AUTOMATED STRUCTURE-BASED CLASSIFICATION USING ChEBI

ONTOLOGY

Venkatesh MuthukrishnanSoftware Engineer - ChEBI

CLASSIFICATION IN ChEBI

CHALLENGES WITH

MANUAL CLASSIFICATION

INCOMPLETE& INCONSISTENT …

BLOCKS BULK LOADING …

http://sourceforge.net/p/chebi/news/2012/11/chebi-release-97-is-now-available/

STRUCTURE BASED AUTO-CLASSIFICATION

PREVIOUS APPROACHES

SOCO SELF-ORGANISING CHEMICAL ONTOLOGIES

SMARTS & OWL

Chepelev et al. BMC Bioinformatics 2012 13:3 doi:10.1186/1471-2105-13-3

PROPOSED APPROACH

SCHEMA

DEFINITIONSeg: ketone organic_molecular_entity and has_part some acetone

RANKED

DEFINITIONS

dicarboxylic acid dianion organic_molecular_entity and has_part exactly 2 acetate and has_charge value "-2"^int

flavonoid organic_molecular_entity and has_skeleton some flavones

benzoquinones organic_molecular_entity and ( has_part some 1,2-benzoquinone or has_part some 1,4-benzoquinone )

gamma-lactam organic_molecular_entity and has_part some pyrrolidin-2-one and not ( has_part some succinimide )

WHY MANUALDEFINITION

GENERATION

NO MCS

https://github.com/downloads/asad/SMSD/SMSD20120718.zip

http://dalkescientific.com/writings/diary/archive/2012/05/13/mcs_chebi.html

CHALLENGING CLASSES

PLANNED INTEGRATION INTERNAL DATA LOADING SUBMISSION TOOL & CURATOR TOOL

ACKNOWLEDGEMENTS COLLABORATORS

Colin Batchelor, RSCLian Duan, ETHLeonid Chepelev, OttawaMichel Dumontier, StanfordDespoina Magka, Oxford

FUNDING BBSRC “Continued development of ChEBI towards better usability for the systems biology and metabolic modelling communities” BB/K019783/1

THANK YOU