PubRef.org

This article has multiple issues. Please help improve it or discuss these issues on the talk page. (Learn how and when to remove these template messages) This article's use of external links may not follow Wikipedia's policies or guidelines. Please improve this article by removing excessive or inappropriate external links, and converting useful links where appropriate into footnote references. (June 2018) (Learn how and when to remove this template message) The topic of this article may not meet Wikipedia's notability guideline for web content. Please help to demonstrate the notability of the topic by citing reliable secondary sources that are independent of the topic and provide significant coverage of it beyond a mere trivial mention. If notability cannot be shown, the article is likely to be merged, redirected, or deleted. Find sources: "PubRef.org" – news · newspapers · books · scholar · JSTOR (September 2015) (Learn how and when to remove this template message) (Learn how and when to remove this template message)

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.^[1]

They used the same name PubRef which was a service provided by PubMed for linking bibliographies, defeated by the independent service Crossref.^[2]

PubRef was a composition and project management application used by researchers and students for scholarly writing and communication. 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[edit]

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, transparency and re-usability in digital science publishing.

Manuscript writing[edit]

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[edit]

This minimal formatting example repurposes a classic paper by Stephen Hawking and Roger Penrose The Singularities of Gravitational Collapse and Cosmology:^[3]

# The journal meta descriptor declares what journal the  # manuscript should be submitted to. !journal title: Proceedings of the Royal Society of London 

# The article meta descriptor defines the title, keywords, and categorization !article type: Original Research title: The Singularities of Gravitational Collapse and Cosmology 

# A Meta Block that describes the corresponding author. !author corresponding: yes first: Stephen last: Hawking degrees: PhD affiliation: cambridge --- !author first: Roger last: Penrose degrees: PhD affiliation: birbeck 

# A Meta Block that describes an organizational affiliation.   # The 'id' makes it referenceable within the document. !affiliation id: cambridge university: Cambridge University institute: Institute of Theoretical Astronomy --- !affiliation id: birbeck college: Birbeck College dept: Department of Mathematics 

  # 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[edit]

Once the essential frontmatter meta elements have been declared, manuscripts can be automatically submitted to academic publishers.^[4] 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.^[5]

References[edit]