https://github.com/corybrunson/pubmed.network
analysis of PubMed data
https://github.com/corybrunson/pubmed.network
pubmed reproduction-code
Last synced: 2 months ago
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analysis of PubMed data
- Host: GitHub
- URL: https://github.com/corybrunson/pubmed.network
- Owner: corybrunson
- License: gpl-2.0
- Created: 2015-01-30T13:52:40.000Z (over 10 years ago)
- Default Branch: master
- Last Pushed: 2015-03-12T20:55:51.000Z (about 10 years ago)
- Last Synced: 2025-02-05T00:41:44.616Z (4 months ago)
- Topics: pubmed, reproduction-code
- Language: R
- Homepage:
- Size: 1.89 MB
- Stars: 0
- Watchers: 4
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
pubmed.network
=======
This R package contains functions for network analysis of PubMed data.
## Description
An ongoing network analysis of an excerpt of the [PubMed bibliographic database] [2] makes use of the [Author-ity database] [1] to disambiguate author names. The data consolidation consists in omitting
* PMIDs (PubMed publication identification numbers) from the PubMed excerpt that do not appear, or do not appear as many times as they should (once for each author), in Author-ity; and
* PMIDs from Author-ity that do not appear in the PubMed excerpt.
Further steps will be discussed as they are performed.
[1]: http://arrowsmith.psych.uic.edu/arrowsmith_uic/author2.html
[2]: http://www.ncbi.nlm.nih.gov/pubmed/
## Install
The repo is arranged as an R package and can be installed using the [devtools](http://cran.r-project.org/web/packages/devtools/index.html) package:
```r
if(!require(devtools)) {
install.packages('devtools')
stopifnot(require(devtools))
}
install_github('corybrunson/pubmed.network')
```
If you experience any problems with the installation process (that aren't resolved by `?` and searching, e.g., [StackExchange] [3], please let me know.
[3]: http://stackexchange.com/
## References
The Author-ity database is credited to:
* Torvik VI, Smalheiser NR. "Author name disambiguation in MEDLINE." ACM Transactions on Knowledge Discovery from Data 2009; **3**(3):11.
* Smalheiser NR, Torvik VI. "Author name disambiguation." In *Annual Review of Information Science and Technology* (B. Cronin, Ed.), Vol. 43 (2009), pp. 287-313.