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PubMed Status

Technical Notes

PubMed Status - [Editor's Note added on February 20, 2001.]

2001 MeSH in LocatorPlus

Revision to NLM's License Agreement to Lease NLM Databases in Machine-Readable Form

PubMed Status Update

Small Number of PubMed Citations Receive New Entrez Date (EDAT)

New Version of the NLM Gateway Released

Expanded Access to MeSH

MEDLINE Updates Resume in PubMed

January 18, 2001 [posted]
February 20, 2001 [Editor's Note added]

Effective Tuesday, January 16, 2001, the National Center for Biotechnology and Information (NCBI) temporarily stopped the daily updating of PubMed with new publisher-supplied and in-process citations as they work on making the necessary changes to reload MEDLINE data following 2000-to-2001 year-end maintenance. We expect this interruption to last until about January 26, 2001, if all goes well, or later, if we encounter problems. An article describing PubMed changes happening as part of this reload will soon be available in the NLM Technical Bulletin. We predict that the system will be replaced and publicly searchable before the end of January. Then daily updates with publisher-supplied and in-process citations will resume. Also, the newly indexed MEDLINE citations from the beginning of the 2001 indexing year will be added and weekly updates for these indexed citations will resume according to the published update schedule. For searches limited to MeSH headings, users will then start retrieving newly indexed citations whether using the PubMed query box or the current awareness Cubby feature.

[Editors Note: Please see the Technical Note PubMed Status Update in this issue of the NLM Technical Bulletin for the most current information.]

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2001 MeSH in LocatorPlus

February 01, 2001 [posted]

As of December 18, 2000, MeSH subject authority records in LocatorPlus, the online public access catalog module of NLM's Voyager integrated library system, were changed to reflect 2001 MeSH. These changes are also reflected in the LocatorPlus records accessed via the NLM Gateway.

Use MeSH 2001 when searching for books, journals, audiovisuals, or other resources by MeSH subject in LocatorPlus or in the NLM Gateway.

MeSH 2001 is the subject authority, or controlled vocabulary, for headings in LocatorPlus in the following fields:

MARC21 field contains
650 main headings or main headings and topical subheadings
651 geographic qualifiers
655 Publication Types

For more information on how to search for fields in NLM LocatorPlus, see http://www.nlm.nih.gov/services/lpfields.html#heading.

In the 2001 Medical Subject Headings Annotated Alphabetic List, users are advised to annotate the printed tool as follows:

  • In the list headed "Publication Types - Genre Terms"identified as "Generally Used for Cataloging" (p. I-28), add the genre term "Evaluation Studies". This term will be included in the list in the next edition of the Medical Subject Headings Annotated Alphabetic List.

  • In the section headed "Publication Types - Scope Notes", add the new Publication Type "Validation Studies" with the scope note "Used by Special Data Producers Only". Catalogers do not use this Publication Type at this time. This term will be correctly annotated in the next edition of the Medical Subject Headings Annotated Alphabetic List.

For more information on how NLM catalogers apply MeSH, see http://www.nlm.nih.gov/tsd/cataloging/catmesh.html.

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Revision to NLM's License Agreement to Lease NLM Databases in Machine-Readable Form

February 01, 2001 [posted]

The National Library of Medicine's License Agreement to Lease NLM Databases in Machine-Readable Form has been revised. A sentence has been added at the end of section E3. The section now reads:

E. RESTRICTIONS ON USE, DUPLICATION, AND REDISTRIBUTION OF MACHINE-READABLE DATA
3. The Licensee shall inform its users that the duplication, resale, or redistribution of data obtained under this Agreement must conform to fair use guidelines and U.S. and international copyright law. Any duplication, resale, or redistribution by the Licensee or its users who provide information services or products from NLM databases obtained directly or indirectly from the Licensee must also conform to NLM's quality assurance requirements listed in Paragraphs D.2.a. through D.2.o., copyright constraints listed in Paragraph F., and usage reports listed in Paragraph J. Written approval from NLM is required before a non-U.S. licensee duplicates, resells, or redistributes NLM data (except cataloging records) to others.

Per Section M of the License, the modification is binding upon publication in the NLM Technical Bulletin.

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PubMed Status Update

February 16, 2001 [posted]

On November 7, 2000, NLM temporarily stopped adding fully indexed citations to PubMed and on January 16, 2001, the Library stopped the daily updating of PubMed with new publisher-supplied and in-process citations. These actions were taken to accommodate both NLM's internal maintenance cycle known as Year-End Processing (YEP) and the replacement of our system that manages the data entry, indexing, and quality control of journal citations. Although we expected these interruptions to last only through January 26, 2001, the updating of publisher-supplied, in-process and fully indexed citations to PubMed was delayed past this date.

On February 2, 2001, the MEDLINE data were reloaded into PubMed. This reload included MEDLINE citations through the end of the 2000 indexing year which were updated to reflect changes to 2001 MeSH. Also, the 2001 MeSH vocabulary was incorporated into PubMed's MeSH Browser and MeSH translation table.

On February 7, 2001, we resumed loading new citations into PubMed with a small number (approximately 2,000) of publisher-supplied citations. On February 13, 2001 we loaded another 11,000 publisher-supplied citations into PubMed. We loaded the remaining backlog of publisher-supplied citations and resumed our regular update schedule for these citations on February 15, 2001.

The newly indexed MEDLINE citations from the beginning of the 2001indexing year and the backlog of in-process citations will be added to PubMed soon and updates for these citations will resume according to the published update schedule.

Please see the Changes to PubMed for 2001 article in this issue of the NLM Technical Bulletin for a description of the changes happening as part of the reload and NLM's new Data Creation and Maintenance System (DCMS).

The MEDLINE reload data were sent to licensees the week of February 5, 2001. The MEDLINE in-process citations and newly indexed citations since the beginning of the 2001 indexing year will be made available for licensees to ftp as soon as NLM has successfully added the data to PubMed. Licensees are reminded that NLM sends them e-mail notifications regarding data distribution issues and schedules. These notifications are also posted on NLM's Web site for licensees at http://www.nlm.nih.gov/bsd/licensee.html.

We appreciate your patience and understanding as NLM navigates through this major reinvention initiative. This is the final leg of our migration from the old, mainframe MEDLINE computer applications to more modern information technology architecture. It has been a long journey and this most recent year-end cycle took longer than usual as we juggled transition issues. As NLM's own 2001 system has been delayed, users should expect similar delays in the delivery of products from other vendors as they make their own adjustments.

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Small Number of PubMed Citations Receive New Entrez Date

February 21, 2001 [posted]

All PubMed citations have an EDAT (Entrez Date) field to indicate the date the citation first entered PubMed. It was recently discovered that approximately 4,000 PubMed citations did not have an EDAT value. A record without an EDAT cannot be retrieved by a search. In order to correct this as quickly as possible, these records were assigned a new EDAT value of 2001/02/07.

Approximately 3,000 of these citations stand out because they are MEDLINE citations and their MHDA (the date the citation was indexed with MeSH Terms and elevated to MEDLINE status) is now older than the EDAT.

Example:

PMID- 10819728
EDAT- 2001/02/07 11:00
MHDA- 2000/05/20 9:00

This may result in citations with this EDAT (2001/02/07) being retrieved a second time by a Cubby stored search, or by a search that includes a date range or limit.

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New Version of the NLM Gateway Released

February 21, 2001 [posted]

A new version of the NLM Gateway was released on February 2, 2001. Changes include the following:

  • A new collection, "HSR Meetings," was added to the NLM Gateway in the Meeting Abstracts category. The HSR Meetings collection includes the meeting abstracts from the former HealthSTAR database.
  • A new collection, "DIRLINE," was added to the NLM Gateway in the Consumer Health category. The DIRLINE collection is a directory of health-related organizations. The DIRLINE fact sheet provides additional information on this resource.
  • Two new field qualifiers were added for searching. You may now search by Unique Identifier ([UI]) and by Substance Name ([NM]). The NLM Gateway Help provides information on searching by fields.
  • The search box was added to the Locker, Preferences, and Login pages.
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Expanded Access to MeSH

February 21, 2001 [posted]

The MeSH Section continues to provide access via the MeSH Browser for two years of the MeSH vocabulary: the current year (default) and an alternate year accessible by a link on the MeSH Browser Home Page.

The access will follow a rotation as successive years of MeSH are created. Old MeSH (the previous year's vocabulary) will be available until October. New MeSH (the next year's vocabulary) will be available from October through December, after which it will become Current MeSH.

MeSH Browser File January-September October-December
Primary Current MeSH [2001] Current MeSH [2001]
Alternate Old MeSH [2000] New MeSH [2002]

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MEDLINE Updates Resume in PubMed

February 28, 2001 [posted]

We have resumed updating PubMed with MEDLINE citations. On February 28, over 120,000 indexed (MEDLINE) citations were loaded in PubMed. MEDLINE citations will return to a weekly update schedule in PubMed.

We, again, apologize for the delay in the resumption of updates, and thank you for your patience as we continue with the transition to our new organization of databases (http://www.nlm.nih.gov/pubs/techbull/mj00/mj00_buckets.html).

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