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Distinguishing the Databases:
PubMed and PubMed Central are not the same database.
PubMed is a bibliographic database that indexes citations and abstracts of published articles but does not include full-text. Articles do not need to be NIH funded to be listed in PubMed.
PubMed Central is a full-text database that contains the complete text of NIH-funded, peer-reviewed manscripts.
An article can be in PubMed alone, PubMed Central alone, or in both.
NIHMS is a submission system for PubMed Central only.
Distinguishing the Identifiers:
PMID = permanent PubMed citation/abstract identifier
PMCID = permanent PubMed Central full-text article identifier
NIHMSID = temporary manuscript submission identifier given to a manuscript processing through the NIHMS system to PubMed Central.
The two primary tools that are used to collect, manage, and submit articles are:
MyBibliography within MyNCBI
My NCBI provides a free account with customized services for many databases operated by the National Library of Medicine's National Center for Biotechnology Information, including PubMed, PubMed Central and SciENcv. It allows you to save searches, collections of search results, create automated searches with e-mail alerts, create and manage NIH Biosketches, and most vital to the NIHPAP, manage your personal publications within My Bibliography.
The NIH Manuscript Submission System (NIHMS)
The NIH Manuscript Submission System (NIHMS) is where authors and publishers submit electronic version of peer-reviewed final manuscripts for entrance into PubMed Central. Some publishers handle the entire submission process while others require differing levels of author involvement. Any author on a paper may take responsibility for completing the submission process.