Reference

Last updated on 2025-04-30 | Edit this page

Glossary

Author Carpentry
An instructional initiative by Caltech Library focused on integrating open science values into scholarly writing, editing, and publishing workflows.

BibTeX
A reference management format used with LaTeX documents for citing and formatting bibliographies.

CRediT (Contributor Roles Taxonomy)
A standardized taxonomy that defines 14 contributor roles (e.g., Conceptualization, Data Curation, Writing – Original Draft) to improve transparency in author contributions.

Conflict of Interest (COI)
A situation in which an individual’s personal, financial, or professional relationships may compromise or bias their research or review responsibilities.

DOI (Digital Object Identifier)
A persistent identifier used to uniquely identify electronic documents, such as journal articles or datasets.

LaTeX
A typesetting system commonly used in academia for producing scientific and mathematical documents with high typographical quality.

Markdown
A lightweight markup language with plain-text formatting syntax, often used for writing documents intended to be converted into HTML or PDF.

Open Access
A publishing model that makes research outputs freely available online, removing access barriers for readers.

Open Peer Review
A set of peer review practices that emphasize transparency, including revealing reviewer identities or publishing review reports.

Open Science
A movement to make scientific research more accessible, transparent, reproducible, and inclusive through open data, open methods, open source tools, and open access publishing.

Pandoc
An open-source tool that converts files from one markup format to another (e.g., Markdown to PDF or DOCX), commonly used in scholarly writing workflows.

Preprint
A version of a scholarly paper that precedes formal peer review and publication in a scientific journal. Often shared to solicit early feedback.

RIS
A standardized tag format for citations, used to exchange bibliographic data between reference management tools.

WYSIWYG (What You See Is What You Get)
A user interface that allows authors to directly manipulate the layout of a document or webpage while editing.

WYSIWYM (What You See Is What You Mean)
A document authoring approach that prioritizes semantic structure over visual appearance, enabling easier reuse, conversion, and machine readability.

References

  1. Ketchum AM. The research life cycle and the health sciences librarian: responding to change in scholarly communication. J Med Libr Assoc. 2017 Jan;105(1):80–83. https://doi.org/10.5195/jmla.2017.110
  2. The Open Science Toolkit. Center for Open Science. https://osf.io/a4ftw/
  3. Author Carpentry Workshop. https://github.com/kmiller621/author-2022-05-16-online
  4. Think. Check. Submit. Journal Evaluation Checklist. https://thinkchecksubmit.org/journals/
  5. Garfield E. The history and meaning of the journal impact factor. JAMA. 2006 Jan;295(1):90–93. https://jamanetwork.com/journals/jama/article-abstract/202114
  6. CommonMark Markdown Tutorial. https://commonmark.org/help/tutorial/
  7. Sustainable Authorship in Plain Text using Pandoc and Markdown. Programming Historian. https://programminghistorian.org/en/lessons/sustainable-authorship-in-plain-text-using-pandoc-and-markdown
  8. Manuscript template resources:
  1. JMSACL RMarkdown Example. https://github.com/drdanholmes/jmsacl_reproducible_research
  2. Learn LaTeX. https://www.learnlatex.org/en/lesson-02
  3. LaTeX Structure Exercise. https://www.learnlatex.org/en/lesson-04
  4. JDLang LaTeX Course:
  1. Wiley Author Services: Authorea. https://authorservices.wiley.com/author-resources/Journal-Authors/Prepare/authorea.html
  2. Knowledge Futures: PubPub. https://www.knowledgefutures.org/pubpub/
  3. The Open Journal. https://www.theoj.org/
  4. Programming Historian Author Guidelines. https://programminghistorian.org/en/author-guidelines
  5. Tennant JP, et al. A multi-disciplinary perspective on emergent and future innovations in peer review. F1000Research. 2017. https://doi.org/10.12688/f1000research.11369.2
  6. Ross-Hellauer T. What is open peer review? A systematic review. F1000Research. 2017. https://doi.org/10.12688/f1000research.12037.3
  7. Nature Editorial. Peer review and the acceptance of submitted manuscripts. Nature. 2002. https://doi.org/10.1038/6295
  8. ICMJE: Defining the Role of Authors and Contributors. https://www.icmje.org/recommendations/browse/roles-and-responsibilities/defining-the-role-of-authors-and-contributors.html
  9. LibreOffice vs. Microsoft Office Feature Comparison. https://wiki.documentfoundation.org/Feature_Comparison:_LibreOffice_-_Microsoft_Office