Chemical Ontologies

I533 Seminar

21.Feb.2006

Kent Holaday

Overview

• Define Ontology

• Knowledge Representations

• Applications of Ontologies

• Chemical Ontologies

Ontology Defined

Merriam-Webster Online Dictionary1 : a branch of metaphysics concerned with the nature and relations of being2 : a particular theory about the nature of being or the kinds of existents

Ontology Defined (cont.)

Google Definitions on the web• An ontology is a controlled vocabulary that describes objects

and the relations between them in a formal way, and has a grammar for using the vocabulary terms to express something meaningful within a specified domain of interest. Source: members.optusnet.com.au/~webindexing/Webbook2Ed/glossary.htm

• Ontology is the newest label attached to some KOSs. Ontologies are being developed as specific concept models by the Knowledge Management community. They can represent complex relationships between objects, and include the rules and axioms missing from semantic networks. Ontologies that describe knowledge in a specific area are often connected with systems for data mining and knowledge management.Source: www.und.nodak.edu/dept/library/Departments/abc/SACSEM-SemInGlossary.htm

Knowledge Representations

INFORMAL• Tagging• Folksonomies

Examples• del.icio.us• flickr• Yahoo My Web 2.0

FORMAL• Lists• Thesauri• Taxonomies• Ontologieshttp://www.biowisdom.com/ontology/faq_q1.htm

Examples• IUPAC, MeSH, LCSH,

XML schema/DTD

IUPAC Nomenclature

• Compendium of Chemical TerminologycarbonElement number 6 of the periodic table of elements (electronic ground state1s2 2s2 2p2).For a description of the various types of carbon as a solid the term carbonshould be used only in combination with an additional noun or a clarifyingadjective.See also amorphous carbon, carbon fibres, carbon material, glasslikecarbon, graphitic carbon, non-graphitic carbon, pyrolytic carbon.1995, 67, 479

• Nomenclature of Inorganic Compounds• Nomenclature of Organic Chemistry

http://www.iupac.org/publications/books/seriestitles/nomenclature.html

MeSH Tree Structures

2006

1.   Anatomy [A] 2.   Organisms [B] 3.   Diseases [C] 4.   Chemicals and Drugs [D]

oInorganic Chemicals [D01]  + oOrganic Chemicals [D02]  + oHeterocyclic Compounds [D03]  + oPolycyclic Compounds [D04]  + oMacromolecular Substances [D05]  + oHormones, Hormone Substitutes, and Hormone Antagonists [D06]  + oEnzymes and Coenzymes [D08]  + oCarbohydrates [D09]  + oLipids [D10]  + oAmino Acids, Peptides, and Proteins [D12]  + oNucleic Acids, Nucleotides, and Nucleosides [D13]  + oComplex Mixtures [D20]  + oBiological Factors [D23]  + oBiomedical and Dental Materials [D25]  + oPharmaceutical Preparations [D26]  + oChemical Actions and Uses [D27]  +

5.   Analytical, Diagnostic and Therapeutic Techniques and Equipment [E] 6.   Psychiatry and Psychology [F] 7.   Biological Sciences [G] 8.   Physical Sciences [H] 9.   Anthropology, Education, Sociology and Social Phenomena [I] 10.   Technology and Food and Beverages [J] 11.   Humanities [K] 12.   Information Science [L] 13.   Persons [M] 14.   Health Care [N] •   Publication Characteristics [V] 1.   Geographic Locations [Z]

Caffeine

CAS: 58-08-2

C8H10N4O2

Synonyms:• 3,7-dihydro-1,3,7-trimethyl-1H-purine-2,6-dione• Methyltheobromin• guaranine

Visual vs Linguistic

Source: Krallinger, M. et al. (2005) Text-mining approaches in molecular biology and biomedicine. DDT 10(6) 440

Data Sources

Structured• Medline• SwissProt• ChemID Plus• Medline Plus• Chemical Abstracts• NCBI databases• Misc. databases

Unstructured• Text documents• Journal articles• Lab notebooks• Web pages• Database BLOBs• Email

Source: Gardner, S. (2005) Ontologies and semantic data integration. DDT 10(14) 1004

Semantic Web

Figure 1: The Semantic Web "layer cake" as presented by Tim Berners-Lee.

Source: Hendler, J. (2001) Agents and the semantic web. http://www.cs.umd.edu/users/hendler/AgentWeb.html

Chemical Ontology

• Describe chemical objects and relationships• Enable the search across multiple data sources• Bridge some of the graphical versus linguistic

representations

two-ring heterocyclic compounds isoquinolines isoquinoline alkaloids morphinans morphine

grouped_by_chemistry

Fragment of Chemical Ontology

molecules organic molecules heterocyclic compounds bridged-ring heterocyclic compounds morphinans morphineIsA

O

N

OH

OH

CH3

H

NHH

morphine

morphinan

IsA

Source: Ennis, M. (2004) ChEBI A Dictionary of Chemical Entities with an Associated Ontology. SOFG-2, Philadelphia, October 23-26 2004

• Chemical Entities of Biological Interest – an EBI database/dictionary of ‘biochemical compounds’ and other chemical entities of biochemical interest with an associated ontology

• ChEBI’s goal is to provide standard terminology of (bio)chemical compounds that should finally be used in biological databases

ChEBI: What is it?

Source: Ennis, M. (2004) ChEBI A Dictionary of Chemical Entities with an Associated Ontology. SOFG-2, Philadelphia, October 23-26 2004

Relationships in ChEBI ontology

To be implemented…• IsPartOf - group to molecule; group to group; group to

class• IsEnantiomerOf - molecule to molecule; cycles allowed• IsTautomerOf - molecule to molecule; cycles allowed• IsConjugateBaseOf/IsConjugateAcidOf - molecule

to molecule (e.g. anion to acid)• IsParentHydrideOf - molecule to molecule (later?)

Current• IsA : inherited from Chemical Ontology - class to

class; instance to class

Source: Ennis, M. (2004) ChEBI A Dictionary of Chemical Entities with an Associated Ontology. SOFG-2, Philadelphia, October 23-26 2004

CH3

O

NH2H

O

OHCH2

OH

NH2H

O

O-

CH3

O

NH2H

O

O-

CH2

OH

NH2H

O

OH

CH3

O

H NH2

O

OHCH2

OH

H NH2

O

O- CH2

OH

H NH2

O

OH CH3

O

H NH2

O

O-

L-Amino acid

D-Amino acid

Amino acid

CO2H

OH =O

NH2 CO2¯

is_a is_part_of is_enantiomer_of

is_conjugate_base_of is_tautomer_of

Source: Ennis, M. (2004) ChEBI A Dictionary of Chemical Entities with an Associated Ontology. SOFG-2, Philadelphia, October 23-26 2004

Source: http://www.cse.buffalo.edu/~rapaport/663/F03/ontology.html