Health Sciences Librarians and PubViz,  a Novel Medline Exploration Engine Jean Song Bioinformationist, Health Sciences Li...
Overview <ul><li>The Bioinformationist </li></ul><ul><li>The National Center for Integrative Biomedical Informatics (NCIBI...
Bioinformationist <ul><li>Early 2007, pilot project collaboration </li></ul><ul><li>Health Sciences Libraries and NCIBI </...
<ul><li>A National Center for Biomedical Computing (NCBCs) in the NIH Roadmap </li></ul><ul><li>University of Michigan’s C...
NCIBI Goals <ul><li>Development </li></ul><ul><ul><li>Software tools </li></ul></ul><ul><ul><li>Data integration methods <...
NCIBI Structure <ul><li>Core 1 – Computer and Information Science </li></ul><ul><li>Core 2 – Bioinformatics & Knowledge Ac...
Tools and Technology <ul><li>Tools and Technology Seminar Series </li></ul><ul><ul><li>Weekly: Noon to 1pm on Thursday </l...
PubViz: What it is <ul><li>Development interactive visual search interface for Medline </li></ul><ul><li>Summarize search ...
 
PubViz Visualization Tools
References <ul><li>http:// www.pubviz.org </li></ul><ul><li>Xuan W, Wang P, Watson SJ, Meng F. An active visual search int...
Getting Started <ul><li>Tools and Tech prompted questions </li></ul><ul><ul><li>Major qualifier </li></ul></ul><ul><ul><li...
The Collaboration <ul><li>External data access </li></ul><ul><ul><li>Mirlyn, other databases, CatFile Plus </li></ul></ul>...
The Collaboration (cont’d) <ul><li>Interface usability </li></ul><ul><ul><li>Barbara Mirel </li></ul></ul><ul><ul><li>Othe...
Future Work <ul><li>Continued algorithm evaluation </li></ul><ul><ul><li>Check tags </li></ul></ul><ul><ul><li>Major headi...
Acknowledgements <ul><li>Dr. Fan Meng </li></ul><ul><li>Dr. Barbara Mirel </li></ul><ul><li>Weijian Xuan </li></ul><ul><li...
Upcoming SlideShare
Loading in...5
×

HSL and PubViz: a novel Medline Exploration Engine

1,303

Published on

MLA 2008 Annual Meeting section paper

Published in: Health & Medicine, Education
0 Comments
1 Like
Statistics
Notes
  • Be the first to comment

No Downloads
Views
Total Views
1,303
On Slideshare
0
From Embeds
0
Number of Embeds
0
Actions
Shares
0
Downloads
9
Comments
0
Likes
1
Embeds 0
No embeds

No notes for slide
  • HSL and PubViz: a novel Medline Exploration Engine

    1. 1. 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
    2. 2. Overview <ul><li>The Bioinformationist </li></ul><ul><li>The National Center for Integrative Biomedical Informatics (NCIBI) </li></ul><ul><li>PubViz </li></ul><ul><li>Collaboration </li></ul><ul><li>Future Work </li></ul>
    3. 3. Bioinformationist <ul><li>Early 2007, pilot project collaboration </li></ul><ul><li>Health Sciences Libraries and NCIBI </li></ul><ul><li>Purpose: test the viability of a bioinformationist to increase research support in bioinformatics </li></ul><ul><li>Recruitment </li></ul><ul><li>Initial work </li></ul><ul><li>Position funding </li></ul>Bioinformationist NCIBI HSL
    4. 4. <ul><li>A National Center for Biomedical Computing (NCBCs) in the NIH Roadmap </li></ul><ul><li>University of Michigan’s Center for Computational Medicine and Biology (CCMB) </li></ul><ul><li>Problem-centric development based on Driving Biological Problems </li></ul>National Center for Integrative Biomedical Informatics
    5. 5. NCIBI Goals <ul><li>Development </li></ul><ul><ul><li>Software tools </li></ul></ul><ul><ul><li>Data integration methods </li></ul></ul><ul><ul><li>Systems modeling environments </li></ul></ul><ul><li>Suite of Tools to better understand complex biomedical processes </li></ul><ul><ul><li>Web-accessible knowledge analysis </li></ul></ul><ul><ul><li>Collaborative work environments </li></ul></ul><ul><ul><li>Create and utilize computationally-enabled models and workflows </li></ul></ul>
    6. 6. NCIBI Structure <ul><li>Core 1 – Computer and Information Science </li></ul><ul><li>Core 2 – Bioinformatics & Knowledge Acquisition </li></ul><ul><li>Core 3 – Driving Biological Problems </li></ul><ul><li>Core 4 – Computational Infrastructure </li></ul><ul><li>Core 5 – Education </li></ul><ul><li>Core 6 – Outreach and Dissemination </li></ul><ul><li>Core 7 – Administration </li></ul>
    7. 7. Tools and Technology <ul><li>Tools and Technology Seminar Series </li></ul><ul><ul><li>Weekly: Noon to 1pm on Thursday </li></ul></ul><ul><ul><li>Streamed live </li></ul></ul><ul><ul><li>http://www.ncibi.org </li></ul></ul><ul><li>PubViz: a graphic search engine of Medline database </li></ul><ul><ul><li>Presented on 3/29/07 </li></ul></ul><ul><ul><li>http://connect.umms.med.umich.edu/ncibitt032907flv/ </li></ul></ul><ul><ul><li>Weijian Xuan and Fan Meng Molecular & Behavioral Neuroscience Institute (MBNI) </li></ul></ul>
    8. 8. PubViz: What it is <ul><li>Development interactive visual search interface for Medline </li></ul><ul><li>Summarize search results based on different biomedical concepts </li></ul><ul><ul><li>Protein interaction </li></ul></ul><ul><ul><li>Pathway/cellular processes </li></ul></ul><ul><ul><li>Anatomical location </li></ul></ul><ul><ul><li>Biological process or disease </li></ul></ul><ul><li>Explore Medline using external databases </li></ul><ul><li>Targeted for high throughput biomedical data </li></ul><ul><li>Online application </li></ul><ul><li>Built in visualization tools </li></ul>
    9. 10. PubViz Visualization Tools
    10. 11. References <ul><li>http:// www.pubviz.org </li></ul><ul><li>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 </li></ul>
    11. 12. Getting Started <ul><li>Tools and Tech prompted questions </li></ul><ul><ul><li>Major qualifier </li></ul></ul><ul><ul><li>Subheadings </li></ul></ul><ul><li>Developers wanted additional information </li></ul><ul><ul><li>Expert searcher opinions on interface use </li></ul></ul><ul><ul><li>Comparisons of search results </li></ul></ul><ul><ul><li>Additional external data sources </li></ul></ul><ul><li>Partnership deemed beneficial </li></ul>
    12. 13. The Collaboration <ul><li>External data access </li></ul><ul><ul><li>Mirlyn, other databases, CatFile Plus </li></ul></ul><ul><ul><li>Facilitated discussions with systems librarians </li></ul></ul><ul><li>Algorithm Evaluation </li></ul><ul><ul><li>Similarity measures used in PubViz </li></ul></ul><ul><ul><ul><li>Document similarity </li></ul></ul></ul><ul><ul><ul><li>MeSH term relatedness </li></ul></ul></ul><ul><ul><li>Provide search questions </li></ul></ul><ul><ul><ul><li>Reference </li></ul></ul></ul><ul><ul><ul><li>Mediated Searches </li></ul></ul></ul><ul><ul><ul><li>Discussion lists </li></ul></ul></ul><ul><ul><li>Provide search results </li></ul></ul>
    13. 14. The Collaboration (cont’d) <ul><li>Interface usability </li></ul><ul><ul><li>Barbara Mirel </li></ul></ul><ul><ul><li>Other visualization search engines </li></ul></ul><ul><ul><li>Institutional trial of RefViz </li></ul></ul><ul><ul><li>Informal focus group on PubMed interface design </li></ul></ul><ul><li>Grant applications </li></ul><ul><ul><li>CCMB Pilot Project </li></ul></ul><ul><ul><li>NIH R01 </li></ul></ul>
    14. 15. Future Work <ul><li>Continued algorithm evaluation </li></ul><ul><ul><li>Check tags </li></ul></ul><ul><ul><li>Major headings </li></ul></ul><ul><li>Additional focus groups </li></ul><ul><li>Heuristic evaluation </li></ul><ul><li>Grant applications </li></ul>
    15. 16. Acknowledgements <ul><li>Dr. Fan Meng </li></ul><ul><li>Dr. Barbara Mirel </li></ul><ul><li>Weijian Xuan </li></ul><ul><li>Marci Brandenburg </li></ul><ul><li>Health Sciences Libraries </li></ul><ul><li>National Center for Integrative Biomedical Informatics NIH Grant # U54-DA021519 </li></ul>
    1. A particular slide catching your eye?

      Clipping is a handy way to collect important slides you want to go back to later.

    ×