The links below will help you obtain the necessary copyright permissions to submit your manuscript to PubMed Central. There is a link list of journals that automatically submits manuscripts for authors into PubMed Central. If your article is published in one of these journals, you do not need to do anything else to comply with the NIH Public Access Policy.
NIH stresses that it is your responsibility, as the author, to ensure that you have the right to deposit your manuscript with PMC. Some publishers require that you transfer copyright prior to acceptance of publication; NIH warns that you should avoid such journals if their contract does not allow you to deposit articles in PubMed Central. Other publishers in their publication agreements ask you to warrant that there are no prior agreements concerning the publication and that the publisher will own all rights. If you submit a manuscript to PMC prior to signing such an agreement, you would be in breach of the agreement and in violation of NIH policy. If your publisher does not participate in PMC, there are three options you can use to be in compliance.
Read your publication agreement carefully. Make sure that you have the right to deposit your article with PMC. The SHERPA/RoMEO site at http://www.sherpa.ac.uk/romeo.php has information on the policy of many journals regarding PMC deposit.
If there is any question about your rights, add the following language to the publication agreement: "Journal acknowledges that Author retains the right to provide a copy of the final manuscript to the NIH upon acceptance for Journal publication, for public archiving in PubMed Central as soon as possible but no later than 12 months after publication by Journal."
Alternatively, attach the Scholar's Copyright Addendum Engine Delayed Access Addendum to the publication contract. The Addendum is a legal instrument that acknowledges any prior grants (including those required by funding agencies). It also provides you with other important rights, including the right to use your article in your own teaching and research, the right to build on the article in future publications, and the right to deposit the PDF version from the publisher with PMC. An online engine that generates the Addendum is found at http://scholars.sciencecommons.org/. Note that the engine currently creates an agreement with a six month delay; this can be changed manually if the journal insists on PMC delaying access for the full twelve months.