PubMatrix: a tool for multiplex literature mining

BMC Bioinformatics. 2003 Dec 10:4:61. doi: 10.1186/1471-2105-4-61.


Background: Molecular experiments using multiplex strategies such as cDNA microarrays or proteomic approaches generate large datasets requiring biological interpretation. Text based data mining tools have recently been developed to query large biological datasets of this type of data. PubMatrix is a web-based tool that allows simple text based mining of the NCBI literature search service PubMed using any two lists of keywords terms, resulting in a frequency matrix of term co-occurrence.

Results: For example, a simple term selection procedure allows automatic pair-wise comparisons of approximately 1-100 search terms versus approximately 1-10 modifier terms, resulting in up to 1,000 pair wise comparisons. The matrix table of pair-wise comparisons can then be surveyed, queried individually, and archived. Lists of keywords can include any terms currently capable of being searched in PubMed. In the context of cDNA microarray studies, this may be used for the annotation of gene lists from clusters of genes that are expressed coordinately. An associated PubMatrix public archive provides previous searches using common useful lists of keyword terms.

Conclusions: In this way, lists of terms, such as gene names, or functional assignments can be assigned genetic, biological, or clinical relevance in a rapid flexible systematic fashion.

Publication types

  • Comparative Study

MeSH terms

  • Cell Line, Tumor
  • Cisplatin / metabolism
  • Cisplatin / therapeutic use
  • Computational Biology / methods*
  • Computer Graphics / classification
  • Computer Graphics / statistics & numerical data
  • Databases, Genetic / classification
  • Databases, Genetic / statistics & numerical data
  • Drug Resistance, Neoplasm / genetics
  • Female
  • Gene Expression Profiling / classification
  • Gene Expression Profiling / statistics & numerical data
  • Gene Expression Regulation / physiology
  • Gene Expression Regulation, Neoplastic / physiology
  • Genes / physiology
  • Genes, Neoplasm / physiology
  • Genomics / classification
  • Genomics / statistics & numerical data
  • Humans
  • Internet
  • Oligonucleotide Array Sequence Analysis / classification
  • Oligonucleotide Array Sequence Analysis / statistics & numerical data
  • Ovarian Neoplasms / drug therapy
  • Ovarian Neoplasms / genetics
  • Ovarian Neoplasms / metabolism
  • Ovarian Neoplasms / pathology
  • Proteomics / classification
  • Proteomics / statistics & numerical data
  • PubMed / classification
  • PubMed / statistics & numerical data
  • Software* / classification
  • Software* / statistics & numerical data


  • Cisplatin