Integrating Literature and Experimental Data

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

Concepts 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. MGREP Concept Mapping Engine Remove Common Words Single Word Variation Combine with Word Order Permutation Radix-tree Match Figure 1. Overview of our free text-to-ontology mapping method

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. 2009 Sep 17;10 Suppl 9:S14.

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

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

PubAnatomy Interface PubAnatomy

Integrating Literature and Experimental Data

Integrating Literature and Experimental Data

Presentation Transcript

experimental data

Integrating Lecture, Laboratory, and Literature using Case Studies

Integrating Writing with Literature

Integrating Experimental Design into Science

1.3 Data Collection and Experimental Design

( ___ ) NRTL (---) UNIQUAC (○) experimental data

Secondary Data, Literature Reviews, and Hypotheses

Experimental Data Analysis

experimental data

Thermo chromatography: Experimental data

Integrating Environmental and Social Data -

Integrating Biodiversity Data

Integrating CADD and GIS Data

Integrating Distributed Data Streams

Formulae from Experimental Data

Integrating Data

Integrating Literature and Experimental Data

Integrating Voice, Video, and Data

Experimental Data Analysis