Announcements to NLM Data Licensees: Year 2013
May 15, 2013
There are 2013 mid-year changes to the NLMMedlineCitationSet DTD used for MEDLINE/PubMed. The January 1, 2013 version of the NLMMedlineCitationSet DTD currently in effect will be replaced by a new DTD dated May 1, 2013. The new DTD will be used for creating new and revised MEDLINE/PubMed records beginning no earlier than 30 days from the date of this announcement (i.e., not earlier than June 14, 2013). The 2013 MEDLINE/PubMed baseline XML data will not be recreated nor re-exported with these mid-year changes. The forthcoming May 1, 2013 DTD is available from a link on http://www.nlm.nih.gov/databases/dtd/.
The DTD changes are itemized in the Revision Notes section near the top of the DTD. The following describes the substantive changes to NLMMedlineCitationSet DTD and MEDLINE/PubMed XML:
The PubModel attribute of Article element has a new valid value of “Electronic-eCollection.” The Electronic-eCollection PubModel is used for electronic-only journals that publish individual articles first and then later collect them into an “issue” that is typically called an eCollection. The ArticleDate is the date the individual article is published and the PubDate is the date the eCollection is published. Please see the description of the Article element at http://www.nlm.nih.gov/bsd/licensee/elements_descriptions.html#article for more information about how these elements and attributes are used in the source area of the PubMed citation display.
The NlmCategory attribute of AbstractText element has a new valid value of “UNASSIGNED.” The UNASSIGNED NlmCategory is used for labels in structured abstracts that NLM has not yet mapped to one of 5 categories, i.e., BACKGROUND, OBJECTIVE, METHODS, RESULTS, or CONCLUSIONS. For more information on structured abstracts, please see http://www.nlm.nih.gov/bsd/licensee/elements_descriptions.html#abstract.
April 11, 2013
On March 31, 2013 the NLM began use of RDA: Resource Description and Access for all original cataloging of modern material, replacing the Anglo-American Cataloguing Rules, 2nd edition (AACR2). Bibliographic records distributed by NLM will continue to contain a mix of RDA and AACR2 records as NLM will accept AACR2 copy without upgrading these records to RDA. Any new authority records created by NLM will follow RDA guidelines, regardless of the rules used to create the bibliographic data. For more information please visit the RDA section on the NLM Cataloging homepage http://www.nlm.nih.gov/tsd/cataloging/mainpge.html.
March 8, 2013
On April 15, 2013, the length of unique identifiers used in the MeSH vocabulary will expand to 10 characters. Details are discussed in the NLM Technical Bulletin article titled "MeSH Unique Identifiers: Length Expanding to Ten Characters" at http://www.nlm.nih.gov/pubs/techbull/ma13/ma13_mesh_ui_expand.html.
January 7, 2013
The updated 2013 MARC base files for Catfile, CatfilePlus, and Serfile are available on the NLM FTP server. These base files are each complete in a single file. Loading the base files on an annual basis is optional for MARC subscribers. If you have correctly loaded each of the update files, there is no need to reload the base files. The MARC file containing all the bibliographic records deleted by NLM between January 1, 2012 and December 31, 2012, will be available no later than February 1, 2013. Licensees who are new recipients of NLM MARC bibliographic records in 2013, as well as ongoing licensees who are discarding their pre-2013 records and reloading with the 2013 base files, do NOT need the delete file. The records in this file were removed from the NLM database prior to the pull of the 2013 base files. If loading new baseline files, you should then load the 2013 update files dated after the date of the base files.
December 17, 2012
MEDLINE/PUBMED DATA CHANGES
NLM will soon include author keywords in MEDLINE/PubMed citations. The keywords are written by authors and supplied by publishers. Author keywords will be exported in records for licensees in the Keyword element of KeywordList. The KeywordList Owner attribute for author keywords is NOTNLM, i.e., <KeywordList Owner="NOTNLM">. NOTNLM is defined as a valid value for KeywordList Owner attribute in the NLMMedlineCitationSet DTD but has not been used by NLM until now. The Keyword MajorTopic attribute for author keywords is N, i.e., <Keyword MajorTopicYN="N">. NLM will begin exporting author keywords no earlier than 30 days from the date of this announcement (i.e., not earlier than January 17, 2013).
MORE MESH 2013 MODIFICATIONS
Two changes were made to the current 2013 MeSH Vocabulary. The entry terms Esomeprazole and Nexium are removed from the descriptor Omeprazole. A new descriptor Esomeprazole Sodium with entry term Nexium is created. MEDLINE/PubMed records will be updated to reflect these changes and will be re-exported to licensees. Licensees who downloaded the 2013 MeSH Descriptor Records should download them once again. As a reminder, the MeSH Files Available to Download are at http://www.nlm.nih.gov/mesh/filelist.html.
December 11, 2012
- AVAILABILITY OF 2013 MEDLINE/PUBMED BASELINE DATA
The 2013 MEDLINE/PubMed baseline files, which replace all previously distributed MEDLINE/PubMed data are now available for FTP. Licensees have been e-mailed the location of the FTP access instructions with additional information.
- 2013 UPDATE FILES
The first group of 2013 update files and the special PMID list text file (see item 3 below) are also available. Please be sure to read the _notes.txt file that is on the server accompanying the first update file medline13n0718. Update files should be processed after the baseline files in ascending file name numeric sequence (see item 3 below for exception) to ensure that all new records are added and the most current and accurate version of each record is retained.
- ADDITIONAL PMID LIST FILE
A text file containing PMIDs of records in MedlineCitation Status = In-Process and MedlineCitation Status = In-Data-Review that have been retained in the 2013 version of PubMed at the time the 2013 baseline files were loaded and that are not exported to licensees in the first batch of update files is available. These records will eventually be exported in update files as completed records in MedlineCitation Status = MEDLINE or MedlineCitation Status = PubMed-not-MEDLINE or as deleted PMIDs in DeleteCitationSet. Licensees who wish to create a database as close as possible to the record content in PubMed on December 10, 2012 will want to include these records now.
The file, named SpecialPubMedPMIDList_2013.txt, resides in the update file directory. Licensees may use the Entrez Utilities to download the records using the list of PMIDs.
*IMPORTANT*: If you elect to add these records to your version of MEDLINE/PubMed, they must be added to your 2013 MEDLINE/PubMed database either 1) immediately after the baseline files and before any update files or, 2) immediately after update files medline13n0718 through medline13n0732 to ensure retaining the most current version of those records as subsequent update files are loaded. Do not add the records identified in SpecialPubMedPMIDList_2013.txt after you have processed medline13n0733 as this may result in retention of an earlier and inaccurate version of the records.
- 2012 MEDLINE/PUBMED FILES TO MOVE TO NEW DIRECTORY
The 2012 update files are moved to a new directory where they will remain for several weeks. Contact NLM at firstname.lastname@example.org if you need access to those files.
Documentation for the MEDLINE/PubMed baseline database is available from links in the Data Availability and Maintenance section of NLM’s information page for MEDLINE/PubMed licensees. Also see the MEDLINE/PubMed Maintenance Overview for information about and points to consider for processing update files. Announcements during the year will be added as they become available.
- MEDLINE/PUBMED BASELINE REPOSITORY (MBR)
The 2013 baseline data will be included at a later date in the MEDLINE/PubMed Baseline Repository (MBR) resources. If you wish to search the baseline data via the MBR Query Tool, be sure to use the same IP address registered with NLM for access to MEDLINE/PubMed from NLM’s FTP server.
- MeSH 2013 MODIFICATIONS
Two changes were made to the current 2013 MeSH Vocabulary. The descriptor Tropical Diseases was removed and the descriptor Tropical Medicine was returned to its 2012 content. If you downloaded the 2013 MeSH Descriptor Records prior to 12/11/2012 you should download them again. As a reminder, the MeSH Files Available to Download are at http://www.nlm.nih.gov/mesh/filelist.html.
CatfilePlus and Serfile XML Baseline Files
The updated XML base files for CatfilePlus and Serfile are available on the NLM FTP server. CatfilePlus is in 4 parts, named "catplusbase1of4.2013.xml", "catplusbase2of4.2013.xml", etc. The Serfile base file is complete in a single file, named "serfilebase.2013.xml". The baseline files contain all records through November 16, 2012 and should be used to completely replace all records previously distributed. The first XML update files for CatfilePlus and Serfile were made available November 23, 2012.