Integrating Literature and Experimental Data Fan Meng, Ph.D. Microarray Laboratory Psychiatry Department and Molecular & Behavioral Neuroscience Institute University of Michigan

High Throughput Data Analysis Overview Raw Data: Expression/Genotype/Sequence Molecular → Gene/Transcript/SNP/Genome System → Pathway/Network/Gene Set Integrative Exploration → Hypothesis freewheeling rigid glamorous dull

MGREP Concept Mapping Engine Single Word Variation Concepts Remove Common Words Combine with Word Order Permutation Radix-tree Match Figure 1. Overview of our free text-to-ontology mapping method Key Idea: While classical concept match algorithms use the time consuming approach of generating concept variations during concept match, mgrep pre-generate concept variations and uses highly efficient string match algorithms to achieve two orders of magnitude increase in speed over MetaMap.

Evaluation of MGREP by NCBO Shah NH, Bhatia N, Jonquet C, Rubin D, Chiang AP, Musen MA (2009) Comparison of concept recognizers for building the Open Biomedical Annotator. BMC Bioinformatics Sep 17;10 Suppl 9:S14. Precision of Mgrep and MetaMap using the 'diseases' dictionary Data SourceMgrepMetaMap Clincal Trials Gold Miner GEO MedLine

MGREP in NCBO Annotator Web Service

PubAnatomy Integrate Medline literature with external data Enable efficient visual query Open architecture

Linking Literature and Experimental Data Mapping Medline to brain structures Integrating multiple data sets – Gene expression from the Allen Brain Atlas – Brain structure relationship from NeuroName – Protein-protein interaction from MiMI Graphic presentation of data – Allen Brain Atlas – Protein-protein interaction network – Gene Co-expression network

PubAnatomy Architecture Visualization components: Flex Server-side web services: algorithms and graphics Backend database: Oracle PubAnatomy UI user selection Internal services User plug-ins service I1 service I2 … plugin U1 plugin U2 … algorithm I1 ithm I2 dataset I1 dataset I2 algorithm U1 algorithm U2 dataset U1 dataset U2 … … open API databases BioNLP Literature … Integration Visualization ComponentsServer-Side Web ServicesBackend Database

PubAnatomy Interface PubAnatomy