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Open Access Highly Accessed Research article

Content-rich biological network constructed by mining PubMed abstracts

Hao Chen and Burt M Sharp

Author Affiliations

Department of Pharmacology, University of Tennessee Health Science Center, Room 115 Crowe Research Building, 874 Union Avenue, Memphis, Tennessee 38163 USA

BMC Bioinformatics 2004, 5:147  doi:10.1186/1471-2105-5-147

Published: 8 October 2004

Additional files

Additional File 1:

A total of 770 known relationships were used to test the recall and precision of Chilibot. A maximum of 5, 10, 20, 30, 40, or 50 most recent PubMed records for each relationship was specified for analysis. The relationships identified by Chilibot are summarized and provided in Microsoft Excel and OpenOffice format.

Format: BZ2 Size: 51KB Download file

Open Data

Additional File 2:

The original results of the above study (non-essential files are deleted to keep the file size under the limit set by BMC bioinformatics).

Format: BZ2 Size: 7MB Download file

Open Data

Additional File 3:

Sub-network graph obtained by filtering figure 1 using the number of supporting publications as a threshold criterion.

Format: JPEG Size: 26KB Download file

Open Data

Additional File 4:

Sub-network graph obtained by filtering figure 1 to selectively display a node of interest (i.e. "cocaine") and other nodes that directly connected to it.

Format: PNG Size: 4KB Download file

Open Data

Additional File 5:

The original Chilibot query results of the term "long-term potentiation (LTP)" and 22 other terms, limiting the latest references analyzed to the years 1990, 1995, 2000, and 2004.

Format: BZ2 Size: 2.4MB Download file

Open Data

Additional File 6:

A graph demonstrating the scale-free topology of relationship networks derived from the biological literature. The network contains 138 nodes and 1912 relationships. A small fraction of the nodes (10 nodes colored in black) accounted for more than 45% of the relationships (solid lines), a characteristic of scale-free topology.

Format: PNG Size: 128KB Download file

Open Data