https://github.com/corybrunson/pubmed.network
analysis of PubMed data
Science Score: 10.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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○DOI references
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✓Academic publication links
Links to: ncbi.nlm.nih.gov -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (6.9%) to scientific vocabulary
Keywords
Repository
analysis of PubMed data
Basic Info
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Metadata Files
README.md
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 makes use of the Author-ity database 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.
Install
The repo is arranged as an R package and can be installed using the devtools 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, please let me know.
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.
Owner
- Name: Cory Brunson
- Login: corybrunson
- Kind: user
- Location: Gainesville, FL
- Company: @LaboratoryForSystemsMedicine
- Website: http://systemsmedicine.pulmonary.medicine.ufl.edu/profile/brunson-jason/
- Twitter: cornelioid
- Repositories: 14
- Profile: https://github.com/corybrunson
Mathematician by training, data scientist by testing. Relatively new to pretty much everything.
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Dependencies
- R >= 3.0.1 depends
- R.utils * depends
- data.table * depends
- igraph * depends
- reshape2 * depends
- R.utils * imports
- data.table * imports
- igraph * imports
- reshape2 * imports
- knitr * suggests