1. Chemical Ontologies I533 Seminar 21.Feb.2006 Kent Holaday

2. Overview Define Ontology Knowledge Representations Applications of Ontologies Chemical Ontologies

3. Ontology Defined Merriam-Webster Online Dictionary 1 : a branch of metaphysics concerned with the nature and relations of being 2 : a particular theory about the nature of being or the kinds of existentsMerriam-Webster Online Dictionary

4. Ontology Defined (cont.) GoogleGoogle 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.htmmembers.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.htmwww.und.nodak.edu/dept/library/Departments/abc/SACSEM-SemInGlossary.htm

5. Knowledge Representations INFORMAL Tagging Folksonomies Examples del.icio.us flickr Yahoo My Web 2.0 FORMAL Lists Thesauri Taxonomies Ontologies http://www.biowisdom.com/ontology/faq_q1.htm Examples IUPAC, MeSH, LCSH, XML schema/DTD

6. IUPAC Nomenclature Compendium of Chemical Terminology carbon Element number 6 of the periodic table of elements (electronic ground state 1s2 2s2 2p2). For a description of the various types of carbon as a solid the term carbon should be used only in combination with an additional noun or a clarifying adjective. See also amorphous carbon, carbon fibres, carbon material, glasslike carbon, 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

7. MeSH Tree Structures 2006 1. Anatomy [A] 2. Organisms [B] 3. Diseases [C] 4. Chemicals and Drugs [D] oInorganic Chemicals [D01] +Inorganic Chemicals [D01] + oOrganic Chemicals [D02] +Organic Chemicals [D02] + oHeterocyclic Compounds [D03] +Heterocyclic Compounds [D03] + oPolycyclic Compounds [D04] +Polycyclic Compounds [D04] + oMacromolecular Substances [D05] +Macromolecular Substances [D05] + oHormones, Hormone Substitutes, and Hormone Antagonists [D06] +Hormones, Hormone Substitutes, and Hormone Antagonists [D06] + oEnzymes and Coenzymes [D08] +Enzymes and Coenzymes [D08] + oCarbohydrates [D09] +Carbohydrates [D09] + oLipids [D10] +Lipids [D10] + oAmino Acids, Peptides, and Proteins [D12] +Amino Acids, Peptides, and Proteins [D12] + oNucleic Acids, Nucleotides, and Nucleosides [D13] +Nucleic Acids, Nucleotides, and Nucleosides [D13] + oComplex Mixtures [D20] +Complex Mixtures [D20] + oBiological Factors [D23] +Biological Factors [D23] + oBiomedical and Dental Materials [D25] +Biomedical and Dental Materials [D25] + oPharmaceutical Preparations [D26] +Pharmaceutical Preparations [D26] + oChemical Actions and Uses [D27] +Chemical 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] 15. Publication Characteristics [V] 16. Geographic Locations [Z]

8. Caffeine CAS: 58-08-2 C8H10N4O2 Synonyms: 3,7-dihydro-1,3,7-trimethyl-1H-purine-2,6-dione Methyltheobromin guaranine Visual vs Linguistic

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

10. 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

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

12. 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

13. Chemical Ontology Describe chemical objects and relationships Enable the search across multiple data sources Bridge some of the graphical versus linguistic representations

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

15. 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

16. 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

17. L-Amino acidD-Amino acid Amino acid CO 2 H OH =O NH 2 CO 2 ¯ 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

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