New PDB Citation MeSH Network Explorer
In January, the PDB contained more than 170,000 structures; ~150,000 had corresponding “primary citations” describing these entries in a peer-reviewed journal.
The National Library of Medicine assigns MeSH (Medical Subject Headings) from a controlled vocabulary to index articles for PubMed. MeSH terms typically appear in a hierarchical tree structure that starts with 16 main branches.
The PDB Citation MeSH Network Explorer flattens these trees into co-occurrence networks of MeSH terms associated with PDB entries. Each node on the graph is a publication, and nodes are linked when they share MeSH terms.
Publications that share similar MeSH terms are clustered together into Groups; the largest groups are color-coded. Depending on the size of the network, groups contain at least one, two, or three common MeSH terms. Clicking on a node reveals information about the publication, clustered group, and related PDB structures. Nodes that have multiple terms in common are located near each other; nodes that have less in common are located further apart.
This new way of visualizing MeSH terms can provide insights into relationships between PDB primary citations.
This MeSH Explorer has been developed for RCSB PDB by Digital Science and is powered by Dimensions, the world’s largest linked research information dataset.