Dataset Open Access

A global network of biomedical relationships derived from text

Percha, Bethany; Altman, Russ B.

This repository contains labeled, weighted networks of chemical-gene, gene-gene, gene-disease, and chemical-disease relationships based on single sentences in PubMed abstracts. All raw dependency paths are provided in addition to the labeled relationships.

PART I: Connects dependency paths to labels, or "themes". Each record contains a dependency path followed by its score for each theme, and indicators of whether or not the path is part of the flagship path set for each theme (meaning that it was manually reviewed and determined to reflect that theme). The themes themselves are listed below and are in our paper (reference below).

PART II: Connects sentences to dependency paths. It consists of sentences and associated metadata, entity pairs found in the sentences, and dependency paths connecting those entity pairs. Each record contains the following information:

  • PubMed ID
  • Sentence number (0 = title)
  • First entity name, formatted
  • First entity name, location (characters from start of abstract)
  • Second entity name, formatted
  • Second entity name, location
  • First entity name, raw string
  • Second entity name, raw string
  • First entity name, database ID(s)
  • Second entity name, database ID(s)
  • First entity type (Chemical, Gene, Disease)
  • Second entity type (Chemical, Gene, Disease)
  • Dependency path
  • Sentence, tokenized

The "with-themes.txt" files only contain dependency paths with corresponding theme assignments from Part I. The plain ".txt" files contain all dependency paths.

This release contains the annotated network for the April 22, 2018 version of PubTator. The version discussed in our paper, below, is an older one - from April 30, 2016. If you're interested in that network, it can be found in Version 1 of this repository. We will be releasing updated networks periodically, as the PubTator community continues to release new versions of named entity annotations for Medline each month or so.

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REFERENCES

Percha B, Altman RBA (2017) A global network of biomedical relationships derived from text. (In press at Bioinformatics.)
Percha B, Altman RBA (2015) Learning the structure of biomedical relationships from unstructured text. PLoS Computational Biology, 11(7): e1004216.

This project depends on named entity annotations from the PubTator project:
https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/

Reference:
Wei CH et. al., PubTator: a Web-based text mining tool for assisting Biocuration, Nucleic acids research, 2013, 41 (W1): W518-W522. doi: 10.1093/nar/gkt44

Dependency parsing was provided by the Stanford CoreNLP toolkit:
https://stanfordnlp.github.io/CoreNLP/index.html

Reference:
Manning, Christopher D., Mihai Surdeanu, John Bauer, Jenny Finkel, Steven J. Bethard, and David McClosky. 2014. The Stanford CoreNLP Natural Language Processing Toolkit In Proceedings of the 52nd Annual Meeting of the Association for Computational Linguistics: System Demonstrations, pp. 55-60.

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THEMES

chemical-gene
(A+) agonism, activation
(A-) antagonism, blocking
(B) binding, ligand (esp. receptors)
(E+) increases expression/production
(E-) decreases expression/production
(E) affects expression/production (neutral)
(N) inhibits

gene-chemical
(O) transport, channels
(K) metabolism, pharmacokinetics
(Z) enzyme activity

chemical-disease
(T) treatment/therapy (including investigatory)
(C) inhibits cell growth (esp. cancers)
(Sa) side effect/adverse event
(Pr) prevents, suppresses
(Pa) alleviates, reduces
(J) role in disease pathogenesis

disease-chemical
(Mp) biomarkers (of disease progression)

gene-disease
(U) causal mutations
(Ud) mutations affecting disease course
(D) drug targets
(J) role in pathogenesis
(Te) possible therapeutic effect
(Y) polymorphisms alter risk
(G) promotes progression

disease-gene
(Md) biomarkers (diagnostic)
(X) overexpression in disease
(L) improper regulation linked to disease

gene-gene
(B) binding, ligand (esp. receptors)
(W) enhances response
(V+) activates, stimulates
(E+) increases expression/production
(E) affects expression/production (neutral)
(I) signaling pathway
(H) same protein or complex
(Rg) regulation
(Q) production by cell population

Files (7.3 GB)
Name Size
part-i-chemical-disease-path-theme-distributions.txt.gz
md5:a36e2e9516ce1d3ebcfa921b5c10467a
70.0 MB Download
part-i-chemical-gene-path-theme-distributions.txt.gz
md5:4f02054eec8b92fafada5cb7098ac7dc
24.8 MB Download
part-i-gene-disease-path-theme-distributions.txt.gz
md5:66949134a3fde6752e8e36d21bc8c2b7
63.7 MB Download
part-i-gene-gene-path-theme-distributions.txt.gz
md5:9be6e7eac7ea044ebaca06a6fa83c34c
53.0 MB Download
part-ii-dependency-paths-chemical-disease-sorted-with-themes.txt.gz
md5:02ebd618f619fca5cadcaa527ad1549c
395.9 MB Download
part-ii-dependency-paths-chemical-disease-sorted.txt.gz
md5:b947d498a7c54b051aab2e75b5cb173f
1.4 GB Download
part-ii-dependency-paths-chemical-gene-sorted-with-themes.txt.gz
md5:b4a43f02f9ecb6ea1737b025e9e445c8
149.9 MB Download
part-ii-dependency-paths-chemical-gene-sorted.txt.gz
md5:51437d31c4f139e4778c15b452c08bbd
847.4 MB Download
part-ii-dependency-paths-gene-disease-sorted-with-themes.txt.gz
md5:4c949f854eb4a60c641a6e147dc81b8d
312.2 MB Download
part-ii-dependency-paths-gene-disease-sorted.txt.gz
md5:d210bb11a0dc39ab8d7500a457a147a7
1.1 GB Download
part-ii-dependency-paths-gene-gene-sorted-with-themes.txt.gz
md5:614f7becd38ad4c4543aec5b2e8781b6
382.1 MB Download
part-ii-dependency-paths-gene-gene-sorted.txt.gz
md5:bdfd25cc6a272483d0c490f138bebeae
2.5 GB Download

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