With the addition of several European sponsoring agencies, including the European Research Council, UKPMC was renamed Europe PMC as of November 1, 2012. Europe PMC is an outgrowth and expansion of UKPMC, which was first launched in January 2007 with sponsorship from the Wellcome Trust and several other funders of biomedical research in the UK. Europe PMC receives all of its final published articles directly from the U.S. PMC archive. It also accepts and processes author manuscripts of journal articles funded by the Europe PMC sponsoring agencies and makes them available to U.S. PMC and PMC Canada. For more information, see PMC International.

NCBI has developed a new web presentation style called PubReader, which offers you an easier way to use your Web browser to read the articles in PMC. Designed particularly for enhancing readability and navigation on tablet and other small screen devices, PubReader can also be used on desktops and laptops and from multiple web browsers. For more information on PubReader, see the article in the November-December issue of the NLM Technical Bulletin.

As of February 1, 2013, the following new members have been appointed to serve on the PMC National Advisory Committee: Ms. Sharon Terry of the Genetic Alliance; Dr. C. Victor Jongneel of the University of Illinois at Urbana-Champaign; Dr. Bevin Engelward of the Massachusetts Institute of Technology; Dr. Randall Morse of the Wadsworth Center; and Dr. Adelita Cantu of the University of Texas. For more information, see PMC National Advisory Committee.

KoreaMed Synapse, a digital archive and reference linking platform of Korean medical journals, is now using NCBI’s new PubReader presentation style to display their full-text journal articles. KoreaMed’s database of 122 journals now includes a blue ‘PubReader’ icon for each full-text article. NCBI launched PubReader in December 2012 as a convenient new way to view full-text articles in PubMed Central on desktops as well as tablets and mobile devices. In tandem with the launch, NCBI made the code used to create PubReader freely available on GitHub.

PMC is pleased to announce the new OA web service, designed to allow tool developers an easier way to find content in the PMC open access subset. Until now, it has not been easy for outside users to determine which articles in the subset are new or have been updated recently. Our new OA web service addresses this need. It provides a simple API to allow you to query the subset, to find PDF or tgz (tarred-gzipped) format files, either by article ID, or by date/time ranges. More information, along with examples, is available from the documentation page, at OA Web Service. Your feedback is welcome; please send it to the PMC Help Desk, at pubmedcentral@ncbi.nlm.nih.gov.

PMC has created a new email list for announcements of new or updated tools and utilities to help you keep better track of improvements to the archive. To find out more information about the list, or to subscribe, please visit PMC-Utils-Announce.

JATS-Con is a conference for users of the Journal Article Tag Suite, that is, users of any of the "NLM DTDs" or NISO Z39.96. JATS-Con will take place on the NIH campus in Bethesda, Maryland on October 22 and 23, 2013.

The full program is now available, as are proceedings from previous years.

There is no charge for the conference; however, space is limited so registration is required.

You may also sign up for a pre-conference tutorial on October 21, 2013. Details are on the Tutorial Registration page.

You can now search for Open Access articles that have certain types of licenses, by using special filters in both PMC and PubMed. These filters are based on license information that is provided to PMC by publishers and other content providers, as encoded by machine-readable identifiers in the source XML of each article. For more information, see our updated Open Access Subset page.

PMC has recently replaced the PMC-News mailing list and its accompanying RSS feed with a new PMC-Announce list and a new RSS feed. Please note that the older list and feed have now been retired. To subscribe to the new announcement list, see https://www.ncbi.nlm.nih.gov/mailman/listinfo/pmc-announce/. To see the new RSS feed, update your news reader to subscribe to https://www.ncbi.nlm.nih.gov/pmc/about/new-in-pmc/?format=rss.

PMC has recently released an updated version of its PubReader view. The new version (1.2) includes a "search this page" feature that allows you to find specific terms within the article. The latest source code is also available from the GitHub repository.

PMC has just released an upgrade to our ID converter, now dubbed the PMCID - PMID -Manuscript ID - DOI Converter. This utility allows you to start with the unique identifier for an article that is in PMC, and find additional unique identifiers that may apply to the article. Improvements include support for DOIs, auto-detection of the ID type based on its format, and enhanced output. It also provides output in any of several different formats: HTML, XML, JSON, or CSV. This tool uses an underlying web service, that is also publicly available for those needing programmatic access to this data. See the ID Converter API documentation.

As of February 21, 2014, PMC became home to three million articles! As listed on our home page, the content has been provided in part by 1441 full participation journals, 277 NIH Portfolio journals and 2470 selective deposit journals. For related information on PMC milestones, see these announcements from 2007 and 2010, respectively.

This year's PMC Advisory Committee meeting will be held on Tuesday, June 10. The meeting will take place in the NLM Board room starting at 9:30 am. Stay tuned for further details.

PMC is happy to announce the addition of a citation exporter feature. This feature makes it easy to retrieve either styled citations that you can copy/paste into your manuscripts, or to download them into a format compatible with your bibliographic reference manager software.

When viewing an Entrez search results page, each result summary will now include a "Citation" link. When, clicked, this will open a pop-up window that you can use to easily copy/paste citations formatted in one of three popular styles: AMA (American Medical Association), MLA (Modern Language Association), or APA (American Psychological Association). In addition, the box has links at the bottom that can be used to download the citation information in one of three machine-readable formats, which most bibliographic reference management software can import.

The same citation box can also be invoked from an individual article, either in classic view (with the "Citation" link among the list of formats) or the PubReader view, by clicking on the citation information just below the article title in the banner.

These human-readable styled citations, and machine-readable formats, will be available through a public API, and we will be providing more details about that in another announcement, on the pmc-utils-announce mailing list. Please subscribe to that list if you are interested.

In order to facilitate text and data mining for articles in the Open Access Subset, we are now providing plain text files for those articles on our FTP site. These files contain the full text of the article, extracted either from the XML source files, or (for those articles that don't have XML) the PDF files. Users are directly and solely responsible for compliance with copyright restrictions and are expected to adhere to the terms and conditions defined by the copyright holder (see the PMC Copyright Notice).

These text files are bundled in gzipped archives. Note that these files are quite large (each greater than one gigabyte). They are available for download as:

• ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/articles.txt.0-9A-B.tar.gz
• ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/articles.txt.C-H.tar.gz
• ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/articles.txt.I-N.tar.gz
• ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/articles.txt.O-Z.tar.gz

These files are updated every week, on Saturday.

For more information, see the Bulk Packages of OA Articles section of our FTP Service page.

PMC includes some journals published by US government agencies that make their articles available under a Creative Commons CC0 (public domain) license. Some other journals also apply a CC0 license to selected articles in PMC. All these articles may be used and reproduced without special permission. However, anyone using the material is requested to properly cite and acknowledge the source.

You may now search for CC0 articles by using special filters in both PMC (cc0 license[filter]) and PubMed (pmc cc0 license[filter]). These filters are based on license information that is provided to PMC by publishers and encoded as machine-readable identifiers in the source XML of each article. For more information, see the Open Access Subset page.

Please bear in mind that these articles, although made available under a CC0 license, may still contain photographs or illustrations copyrighted by other commercial organizations or individuals that may not be used without obtaining prior approval from the holder of the copyright.

The PMC Overview and FAQ have been updated to provide more information on the Scientific Quality Review Process for journals that apply to participate in PMC.

In 2014, PMC implemented a scientific and editorial quality review procedure whereby expert consultants from outside the National Library of Medicine (NLM) conduct an independent review of journals seeking to participate in PMC. This was in response to a significant increase in new publishers and journals applying to participate in PMC, many of which are unknown to NLM in terms of quality and publishing practices. The independent review, which was approved by the PMC National Advisory Committee (see minutes from June 10, 2014), follows an assessment by NLM that the journal meets NLM’s criteria for its collection, as outlined in the Collection Development Manual.

PMC also recently updated the minimum requirement on the number of substantive, peer-reviewed articles needed before a journal can apply to PMC. The new 25-article minimum ensures that the reviewers have a sufficient amount of content on which to base their recommendation for inclusion in PMC. The new minimum article requirement takes effect on January 1, 2016. Publishers are encouraged to use the 25-article minimum as a guideline in the interim when submitting applications.

NIH-supported scientists have made over 300,000 author manuscripts available in PMC. Now NIH is making these papers accessible to the public in a format that will allow robust text analyses.

You can download the PMC collection of NIH-supported author manuscripts as a package in either XML or plain-text format at ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/manuscript/. The collection encompasses all NIH manuscripts posted to PMC that were published in July 2008 or later. While the public can access the manuscripts’ full text and accompanying figures, tables, and multimedia via the PMC website, the newly available XML and plain-text files include full text only. In addition to text mining, the files may be used consistent with the principles of fair use under copyright law.

Please note that these author manuscript files are not part of the PMC Open Access Subset.

The NIH Office of Extramural Research developed this resource to increase the impact of NIH funding. Through this collection, scientists will be able to analyze these manuscripts, further apply NIH research findings, and generate new discoveries.

For more information, please visit the PMC author manuscript collection webpage.

Last month marked the third anniversary of the White House’s Office of Science and Technology Policy (OSTP) memorandum directing Federal agencies with more than $100 million in annual research and development (R&D) expenditures to develop plans for increasing public access to the results of the research they support, including scholarly publications. As a result of this directive, in 2015, PMC started providing support as a public access repository for funding agencies beyond the National Institutes of Health (NIH) and Howard Hughes Medical Institute (HHMI).

As of March 2015, the following additional agencies are using the NIH Manuscript Submission (NIHMS) system to facilitate the deposit in PMC of peer-reviewed manuscripts that fall under their public access policies:

• Agency for Healthcare Research Quality (AHRQ/HHS)
• Centers for Disease Control and Prevention (CDC/HHS),
• Food and Drug Administration (FDA/HHS),
• National Institute of Standards and Technology (NIST), and
• U.S. Department of Veterans Affairs (VA)

Additionally, the following additional HHS and other federal agencies have announced public access plans and committed to using PMC as the repository for agency-funded publications:

• Administration for Community Living (ACL/HHS)
• Assistant Secretary for Preparedness and Response (ASPR/HHS)
• Environmental Protection Agency (EPA)
• National Aeronautics and Space Administration (NASA)

PMC will continue to update the list of participating funding agencies at Public Access and PMC as these agencies begin implementation of their policies.

More information about the current status of public access expansion as a result of the OSTP memo can be found on the White House blog.

PMC has reorganized its FTP Service site for users interested in accessing the Text Mining Collections, which include the original Open Access (OA) Subset. New top-level FTP directories help users quickly locate the content available for bulk download that best suits their research needs. These directories include:

• oa_package - article packages for individual OA articles
• oa_pdf – individual PDFs for OA articles
• oa_bulk – bulk packages of text from OA articles
• manuscript – author manuscripts collected under a funding agency’s public access policy
• historical_ocr – select OCR texts from the PMC Back Issue Digitization project

To make it easier for users to identify and comply with the different licenses that apply to OA articles, new file lists have been created and the file lists for individual OA articles now include a “license-type” field for each article. Similarly, the bulk packages of OA article text have been divided into two sets. One set comprises articles that may be used for commercial purposes (the Commercial Use Collection); the other contains articles that can be used only for non-commercial purposes. See the Open Access Subset page for details.

To allow regular users to transition to the new arrangement, the previous arrangement of files and directories will be maintained in parallel for at least four weeks (i.e., until the end of August 2016).

As of August 2016, PMC is home to four million articles! To make this wealth of full-text content easier to navigate, PMC has rolled out a few updates:

1) Search Result Filters
On all search results pages, you will now see filters (similar to PubMed’s filters) on the left-hand side that allow you to filter your results by article attributes, publication date, research funder, and search fields. These filters replace the Limits page and allow you to more readily:

• find open access articles (PMC has more than 1.35 million open access articles that can be reused according to their license statements),
• explore PMC’s rich historical content from NLM's back issue digitization project,
• browse research supported by PMC-participating funding organizations (click "Customize" to view additional funder options),
• and much more.

You can now also quickly add articles that are under a 12-month or less embargo in PMC to your search results by selecting the “Include embargoed articles” filter option under Text Availability. See the PMC User Guide for more information on these filters.

2) Reference List Display
Using related article data available in PMC, articles that cite papers that have been either retracted or named in a Findings of Research Misconduct issued by the HHS Office of Research Integrity and not yet retracted will now include a red hyperlink to the relevant notice directly from the article’s reference list. This update will help users more easily identify post-publication updates to existing research.

A large-scale update of the file names used for articles available via the PMC FTP service for bulk download was undertaken in early January 2017. The new file naming convention is PMCID-based (e.g., PMC4855680.tar.gz) rather than being built from article citation data (i.e., journal abbreviation_pub date_volume_issue_page). This update was made following user reports that the previous naming convention was resulting in missing contents in cases where citation data was duplicated across multiple articles. The new convention will ensure that file names are unique and that the corpus available via the FTP service is complete.

Since March 2016, the NIH Manuscript Submission (NIHMS) system has added support for researchers from the following federal agencies to deposit in PMC any manuscripts that fall under the agency’s public access policy:

• Assistant Secretary for Preparedness and Response (ASPR/HHS; intramural only at this time)
• Environmental Protection Agency (EPA; intramural only at this time)
• National Aeronautics and Space Administration (NASA; intramural/civil servants and grantees)

Manuscript deposit support for all Administration for Community Living (ACL/HHS) researchers will be available in NIHMS by October 2017 and for Department of Homeland Security researchers in early 2018.

Additionally, the Bill & Melinda Gates Foundation Open Access Policy now requires their grantees to make their published research results available in PMC immediately upon publication under a Creative Commons Attribution (CC-BY) license. Manuscript deposit support is not provided in NIHMS for Gates-funded researchers; rather the final published version of any Gates-funded article is to be deposited directly to PMC by the publisher or a funder-supported data provider without author involvement. More information on this open access policy is available on the Gates Foundation website.

PMC will continue to update the list of participating funding agencies at Public Access and PMC as support is implemented.

In response to the growing interest in the availability of data associated with articles, PMC is reviewing current practices around data and seeking feedback on how to best serve the data needs of the research community.

As part of these efforts, the PMC policy statement on supplementary data was recently updated to more clearly articulate the requirement that any supplementary data (images, tables, video, or other documents / files) that are associated with an article must be deposited in PMC with an article. The search filter "has suppdata[filter]" can be used in PMC to discover records with associated supplementary data files.

In addition to providing supplementary data with an article, NLM is also encouraging journals and authors to make research data available in a public repository and include the relevant data citation(s) in the paper. Guidance for PMC data providers on tagging data citations is available in the Tagging Guidelines. This guidance is based on the JATS4R recommendations on data citations.

Starting this month, the NIH Manuscript Submission (NIHMS) system will also accept deposits of small datasets accompanying deposits of funded author manuscripts for inclusion of PMC. (Guidance for authors is available in the NIHMS FAQ.)

If you have suggestions on future directions in data for PMC to consider, please let us know at pubmedcentral@ncbi.nlm.nih.gov.

PMC Canada, sponsored by the Canadian Institutes of Health Research (CIHR), with operational support provided by the National Research Council (NRC), has been a valued partner in the PMC International network since 2009. CIHR and NRC have now notified NLM of their decision to permanently take PubMed Central Canada (PMC Canada) offline on February 23, 2018. Details of this decision are available on the PMC Canada website.

The decision to decommission PMC Canada does not affect the status or operations of NIH’s PubMed Central (US) or Europe PubMed Central. PMC Canada content will remain in the PMC archive and be publicly searchable on NLM’s PubMed Central (US) and through Europe PMC. CIHR researchers who publish in journals that deposit their articles directly into NIH’s PubMed Central or deposit manuscripts co-funded with current PMC-participating funders will continue to be considered in compliance with the Tri-Agency Open Access Policy on Publications.

NIH and NLM have appreciated our cooperation with CIHR and NRC over the last several years and will continue to identify new opportunities to work together to support open access and research excellence.

As we kick off a new year, we wanted to take this opportunity to look back on 2017, which was a milestone year for PMC.

Last year, PMC made nearly half a million articles available for the public to access with the support of participating journals, publisher programs, and research funders. Also, in addition to expanding support for public access to research results and the linking of those results to the underlying dataset(s), PMC released several other policy and resource updates. These include:

1. Clearer statement of scope for PMC (see also the updated entry in the NLM Collection Development Manual for “Journals”);
2. Guidance for journals on reapplying to PMC;
3. Policy statements on the scientific, editorial, and technical standards for PMC (including details on the journal reevaluation process), the supply of back content, the eligibility of non-English language journals, and the maintenance of publishing schedules;
4. Production data requirements for PMC-participating journals; and
5. Major update to the PMC Article Previewer, a tool that allows publishers to see or “preview” how articles will appear in PMC and resolve data problems prior to submission.

In September, NLM recognized the achievements to date in the Wellcome Trust and NLM Biomedical Journal Digitization project, which has added a dozen new historical titles and more than a half million pages to the PMC archive. The PMC archive now includes content from as far back as the late 18th century.

Many thanks all our participants and users for a wonderful year!

In collaboration with Europe PMC, PMC has rolled out several updates to our article display in order to enhance the transparency and readability of the content.

Navigating from the PMC record to the PubMed record has been made easier by the addition of hyperlinked PubMed IDs (PMIDs) in the upper right-hand corner of article records. Clicking the PMID link will take you to the corresponding citation record in PubMed.

The PMC Disclaimer link has also been moved out of the Copyright and License information section for easier discovery and access. This page describes what content is included in PMC as well as other important NCBI and NLM disclaimer information.

Additionally, two changes have been implemented to improve the functionality of author names. Users can now click on an author name to view the author’s affiliation(s). Users also have the option of running a quick author name search in PMC by clicking the linked author name in “Find articles by [author name]”. In the example pictured above, the search would be for “Sawyer SL”[Author].

And finally, figures and tables have been moved inline in the article display. By moving away from the thumbnail display, PMC hopes to make it easier for users to view figure and table data as they read articles. Users may still click on the figure/table title or “Open in separate window” (as available) link for a closer look.

We hope these updates improve the overall user experience in PMC and look forward to hearing your feedback.

References

Screenshots from:

Qiao, Y., Yang, J., Liu, L., Zeng, Y., Ma, J., Jia, J., … Wang, Y. (2018). Successful treatment with pazopanib plus PD-1 inhibitor and RAK cells for advanced primary hepatic angiosarcoma: a case report. BMC Cancer, 18, 212. http://doi.org/10.1186/s12885-018-3996-3

Stabell, A. C., Meyerson, N. R., Gullberg, R. C., Gilchrist, A. R., Webb, K. J., Old, W. M., … Sawyer, S. L. (2018). Dengue viruses cleave STING in humans but not in nonhuman primates, their presumed natural reservoir. eLife, 7, e31919. http://doi.org/10.7554/eLife.31919

Both articles made available under a CC-BY license.

Looking for journal articles with associated data sets? New search filters in PMC and PubMed aim to increase the discoverability of articles with associated data information.

In PMC, users can now search on or append searches with filters to discover articles with specific types of associated data, i.e., to find

1. articles with associated supplementary material, use “has suppdata”[filter];
2. articles that include a data availability or data accessibility statement, use “has data avail”[filter]; or
3. articles that include data citation(s), use “has data citations”[filter]

Alternatively, users can run a search on “has associated data”[filter] to find all articles with any type of data section described above.

In PubMed, users can now search on or append searches with data[filter] to find articles with related data links in either the Secondary Source ID field or the LinkOut – Other Literature Resources field (both located below the abstract). These data links may be to records in other NLM databases (e.g., GenBank) or external data repositories (e.g., figshare, Dryad).

The provision and availability of associated datasets still varies widely from article to article, but it is our hope that this small step helps improve the discoverability of this material and supports wider community efforts to advance science in new directions.

PMC has released expanded information about its selection process for journals that apply for participation. The current review process has been in place since November 2014 and focuses on the scientific rigor and editorial quality of each journal that applies to participate in PMC. Some of the attributes taken into account as part of this process include the article content, journal policies, language quality, and presentation of content. The same assessment considerations are used for reevaluation of currently participating journals. We encourage you to visit the Journal Selection for PMC page to learn more.

Publishers and journals interested in submitting an application to PMC are also encouraged to review our updated policies on agreement types. These policies provide the eligibility criteria for each type of participation agreement and should be considered alongside the pre-application requirements.

We hope these updates are informative and look forward to hearing your feedback.

Collaboration with publishers and funders to ensure the openness and preservation of the scientific record is one of PMC’s core principles. Open Access Week offers an opportunity to celebrate some of the recent outcomes of these collaborations:

• In July 2018, the PMC corpus of publicly accessible articles hit 5 million articles.
• In May 2018, the PMC Open Access Subset surpassed the 2 million article mark.
• The Author Manuscript Collection now includes more than 500,000 papers for text mining.
• The PMC and Research Funder Policy page underwent an update in September 2018 to increase transparency around funder support in PMC for publishers, authors, and the public.
• Funder policy support in PMC has been extended to the US Department of Homeland Security, in addition to several new US private research funders via the Health Research Alliance.

In FY2018 more than 200 new journals committed to archiving their complete contents in PMC, to be made publicly accessible in 12 months or less.

In the NLM Strategic Plan released earlier this year, we noted that “[c]reating efficient ways to link the literature with associated datasets enables knowledge generation and discovery.” To that end, PMC is now aggregating data citations, data availability statements and supplementary materials, as available, in an Associated Data box. This box will only display on articles that have one or more of these features in the article.

To limit your search to records with an Associated Data box, you can use the new "Associated Data" facet on the search results page:

We hope that exposing this content in a consistent format and in an easy to find and easy to access manner, you will more readily find the datasets you need to further accelerate discovery and advance health. As part of our ongoing commitment to making data findable, accessible, interoperable, and re-usable (FAIR), we encourage you to contact us with your feedback on these updates and with any other suggestions you may have for improving discovery of related data in PMC.

Machine-readability of scholarly outputs is critical to supporting large-scale analysis of the scientific literature. To that end, PMC’s Tagging Guidelines and internal processes have been updated to support the JATS4R recommendations for tagging clinical trial information. NLM encourages PMC-participating publishers, journals, and data providers to review this guidance. Please contact us at pubmedcentral@ncbi.nlm.nih.gov if you have any questions.

On March 18, 2019, PMC will no longer provide bulk packages of Open Access (OA) Subset text and XML at the top level directory of the FTP Service. These files were superseded in August 2016 by the Commercial Use and Non-Commercial Use bulk packages located in the oa_bulk subdirectory. One set comprises articles that may be used for commercial purposes (the Commercial Use Collection); the other contains articles that can be used only for non-commercial purposes. Anyone planning to use OA subset content for non-commercial purposes will need to download both “non_comm_use.*.tar.gz” and “comm_use.*.tar.gz” to access the complete collection. See the Open Access Subset page for additional details. Questions should be directed to pubmedcentral@ncbi.nlm.nih.gov.

PMC has updated the Associated Data box to display unique identifiers assigned to supplemental material files by the publisher when available (e.g., DOI; see PMC6351104). In cases where the publisher has not assigned a unique ID to a supplemental file, NLM will generate and display a Globally Unique Identifier (GUID; see PMC6351564). This update aims to support the reporting of datasets as well as the citation and discovery of this content.

Publishers that are interested in supplying unique IDs for supplemental material files with their PMC submissions should visit the Tagging Guidelines.

Peer review documents, including review reports and editor decision letters, are increasingly being published along with the articles they review. This practice is intended to make the publishing process more transparent. To support these efforts, PMC’s Tagging Guidelines have been updated to include the tagging of peer review documents. NLM encourages PMC-participating publishers, journals, and data providers to review this guidance. Please contact us at pubmedcentral@ncbi.nlm.nih.gov if you have any questions.

On March 13, 2020, the National Science and Technology Advisors from a dozen countries, including the United States, called on publishers to voluntarily agree to make their COVID-19 and coronavirus-related publications and associated data immediately accessible in PubMed Central (PMC) and other appropriate public repositories to support the ongoing public health emergency response efforts.

For more information on which publishers have responded to this call and how to discover COVID-19 and coronavirus-related publications in PMC, see the main COVID-19 Initiative page.

A FAQ is also available. If you have questions not addressed in the FAQ, please contact pmc-phe@ncbi.nlm.nih.gov.

You can learn more about how this initiative fits into the wider NLM response to the current public health emergency in Dr. Patti Brennan's post, "How Does a Library Respond to a Global Crisis?"

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