PubRef.org was a short lived project that is now discontinued.
The website is not accessible anymore. An old version can be accessed from the
Internet Archive
The Internet Archive is an American 501(c)(3) organization, non-profit organization founded in 1996 by Brewster Kahle that runs a digital library website, archive.org. It provides free access to collections of digitized media including web ...
.
They used the same name PubRef which was a service provided by
PubMed
PubMed is an openly accessible, free database which includes primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine (NLM) at the National Institute ...
for linking bibliographies, defeated by the independent service
Crossref.
PubRef was a composition and project management application used by researchers and students for
scholarly writing
Academic writing or scholarly writing refers primarily to nonfiction writing that is produced as part of academic work in accordance with the standards of a particular academic subject or discipline, including:
* reports on empirical fieldwork o ...
and
communication
Communication is commonly defined as the transmission of information. Its precise definition is disputed and there are disagreements about whether Intention, unintentional or failed transmissions are included and whether communication not onl ...
.
PubRef uses an extended form of
Markdown as a primary authoring format and converts this to
JATS, the archive format used by the
US National Library of Medicine.
Research asset containerization
Researchers manage scholarly writing projects within version-controlled file repositories called ''containers'' that function similarly to
git repositories and
docker containers to provide enhanced
reproducibility
Reproducibility, closely related to replicability and repeatability, is a major principle underpinning the scientific method. For the findings of a study to be reproducible means that results obtained by an experiment or an observational study or ...
,
transparency and
re-usability in digital science publishing.
Manuscript writing
A PubRef manuscript is a Markdown file within a ''container'' that contains extra embedded information that describes the essential front matter elements of a scholarly manuscript such as the title
short title list of authors
author affiliations key words. This information is captured in embedded
YAML blocks within the primary manuscript called ''Meta''. Figures, tables, equations and other special content can be similarly embedded within the context of the document via ''Meta'' descriptors.
Minimal example
This minimal formatting example repurposes a classic paper by Stephen Hawking and Roger Penrose ''The Singularities of Gravitational Collapse and Cosmology'':
# Introduction
An important feature of gravitation, for very large concentrations of mass, is that it is essentially *unstable*. This is due...
# This inserts a bibliography within the document. Citations references are
# resolved to a items in a folder named 'references', in the same directory as the
# manuscript file.
!bibliography
src: references
Manuscript publishing
Once the essential frontmatter meta elements have been declared, manuscripts can be automatically submitted to academic publishers.
Articles, supporting data, and dependent code can be published directly on PubRef in the form of ''personal communications'' under the DOI prefix ''10.17920/P9.pubref''.
References
{{Reflist, refs=
[{{cite web , title=PubRef to be Removed from PubMed — , url=https://www.nlm.nih.gov/pubs/techbull/jf01/jf01_pubref.html , accessdate=21 February 2020]
[{{cite web , last1=Internet Archive , title=The easiest way to compose and publish research — in science, technology, and medicine — , url=http://pubref.org/ , website=PubRef.org , archive-url=https://web.archive.org/web/20150929064823/http://pubref.org/ , accessdate=21 February 2020, archive-date=2015-09-29 ]
[{{cite journal , doi=10.1098/rspa.1970.0021 , first=Stephen , last=Hawking , last2=Penrose , first2=Roger , year=1970 , title=The Singularities of Gravitational Collapse and Cosmology , journal=]Proceedings of the Royal Society A
''Proceedings of the Royal Society'' is the main research journal of the Royal Society. The journal began in 1831 and was split into two series in 1905:
* Series A: for papers in physical sciences and mathematics.
* Series B: for papers in life s ...
, volume=314 , issue=1519 , pages=529–548 , bibcode=1970RSPSA.314..529H, doi-access=free
[{{cite web , last1=Aries Press , title=Aries Systems and PubRef Announce Partnership Allowing Authors Direct Submission to Thousands of Scholarly Journals , url=https://www.ariessys.com/views-press/press-releases/aries-systems-and-pubref-announce-partnership-allowing-authors-direct-submission-to-thousands-of-scholarly-journals , website=Aries Systems Corporation , accessdate=21 February 2020]
[{{cite web , last1=California Digital Library , title=EZID Client List , url=http://ezid.cdlib.org/home/client_list , website=California Digital Library , accessdate=10 September 2015 , archive-url=https://web.archive.org/web/20150914205346/http://ezid.cdlib.org/home/client_list , archive-date=14 September 2015 , url-status=dead ]
Scholarly communication
Open-access archives
Open science
Open data
Academic publishing