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I have submitted a poster abstract with my supervisors. The poster abstract got accepted, but we have not presented the poster yet. The poster describes a method we have invented and now we consider applying for a patent. Can we still do this? I know this is not possible if we have published the method in an article, but does an accepted poster abstract count as a publication? I'm a PhD student in Europe.

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    You have discussed this with your supervisor. Have they or you discussed this with whichever university office is responsible for patents?
    – MJeffryes
    May 15, 2016 at 13:41

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You have not yet made what's called a public disclosure of your research, which would render it (from an institutional standpoint) un-patentable. The second you display your poster, or if there is a short paper published along side it, is the second your work becomes publicly disclosed. Also bear in mind that if you have, on some website or another, posted code pertaining to the project, etc. this counts as a public disclosure.

As MJeffryes mentioned in his comment, you should talk with the office at your institution responsible for such endeavors (at mine it is called the research foundation) as soon as possible. The patent process takes quite some time (re: years; just FYI). Anyway, they should be able to fill you in on all that's necessary and the steps you should take, should you want to pursue that course of action.

Edit: As Dan Romik pointed out in the comments, at least in the US, there is a one-year grace period, from when you make a public disclosure, that your work can still be patented-- but anybody could patent it. I found this helpful in terms of clarifying some of the specifics. However, in speaking with the individual in charge of the research foundation at my institution, the impression I got was that, once this public disclosure was made, the foundation was no longer willing to pursue a patent (again, at my particular institution).

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    Even after public disclosure, in the U.S. you would have a year to file a patent application. In some other countries public disclosure results in an immediate loss of the right to patent the invention. See: en.m.wikipedia.org/wiki/Public_disclosure
    – Dan Romik
    May 15, 2016 at 16:14

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