PubGraph Advanced Query

PubGraph Query
  Basic Query
  Advanced Query
  Choosing Colors
Gallery -- Sample Output

If you fill in the form below with vocabulary terms and click submit, PubGraph will produce a a graphical view and analysis of associations among these terms in the PubMed/MEDLINE literature database. PubMed is vast, covering millions of publications and thousands of journals.

By specifying a context that limits the analysis done by PubGraph to specific subsets of publications and/or journals, you can control the meaning and strength of associations determined by PubGraph.

PubGraph also provides a number of options for controlling the display of association graphs.

For examples of use of PubGraph, see the Gallery.

Context for this Analysis -- Limits on all Queries

PubGraph statistics are more accurate when the context is specified accurately.
By specifying the context carefully you can sharpen the precision and recall (and control the meaning) of all queries.

Journal Subset Strategy [SB] Journal/Citation Subset Publication Type [PT]
MeSH Subheading [SH] Dates of Publication [DP] Other Useful Limits
starting     ending

Context (a PubMed query specifying restrictions in addition to any limits above):

Vocabulary Entry

Enter your vocabulary terms (PubMed queries) in the form below.

Note: if you want terms to be treated literally, double-quote them; otherwise PubMed will interpret them with its peculiar semantic methods.     (Explanation: how PubMed interprets queries)

Important PubMed quirk: use UPPERCASE for boolean operators (AND, OR, NOT).

Put each Vocabulary Term on a separate line.

You can also optionally start each line with a Group ID, a single digit 0, 1, ..., 9. (If no initial digit is present, Group ID 0 is used.)

Below you must specify Display of Terms in each Group, letting you control the PubGraph output for each vocabulary term by choosing its Group ID.

If you want additional terms to be loaded into the text box from a text file (with a separate term on each line), choose a filename and click submit below. This form will be redisplayed after including the file contents, giving you the option of making further modifications or file loads before submission for PubGraph analysis.

Display of Terms in each Group

Group ID Color Style Shape
    (how the colors look)

    Clustering for groups:

    Ordering of groups:

    Layout direction used, if groups are ordered:

Which Association Measure to Analyze

Association Measure Explanation
Term co-occurrence Jaccard coefficient
Term covariance covariance of term document-vectors

PubGraph will generate a graph showing how your Terms co-occur in the PubMed/MEDLINE literature if you click submit (provided you have not selected a file for loading).

PubGraph is a project of the UCLA Center for Cognitive Phenomics.
Copyright © 2006-2007 D.S. Parker.