ENQUIRE automatically reconstructs, expands, and drives enrichment analysis of gene and Mesh co-occurrence networks from context-specific biomedical literature
Fig 2
Example of ENQUIRE’s network reconstruction and expansion.
We generated co-occurrence networks using the corpus collected for the case study Ferroptosis and Immune System as input (see main text for additionally specified parameters). The originally reconstructed network and the expanded ones obtained by querying community-connecting graphlets are arranged clockwise. Nodes and edges belonging to previously reconstructed networks are colored in white and grey, respectively. At each network expansion, newly found nodes and edges are indicated in red. Nodes of the five graphlets that resulted in PMID-matching queries are colored in black and labelled, with letters in parentheses (a-e) indicating the graphlets they belong to. We acknowledge the use of Cytoscape and DyNet to layout the networks.