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Scholarly Publishing and Communication

Types of Research Outputs

Articles

Journal Selection

There are a lot of factors to consider when looking for the right venue for your work: do you want to publish open access? Are there any public access policies from your funder? What are some impactful journals in your field? The following are a few other resources to consider when selecting and evaluating journals to publish in.

Journal Matching Tools
More Journal Selection Tools

Journal Evaluation

Think. Check. Submit.

Think. Check. Submit. "helps researchers identify trusted journals and publishers for their research. Through a range of tools and practical resources, this international, cross-sector initiative aims to educate researchers, promote integrity, and build trust in credible research and publications."

Some questions that you should ask when evaluating a journal include:

  • Is it a known journal?
  • Is the publisher easy to contact?
  • Is the peer review process explained?
  • Are the journal's articles indexed in established databases? (Excluding Google Scholar)
  • Are author fees transparent?
  • Do they participate in any professional organizations or industry initiatives?
  • Visit Think. Check. Submit. for the entire checklist.
More Evaluation Guidelines

Datasets

Publishing a Dataset

Researchers may make their datasets publicly available for a variety of reasons, including but not limited to:

  • encouraging peer review of data analysis beyond what is typically possible through a research article alone
  • contributing data for secondary analysis
  • sharing data that did not or will not lead to a publication, but are still valuable
  • complying with data sharing mandates from a funder, publisher, or institution

Often, "publishing" and "sharing" datasets are synonymous. In this guide, both refer to methods of sharing research data that are more robust than simply e-mailing data files among interested colleagues or asking an author for access to the data. In general, we advise researchers to look for a data publication platform that will enable their data to be as open as possible (while respecting confidentiality obligations), for as long as possible, and stored as securely as possible (e.g., so the data files won't become corrupted.) 

Data Repositories

The NNLM data thesaurus defines a data repository as a: "place that holds data, makes data available to use, and organizes data in a logical manner."  

The NIH has guidance for selecting a repository for data resulting from NIH-supported research.

Directories to Locate Repositories

Although not comprehensive, these directories are a good place to start searching for a data repository.  

Generalist Repositories

These repositories host data regardless of type, format, content, or subject matter.  This comparison chart may be helpful when considering more than one repository.  

Domain-Specific Repositories

This is a selective list of domain-specific resources, including genomics and clinical.  To locate more, please use the directories listed above or reach out to a librarian.  

Data Journals

Data journals are a means to share datasets and provide detailed information about the methods and instrumentation used to acquire the data. Below is a selected list of open access data journals for the health sciences.  The journals that are indexed and findable in PubMed are denoted.  

Citing Data

Data citations allow the impact of data to be tracked, are separate from publication citations and enable credit to be given to author(s).

Two citation templates are commonly accepted:

Preprints

Definitions

A preprint is a scientific manuscript containing data and methods that is posted by the author(s) to a public server prior to journal acceptance and official publication.

A preprint server is an open access online distribution center/archive that enable authors to immediately post their findings and receive feedback from the scientific community. 

Preprints are not copy-edited or peer-reviewed prior to posting online, although they undergo a basic screening process to check against plagiarism, offensiveness, and non-scientific content. Authors may make revisions at any point prior to publication, but all versions remain available online.

Visit ASAPbio for more preprint information.

Posting on a Preprint Server

Before posting a preprint, it is crucial to review the journal policies for where you plan to submit your manuscript.

You also need to consider copyright and licensing issues.

Numerous preprint servers with varying posting models are available, including some with pipelines leading to journal publication.  A select few with a biomedical focus are listed here; check the ASAPbio Preprint Directory for more options.

Finding Preprints

Seeing examples may be useful to help you decide where to post your preprint. In addition to directly searching a specific preprint server, you can identify preprints from multiple sources using one of the following search tools.

Protocols

Research Protocols

Research protocols could include step-by-step descriptions of procedures (protocols), guidelines, best practices, workflows, safety precautions, animal handling, and other methods relating to research and education. 

Examples of Publication Options

(Note these resources are NOT typically for clinical protocols)

Repositories
Peer-Reviewed Journals

Pre-Registration of Study Protocols

A pre-registration of a study protocol is a time-stamped record of decisions around study design, methods and analysis, that is created before data are collected or become accessible. The pre-registration document should be publicly available on a registry or repository.  Learn more about pre-registration at the Center for Open Science Preregistration page.

Another option would be to publish a registered report, a type of journal article that involves peer review of the background, study design, methods, and analysis plan before data are collected. Learn more about registered reports at the Center for Open Science Registered Reports page

Examples of Publication Options 

(Note these resources are NOT for registration of clinical trials)

Pre-Registration
Registered Reports

Software

Publishing Software

This guide provides resources for two scenarios in which a researcher may wish to make their research code publicly available:

Contributing code to the community

Have you created a software package that other researchers would find useful? Sharing your code via a public repository is recommended over  sharing it via a personal FTP or lab website because it reduces maintenance, especially if you change institutions; is more discoverable through search engines; often applies version control to code updates or modifications suggested by others; and may provide a DOI or other persistent, unique identifier required by publishers to include in a citation.

Sharing code as supporting resources for a publication

Sharing code makes computational research more reproducible, and it is required by a growing number of top journals. The easiest way to share code, for both authors and readers/reviewers, is by making it available through a public repository. Sharing code only upon request takes up more time for all parties, and often does not work in practice--see Stodden et al. (2018) for an exploration of code-sharing in Science and the frustrations encountered by the research team when attempting to reproduce ostensibly open code.

Software Repositories

This is a partial list of platforms designed for sharing open-source code, organized generally from simple to complex. When choosing a software repository for your code, you may consider the following criteria:

  • Price: most (if not all) of these repositories have a free option. Will it meet your needs, or should you look at the paid options?
  • Usage: some of these repositories are more heavily used by certain fields or programming language communities (CRAN for R users being an obvious example.)
  • Computational power: are you looking for a simple, safe host for your software code, or do you want to run computational analyses on the same platform?
  • DOIs: if having a DOI for your code is important, a platform like Zenodo will suit your needs better than something like Github.

Choosing a License for Research Code

Licenses are essential for laying out how users may use, modify, or share your code. Some licenses are more permissive, while others are more restrictive. They do not give up your copyright, unless you explicitly choose a public domain dedication like CC0 or The Unlicense.

Note that this is not the same as "licensing" in the commercialization sense. For that, please contact the University of Pittsburgh Innovation Institute.