rdflib · Issue #169 · ropensci/software-review (original) (raw)

Summary

• What does this package do? (explain in 50 words or less):

rdflib is simply a wrapper around two existing ropensci packages: redland and jsonld, which should be a user-friendly complement to the low-level interface already provided by redland for working with RDF (semantic/linked data).

• Paste the full DESCRIPTION file inside a code block below:

Package: rdflib
Title: Tools to Manipulate and Query Semantic Data
Version: 0.0.2
Authors@R: person("Carl", "Boettiger", 
                  email = "cboettig@gmail.com", 
                  role = c("aut", "cre", "cph"),
                  comment=c(ORCID = "http://orcid.org/0000-0002-1642-628X"))
Description: The Resource Description Framework, or 'RDF' is a widely used
             data representation model that forms the cornerstone of the 
             Semantic Web. 'RDF' represents data as a graph rather than 
             the familiar data table or rectangle of relational databases.
             The 'rdflib' package provides a friendly and concise user interface
             for performing common tasks on 'RDF' data, such as reading, writing
             and converting between the various serializations of 'RDF' data,
             including 'rdfxml', 'turtle', 'nquads', 'ntriples', 'trig', and 'json-ld';
             creating new 'RDF' graphs, and performing graph queries using 'SPARQL'.
             This package wraps the low level 'redland' R package which
             provides direct bindings to the 'redland' C library.  Additionally,
             the package supports the newer and more developer friendly
             'JSON-LD' format through the 'jsonld' package. The package
             interface takes inspiration from the Python 'rdflib' library.
Depends: R (>= 3.4.1)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
URL: https://github.com/cboettig/rdflib
BugReports: https://github.com/cboettig/rdflib/issues
Imports: redland,
    jsonld,
    methods,
    utils
RoxygenNote: 6.0.1
Suggests: magrittr,
    covr,
    testthat,
    knitr,
    rmarkdown,
    jsonlite,
    httr,
    xml2,
    jqr,
    readr,
    dplyr,
    lubridate,
    DT
VignetteBuilder: knitr

• URL for the package (the development repository, not a stylized html page):

https://github.com/cboettig/rdflib

• Please indicate which category or categories from our package fit policies this package falls under * and why(? (e.g., data retrieval, reproducibility. If you are unsure, we suggest you make a pre-submission inquiry.):

data extraction, because this package parses scientific data file formats. (specifically, formats already parsed by existing rOpenSci packages). This package also enables graph queries using the SPARQL language, somewhat analogous to the rOpenSci jqr package, but for JSON-LD and other linked data formats.

• Who is the target audience and what are scientific applications of this package?

Anyone working with semantic data, including the wide array of scientific ontologies and knowledge-bases. These include reproducibility-focused ontologies like PROV, and a large number of biological ontologies ranging from genes to traits to environmental features.

• Are there other R packages that accomplish the same thing? If so, how does
  yours differ or meet our criteria for best-in-category?

As described above, this package overlaps significantly with the redland package, but should be easier to use.

• If you made a pre-submission enquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted.

Requirements

Confirm each of the following by checking the box. This package:

• does not violate the Terms of Service of any service it interacts with.
• has a CRAN and OSI accepted license.
• contains a README with instructions for installing the development version.
• includes documentation with examples for all functions.
• contains a vignette with examples of its essential functions and uses.
• has a test suite.
• has continuous integration, including reporting of test coverage, using services such as Travis CI, Coeveralls and/or CodeCov.
• I agree to abide by ROpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

Publication options

• Do you intend for this package to go on CRAN?
• Do you wish to automatically submit to the Journal of Open Source Software? If so:
  • The package has an obvious research application according to JOSS's definition.
  • The package contains a paper.md matching JOSS's requirements with a high-level description in the package root or in inst/.
  • The package is deposited in a long-term repository with the DOI: https://doi.org/10.5281/zenodo.1098478
  • (Do not submit your package separately to JOSS)
• Do you wish to submit an Applications Article about your package to Methods in Ecology and Evolution? If so:
  • The package is novel and will be of interest to the broad readership of the journal.
  • The manuscript describing the package is no longer than 3000 words.
  • You intend to archive the code for the package in a long-term repository which meets the requirements of the journal.
  • (Please do not submit your package separately to Methods in Ecology and Evolution)

Detail

• Does R CMD check (or devtools::check()) succeed? Paste and describe any errors or warnings:
• Does the package conform to rOpenSci packaging guidelines? Please describe any exceptions:
• If this is a resubmission following rejection, please explain the change in circumstances:
• If possible, please provide recommendations of reviewers - those with experience with similar packages and/or likely users of your package - and their GitHub user names:
• Scott Chamberlain, @sckott
• Peter Slaughter, @gothub
• Bryce Mecum, @amoeba
• Anna Krystalli, @annakrystalli