Health Sciences Librarians and PubViz, a Novel Medline Exploration Engine

Jean SongBioinformationist, Health Sciences LibrariesNational Center for Integrative Biomedical InformaticsUniversity of Michiganjeansong@umich.edu

May 19, 2008

Overview

The Bioinformationist The National Center for Integrative

Biomedical Informatics (NCIBI) PubViz Collaboration Future Work

Bioinformationist

Early 2007, pilot project collaboration Health Sciences Libraries and NCIBI Purpose: test the viability of a

bioinformationist to increase research support in bioinformatics

Recruitment Initial work Position funding

BioinformationistBioinformationist

NCIBI

HSL

A National Center for Biomedical Computing (NCBCs) in the NIH Roadmap

University of Michigan’s Center for Computational Medicine and Biology (CCMB)

Problem-centric development based on Driving Biological Problems

National Center for Integrative Biomedical Informatics

NCIBI Goals

Development Software tools Data integration methods Systems modeling environments

Suite of Tools to better understand complex biomedical processes Web-accessible knowledge analysis Collaborative work environments Create and utilize computationally-enabled models

and workflows

NCIBI Structure

Core 1 – Computer and Information Science Core 2 – Bioinformatics & Knowledge Acquisition Core 3 – Driving Biological Problems Core 4 – Computational Infrastructure Core 5 – Education Core 6 – Outreach and Dissemination Core 7 – Administration

Tools and Technology

Tools and Technology Seminar Series Weekly: Noon to 1pm on Thursday Streamed live http://www.ncibi.org

PubViz: a graphic search engine of Medline database Presented on 3/29/07 http://connect.umms.med.umich.edu/ncibitt032907flv/ Weijian Xuan and Fan Meng

Molecular & Behavioral Neuroscience Institute (MBNI)

PubViz: What it is

Development interactive visual search interface for Medline

Summarize search results based on different biomedical concepts Protein interaction Pathway/cellular processes Anatomical location Biological process or disease

Explore Medline using external databases Targeted for high throughput biomedical data Online application Built in visualization tools

PubViz Visualization Tools

References

http://www.pubviz.org Xuan W, Wang P, Watson SJ, Meng F.

An active visual search interface for Medline. Comput Syst Bioinformatics Conf 2007; 6:359-69. PMID: 17951838

Getting Started

Tools and Tech prompted questions Major qualifier Subheadings

Developers wanted additional information Expert searcher opinions on interface use Comparisons of search results Additional external data sources

Partnership deemed beneficial

The Collaboration

External data access Mirlyn, other databases, CatFile Plus Facilitated discussions with systems librarians

Algorithm Evaluation Similarity measures used in PubViz

Document similarity MeSH term relatedness

Provide search questions Reference Mediated Searches Discussion lists

Provide search results

The Collaboration (cont’d)

Interface usability Barbara Mirel Other visualization search engines Institutional trial of RefViz Informal focus group on PubMed interface design

Grant applications CCMB Pilot Project NIH R01

Future Work

Continued algorithm evaluationCheck tagsMajor headings

Additional focus groups Heuristic evaluation Grant applications

Acknowledgements

Dr. Fan Meng Dr. Barbara Mirel Weijian Xuan Marci Brandenburg Health Sciences Libraries National Center for Integrative Biomedical Inform

aticsNIH Grant # U54-DA021519