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rols

An R package to query EBI's Ontology Lookup Service (OLS)

https://github.com/lgatto/rols

Science Score: 23.0%

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
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    3 of 21 committers (14.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.0%) to scientific vocabulary

Keywords from Contributors

bioconductor-packages bioconductor proteomics mass-spectrometry genomics metabolomics gene bioinformatics transcriptomics visualisation
Last synced: 10 months ago · JSON representation

Repository

An R package to query EBI's Ontology Lookup Service (OLS)

Basic Info
Statistics
  • Stars: 11
  • Watchers: 4
  • Forks: 5
  • Open Issues: 11
  • Releases: 0
Created about 14 years ago · Last pushed about 2 years ago
Metadata Files
Readme

README.md

codecov

The Ontology Lookup Service

The Ontology Lookup Service (OLS), developed at the European Bioinformatics Institute (EBI), is a unified web interface to query multiple ontologies from a single location. The new version of the OLS uses a REST API.

The rols package uses functionality from the httr package to query the OLS directly from R.

See the package's page on GitHub for details, documentation and vignette.

Installation

rols is available from the Bioconductor repository. The package and its dependencies can be installed

if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("rols")

See also the rols Bioconductor page for on-line access to the vignette and the reference manual.

Help

  • rols comes with plenty of documentation. Have a start with the vignette vignette("rols", package="rols").

  • Please direct your questions to the Bioconductor support site.

  • For feature requests and bug reports, use GitHub issues

Owner

  • Name: Laurent Gatto
  • Login: lgatto
  • Kind: user
  • Location: Belgium
  • Company: de Duve Institute, UCLouvain

Open science, reproducible research, bioinformatics, computational biology, proteomics, more omics, emacs, a lot of R, running and parenting.

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 472
  • Total Committers: 21
  • Avg Commits per committer: 22.476
  • Development Distribution Score (DDS): 0.578
Past Year
  • Commits: 7
  • Committers: 4
  • Avg Commits per committer: 1.75
  • Development Distribution Score (DDS): 0.714
Top Committers
Name Email Commits
Laurent l****0@c****k 199
Laurent Gatto l****o@d****e 56
Laurent Gatto l****o@g****m 48
l.gatto l****o@b****8 43
Laurent Gatto l****o@u****e 37
d.tenenbaum d****m@b****8 32
Dan Tenenbaum d****a@f****g 20
Nitesh Turaga n****a@g****m 14
Herve Pages h****s@f****g 4
J Wokaty j****y@s****u 2
Hervé Pagès h****s@f****g 2
Andrew Clugston a****4@p****u 2
hpages@fhcrc.org h****s@f****g@b****8 2
vobencha v****n@r****g 2
J Wokaty j****y 2
vobencha v****a@g****m 2
tiago t****t@g****m 1
LiNk-NY m****9@g****m 1
m.carlson m****n@b****8 1
Kayla-Morrell k****l@r****g 1
Marc Carlson m****n@f****g 1
Committer Domains (Top 20 + Academic)
fhcrc.org: 4 roswellpark.org: 2 pitt.edu: 1 fredhutch.org: 1 sph.cuny.edu: 1 uclouvain.be: 1 dnavision.be: 1 cam.ac.uk: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 48
  • Total pull requests: 3
  • Average time to close issues: 11 months
  • Average time to close pull requests: about 1 hour
  • Total issue authors: 16
  • Total pull request authors: 3
  • Average comments per issue: 1.17
  • Average comments per pull request: 0.67
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 0
  • Average time to close issues: 21 minutes
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 0
  • Average comments per issue: 1.33
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • lgatto (23)
  • LTLA (3)
  • quirinmanz (2)
  • shbrief (2)
  • ssun1116 (1)
  • christianholland (1)
  • tiagochst (1)
  • andysw90 (1)
  • AndrewC160 (1)
  • ramiromagno (1)
  • zhangmimm6 (1)
  • azankl (1)
  • maxfarrell (1)
  • moldach (1)
  • pstils (1)
Pull Request Authors
  • tiagochst (1)
  • AndrewC160 (1)
  • lgatto (1)
Top Labels
Issue Labels
enhancement (4) bug (2)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 67,187 total
  • Total dependent packages: 3
  • Total dependent repositories: 0
  • Total versions: 7
  • Total maintainers: 1
bioconductor.org: rols

An R interface to the Ontology Lookup Service

  • Versions: 7
  • Dependent Packages: 3
  • Dependent Repositories: 0
  • Downloads: 67,187 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 5.2%
Downloads: 15.7%
Maintainers (1)
laurent.gatto@uclouvain.be
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • methods * depends
  • Biobase * imports
  • BiocGenerics >= 0.23.1 imports
  • httr * imports
  • jsonlite * imports
  • progress * imports
  • utils * imports
  • BiocStyle >= 2.5.19 suggests
  • DT * suggests
  • GO.db * suggests
  • knitr >= 1.1.0 suggests
  • lubridate * suggests
  • rmarkdown * suggests
  • testthat * suggests