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PDB Citation MeSH Network Explorer: User Guide

Explore PDB MeSH Networks | Overview | Filtering and Data | User Guide | Search PDB by MeSH

Most entries in the Protein Data Bank (PDB) has been cited in a peer-reviewed publication. We have taken each of these publications, and created a co-occurence network of Medical Subject Headings (MeSH) terms: each node on the graph is a publication, and nodes are linked when they share MeSH terms.

There are 15 branches of MeSH terms; we created one network for each. Each network can be explored individually.

Navigation Guide

B - Organisms

Only publications with at least one MeSH term in the branch 'B - Organisms' are represented here.
On the graph, publications that share similar MeSH terms are clustered together.
Links are not displayed.
We created groups of publications that share similar MeSH terms; the largest groups are color-coded.

Tooltips

Hovering on a node gives basic information about the node:

  • the group number (randomly assigned, at each branch level),
  • its MeSH terms (regardless of the branch),
  • and the publication it corresponds to.
When one clicks on a node (=publication), the network highlights only the publications it shares MeSH terms with and indicates:
  • the publication it corresponds to,
  • the group number (randomly assigned, at each branch level),
  • the most common MeSH terms in this group,
  • the molecules related to this publication,
  • and its MeSH terms (regardless of the branch).
The 15 branches can be selected on the left panel, to change the network. Some branches are slower to load, often because they have too many connections.
Specific MeSH terms can be selected either with the dropdown below the branch selector, or in the list of MeSH terms associated to a publication when one is selected. Here, we have selected "Escherichia coli".
The groups can also be highlighted. The list of groups is in the panel on the top right.
Here we have clicked on the group "49 Humans; SARS-CoV-2; Betacoronavirus", which has 90 publications.

Organisms network

The networks can be explored here