Technical Notes - e1

PubMed: Truncation, Automatic Explosion, Mapping, and MeSH Headings - e2

MLA 1998 [corrected 1998/07/14] - e3

BIOETHICSLINE Regenerated - e4

• New and Noteworthy in PubMed
• PubMed Sneak Preview Available on the Web
• PubMed Help Updated May 5, 1998
• PubMed Help Sheet for Command Language Searchers
• PubMed and Internet Grateful Med Training Workbooks Available
• National Library of Medicine Data Distribution Program
• OLDMEDLINE Database Moves Back in Time
• TOXLINE Rebuilt
• TOXNET Moved to New Computer Platform
• Unused Codes Deactivated
• Institutional Student Codes to be Discontinued on 10/1/98

New and Noteworthy in PubMed

From the PubMed Home Page click on New and Noteworthy and then click on theApril 6 link for the latest information on searching MeSH/subheading combinations, Truncation and System Fixes. For more detailed information on truncation see the article PubMed: Truncation, Automatic Explosion, Mapping, and MeSH Headings in this issue.

PubMed Sneak Preview Available on the Web

If you click on New and Noteworthy from the PubMed Web site, you will be able to read about the PubMed enhancements that are currently in progress. Check here to see if anything on your PubMed wish list is already in the works. The preview will be updated with projected release dates, new enhancements, and changes to the existing plans as the information becomes available. Your comments and suggestions are welcome and can be sent directly to custserv@nlm.nih.gov.

PubMed Help Updated May 5, 1998

From the PubMed Home Page click on Help to read or print the latest information on basic and advanced search features in PubMed, including using the MeSH browser.

PubMed Help Sheet for Command Language Searchers

Go to [This link was removed because it is no longer valid.] to view a chart comparing PubMed with ELHILL formulations. It's perfect for answering those "this is how I did it before, now how can I do the same thing in PubMed?" questions. The chart is in pdf format and may require you to install a plug-in to read it, if you don't already have the capability to view pdf documents in your Web browser. The chart was developed by Nancy Ralston and Molly Youngkin at the National Network of Libraries of Medicine, Midcontinental Region, at the University of Nebraska Medical Center.

For other helpful information about PubMed and IGM, please check out the National Network of Libraries of Medicine (NN/LM) Web site: http://nnlm.gov/. This site contains links to information on using the NLM Web-based search engines (including the above mentioned chart) from the NN/LM and other institutions.

PubMed and Internet Grateful Med Training Workbooks Available

PubMed and Internet Grateful Med training workbooks are now available for downloading from the National Library of Medicine's (NLM) Web site.

The workbooks, used in the two NLM/National Online Training Center PubMed/IGM classes (2-day Introduction class and the 1-day Transition class), are available in three formats: PDF, WordPerfect, and PostScript.

Look for an HTML version in the future. These workbooks are not copyrighted. Feel free to use any part of the workbooks -- you may customize part of the workbook for training programs, demos, or workshops you conduct. Or you may use the workbooks as a self-training guide if you can't get to a class or your scheduled class is several months away. The workbooks are found at: http://www.nlm.nih.gov/pubs/web_based.html.

Also, look at the revised and updated online Help in PubMed. The online Help can also serve as an excellent training tool.

National Library of Medicine Data Distribution Program

The National Library of Medicine (NLM) is announcing the release of its revised "License Agreement to Lease NLM Databases." This license, dated March 13, 1998, supersedes the previous license last revised April 1, 1994. Existing licensees will not be asked to sign the new license. However, please note that the terms of the new license are binding upon publication in the Web-based NLM Technical Bulletin, as per the 1994 license.

The following summarizes the changes in the revised license:

1. Section C.5 accounts for the possibility that NLM may use a contractor for distribution of leased data in the future and that the data may be distributed electronically.
2. Section D.1.c reflects the fact that a code is no longer required for licensees to access NLM's publicly available system for record verification. PubMed and Internet Grateful Med, our two free Web-based retrieval systems, do not require a code.
3. References to TOXLIT and CHEMLINE have been deleted from Sections E and G. NLM no longer provides access to these files on our retrieval systems nor do we lease them.
4. ChemID is referenced in Section E as a database for which downloading is not permissible without approval from two of the suppliers.
5. The wording of the notice in Section E.4 which licensees are required to issue regarding downloading and subsequent re-use of NLM-supplied data has been revised. Sections E and F now refer to the NLM statement on Copyright of Abstracts and Downloading Small Amounts of MEDLARS Data for Redistribution for additional information regarding these topics.
6. Section G.2 has been deleted. This section addressed the foreign surcharge in effect prior to October 1, 1997. Because NLM no longer requires licensees to pay a surcharge for usage of licensees' products and services outside the U.S., this section (and all references to it) has been removed from the license. Section G has been renumbered.
7. Sections H and K acknowledge the fact that NLM may offer a media other than tape to distribute the leased data.
8. Section M now states that the NLM Technical Bulletin (in which amendments to the License are announced) is a Web-based publication available at http://www.nlm.nih.gov/pubs/techbull/tb.html.

Currently, there are 58 NLM licensees, 43 of whom lease MEDLINE. Formally recognized International MEDLARS Centers, commercial enterprises, and academic institutions are among our licensees. The licensees make NLM data available within their own organizations and also to the public via online and Web-based systems, and CD-ROM products. Under certain circumstances it is permissible to download NLM data for redistribution outside of the formal licensing program. This situation is covered in our statement on Copyright of Abstracts and Downloading Small Amounts of MEDLARS Data for Redistribution. Information about leasing databases and downloading for redistribution beyond personal use is available from the NLM Web site at http://www.nlm.nih.gov/databases/leased.html. Please note that in this context downloading for redistribution pertains to licensees, not to the work a librarian or information professional does for a client's personal use.

OLDMEDLINE Database Moves Back in Time

OLDMEDLINE was made available in December 1996, with over 300,000 citations published in the 1964 and 1965 Cumulated Index Medicus (CIM) (see NLM Technical Bulletin, 1996 Nov-Dec; (293):1,4-6). In completion of the next phase of NLM's goal to provide online access to citations published in Index Medicus before 1966, over 250,000 citations published in the 1962 and 1963 CIM will be added to OLDMED in Summer 1998.

Differences
The 1964 and 1965 CIM data were converted from the original data tapes largely "as is," meaning with minimal data cleanup and validation. Yet NLM was able to provide some data validation because the 1964 and 1965 data included Journal Title Codes (JC), which were used to link to SERLINE to provide current Title Abbreviation (TA), ISSN (IS), and Country (CY) data in matching citations in OLDMED. The 1962 and 1963 citations have been keyed from the printed indexes that did not include JC information. Title Abbreviations (TA) in 1962 and 1963 citations were not matched against current SERLINE information, and 1962-1963 citations do not contain any ISSN or CY data either.

Date of Publication (DP)

The original DP format in OLDMEDLINE has been reformatted to display and search in the same way as DP in MEDLINE and MEDLINE Backfiles, e.g.,

DP -1962 May 14.

Year (YR) is directly searchable in either 2-or 4-digit format, e.g.,

(YR) 63

(YR) 1963

MeSH Headings, Subheadings and Keywords
As in 1964 and 1965 citations, the original MeSH Headings (MH) assigned to the 1962 and 1963 CIM citations are contained in the Keywords (KW) field. This is because these original Headings have not been maintained for over 30 years, and many are not current in 1998 MeSH. NLM has begun the task to map the original MeSH to current MeSH, and to add current MeSH Headings to OLDMED in the future.

Note that citations indexed for the 1963-1965 CIM were assigned MeSH Headings (MH) only, and did not include Subheadings (SH). Citations indexed for the 1962 CIM were indexed using Subheadings. These MH/SH combinations are contained in the Keywords (KW) field, but are not directly searchable using the MH/SH combinations. Only the MeSH Heading (MH) portion of the MH/SH combination may be searched directly, e.g.

Heart/abnormalities may be searched directly as heart (KW)

Searchers may prefer to truncate the KW search term, e.g.

Heart: (KW)

or

may use CONTAINS, e.g.

HEART: (KW) contains abnormalities (KW)

Remember that not all Subheading values used in 1962 citations are Subheadings in 1998 MeSH.

As was announced when OLDMED first became available, these older data have been made available "as is." It is unlikely that NLM will have the resources to undertake any significant data error correction effort in the near future. Any errors reported by users will be kept on file, although the corrections cannot be made to the database now.

The Entry Month in OLDMED identifies the CIM in which the citation was printed:

EM -196512 = 1965 CIM

EM -196412 = 1964 CIM

EM -196312 = 1963 CIM

EM -196212 = 1962 CIM

Future Enhancements
Work has already begun to key the approximately 225,000 citations from the 1960 and 1961 CIM. NLM expects to add these citations to OLDMED in the fall of 1998. The OLDMEDLINE file is currently available for searching on Internet Grateful Med; the OLDMED citations are expected to be integrated in PubMed in the fall. Watch for the announcement for this.

TOXLINE Rebuilt

TOXLINE and TOXLINE65 have been rebuilt in order to provide 1998 MeSH indexing on the records in the TOXBIB, DART and BIOSIS subfiles. During the rebuilding of TOXLINE, the TSCATS subfile was also replaced. The first update following this rebuilding was in May 1998, and will include data from the CRISP subfile for 1997. The FEDRIP and RISKLINE subfiles are expected to be added to TOXLINE sometime in the summer. The May update included data intended for TOXLINE updates in March and April as well as the May data. TOXLINE now contains 1,792,910 records. TOXLINE65, a closed database now contains 719,740 records.

The subfile counts are shown below along with the total count for the rebuilt files in April 1998.

TOXLINE Rebuilt File

TOXBIB          776,460

ANEUPL            1,987

BIOSIS          458,159

CIS              16,902

CRISP            17,958

DART             29,316

EMIC             34,038

EPIDEM            9,082

ETIC             21,444

HEEP             49,778

HMTC              4,018

IPA             152,168

NIOSH            88,563

NTIS            101,683

PESTAB            1,536

PPBIB               140

TSCATS           29,678





TOTAL         1,792,910

TOXLINE65 Rebuilt File

TOXBIB          407,857

ANEUPL            1,606

BIOSIS               41

CIS                  46

EMIC             37,830

ETIC             28,145

HAPAB            10,856

HEEP            117,881

IPA              51,790

NIOSH            26,502

NTIS             12,321

PESTAB           22,317

PPBIB             2,368



TOTAL           719,740

TOXNET Moved to New Computer Platform

The TOXNET system with its 20 files of factual and bibliographic information related to toxicology, hazardous chemicals, and the environment, began life in 1985 on a minicomputer, eventually moved to a group of networked microprocessors, and has now been ported to its newest platform. On June 1, 1998, TOXNET was tranferred to a UNIX environment, using a SUN Enterprise 3000 as the "live" server and a SUN Ultra II Station as the "development" server. UNIX is generally considered to have a relatively open platform with a high degree of data connectivity. TOXNET will continue to utilize the M (formerly MUMPS) operating system/programming language.

This change to a UNIX-based system will be transparent to users. An important benefit is expected to be more efficient search capabilities, translating into improved response time. The new platform will also allow NLM to take advantage of utilities that facilitate Web-based development, such as the TOXNET Web Simple Interface currently being tested, and scheduled for public release later in the year.

There will be no change in the procedure for accessing TOXNET via modem using the FTS2000 MEDLARS number (1-800-525-0216), nor will there be any change in telneting to NLM/MEDLARS at medlars.nlm.nih.gov and from there to TOXNET.

Telneting to TOXNET, however, at toxnet.nlm.nih.gov, via a direct connection or through the SIS Web Site at sis.nlm.nih.gov, will involve a slight change in procedure. After TELNETing to the TOXNET address, a new "login:" prompt will appear. At this point, you should enter the word search. The standard TOXNET welcome message will display and you will be prompted for your USERID/PASSWORD, as usual. See below:

TELNETing to TOXNET Using the toxnet.nlm.nih.gov Address:

  Welcome to the TOXNET Search system.

  Enter search at login prompt.



  login: search          

  Last login: Mon May 4 08:50:32 from 206.6.69.134

  Sun Microsystems Inc.   SunOS 5.6  Generic August 1997



       WELCOME TO THE NATIONAL LIBRARY OF MEDICINE'S

            TOXICOLOGY DATA NETWORK (TOXNET)



       PLEASE ENTER USERID/PASSWORD

       @@@@@@@@@@@@@@@@@@@@@@@@@@@

Also, note that the local access number for Washington, DC area users, 301-480-4360, has been discontinued.

Unused Codes Deactivated

On October 1, 1997, billed MEDLARS User ID codes issued before October 1994 and not used for the past three years were deactivated. A second purging of unused codes was done in April. This second group of purged codes were originally distributed at outreach classes, but NLM never received billing and/or address information for them. Most of these codes have been held for a long time without ever being used. If you have problems with a code not working and you are unable to access the NLM databases you need via the free search engines available on the Web, please contact NLM at custserv@nlm.nih.gov or call 1-888-346-3656 for assistance with your code question. To register online and receive a new code immediately, go to https://access.nlm.nih.gov [This link was removed because it is no longer valid.]; you must supply a credit card number to use the online registration system. The only reason to go to this address for a code is to search ELHILL databases NOT yet available on the Web. Users who need codes for Loansome Doc should go to http://tendon.nlm.nih.gov/ld/loansome.html. [This link was removed because it is no longer valid.]

Institutional Student Codes to be Discontinued on 10/1/98

NLM will deactivate all previously distributed institutional student codes on October 1, 1998. As noted in the NLM Technical Bulletin 1997 Sep-Oct;(298):2, the Library stopped issuing new institutional student accounts effective October 1, 1997. The Library is encouraging instructors to teach PubMed and Internet Grateful Med.

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