NLM produces a baseline set of MEDLINE/PubMed citation records in XML format for download on an annual basis. The annual baseline is released in December of each year. Each day, NLM produces update files that include new, revised and deleted citations. See our documentation page for more information.

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NLM Data News

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March 5, 2018: Release of Mid-Year PubMed DTD and Upcoming Inclusion of MathML 3.0 Element Tags in PubMed XML

On June 1, 2018, we will begin displaying formulas in citation titles, abstracts, and keywords in PubMed. Today, formulas are replaced with [Formula: see text]. With this enhancement to PubMed, you will see formulas in the PubMed summary and abstract displays when these data are available. We will also be including the MathML 3.0 element tags in PubMed XML.

To support the addition of MathML tagging in our XML, we have created a new, forthcoming DTD which will be in use after June 1, 2018. You can download the forthcoming DTD for June 2018 now. Existing content will be valid against the new DTD. You can also download sample XML files with MathML 3.0 tags.

February 8, 2018: Removal of <OtherID Source="NLM"> Data Element from Prospective Records

Beginning with file pubmed18n1022.xml, NLM will no longer populate the <OtherID Source=> with the attribute of "NLM". We will not remove and reissue citations that currently have an OtherID source of NLM but it will be removed from respective records in the PubMed web interface. Currently and in future use, users should refer to the <ArticleID> element as the authoritative Article Identification for the record.

January 31, 2018: Hiatus of Posted Daily Export Files

Due to a technical problems we have not posted PubMed Daily Export files for the date range January 29-30, 2018. Export and posting of the Daily Update files will resume January 31, 2018. Catch-up records will be included with a date on server of 1/31/18.

January 23, 2018: Missing Delete Notifications

Due to a processing error, for the large majority of January Delete Citations were erroneously excluded from the PubMed Daily Update files. This error has been corrected and the catch-up deletes are located in daily export file pubmed18n1000.xml with a server date of January 18, 2018. Regular Delete Citations are included in the update files loaded after January 18, 2018.

January 4, 2018: Large Export Files dated 1/4/18

The PubMed export files with a date of January 4, 2018 will be larger than normal due to a processing code change to approximately 70 journals. The citation maintenance will affect approximately 67,000 records changing the current status from In-Data-Review to In-process.

January 2, 2018: Health Services Research Projects in Progress (HSRPRoj) Dataset Available for Download

NLM has released the HSRPRoj data for download. HSRProj is a dataset of ongoing health services research and public health projects containing descriptions of research in progress funded by federal and private grants and contracts. The dataset consists of over 33,000 records and is in XML format. More information about HSRProj and how to download the data can be found at Download HSRProj Data. Any questions or comments can be sent to nlmdatadistrib@nlm.nih.gov.

November 28, 2017: 2018 Production Year PubMed Data Release

NLM has released the 2018 production year PubMed Baseline files. The complete 2018 baseline consists of files pubmed18n0001 - pubmed18n0928. In addition to the XML files there are corresponding MD5 checksum and statistics files for each XML export file. At a future time we will release consolidated and comprehensive analysis of the 2018 PubMed baseline snapshot (see: Statistical Reports on MEDLINE/PubMed Baseline Data).

The first set of 2018 PubMed Update file exports have also been posted. The first 2018 update file is pubmed18n0929.

NOTE: All baseline files must be downloaded and processed PRIOR to loading the first and subsequent update files.

We have also posted a set of PubMed Sample data. This is a small sampling of PMIDs representing the changes in data elements and their attributes.

November 16, 2017: 2018 Production Year PubMed Baseline Release Information

We are anticipating the release of the 2018 PubMed Baseline files to be November 28, 2017. This is subject to change as we get closer to the release date. Additional information regarding the number, location and statistics about the contents of the files will be posted here at the same time we announce their posting.

In preparation of the baseline, updates to the indexing of records being exported stopped on November 14, 2017 with the release of file medline171385.xml.gz. Subsequent files contain new records and updated records in all statuses. These "held" indexed records will be released as part of the 2018 baseline files.

2018 sample data using the PubMed 2018 DTD is expected to be posted during the week of November 20, 2017. A message will be posted here as soon as the 2018 sample data is available.

To better reflect the citations NLM exports, file names for the ftp server will be updated beginning with the 2018 baseline.

• Baseline files will begin with pubmed18n0001.xml.gz
• Daily update files will continue with this naming convention: pubmed18nxxxx.xml.gz
• Associated .md5 files will follow this convention beginning with pubmed18n0001.xml.gz.md5
• Stats files will follow this convention beginning with pubmed18n0001_stats.html

Questions regarding any of this information can be sent to nlmdatadistrib@nlm.nih.gov

November 15, 2017: 2018 Production Year MeSH XML Available for Download

The 2018 Medical Subject Headings (MeSH) XML files have been posted to the FTP server and are available for download. The files are located at ftp://nlmpubs.nlm.nih.gov/online/mesh/MESH_FILES/xmlmesh/
Complete details about the terminology changes and updates can be found on the Medical Subject Headings homepage.

October 23, 2017: 2018 Production Year PubMed DTD

The 2018 PubMed DTD has been released. PubMed 2018 DTD This DTD is effective with the posting of the 2018 PubMed Baseline files, expected to be posted on or before December 17, 2017. The one major change from the current 2017 PubMed DTD is the removal of the <DateCreated> element within the MedlineCitation sub-document wrapper element. Being retained is the <PubMedPubDate PubStatus="entrez"> date within the within the PubmedData sub-document wrapper element. This date will denote the date the citation was added to the existing dataset. Questions and concerns should be immediately sent to the NLM Data Distribution team at nlmdatadistrib@nlm.nih.gov.

September 29, 2017: Initial Planning for 2018 MEDLINE/PubMed Baseline File Reload

We are still finalizing the production schedule for the 2018 MEDLINE/PubMed baseline export but wanted to disseminate initial key points.

DTD Changes: We do not anticipate any structural changes to the 2018 production year PubMed DTD. For consistency and clarity we will update the date on the file name as well as any dates referenced in the DTD.
Baseline File Release: We anticipate the release of the complete 2018 MEDLINE/PubMed Baseline Not Later Than December 17, 2017. As production proceeds we may be able to release the files earlier but not earlier than December 1, 2017. Statistics for the baseline will be posted at a future date, generally within a month of the baseline's release.
2018 Medical Subject Heading (MeSH) File Release for Download: A message will be posted to this area when 2018 MeSH is ready for download.

For additional information regarding the Year End Processing of PubMed please see: MEDLINE/PubMed Year-End Processing Activities for 2018. This article will be updated throughout the process.

If you have questions or would like to schedule a time to talk to NLM Data Distribution staff regarding this process please email nlmdatadistrib@nlm.nih.gov.

September 27, 2017: Announcement for users of NLM Cataloging Data in coordination with MEDLINE/PubMed Data

As part of our efforts to prepare our cataloging data for a linked data environment, NLM has determined that some of the MARC coding for our subject fields is not accurate and will not create true triple statements in an RDF environment.

Historically, all MARC 6XX fields used in NLM bibliographic records have been assigned a second indicator of “2,” defined as Medical Subject Headings (MeSH). This is true for data in the 650, 651, and 655 fields which are all taken from the MeSH vocabulary. However, data in the 600, 610, 611, and 630 fields does not come from MeSH, it comes from the National Authority File (NAF). Therefore, coding these fields with a second indicator of “2” is erroneous information. A second indicator of “0” (Library of Congress Subject Headings) would also not be correct. Although LC uses with the NAF form for these subjects, LCSH practices for construction of name and title access points allow additions to these fields that NLM does not permit.

To accurately portray these subject fields the second indicator should be “7” (Source specified in $2) with an accompanying $2 naf added to the 6XX field and NLM would like to make these changes in its files.

NLM recognizes that some libraries may rely on the second indicator in the 6XX fields for internal processing. Before making changes to our records we are asking for community input on the impact to your organization or institution if indicators on the 600, 610, 611, and 630 fields were updated from “2” to “7” with the addition of a $2 naf. There may be positive as well as negative impacts. Libraries that are already converting MARC data into triples or have plans to do this in the near future will find that having accurate indicators in the records will more likely allow link resolvers to automatically find the correct data.

Comments about this proposed change to NLM records should be sent to Diane Boehr by Oct. 31, 2017. No changes to cataloging records will be made until the comments are reviewed. Ample notification will be provided before any MARC changes are made.

September 21, 2017: Large export files dated September 22, 2017

A large set of citations will be included in the export files posted with a server date of 9/22/2017. These citations have updates or corrections to grants data (we anticipate that more than 170,000 records will be updated).

August 23, 2017: Documentation Updated: Element Descriptions

We have updated the documentation defining and providing background information about the XML elements used in the current (2017) production year of PubMed. The documentation can be found at MEDLINE/PubMed XML Data Elements. Any comments, questions or comments can be directed to nlmdatadistrib@nlm.nih.gov.

August 23, 2017: Large export files dated August 23, 2017

DATE CORRECTED:
There will be larger than normal export files with posted server dates of August 23, 2017. The large exports are due to citation maintenance on records that currently are in a status of <In-Data-Review>. The bulk maintenance and export will change these citations from <In-Data-Review> to <PubMed-Not-MEDLINE>. We are expecting approximately 84,000 citations to be affected. These updated citations will be comingled in the export files with the standard daily citation updates and should be processed accordingly.

August 16, 2017: Large export files dated August 16, 2017 and August 17, 2017

There will be larger than normal export files with posted server dates of August 16, 2017 and August 17, 2017. The large exports are due to citation maintenance on records that currently are in a status of <In-Data-Review>. The bulk maintenance and export will change these citations from <In-Data-Review> to <PubMed-Not-MEDLINE>. These updated citations will be comingled in the export files with the standard daily citation updates and should be processed accordingly.

July 14, 2017: ISSN Element missing from some records in export files after June 22, 2017

Beginning with export file medline17n1172.xml with a server date of June 22, 2017 and continuing until present we have identified citation data which has erroneously excluded the <ISSN> element. We will fix this error during the week of July 17, 2017 and will post another message upon completion. Any questions can be directed to the Data Distribution team at nlmdatadistrib@nlm.nih.gov or by clicking on the NLM Customer Support link (at the top of this page).

June 23, 2017: PubMed Data Begins Sunday Exports on June 25, 2017

Beginning Sunday June 25, 2017 NLM will begin exporting and posting PubMed Daily Update Files 7 days a week. PubMed Daily Update files include all new, revised and deleted citations added to the PubMed dataset on a daily basis. The Daily Update files can be found at ftp://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/

April 12, 2017: Statistical Reports on MEDLINE/PubMed 2016 and 2017 Baseline Data Posted

Annual statistical reports based upon the data elements in the 2016 and 2017 baseline versions of MEDLINE/PubMed are available. Please email us with any questions or concerns regarding the reported data.

February 24, 2017: Large Export Files

A large set of citations will be included in the export files posted with a server date of 2/24/2017. Approximately 70,000 citations will receive Conflict of Interest (COI) statements added to their bibliographic data. See the Technical Bulletin article MEDLINE Data Changes — 2017 for more information.

February 14, 2017: Large Export Files

A large set of citations were included in the export files with a server date of 2/14/2017. The citations received an update or correction to the DOI information. Approximately 180,000 citations were updated.

February 10, 2017: Large Export Files

A large set of citations were included in the export files with a server date of 2/9/2017. These citations had a change in the status of the record the majority of which were moved from In-Data-Review to a status of In-Process (approximately 120,000).

February 8, 2017: Large Export Files

Due to a an internal change in processing codes Daily Update files with a server date of 2/8/2017 will include a large number (approximately 120,000) of update citations. A large group of citations are being moved to either a status of In-Process or PubMed-Not-MEDLINE.

February 2, 2017: Large Export Files Containing Delete Citations

Due to routine citation maintenance Daily Update files with a server date of 2/2/2017 will include a large number (approximately 38,000) deleted citations. Many of these deleted citations come from out of scope articles to include meeting abstracts. See <DeleteCitation>.

January 27, 2017: Export Files Containing Delete Citations

Due to an inadvertent programming error the Daily Update files medline17n0893.xml (dated 12/19/2016) through medline17n0990.xml (dated 1/26/2017) did not include deleted citations. Daily Update file medline17n0991.xml will include catch-up deleted citations (approximately 18,000 citations). Future Daily Update files will provide these citations, as needed. See <DeleteCitation>.

December 21, 2016: Release of 2017 MEDLINE/PubMed Update Files

The 2017 MEDLINE/PubMed Update files are available for download and use. The first Update file to be loaded after loading the complete set of 2017 MEDLINE/PubMed Baseline files is medline17n0893.xml. The first set of Update files contain citations which were held during Year End Processing (YEP). Please note: the first set of Update files (dated 12/19/2016) reference the DTD location http://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_170101.dtd. Subsequent files will correctly reference the DTD location https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_170101.dtd.

December 15, 2016: Release of 2017 MEDLINE/PubMed Baseline Files

The 2017 MEDLINE/PubMed Baseline files are available for download and use. The complete baseline consists of files medline17n0001 through medline17n0892 . Production and distribution of Daily Update Files, which will include citations held during Year End Processing (YEP) is expect to resume December 20, 2016.

December 6, 2016: 2017 Small Sample Data Available and Large Set of Export Files

2017 Small Sample Set of MEDLINE/PubMed data is now available for use. The file can be found at: ftp://ftp.ncbi.nlm.nih.gov/pubmed/.baseline-2017-sample/. Note: this data can be used to validate the 2017 PubMed DTD (>pubmed_170101.dtd). Elements added for the 2017 DTD will not contain data.

We expect to export and post a larger than normal set of records on December 6, 2016. The large export updates approximately 80,000 records to add clinicaltrails.gov IDs. The addition of this data will be made to the <DataBankList> element and will receive an update <DateRevised> on the date of export.

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December 1, 2016: 2017 MeSH Term applied to Update Files

Due to a programming error 2017 MeSH terms were inadvertently applied to PubMed XML Update files medline16n1430.xml through medline16n1583.xml. We are currently working to revert those citations affected by this update and will issue corrected records with today's update files (starting with medline16n1584.xml). As soon as this work is complete we will validate the 2017 Small Sample set and make available for download as soon as possible. Please email us @ nlmdatadistrib@nlm.nih.gov with questions or concerns.

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November 30, 2016: 2017 Small Sample Set

Due to technical issues we have not posted the small sample set of MEDLINE/PubMed citations. We are working on producing and conducting quality control of the file and will provide daily updates on the status until it is posted and available for use against the 2017 PubMed DTD.

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November 14, 2016: Missing Update Files

Due to technical issues we have not posted a MEDLINE/PubMed export files since November 8, 2016. We will post catch-up files today for the records later today.

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November 10, 2016: Release of 2017 DTD

We will be making a number of changes to the DTD for the 2017 MEDLINE/PubMed baseline XML data. Beginning with the release of the 2017 MEDLINE PubMed Baseline, all MEDLINE/PubMed data available via FTP or through the E-utilities API will use the same DTD:

pubmed_170101.dtd

This DTD is backward compatible with the pubmed_160101.dtd that is currently used for the E-utilities API. It also includes all of the data elements from the nlmmedlinecitationset_160101.dtd, with the exception of the <MedlineCitationSet> element, which will be deprecated. Most changes to the DTD involve the addition of new elements and attributes. See the DTD for a list of new data elements. Documentation for new data elements is forthcoming.

We intend to release a small sample set of records using the 2017 DTD mid-late November 2016.

We expect the 2017 MEDLINE/PubMed baseline data to become available in mid-December.

Please see NLM Technical Bulletin article Changes to the NLM Data Distribution Program for further details regarding changes to this program.

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November 3, 2016: 2017 DTD

We anticipate announcing significant changes to the MEDLINE DTD for 2017. This change will reflect not just changes to the structure of the data but also for the contents of the data included in export files. We anticipate having the 2017 DTD and a small sample set of data available the week of November 7, 2016. Documentation and specifically the definition and description of XML elements will be posted shortly thereafter. As always if you have specific questions or concerns regarding these changes you may contact us directly at nlmdatadistrib@nlm.nih.gov.

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October 1, 2016: CHANGE TO MEDLINE/FTP Location

Effective October 6, 2016, Daily MEDLINE/PubMed Daily Update files are located at ftp://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/. The first Update file is medline16n1183.

• Users who are current with Update files prior to transition to the new FTP server (last Update file on previous FTP server is medline16n1182) will begin downloads with medline16n1183.
• Users who have not downloaded the last Update file from previous MEDLINE/PubMed FTP server will need to validate the last Update file downloaded and then begin with the next Update file in sequential order. The complete set of 2016 Update files are available on ftp://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/

The 2016 MEDLINE/PubMed Baseline files new location is: ftp://ftp.ncbi.nlm.nih.gov/pubmed/baseline/

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October 1, 2016: INCLUSION OF PUBLISHER SUPPLIED RECORDS

On October 6, 2016 NLM is exporting Publisher supplied citations in the Daily Update files with the MedlineCitation Status attribute: Publisher. This will include all records defined as Publisher (see: https://www.nlm.nih.gov/bsd/licensee/elements_descriptions.html#medlinecitation)

EXCEPT: Citations to books and book chapters in the NCBI Bookshelf.

Records in the status of Publisher prior October 4, 2016 will need to be imported using the E-Utilities API.

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October 1, 2016: LARGE SET of UPDATE FILES

The week of October 10, 2016 NLM is exporting a large number of revised records (approximately 540,000 records) to reflect an internal update to the full journal name (data are in the <Title> element). These records are being exported as standard Daily Update files and comingled with standard daily updates (new, other changed, and delete records).

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October 1, 2016: Termination of License for NLM Data

The NLM Data License has been replaced by Terms and Conditions. No registration is required to access data available from NLM's FTP servers. Users will not be required to renew a license agreement at the end of the year.