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Author's Corner: Glossary

Writing, publishing and sharing resources for Fred Hutch authors.

Terms Related to Open Access

Author Agreement - See also "Publication Agreement"

DOI - The Digital Object Identifier

A DOI is an alphanumeric name that identifies digital content, such as a book or journal article. The DOI is paired with the object's electronic address, or URL, in an updateable central directory, and is published in place of the URL in order to avoid broken links while allowing the content to move as needed. DOIs are created and distributed by publishers to provide unique, permanent references to scholarly articles (or other works) as hosted on publisher's web sites/electronic journals (from

For example:
Dalal Y, Furuyama T, Vermaak D, Henikoff S.
"Inaugural Article: Structure, dynamics, and evolution of centromeric nucleosomes". Proceedings of the National Academy of Sciences of the United States of America (0027-8424), 104 (41), p. 15974.
PMID: 17893333
PMCID: PMC1993840
DOI: 10.1073/pnas.0707648104

Final peer-reviewed manuscript - The investigator's final manuscript of a peer-reviewed article accepted for journal publication, including all modifications from the peer-review process. This is the final version of the manuscript the author submits before the publisher creates the galley proofs.

Final published article - The journal's authoritative copy of the article, including all modifications from the publishing peer-review process, copyediting and stylistic edits, and formatting changes.

Institutional Repository - An institutional repository is an online locus for collecting, preserving, and disseminating -- in digital form -- the intellectual output of an institution, particularly a research institution. (from Wikipedia). The Arnold Library hosts the Fred Hutchinson Cancer Research Center's institutional repository at

NIH Public Access Policy (aka PMC Deposit Mandate)

The NIH Public Access Policy ensures that the public has access to the published results of NIH funded research. It requires scientists to submit journal articles that arise from NIH funds to the digital archive PubMed Central. The Policy requires that these articles be accessible to the public on PubMed Central to help advance science and improve human health. (from and more details at

The policy is intended to: 1) create a stable archive of peer-reviewed research publications resulting from NIH-funded research to ensure the permanent preservation of these vital published research findings; 2) secure a searchable compendium of these peer-reviewed research publications that NIH and its awardees can use to manage more efficiently and to understand better their research portfolios, monitor scientific productivity, and ultimately, help set research priorities; and 3) make published results of NIH-funded research more readily accessible to the public, health care providers, educators, and scientists (from

Does the Policy Apply to Me?
The Policy applies to you if your peer-reviewed article is based on work in one or more of the following categories:

  • Directly funded by an NIH grant or cooperative agreement active in Fiscal Year 2008 (October 1, 2007- September 30, 2008) or beyond;

  • Directly funded by a contract signed on or after April 7, 2008...

Specifically, this policy applies to all research grant and career development award mechanisms, cooperative agreements, contracts, Institutional and Individual Ruth L. Kirschstein National Research Service Awards, as well as NIH intramural research studies. (from

The Law
The NIH Public Access Policy implements Division G, Title II, Section 218 of PL 110-161 (Consolidated Appropriations Act, 2008) which states:
SEC. 218. The Director of the National Institutes of Health shall require that all investigators funded by the NIH submit or have submitted for them to the National Library of Medicine's PubMed Central an electronic version of their final, peer-reviewed manuscripts upon acceptance for publication, to be made publicly available no later than 12 months after the official date of publication: Provided, That the NIH shall implement the public access policy in a manner consistent with copyright law.

Important Dates

  • As of April 7, 2008, all articles arising from NIH funds must be submitted to PubMed Central upon acceptance for publication.

  • As of May 25, 2008, NIH applications, proposals, and progress reports must include the PubMed Central reference number when citing an article that falls under the policy and is authored or co-authored by the investigator, or arose from the investigator's NIH award. This policy includes applications submitted to the NIH for the May 25, 2008 due date and subsequent due dates.

Learn more about the NIH Public Access Policy at:

NIHMS - NIH Manuscript Submission System

The National Institutes of Health (NIH) developed the NIH Manuscript Submission System (NIHMS) to facilitate the submission process of final, peer-reviewed manuscripts. NIHMS allows users to deposit and manage manuscripts. Any additional files that contain figures, tables, or supplementary information should also be included with the manuscript. (from NIH Public Access FAQ)

NIHMS ID - NIH Manuscript Submission System Reference Number

This number is generated as soon as a manuscript is submitted to PubMed Central. PMCID numbers are assigned later in the PMC intake process. When citing papers in NIH grant applications, proposals and progress reports, if a PMCID number is not yet available, use the NIHMS (NIHMS ID) instead. (from NIH Public Access FAQ)

Open Access (OA)

An Open Access (article) is one that meets the following two conditions:

  1. The author(s) and copyright holder(s) grant(s) to all users a free, irrevocable, worldwide, perpetual right of access to, and a license to copy, use, distribute transmit and display the work publicly and to make and distribute derivative works, in any digital medium for any responsible purpose, subject to proper attribution of authorship, as well as the right to make small numbers of printed copies for their personal use.
  2. A complete version of the work and all supplemental materials, including a copy of the permission as stated above, in a suitable standard electronic format is deposited immediately upon initial publication in at least one online repository that is supported by an academic institution, scholarly society, government agency, or other well-established organization that seeks to enable open access, unrestricted distribution, interoperability, and long-term archiving (for the biomedical sciences, PubMed Central is such a repository). (from The Bethesda Statement).

Open access options and alternatives
Open access to a research article can be achieved in a variety of ways depending on the arrangements authors make with journal publishers and/or a publisher's open access policies. Please note that NIH funded articles, regardless of their open access status, must be deposited into PMC to meet the NIH Public Access Policy requirements. Some examples include:

  • Institutional (e.g. or Discipline based Repositories (e.g. PubMed Central)

  • Open Access Journals (e.g. PLoS Biology) - all articles in these journals are open access immediately upon publication. Some open access publisher operate as non-profits while others are for-profit, commercial enterprises.

  • Open Access Articles after Embargo (e.g. PNAS with 6 month embargo). - Some journals choose to make articles available open access after a proscribed embargo period.

  • Paid Open Access to Articles - Some commercial publishers offer to make articles open access immediately upon publication for a fee (currently $1,000-3,000 per article) paid by the author. Typically, authors are not required to pay this fee in order to fulfill their PMC deposit requirement. If an author chooses to pursue this option, the staff in the Office of Sponsored Research can help in determining whether these fees are allowable on a specific grant.

Publication Agreement - An agreement that transfers some or all of an author's copyright or use rights to the publisher. This agreement might also be titled "Copyright Transfer Agreement," "License to Publish," "Journal Publishing Agreement," "Copyright Assignment," etc. This agreement should be read carefully by the author before signing to ensure that the author retains appropriate public access rights. Although the agreement is provided by the publisher, it may still be amended by negotiation.

PMCID - PubMed Central Reference Number

Please note this is NOT the PMID number. The same article may have both a PMID and a PMCID. Use the PMCID when citing articles in NIH grant applications, progress reports and proposals

For example:
Dalal Y, Furuyama T, Vermaak D, Henikoff S.
"Inaugural Article: Structure, dynamics, and evolution of centromeric nucleosomes". Proceedings of the National Academy of Sciences of the United States of America (0027-8424), 104 (41), p. 15974.
PMID: 17893333
PMCID: PMC1993840
DOI: 10.1073/pnas.0707648104

PMID - The PubMed Identification Number

This number relates to each indexed paper's citation entry in PubMed (the National Library of Medicine's portal to the MEDLINE database). This number is NOT the same as the PMCID number.

For example:
Dalal Y, Furuyama T, Vermaak D, Henikoff S.
"Inaugural Article: Structure, dynamics, and evolution of centromeric nucleosomes". Proceedings of the National Academy of Sciences of the United States of America (0027-8424), 104 (41), p. 15974.
PMID: 17893333
PMCID: PMC1993840
DOI: 10.1073/pnas.0707648104

PubMed - PubMed is a free search engine for accessing the MEDLINE database of citations and abstracts of biomedical research articles. It is a companion to, but separate from PubMed Central. Learn more about PubMed at

PubMed Central (PMC) - PubMed Central is an archive of full-text biomedical journal articles and manuscripts available online without a fee. Articles on PubMed Central contain links to other scientific databases (such as GenBank and PubChem). Articles collected under the NIH Public Access Policy are archived on PubMed Central. PubMed Central is NOT PubMed, rather it is a separate companion resource. Many of the full text links in PubMed point across to PubMed Central. More information about PubMed Central is available at

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