Health Sciences Librarians and PubViz, a Novel Medline Exploration Engine Jean Song Bioinformationist, Health Sciences Libraries National Center for Integrative Biomedical Informatics University of Michigan [email_address] May 19, 2008

Overview The Bioinformationist The National Center for Integrative Biomedical Informatics (NCIBI) PubViz Collaboration Future Work

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 Bioinformationist NCIBI HSL

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

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

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

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

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

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)

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

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

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

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

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

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 evaluation Check tags Major headings Additional focus groups Heuristic evaluation Grant applications

Continued algorithm evaluation

Check tags

Major 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 Informatics NIH Grant # U54-DA021519

Dr. Fan Meng

Dr. Barbara Mirel

Weijian Xuan

Marci Brandenburg

Health Sciences Libraries

National Center for Integrative Biomedical Informatics NIH Grant # U54-DA021519