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pubchem_literature — PubChem compound-literature links (2025)

Description

A bipartite network of the chemical compounds of PubChem, the open chemistry database of the U.S. National Center for Biotechnology Information (NCBI), and the articles of PubMed linked to them. An edge connects a compound with an article that refers to it, as given in PubChem's list of links between compounds (CIDs) and PubMed articles (PMIDs).

The links come from four kinds of sources, given by the edge property type:

  1. articles provided by the depositors of the substances of PubChem (e.g. the publication that describes the substance),
  2. articles indexed in PubMed with a MeSH heading linked to the compound,
  3. articles linked by the publishers of the journals (e.g. compounds described in the article),
  4. articles associated with the compound through the BioAssays of PubChem.

A compound and an article linked by several kinds of sources are connected by several edges, one per kind. Only the compounds and articles with at least one link are nodes. The names of the compounds are those chosen as titles of their summary pages in PubChem (empty for the few compounds without a title).

The network has the following properties:

  • is_compound: whether the node is a compound (otherwise it is an article).
  • cid: the PubChem compound identifier (CID) of the compound (-1 for articles); its page is https://pubchem.ncbi.nlm.nih.gov/compound/<cid>.
  • pmid: the PubMed identifier of the article (-1 for compounds).
  • name: the name of the compound (the title of its PubChem page; empty for articles).
  • Edge type: the kind of source of the link, 1 to 4 as above.
Tags
Informational Chemical Unweighted Multigraph Metadata
Citation
  • S. Kim, J. Chen, T. Cheng, A. Gindulyte, J. He, S. He, Q. Li, B. A. Shoemaker, P. A. Thiessen, B. Yu, L. Zaslavsky, J. Zhang, E. E. Bolton, "PubChem 2025 update." Nucleic Acids Research 53, D1516-D1525 (2025) 10.1093/nar/gkae1059 Sci-Hub
Upstream URL OK
https://pubchem.ncbi.nlm.nih.gov/
https://ftp.ncbi.nlm.nih.gov/pubchem/Compound/Extras/
Upstream license
Public domain (NCBI); data provided by depositors may be subject to their own terms, https://www.ncbi.nlm.nih.gov/home/about/policies/
Networks
Tip: hover over a column header for a description.
Column legend
$\left<k\right>$
Mean degree
$\sigma_k$
Standard deviation of the degrees
$\lambda_h$
Largest eigenvalue of the Hashimoto (non-backtracking) matrix
$\tau$
Random walk mixing time
$r$
Degree assortativity
$c$
Global clustering coefficient
$\oslash$
(Pseudo-) diameter
$S$
Relative size of the largest component
NPs
Node properties
EPs
Edge properties
Name Nodes Edges $\left<k\right>$ $\sigma_k$ $\lambda_h$ $\tau$ $r$ $c$ $\oslash$ $S$ Kind Mode NPs EPs gt GraphML GML csv
pubchem_literature 13,789,196 51,878,601 7.52 441.33 1291.52 716.76 -0.15 0.00 19 1.00 Undirected Bipartite is_compound cid pmid name type 191.8 MiB 326.9 MiB 309.9 MiB 328.8 MiB