1. Ontology, RDF, SW for Chemical Structures
T N Bhat & J. Barkley
NIST
Query tool
Use Case
Publications

2. Major Features, Goal – to Reduce User Frustration
We have established a use case at the HCLS Website - Chemical taxonomies
Combining of Rule-based terms with Vocabulary-based terms to define elements of RDF
Organization of the elements of RDF into predictable ontology using concepts from use cases
Developing tools and techniques to present the information using familiar database environments
Allows easier portability and implementation of the information by the community
Illustrating the concept using high profile data such as for AIDS inhibitors and Protein Data Bank contents

3. Combining of Rule-based with Vocabulary-based elements to define RDF
Chemical structures are definable by atomic connectivity – thus structures are suitable for identification using graph theory – InChI
Suitable for machine reasoning
Graphs are hard to digest for humans – therefore proposal is to combine InChI with familiar vocabularies such as Ala, Phenyl, Adenine
Also include synonyms in the vocabulary for greater coverage among diverse users
Vocabularies make it easier for humans to recognize the information

4. InChI – a Scalable URI
InChI is generated using a software that decodes the chemical connectivity information in certain layers such as chirality, ring structure, atom type and then re-codes them to form a text string
InChI is a naming standard for chemicals recommended by IUPAC

5. InChI – a rule-based URI
_1_2FC10H11NO2_2Fc11-10_2812_ _287_296-9_2Fh1-4_2C9H_2C5-6H2_2C_28H2_2C11_2C12_29

6. Vocabulary-based Definitions
For decades scientists have been developing names to identify structures and their images
Simple names
His
Ala
DNA
ATP
Semi-rule-based IUPAC names
2-amino-3-methylpentanamide
4-amino-3-hydroxy-6-methylheptanoic_acid
1-[(Benzenesulfonyl-methyl-amino)-phenyl-butyl]-piperidin-4-yl}-propyl-carbamic acid, naphthalen-1-ylmethyl ester
Names facilitate text-based queries of desired components
Names when used together with InChI provide a smoother integration of machine and human needs

7. Use-Case for SW; Treatment for AIDS is a work in progress
Treatments for AIDS are of two types
Prevention – the most effective
Containment
Drugs to contain, and reduce the viral load
Majority of the drugs ( ~17) target either HIV protease or RT
Complete suppression of either of these viral enzymes could cure AIDS
But drug resistance leads only to partial suppression of the enzymes
All the drug design efforts for AIDS are based on structures
Data needed for drug-design is scattered over many Web resources and users often wean through the data manually
Therefore AIDS drug design is an ideal target for Semantic Web and novel new database related technologies
SW connection between NIST and NIAID AIDS database
Choose the problem that matters
Website

8. Annotation Technique/Developing Structural Ontology
Define compounds using chemical features of interest to use cases
Fragment, subgroup, class
000503
030798
000505
1A8K

9. Modeling with Protégé – Suitable for Text-based Ontology

10. Web tools Structures are different from text based info
Structures are not amenable to text-based query/rendering techniques
Majority of the structural users never heard (nor want to hear!) about SPARQL – query language for RDF
Commonly preferred/expected way to query is by ‘click’
Semantic Web for Structures needs new Web tools that allow navigation by clicking on structural features

11. Chem-BLAST for Structural Semantic Web
Prasanna et al. PROTEINS 60, 1-4 (2005).
Prasanna et al. PROTEINS 63(4), (2006).
Download publications

12. Future Plans
Extend the work to chemical structures from Protein Data Bank
If interest exists hold a workshop at NIST Proposed dates - last two weeks of March 2008
Workshop will be in conjunction with the NIST wide Ontology week
Possible collaboration with IUPAC (International Union of Pure and Applied Chemistry ) and ChEBI
Contact: Colin Batchelor
RSC Publishing, Royal Society of Chemistry
Community participation is essential for further development
Contact (US)