Science Publishing: Green and Gold -- An Open Access Primer


The landscape of scientific publishing is rapidly changing. Journals are increasingly moving to an open access model, ensuring that readers can freely access and reuse content – where content includes not just the article but the underlying data that led to the insights in the article. Many journals and funders now require the sharing of datasets on which published results are based, particularly in the field of genomics, thereby increasing opportunities for study replication and additional discoveries. And in tandem with this growing culture of openness, publishers are experimenting with more transparent peer review processes and new ways to measure the impact of the work of scientists.

In this new column, authored by scientific communication, data science, and copyright experts from the UCSF Library, we will delve into these topics and related scientific communication issues that are of interest to the UCSF community. You can look forward to future columns on data sharing, reuse of public data, and copyright issues.

For this inaugural column we’re going to focus on flavors of open access (OA) publishing. You’re probably familiar with OA journals such as PLOS ONE (, BioMed Central (, and eLife ( These journals make all of their content available at no cost to readers immediately upon publication and assign a Creative Commons Attribution License (CC-BY) that allows authors and consumers to share and adapt the material without asking permission, so long as appropriate credit is given.

The CC license type is important because one of the significant benefits of OA is the ability to data mine large amounts of content. While eLife does not charge authors (it is supported by three funding agencies), it’s common for the desirable open access journals such as those in the PLOS and BioMed Central families to charge authors an article processing charge to cover the costs of publishing the article and making it freely available. This model of OA publishing is often referred to as “gold open access”.

A companion version is “green open access”. Green OA is the process of making a version of a published article available in an OA repository. A repository may be discipline specific, such as arXiv, or institution based, and it provides free access to documents uploaded from authorized sources. UC runs an OA platform called eScholarship ( that serves as the institutional repository for “previously published works” by any UC author. Are you motivated to share your works? Check it out!

There is no payment required to practice green OA publishing. If you’ve read through the copyright transfer agreement required for publishing in a subscription journal, you may have seen green OA rights outlined. Publishers typically only allow the final manuscript--post peer-review but pre-publisher typesetting and copyediting--to be deposited in a non-commercial repository or website. And they might specify an “embargo” period of six to twelve months after publication before you can make the manuscript available. Examples of journals that provide green OA rights include JBC, Nature Publishing, and NEJM. It’s best to read the specific rights outlined in each publication’s agreement, or search the publication in the SHERPA/RoMEO database (

In May 2012, UCSF Academic Senate faculty declared their commitment to disseminating their research and scholarship as widely as possible by voting unanimously in favor of an Open Access Policy. This is a green OA policy for scholarly articles. It outlines the rights of faculty authors to reserve copyrights and to assert broader control their work. Faculty continue to publish in whichever journal they choose but have granted a prior license that allows them to deposit a final version of their papers in eScholarship or another OA repository immediately upon publication. This policy differs from the NIH Public Access Policy in that there is no 12 month embargo period before papers can be read openly (though it doesn’t change the NIH’s requirements). It also allows faculty to maintain control over sharing their works without having to ask for publisher permission. Learn more at

UCSF’s movement sparked the passing of an almost identical policy across the UC Academic Senate in July 2013. (Two minor differences are UCSF’s requirement to deposit a paper for archival purposes even if opting out and a strictly non-commercial license for content). UCSF is one of three campuses, along with UCLA and UC Irvine, that implemented a publication management system to help faculty track their publications and upload their papers into eScholarship using a single interface. The system went live Oct. 20, and faculty will receive email notifications alerting them when new publications are identified.

Moving beyond faculty, there is a proposed Presidential Policy on Open Access that will extend the same license to all employees of the UC system who author scholarly articles but who are not members of the Academic Senate. Students, postdocs, and research staff will be affected by this policy, so it’s important for these groups to review the details of the proposed policy at Comments will be accepted by until January 15, 2015.

For comments or questions about the UCSF Open Access Policy, email