HSL and PubViz: a novel Medline Exploration Engine
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Transcript of HSL and PubViz: a novel Medline Exploration Engine
Health Sciences Librarians and PubViz, a Novel Medline Exploration Engine
Jean SongBioinformationist, Health Sciences LibrariesNational Center for Integrative Biomedical InformaticsUniversity of [email protected]
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