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Figure 1 | BMC Bioinformatics

Figure 1

From: Content-rich biological network constructed by mining PubMed abstracts

Figure 1

The network map of a biological network constructed by Chilibot. Chilibot queried the entire PubMed abstract database to identify a network of relationships amongst a set of genes reported to be regulated by cocaine [44], a biological concept ("plasticity"), and a drug ("cocaine"). Lines connecting rectangular nodes indicate relationships between the genes shown, and each icon in the middle of a line represents the character of the relationship. Interactive relationships (circles) are neutral (gray), stimulatory (green), inhibitory (red) or both stimulatory/inhibitory (yellow). The number within each icon indicates the quantity of abstracts retrieved for documenting that relationship. Icons containing the plus sign ("+") represent "parallel relationships". Gray rhomboidal icons indicate that only co-occurrence was detected. All arrowheads indicate the direction of the interaction, and some are bi-directional. The green or pink colors of rectangular nodes represent up- or down-regulation of the genes identified therein, respectively, based on experimental data provided by the user. More saturated colors are associated with larger changes. Nodes with no expression values (e.g., "cocaine") are in cyan. The terms and icons are linked to documentation when viewed in a web-browser. See supplementary information for subnetwork maps generated by Chilibot.

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