Soon, the comments being made in PubMed’s pilot scientific discussion forum will be visible to all PubMed users. You can read about that in a previous post. In the meantime, let’s look at how authors are using the Commons with their own scientific publications – and authors’ responses to comments by others.
Last week, there had been just shy of 400 comments live in PubMed. Almost one in five were made by an author of the publication concerned (73/394). The most common contribution – half of the authors’ comments – was adding study data, a link to full free text, further materials or updates related specifically to that publication.
Some typical examples:
- In October, Jones added the full dataset of a randomized controlled trial on helping people quit smoking before surgery;
- On 5 November, Mendes added this link to updated data to a 2008 publication on a genome-scale reconstruction of the metabolic network of yeast (S. cerevisiae);
- Eisen added a link to data for figures in a 2013 article on methods for generating phylogenetic trees – and he added a link to a blog post about the background to a publication on methods for searching for and exploring metagenomic data;
- At the end of October, Bastian added a link to updated data on the increase in systematic reviews of health interventions for a key figure in a 2010 article; and
- Pachter reported in November that the database for analyzing large genomic regions described in a 2003 article was no longer available, with a link to a recommended alternative.
For just over another quarter of the comments, authors took the opportunity to link the record of one study with other work they had done previously or subsequently, or information from others they thought provides useful context. Here are a couple of examples:
- Stein, the lead author of a 2006 article on Golden Rice, points readers to a “subsequent, longer and more detailed article” with a development focus and a review published in 2013 – neither of those articles is in the biomedical literature that PubMed covers; and
- Panzica reported in November that the results of that group’s 2008 study partly supersede the results of a study about hormones and mice from 2002.
Authors almost universally did not use the comment function purely to say on their own record that the publication was good (only two did). Just under 10% used it to notify errata, or to notify readers that they now believed the conclusions of their publication are not valid. Here’s an excerpt from one: it’s from Andrew Kniss, an author of a 2006 paper on the effect of an herbicide on sugarbeet bred to be resistant to it.
“This paper (on which I am a co-author) was an early report based solely on greenhouse and laboratory studies. Glyphosate applied to glyphosate-resistant sugarbeet increased disease under greenhouse conditions in this work. Our conclusions with respect to field management of the disease went beyond what the limited data could support. Subsequent research has shown over five field seasons, two growing regions, and 6 sugarbeet cultivars that the effect presented here is unlikely to occur in the field…”
What about responding to comments made by others? With relatively few people currently using PubMed Commons, a lot of responses can’t be expected yet. There have been some interesting exchanges, though, with the seven authors who have engaged with commenters.
These include a discussion with Huber about a method of statistical analysis for sequencing data, and an answer by Meissner to questions by Ward on a 2013 paper from his lab on the cell invasion of a protozoan parasite responsible for several diseases in humans and animals (apicomplexan parasites).
Eyre-Walker and Stoletzki provided a graceful response to a comment by Cherry disagreeing with their interpretation of data and the conclusion that followed: “We thank the author for his insightful comments. Unfortunately Dr. Cherry is correct.”
If you make a comment, you can invite an author of the publication to respond using the “Invite an author to comment” link near the comment box. With that invitation, you both let them know you have commented and enable them to join PubMed Commons at the same time.
If you’re keen to be sure you see any further commenting on that article – or you’re an author wanting to see if there are comments on your articles – we have a blog post showing you how to search for comments and set up alerts with My NCBI.
Follow us here or on Twitter (@PubMedCommons) for more news, and the public release of the comments coming soon.
The PubMed Commons team
How to join PubMed Commons (Note – if you are an author of a publication in PubMed Commons, your email may be in the list explained in this post)