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pmparser

https://github.com/hugheylab/pmparser

Science Score: 39.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.8%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
Statistics
  • Stars: 18
  • Watchers: 3
  • Forks: 2
  • Open Issues: 1
  • Releases: 2
Created about 6 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog

README.md

pmparser

check-deploy codecov Netlify Status CRAN Status drat version

pmparser enables one to easily create and maintain a relational database of data from PubMed/MEDLINE. pmparser can download the publicly available XML files, parse them, incorporate PubMed's regular updates, and combine the data with the NIH Open Citation Collection. PMDB, our implementation of the database, is available on Zenodo (as a PostgreSQL dump) and on Google BigQuery. For a detailed description of pmparser and PMDB, check out the article.

Installation

Option 1: CRAN

r install.packages('pmparser')

Option 2: Hughey Lab Drat Repository

  1. Install BiocManager.

    r if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager')

  2. If you use RStudio, go to Tools → Global Options... → Packages → Add... (under Secondary repositories), then enter:

- Name: hugheylab
- Url: https://hugheylab.github.io/drat/

You only have to do this once. Then you can install or update the package by entering:

```r
BiocManager::install('pmparser')
```

Alternatively, you can install or update the package by entering:

```r
BiocManager::install('pmparser', site_repository = 'https://hugheylab.github.io/drat/')
```

Usage

See the examples and detailed guidance in the reference documentation.

Owner

  • Name: Hughey Lab
  • Login: hugheylab
  • Kind: organization

GitHub Events

Total
  • Issues event: 2
  • Watch event: 2
  • Issue comment event: 2
  • Push event: 4
  • Fork event: 1
Last Year
  • Issues event: 2
  • Watch event: 2
  • Issue comment event: 2
  • Push event: 4
  • Fork event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 338
  • Total Committers: 4
  • Avg Commits per committer: 84.5
  • Development Distribution Score (DDS): 0.456
Past Year
  • Commits: 17
  • Committers: 1
  • Avg Commits per committer: 17.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Josh Schoenbachler j****r@g****m 184
Jake Hughey j****y@g****m 149
Ubuntu u****u@i****l 4
Elliot Outland e****d@g****m 1
Committer Domains (Top 20 + Academic)
ip-172-31-28-115.us-east-2.compute.internal: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 64
  • Total pull requests: 29
  • Average time to close issues: 26 days
  • Average time to close pull requests: 5 days
  • Total issue authors: 13
  • Total pull request authors: 2
  • Average comments per issue: 1.67
  • Average comments per pull request: 2.03
  • Merged pull requests: 25
  • Bot issues: 17
  • Bot pull requests: 0
Past Year
  • Issues: 4
  • Pull requests: 1
  • Average time to close issues: 11 months
  • Average time to close pull requests: 31 minutes
  • Issue authors: 3
  • Pull request authors: 1
  • Average comments per issue: 1.25
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • github-actions[bot] (17)
  • jakejh (16)
  • JSchoenbachler (10)
  • KimBenjaminTang (4)
  • dhimmel (3)
  • globbestael (3)
  • ravwojdyla (3)
  • hope-data-science (3)
  • alinangle (1)
  • nicklamiller (1)
  • hadley (1)
  • jcalebsmith (1)
  • sitch (1)
Pull Request Authors
  • JSchoenbachler (17)
  • jakejh (12)
Top Labels
Issue Labels
lint (20)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 376 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 11
  • Total maintainers: 1
cran.r-project.org: pmparser

Create and Maintain a Relational Database of Data from PubMed/MEDLINE

  • Versions: 11
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 376 Last month
Rankings
Stargazers count: 15.1%
Forks count: 17.8%
Average: 28.2%
Dependent packages count: 29.8%
Dependent repos count: 35.5%
Downloads: 42.9%
Maintainers (1)
jakejhughey@gmail.com
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.6 depends
  • DBI >= 1.1.0 imports
  • R.utils >= 2.10.1 imports
  • RCurl >= 1.98 imports
  • curl >= 4.3.2 imports
  • data.table >= 1.12.2 imports
  • foreach >= 1.5.0 imports
  • glue >= 1.4.2 imports
  • iterators >= 1.0.12 imports
  • jsonlite >= 1.7.0 imports
  • withr >= 2.3.0 imports
  • xml2 >= 1.3.3 imports
  • RMariaDB >= 1.0.9 suggests
  • RPostgres >= 1.2.0 suggests
  • RSQLite >= 2.2.0 suggests
  • bigrquery >= 1.3.2 suggests
  • doParallel >= 1.0.16 suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat >= 2.3.2 suggests