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Announcements to NLM Data Licensees: Year 2012

(05/03/12) MEDLINE/PubMed Update File May 3, 2012
(02/17/12) MEDLINE/PubMed Data Changes
(01/09/12) Catfile, CatfilePlus, and Serfile MARC 2012 Baseline Files Now Available
(12/23/11) MeSH Descriptor Corrected
(12/14/11) MEDLINE/PubMed Baseline Data; CatfilePlus and Serfile XML Baseline Files

2011 Announcements

MEDLINE/PubMed Update File May 3, 2012

May 3, 2012

There will not be a MEDLINE/PubMed update file on the server today, May 3, 2012, due to technical difficulties at NLM. We will resume our regular update schedule when these problems are resolved.

MEDLINE/PubMed Data Changes

February 17, 2012

The following data changes are in effect:

  1. Now using VersionID and VersionDate attributes of the MedlineCitation element and values other than “1” for the Version attribute of the PMID element.

    NLM creates an individual citation for each article’s version and links the versions via attributes for the MedlineCitation and PMID elements (http://www.nlm.nih.gov/archive/20110328/bsd/licensee/announce/2010.html#2010CHANGES). Until now we had only PMID Version="1" and did not use the new attributes for the MedlineCitation element, for example:

    <MedlineCitation Owner="NLM" Status="PubMed-not-MEDLINE">
<PMID Version="1">20029614</PMID>

    Starting in February 2012, we use the VersionID and VersionDate attributes of the MedlineCitation element and values other than "1" for the Version attribute of the PMID element, for example:

    <MedlineCitation Owner="NLM" Status="In-Data-Review" VersionID="10" VersionDate="2010/04/19">
<PMID Version="10">20029614</PMID>

    Information on versioning in PubMed is available in the NLM Technical Bulletin article title "Versioning in PubMed" at http://www.nlm.nih.gov/pubs/techbull/jf12/jf12_pm_versioning.html.

  2. Version number for OtherID Source="NLM".

    PubMed Central identifiers in the OtherID element may now include a version number in the format pmcid.version, e.g.:

    <OtherID Source="NLM">PMC2762775.2</OtherID>

    We will update the MEDLINE®PubMed® XML Element Descriptions and their Attributes at http://www.nlm.nih.gov/bsd/licensee/elements_descriptions.html as soon as possible.

Catfile, CatfilePlus, and Serfile MARC 2012 Baseline Files Now Available

January 9, 2012

The updated 2012 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, 2011 and December 31, 2011, will be available no later than February 1, 2012. Licensees who are new recipients of NLM MARC bibliographic records in 2012, as well as ongoing licensees who are discarding their pre-2012 records and reloading with the 2012 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 2012 base files. If loading new baseline files, you should then load the 2012 update files dated after the date of the base files.

MeSH Descriptor Corrected

December 23, 2011

There was an incorrect MeSH descriptor in the 2012 XML MeSH Descriptor Records. The MeSH heading “Positron-Emission Tomography/Computed Tomography” includes a forward slash (/) and this is incorrect. NLM corrected the heading to “Positron-Emission Tomography and Computed Tomography.” If you downloaded the 2012 MeSH Descriptor Records prior to 12/19/2011 you should download them again, or correct this descriptor. As a reminder, the MeSH Files Available to Download are at http://www.nlm.nih.gov/mesh/filelist.html.

MEDLINE/PubMed Baseline Data; CatfilePlus and Serfile XML Baseline Files

December 14, 2011

2012 MEDLINE/PubMed Baseline Data

  1. AVAILABILITY OF 2012 MEDLINE/PUBMED BASELINE DATA
    The 2012 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.

  2. 2012 UPDATE FILES
    The first group of 2012 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 medline12n0685. 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.

    SPECIAL NOTE: The 33 records listed below by PMID and distributed in the update files medline12n0685 through medline12n0705 include the MeSH heading “Positron-Emission Tomography/Computed Tomography.” The forward slash (/) in the heading is incorrect. We corrected the heading to “Positron-Emission Tomography and Computed Tomography” and exported the records again in update file medline12n0706.

    PMID PMID PMID PMID PMID
    20884128 20888130 20933343 21440334 21440958
    21465110 21468763 21514975 21514978 21553087
    21553158 21553160 21565398 21567252 21617977
    21626438 21632132 21655905 21719136 21784544
    21786095 21786097 21825837 21825838 21825839
    21825852 21825853 21825855 21855972 21876401
    21914229 21926377 22046717    


  3. 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 2012 version of PubMed at the time the 2012 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 14, 2011 will want to include these records now.

    The file, named SpecialPubMedPMIDList_2012.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 2012 MEDLINE/PubMed database either 1) immediately after the baseline files and before any update files or, 2) immediately after update files medline12n0685 through medline12n0702 to ensure retaining the most current version of those records as subsequent update files are loaded. Do not add the records identified in SpecialPubMedPMIDList_2012.txt after you have processed medline12n0703 as this may result in retention of an earlier and inaccurate version of the records.

  4. 2011 MEDLINE/PUBMED FILES TO MOVE TO NEW DIRECTORY
    The 2011 update files have moved to a new directory where they will remain for several weeks. Contact NLM at NLMdatadistrib@nlm.nih.gov if you need access to those files.

  5. DOCUMENTATION
    Documentation for the MEDLINE/PubMed baseline database is available from links in the Data Availability and Maintenance section of the NLM 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.

  6. MEDLINE/PUBMED BASELINE REPOSITORY (MBR)
    The 2012 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 the NLM FTP server.

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 "catplusbase1of4.2012.xml", "catplusbase2of4.2012.xml", etc. The Serfile base file is complete in a single file, named "serfilebase.2012.xml". The baseline files contain all records through November 18, 2011 and should be used to completely replace all records previously distributed. The first XML update files for CatfilePlus and Serfile were made available November 25, 2011.