Mark2Cure’s first academic paper is finally published. For those of you who have been with us for a while, you may recall the posting of our preprint to biorxiv last January, so why was it only ‘published’ recently? Since all of our contributors are helping to make sense of the biomedical literature, I’d like to share the experience of writing, submitting, and publishing an academic research article, and why preprints and open access matter.

Let’s start with some informal (and partially biased) definitions.

  • Academic Research Article – An unstructured text-based knowledge dump of what a researcher learned after conducting some experiments. The draft (or manuscripts) for these are usually reviewed and improved by all the co-authors, before being submitted to a journal. In highly competitive journals, there will be a first-pass review of the manuscript (pass/no pass type thing), and then the manuscript may be handed to an editor to be sent out for review by fellow researchers.
  • Abstract – A summary of the key findings of an academic research article. Abstracts are generally accessible by all, even if the research article is not. Mark2Cure ‘docs’ are based on abstracts because these are consistently openly accessible.
  • Meta data – information about information. If an academic research article is a knowledge dump, meta data is information about that knowledge dump. For example, title, authors, key words, etc. can be meta data for a research article.
  • Peer Reviewer – a fellow researcher who takes the time to read a manuscript that has been submitted to an academic journal, and critiques the content based on their expert knowledge. It’s not a perfect system and there’s a hilarious site dedicated to unhelpful reviews, but a good reviewer is very useful for improving a manuscript.
  • Pubmed – An NIH-run indexing service that collects abstracts and the meta data about the associated research article. Note that Pubmed, does NOT index every journal (since there are also garbage/predatory journals that don’t care about content). Pubmed indexes the articles/abstracts from the reputable journals primarily in the biomedical research space. Hence, there may still be important papers holding clues for biomedical research which are published in reputable non-biomedical journals, not indexed in Pubmed.
  • Pubmed Central – A repository for published research articles. Since the NIH required that the public be able to access the research they helped to fund, research articles stemming from work sponsored by the NIH must be deposited into Pubmed Central by the publishers. Awesome, right?
  • Preprint service – An online service that publishes un-reviewed manuscripts. In the old paradigm of academic publishing, no one would (save the reviewer) be able to see or read the manuscript until it was published by the journal. I optimistically assume the rationale behind this was to prevent badly written up research, or poorly conducted research from being headlined in the media. But there were major drawbacks to the old publication paradigm. Due to accessibility issues (many researchers could not access their own published papers), so many researchers started publishing their work in preprints which makes it available and easy to share. Also, using a preprint service is helpful for disseminating research, especially since the peer review, revision, and publication process can be very slow.
  • Open Access – When the published academic research article can be read and accessed without some sort of expensive subscription, or paying money. (There’s more to open access than just the payment part, but this is good enough for now).
Why did it take almost two years for our Beta study to get published?
  1. Our small team prioritized moving Mark2cure forward over writing the manuscript for the Beta study, once we found that citizen scientists could do the task very well. That was why the manuscript wasn’t prepared until the end of Mark2Cure’s launch year.
  2. We submitted to a brand new journal. In support of the citizen science field, we submitted to the Citizen Science Association’s brand new journal. This means the kinks in the process have not been worked out, and there probably isn’t enough reviewer, editor, staff support available to make the process happen quickly. Because the Su Lab follows and advocates open science, our manuscript was deposited in the biorxiv preprint server, and the data shared in figshare.
A year in the publication process

As the proposal editor for GENE’s Gene Wiki Review series, I know how time-consuming it can be to find a reviewer. In some cases, you can go through a list of over 25 experts before you find one or two willing to review a paper. Researchers voluntarily review papers (often without any credit, though there are currently efforts to change this), so it may also take them time to review a paper. Although the Mark2Cure beta manuscript was submitted at the end of January, we did not get the reviews until the end of April.

Fortunately, the reviews were all very helpful critiques of our work. We revised our manuscript and resubmitted it mid-June, and it was accepted for publication within a few days of the submission. From that point on, the manuscript was in copy-editing and formatting process, which ended in December. For a well-established journal, this process is usually fairly fast; however, Citizen Science: Theory and Practice is new and probably does not have the level of staffing/support available to well-established journals.

TL;DR – Deposit in preprint servers, publish open access, and participate in the review process to help research move through the publication process efficiently. Mark2Cure beta study participants, you can view the fruits of your labor for free here.