Q: How to write a mail requesting the manuscript be published after the patent is accepted?

Ideally, if your research involves you to file a patent, you should first apply for the patent and have it accepted (if it is indeed accepted) and only then write and submit the manuscript. This is both to protect the potential novelty of your application and to submit a manuscript that discusses a novel solution, which is what publishers look for in each manuscript. However, you can also check with your country’s patent authority – in your case, Japan Patent Office – for the exact regulations regarding patient publication.

Coming to your question, as you are presently revising the manuscript, it has undergone a peer review. This means that the journal is possibly interested in publishing your paper and has therefore spent some resources in handling your manuscript so far. As you decided to file a patent after submitting the manuscript, you may now need to withdraw the paper. If or when the patent is accepted, you could update the manuscript for both the revisions and the patent information and then submit again, but as a new submission.

So, you will need to write to the editor providing these details and discussing the alternatives. If needed, you could express your apologies for the potential oversight. If you describe the situation in a genuine manner, including why you decided to file for the patent during the submission and peer review process, the editor should most likely understand your situation and allow you to submit again if or when your patent is accepted. They may also guide you on how exactly to go about it.

Additionally, you need to keep the following points in mind for the application and publication of a patent.

• If you are affiliated with a university or institute, check their rules for patent ownership. Based on the exact nature of your research, you may need to determine the exact ownership of the patent, whether you or your affiliation.
• While it seems you submitted your manuscript to a reputed publisher, do check for this once again. In case you submitted to a predatory publisher, once you inform them of your patent application and subsequent withdrawal, they may use coercive tactics to take advantage of your situation, such as by asking you to pay article processing charges (APCs) for the work done so far, publishing the paper before your patent application is decided (thus potentially compromising the novelty of your patent), and so on. You may use this checklist to identify a bogus journal: 10 Point checklist to identify predatory publishers

You may also refer to the following resources for more information on the application and publication of patents:

• Patents 101: What are patents and how do you acquire them?
• How to prepare a provisional patent application
• Can my patent-related contents be published in a journal?

All the best for both the patent application and the journal communication!