Bern, Switzerland– Excited states of polyenes/stilbene based on extension to

EHMO method (two-electron integrals of Slater basis functions)

– BICON-CEdiT extended-Hückel band structure package (two-body repulsive term, symmetry analysis of crystal orbitals)

• Applied quantum chemistry (MPG/HU Berlin, ETHZ)– Ab initio calculation of acidic and oxidic catalysts, derivation

of interatomic potential functions: Turbomole, GULP, CRYSTAL, QM/MM, MSI Insight, MPI


Competences InfoCenter• Chemical Information

– Database Development (Relational Databases)– Web Publishing XML/XSLT– Subject Specialist: Classification– Database Retrieval– Evaluation of Commercial (Chemical) Information Systems,

Cooperation with Producers• Scopus (Elsevier)• Science of Synthesis (Thieme)• DiscoveryGate (MDL)• SciFinder Scholar (Chemical Abstracts)

• Staff: 5 scientists/4 librarians/1 apprentice/1 trainee• Operation of Chemical Information DB servers for Swiss

universities (e.g. CrossFire)


Examples


General workflow scheme


Problems• Data flows only partially use standardized data formats

– CML as minimal standard– CMLComp?– free XML extensions

• Workflow implementations individual, steps not exchangeable– Environment– Computational software used– Concepts used in software

• Archiving/Retrieval?– Structure/substructure search– Projection of structural features to QC properties (basis set,

size, structure canonicalization)


Toolbox of general workflow steps

Interfaces?Actions?


General Workflow Step


Ontology : Representing KnowledgeFormal, explicit specification of a shared conceptualization*

– Conceptualization: Abstract model of phenomenon, relevant concepts identified

– Explicit: Type of concepts and constraints on use defined– Formal: Machine-readable– Shared: Consensus about knowledge

* O. Corcho et al, in Ontologies for Software Engineering and Software Technology, by C.Calero et al. (Eds.), Springer, 2006.

Definition of syntax and semantics of concepts and relationshipsbetween concepts.**

– Concepts ⇒ Vocabulary– Relationships ⇒ Statements using the vocabulary

** Baclawski, Niu, Ontologies for Bioinformatics, MIT Press, Cambridge MA, 2006


Categories of ontologies*

• Lightweight → Heavyweight– Controlled vocabularies– Glossaries– Thesauruses– Informal hierarchies– Formal hierarchies– Frames– Ontologies with value constraints– Ontologies with generic logic constraints

* F. Ruiz, J.R. Hilera, in Ontologies for Software Engineering and Software Technology, by C. Calero et al. (Eds.), Springer, 2006.


Ontologies in chemical informatics• CML (implicit)*• CMLComp (implicit)*• CMLComp dictionary*• Related dictionaries: units, software, ...*

* Peter Murray-Rust, Henry Rzepa

<scalar dataType="xsd:float" title="Mulliken charge" dictRef="ccml:mulliken" units="units:electron">0.5</scalar>

<entry id="mulliken" term="Mulliken Charge"><annotation>

<appinfo><scalar dataType="xsd:float" unitType="charge"/>

</appinfo></annotation><alternative type="abbreviation">mull</alternative><definition>Mulliken Charge</definition><description>Mulliken's method for calculating atom-based

charges</description></entry>


Demo


PPSI web interface


PPSI XML


Contributions and Aims

• Identify concepts of QC/physical properties– Software– Literature

• Provide semantic classification of QC classes and properties

• Provide registry of property definitions, synonyms, scopes, units, ranges and association with CompChem software

• Provide dictionary of CompChem CML terms


Implementation: Questions

• Files+ Performance- Updates: Distribution- Different versions

• Database/Web Service + Central update, one version + Standardized (data & protocol)- Performance (#queries/workflow? #data returned?)

- Format- Data: RDF, OWL, ?- Protocol: SOAP/WSDL, ?


Acknowledgements

• Jana Sonnenstuhl• Arun Kumar

physical chemical properties ontology - zib.de · m. brändle, physical chemical properties...

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