This question invariably comes up at some point in any discussion of open notebook science. This concern is usually voiced in reference to the high-visibility magazines, which many scientists seem to assume will have very restrictive conditions. A quick read of their policies shows otherwise. Here are the links to pre-publication policies of major journals, with my short summaries & comments.
Nature - Go right ahead. Explicit protection clause for open/collaborative blogs/wikis. Just don’t talk to the press – guess that could include tweeting. Also Nature would like to see those links when you submit.
PNAS - Nope, not prior publication here either. In fact, PNAS has one of the most liberal stances on prepublication which is well worth reading. Even summaries of the work in the media encouraged – they only remind authors not to forget to publish!
Science - The policy listed there sounds more conservative (phrases like “most cases” and “contact the editors” don’t inspire confidence). Luckily, actually contacting the editors does: Deputy editor Brooks Hanson writes to me:
We allow posting on not-for-profit pre-print archives, so posting on arxiv.org is fine at any time. we ask that if you post before acceptance that you do not indicate that the paper is submitted to Science.
As to lab notebooks, it would probably depend on what was in the “notebook” but if it were just notes or thoughts, it would probably not be a great concern.
Many discipline-specific journals don’t state their policy on this as clearly in their advise to authors. Of course writing to the editors is the best way to get clarification, but I think their are reasonable proxies to guess what’s okay and what’s not.
Posting on preprint servers in advance of submission is probably a greater threat to the journal’s exclusive control of the content than the less-digestible and less accessible (decentralized) posting of an open notebook, and as it’s a more widespread practice it may be a good signal to look for. F1000 also compiled a list of journals that would consider archiving a poster as prepublication, which could be used as another proxy – if they are okay with posters, notebooks are probably in the clear. The Sherpa/Romeo project provides links to the pre-publication policies of many journals. Its database also identifies which journals allow what level of public archiving. Search for your favorite journals there. To the extent that “Yellow” refers “at the time of submission,” rather than post-publication, one might assume that publisher wouldn’t much object to an open notebook. Of course, I’d love clarification.
Can archive pre-print and post-print or publisher’s version/PDF
Can archive post-print (ie final draft post-refereeing) or publisher’s version/PDF
Can archive pre-print (ie pre-refereeing)
Archiving not formally supported
For instance, looks like the Royal Society journals are okay too. They receive a Green status, permits pre-review author’s copy on preprint servers. Published copy uses Creative Commons Attribution (cc-by) licensing. Their duplicate publishing statement makes no reference to archives, only other publishers.