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Announcements to NLM Data Licensees: Year 2015


MEDLINE/PubMed Update File

Today's file, medline15n1206.xml, contains records only in MedlineCitation Status In-Data-Review or In-process. MedlineCitation Status definitions are at http://www.nlm.nih.gov/bsd/licensee/elements_descriptions.html. Subsequent daily update files for the duration of the 2015 production year will also contain only In-Data-Review and In-process records until the release of the first 2016 update files. The 2016 baseline database files and the first 2016 update files will be available on December 16 or December 17, 2015.
Information pertaining to the end-of-year schedule for distribution of MEDLINE/PubMed data and DTD/XML changes for 2016 is available in the 10/1/15 announcement at 2016 DTD and XML Changes; Forthcoming 2016 Baseline and Update Files; Continuing to Lease NLM Data in 2016.

Renew License to Continue Access to 2016 Data (for current MEDLINE®/PubMed®, Catfile, CatfilePlus, Serfile, CCRIS, ChemIDplus Subset, GENE-TOX, HSDB® Subset, LactMed® and TOXLINE® Subset Licensees)

November 12, 2015

Licensees who entered into the current License Agreement for NLM Data on or before August 31, 2015 need to renew their license no later than December 11, 2015 to be retained as licensees and to have access to the 2016 data files. An e-mail announcing access to the renewal instructions was sent to those who need to renew. An online system is used to renew or to cancel your existing license. The system will be in operation through 12:00 pm (Noon) EST Friday December 11, 2015. If you do not renew by then you will need to submit a new license request to again license the NLM data. If you entered into the current License Agreement for NLM Data on September 1, 2015 or later you do not need to renew for 2016. In this case, you were not sent the e-mail and can ignore the instructions below; your license remains in effect, and access to the 2016 data files will continue without interruption.

RENEWAL INSTRUCTIONS FOR LICENSEES
  1. Go to the renewal system Web page (//wwwcf.nlm.nih.gov/nlm_licensee/renewal/index.cfm) no later than 12:00 pm (Noon) EST December 11, 2015.
  2. Sign into the renewal system. Enter your license code and the licensee’s first and last names exactly as shown in the individual e-mail sent to each licensee on November 12, 2015. Sign in will not work if the secondary representative’s name is entered.
  3. Follow the prompts to renew or cancel your license.

If you elect to renew, you will be asked to re-accept the terms of the license agreement and to review your license profile before electing to renew with or without changes to your profile information. Changes to e-mail address, selecting additional data to lease, or changing an IP address used to get to the data files will take effect immediately. An e-mail confirmation of the renewal will be sent to the license representatives.

If you elect to cancel your license, you will no longer have access to licensed data files on December 16, 2015 and your license will be cancelled on that date. An e-mail confirmation of the cancellation will be sent to the license representatives. See Section 12 E of the License (//www.nlm.nih.gov/databases/license/license.pdf) for required actions upon termination of the license. Section 6 is also pertinent if you have redistributed data received under this license, or data derived from the NLM-supplied data.

On December 16, 2015 NLM will cancel licenses of those who have not renewed or cancelled on their own by December 11, 2015. There will be no grace period after December 11 as the renewal system will no longer be operational. Licensees who intended to renew but did not do so on time will need to initiate a new license request (//www.nlm.nih.gov/databases/license/license.html).

2016 DTD and XML Changes; Forthcoming 2016 Baseline and Update Files; Continuing to Lease NLM Data in 2016

October 1, 2015

Topics covered:

  1. DTD and XML Changes for the NLM 2016 Production Year
  2. Forthcoming 2016 Baseline and Update Files
  3. Schedule Changes for Daily MEDLINE/PubMed Update Distributions in November 2015
  4. Continuing to Lease NLM Data in 2016
  5. Information Page for Licensees
  6. License Code Reminder

  1. DTD AND XML CHANGES FOR THE NLM 2016 PRODUCTION YEAR

    There are no changes expected for 2016 to the DTDs used for CCRIS, ChemID Subset, Gene-Tox, HSDB®, LactMed®, and TOXLINE® Subset data. There are changes to the DTDs used for MEDLINE/PubMed, CatfilePlus in XML, and Serfile in XML for the 2016 production year. The January 1, 2015 versions of the NLMMedlineCitationSet and NLMCatalogRecordSet DTDs currently in effect will be replaced by DTDs dated January 1, 2016. The new DTDs will be used to validate the 2016 versions of the baseline MEDLINE/PubMed, CatfilePlus in XML, and Serfile in XML data and their subsequent updates during the 2016 production year. The forthcoming 2016 DTDs are available from links on //www.nlm.nih.gov/databases/dtd/. The MEDLINE/PubMed XML Data Elements pages and the CatfilePlus and Serfile in XML Format Element Descriptions document will be edited to reflect these changes in the future. Licensees will be advised when sample files of XML records using the 2016 DTDs become available. NLM will announce changes in PubMed search functionality and display based on the 2016 DTD in the NLM Technical Bulletin later this fall after those decisions are final.

    1. Change to NLMMedlineCitationSet DTD AND MEDLINE/PubMed XML
      The DTD change for the 2016 production year is defined in the Revision Notes section near the top of the DTD. The following describes the substantive change to NLMMedlineCitationSet DTD and MEDLINE/PubMed XML:
      1. The valid value QCIM will be added to the Source attribute of the OtherID element.
        The added value will indicate citations from the Quarterly Cumulative Index Medicus.
        
DTD:
<!ELEMENT    OtherID (#PCDATA)>
<!ATTLIST    OtherID
Source (NASA | KIE | PIP | POP | ARPL | CPC | IND | CPFH | CMLM | NRBL | NLM | QCIM) #REQUIRED>
    2. Changes to NLMCatalogRecordSet DTD and CatfilePlus and Serfile XML
      The DTD changes for the 2016 production year are itemized in the Revision Notes section near the top of the DTD. The following describes the substantive changes to NLMCatalogRecordSet DTD and CatfilePlus and Serfile XML.

      1. A valid value of the IndexingStatus attribute will change from Continued-by-another-indexed-title to Continued-by-another-title.
        NCRS is changing this in conjunction with the same change being made to the 2016 Serials DTD.

        DTD: 
<!ELEMENT    ISSN (#PCDATA)> 
<!ATTLIST    IndexingSourceName
IndexingStatus (Ceased-publication | Continued-by-another-title | Currently-indexed | Deselected) #IMPLIED>

      2. Add ISSN child element to TitleRelated
        We want to help the user find and correctly identify related titles named in our MARC data by providing the ISSN of the related title as a subelement of the TitleRelated element. The ISSN element already exists in the NCRS DTD, so this change will simply add another use of it as a child element of TitleRelated, with usage optional and not repeatable. The ISSN element includes attribute data which is not available from these originating MARC fields; therefore, when ISSN is a subelement of TitleRelated, the IssnType attribute value will always be ‘undetermined’ and there will be no ValidYN attribute.

        DTD: 
<!ELEMENT    ISSN (#PCDATA)> 
<!ATTLIST    ISSN
IssnType (Electronic | Print | Undetermined | #REQUIRED
ValidYN (Y | N) Y> 
<!ELEMENT    TitleRelated (Title, OtherInformation?, RecordID*, ISSN?)>

  2. FORTHCOMING 2016 BASELINE AND UPDATE FILES
    1. MEDLINE/PubMed
      After NLM completes its annual database maintenance activities, we expect to release the 2016 baseline files for MEDLINE/PubMed maintained with 2016 MeSH vocabulary and other changes to renewing licensees in mid-December (on December 15 or 16 -- within 24 to 48 hours after PubMed is updated with 2016 data). Daily update files for the 2016 production year will also begin at this time. A complete baseline reload to replace all previously received 2015 production year data ensures you have the most current and accurate version of all records and is required per Appendix B of the License Agreement for NLM Data.

    2. CatfilePlus and Serfile
      Beginning with the December 2015 distribution of new records in CATFILE and SERFILE, NLM subject terms will be distributed with topical subjects recorded in 650 $a or 650 $a $x; geographic subjects recorded in 651 $a or 651 $a $x; and publication type/genre terms record in 655 $a. Artificially reconstructed subject strings with 650 $z and $v will no longer be provided. In January 2016, the entire CATFILE and SERFILE databases will be released with these updates made to all the records. Libraries that want their data to be consistent with the NLM files are encouraged to download the full update.

    3. Other databases
      As routine, all XML files distributed to licensees during 2016 for CCRIS, ChemID Subset, Gene-Tox, HSDB®, and TOXLINE® Subset will be complete replacement files. New files, if available, will be on the server for licensees on or about the 28th of the month. Some of these databases are updated irregularly and/or infrequently.

  3. SCHEDULE CHANGES FOR DAILY MEDLINE/PUBMED UPDATE DISTRIBUTIONS IN NOVEMBER 2015
    As is the case each year, in mid-November NLM will suspend distribution of new and revised MEDLINE/PubMed records in MedlineCitation Status = MEDLINE, MedlineCitation Status = PubMed-not-Medline, and MedlineCitation Status = OLDMEDLINE as preparations are made for the new production year. The last records in these three statuses, as well as PMIDs of records to delete for the current 2015 production year are expected to be available Wednesday, November 17. Not later than Monday, November 23, NLM will begin to export only records in In-process and In-Data-Review status until availability of the MEDLINE/PubMed 2016 baseline files in mid-December (on or about December 15 or 16). Daily update files containing new and maintained records in all statuses and PMIDs of deleted records will commence upon release of the baseline files to licensees.

  4. CONTINUING TO LEASE NLM DATA IN 2016
    Licensees must confirm continued interest in leasing NLM data during the 2016 production year by renewing their license agreement following instructions that will be provided in November. Only those who renew will have access to the 2016 data, and licenses of non-responders will be terminated (and accordingly, access to the 2016 data will be denied). Per Section 13E of the License Agreement for NLM Data, licensees who cancel their license or whose license is terminated by NLM are to:
    1. Discontinue use of any promotional or other materials that refer to such data within thirty (30) days, and
    2. Cease use of data or information/data derived from data licensed under this license in all applications no later than ninety (90) days. Following that, licensees must promptly destroy and erase all data obtained under this license as well as any data contained in any derivative applications under the licensee’s control. (This does not apply to Catfile, CatfilePlus or Serfile data.)

  5. INFORMATION PAGE FOR LICENSEES
    Please visit the NLM information page for licensees //www.nlm.nih.gov/bsd/licensee/. Licensees should follow the links on this page for data element descriptions, update charts, announcements to licensees, and other documentation/resources relating to NLM leased data.

  6. LICENSE CODE REMINDER
    A unique alpha-numeric code including the letters "NLM" is assigned to each license and appears at the top of license-related e-mails sent by NLM. Please keep a record of your license code and reference it when corresponding with NLM about matters relating to your license or leased databases.

Now Licensing LactMed®

June 8, 2015

Starting June 8, 2015 The National Library of Medicine will begin licensing the Toxicology Data Network (TOXNET) subset Drugs and Lactation Database (LactMed®). Current Licensees may email the NLM Data Distribution team at nlmdatadistrib@nlm.nih.gov and request to have the dataset added to their license. New licensees may request the dataset when applying for a license. Additional information about LactMed® may be found at Fact Sheet: Drugs and Lactation Database (LactMed®).

Scheduled Maintenance at NLM March 14, 2015 from 8 am to 5 pm ET

March 12, 2015

On Saturday March 14, 2015 from 8 am to 5 pm ET, licensees will be unable to download files from our public ftp sites. Furthermore, depending on the length of outage, we may not be able to post new MEDLINE/PubMed update files on Saturday March 14, 2015. If we are unable to post to the servers these files will be posted to the ftp site at noon ET Sunday March 15, 2015.

MEDLINE/PubMed Update File

March 9, 2015

The MEDLINE/PubMed update files medline15n0933 and medline15n0934 were not placed on the server over the weekend (March 7-8, 2015) due to technical difficulties at NLM. We will resume our regular update schedule on March 9, 2015.

NIH Announces Request for Information Regarding Deliberations of the Advisory Committee to the NIH Director (ACD) Working Group on the National Library of Medicine

February 18, 2015

The National Institutes of Health (NIH) has issued a call for participation in a Request for Information (RFI), allowing the public to share its thoughts with the NIH Advisory Committee to the NIH Director Working Group charged with helping to chart the course of the National Library of Medicine, the world’s largest biomedical library and a component of the NIH, in preparation for recruitment of a successor to Dr. Donald A.B. Lindberg, who will retire as NLM Director at the end of March 2015.
For more information, including how to submit a response, please visit http://www.nlm.nih.gov/news/nih_rfi_nlm_working_group.html


2015 MEDLINE/PubMed Baseline Data; CatfilePlus and Serfile XML Baseline Files

December 17, 2014

  1. AVAILABILITY OF 2015 MEDLINE/PUBMED BASELINE DATA
    The 2015 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. 2015 UPDATE FILES
    The first group of 2015 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 medline15n0780. 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.

  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 2015 version of PubMed at the time the 2015 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 17, 2014 will want to include these records now.

    The file, named SpecialPubMedPMIDList_2015.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 2015 MEDLINE/PubMed database either 1) immediately after the baseline files and before any update files or, 2) immediately after update files medline15n0780 through medline14n0852 to ensure retaining the most current version of those records as subsequent update files are loaded. Do not add the records identified in SpecialPubMedPMIDList_2015.txt after you have processed medline15n0853 as this may result in retention of an earlier and inaccurate version of the records.

  4. 2014 MEDLINE/PUBMED FILES TO MOVE TO NEW DIRECTORY
    The 2014 update files are 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 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.

  6. MEDLINE/PUBMED BASELINE REPOSITORY (MBR)
    The 2015 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.

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 "catplusbase1of4.2015.xml", "catplusbase2of4.2015.xml", etc. The Serfile base file is complete in a single file, named "serfilebase.2015.xml". The baseline files contain all records through December 5, 2014 and should be used to completely replace all records previously distributed. The first XML update files for CatfilePlus and Serfile were made available December 5, 2014.