Dear All,
The text of the latest Technical Bulletin from the US National Library of
Medicine is given below.
Happy New Year everyone, and best wishes.
- Rupert Lee
Research Service
The British Library
National Library of Medicine
Technical Bulletin 335 - November - December 2003
Four new features and two new collections in latest NLM Gateway release
A new version of NLM Gateway was released in early November and introduced
four new features:-
* Display of the Limits for the current search
* Author name truncation
* Display of direct links for PubMed Central articles on Document
Ordering page
* Spell check for user input
Display of the Limits for the current search
Whereas in the past users could not see which Limits were in effect while
they were entering search terms into the NLM Gateway search query box, a
Limits checkbox as well as a list of Limits currently in use are now
displayed directly beneath the query box.
Author name truncation
The user may enter only the last name or the last name and the first initial
if the middle initial is not known. The Gateway will truncate an author (or
investigator) search for Journal Citations, Meeting Abstracts and HSRProj
(Other collections). Books/Serials/AVs does not support author searching.
There is no author or investigator field in the MEDLINEplus collections,
Clinical Trials.gov or DIRLINE.
Display of direct links for PubMed Central articles on Document Ordering
page
When the user selects items and uses the Order Documents function(either on
the Results Display of in the Locker), the Document Ordering page containing
selected items is displayed. Articles that are free in PubMed Central are
flagged with a link to the article and do not need to be ordered.
Spell check for user input
The Gateway processes search terms through a spell check function. If a
possible spelling error is found, Gateway displays a notice at the top of
the Results Summary page. Clicking on the Details button after the notice
reports the term(s) entered incorrectly and offers suggested corrections.
In addition to the new features, access to two new collections, MEDLINEplus
Health Tutorials and MEDLINEplus Current Health News is now available in the
Consumer Health category.
HIV and Infection Meeting Abstract added to NLM Gateway
During October almost 1700 new records were added to the Meeting Abstracts
collection from the National HIV Prevention Conference and the 10th
Conference on Retroviruses and Opportunistic Infections.
To search for abstracts from a particular professional meeting, enter the
title abbreviation of the professional meeting followed by the field
qualifier. To further limit your retrieval, you may choose to limit to a
specific year or range of years.
For more information on searching for meeting abstracts go to
http://gateway.nlm.nih.gov/gw/Cmd?FAQ.x#Meeting
<http://gateway.nlm.nih.gov/gw/Cmd?FAQ.x>.
New features added to MedlinePlus and MedlinePlus en Espanol
MedlinePlus has added several new features as follows:-
* Easy to read pages in both English and Spanish bringing together the
popular Interactive Health Tutorials and other easy to read materials by
topic.
* The Organisations page, available from the "Other Resources" tab,
now includes all organizations with pages linked in MedlinePlus. The
alphabetical pages include printer-friendly and e-mail links.
* Sign up for weekly lists of news and links on selected topic.
On MedlinePlus en Espanol
* Information on hundreds of prescription and over-the-counter
medications is coming to MedlinePlus en Espanol.
* Spanish-speaking users can now subscribe to a daily news feed of
health and wellness articles. Subscription information can be found at
http://www.nlm.nih.gov/medlineplus/spanish/listserv.html
Linking up with the Bookshelf
There are now over thirty books on the Bookshelf and many more in the
pipeline. Books such as the NCBI Handbook provides a guide to the resources
available at NCBI, which are continually being updated.
Alongside the rapid expansion of content, there have also been many
technical developments. One such development is the links between the
Bookshelf and PubMed and PubMed Central. This enables the reader to jump
effortless between books, abstracts and full text journal articles.
Citations in books that have a PubMed or PubMed Central record are linked up
either as a hyperlink in the reference list or as a direct link from the
citation to the text.
More information on the links between Bookshelf and PubMed is available in
the Bookshelf overview.
2004 Index Medicus prices now available
2004 Index Medicus prices have recently been announced - details and
ordering procedures can be obtained through the Government Printing Office
at http://www.nlm.nih.gov/pubs/pubcat.html#ordering
More organisms added to LocusLink
Xenopus laevis (African clawed frog) and Strongylocentrotus purpuratus (sea
urchin) have been added to the list of LocusLink organisms, bringing the
total to ten.
"Upload holdings" feature added to LinkOut
A new LinkOut feature allows any library, even those that are not NLM
SERHOLD participants, to display its print holdings information in LinkOut.
Libraries that currently link to their print holdings by registering their
SERHOLD information with LinkOut do not need to make any changes.
With Upload Holdings, libraries can connect PubMed users with their print
holdings information. To participate libraries need to
* Register for LinkOut
* Prepare a text file of their holdings
* Upload the text file via the LinkOut Library Submission Utility
Libraries interested in this new feature can find more information at
http://www.ncbi.nlm.nih.gov/entrez/linkout/doc/liblinkout.html#UploadHolding
s <http://www.ncbi.nlm.nih.gov/entrez/linkout/doc/liblinkout.html> or the
LinkOut home page at <http://www.ncbi.nlm.nih.gov/entrez/linkout/>
NLM SERHOLD libraries can continue to use the Link-Out-SERHOLD interface
(http://www.ncbi.nlm.nih.gov/entrez/linkout/doc/liblinkout.html#LinkOutSERHO
LD <http://www.ncbi.nlm.nih.gov/entrez/linkout/doc/liblinkout.html>) to
display their SERHOLD holdings in LinkOut.
For more information go to [log in to unmask] <mail
to:[log in to unmask]>.
Case report [mh] replaced by Case reports [pt]
Beginning with 2004 data, MEDLINE citations indexed to the MeSH heading
"Case Report" are now indexed to the Publication type "Case reports". Over
one million records will be changed. Entry terms will remain the same.
Unqualified PubMed queries for case report or case reports will continue to
retrieve the same records.
NB: Stored searches eg in the Cubby that include case report [mh] should be
updated to case reports [pt] to reflect the change.
Status tags on PubMed citations
Set out below are the possible status tags found on PubMed citations along
with how to search for the respective subset beginning with the availability
of 2004 data.
Search tag How to search
[PubMed - as supplied by the publisher] Publisher [sb]
[PubMed - in process] In process [sb]
[PubMed - indexed for MEDLINE] Medline [sb]
[PubMed] Pubmednotmedline [sb]
[PubMed - OLDMEDLINE for pre 1966] Oldmedline [sb]
For an explanation of the status tags, see Citation Status Subsets under
Subsets in PubMed's Help
Truncation in PubMed increases to 600 variations
PubMed can now retrieve truncated words (eg mimic) using up to 600
variations of a root word.
NB: Truncation turns off PubMed's automatic term mapping feature. For more
information about using truncation look at PubMed's Help at
http://www.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html#Truncation
<http://www.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html>.
Hazardous Substances Data Bank Chemicals available via LinkOut
PubMed users now have access to information for over 3000 Hazardous
Substances Data Bank (HSDB) chemical substances. Links to these substances
were added to LinkOut in September 2003.
How to use LinkOut to retrieve HSDB information:
* Click on the word "Links" to the right of each citation.
* Then choose LinkOut from the menu that appears.
* Look for the heading, MOLECULAR BIOLOGY DATABASES.
* HSDB links, if present, will appear under the TOXNET heading.
To read more about the Hazardous Substances Data Bank see the HSDB fact
sheet at <http://www.nlm.nih.gov/pubs/factsheets/hsdbfs.html>.
What's new for 2004 MeSH
The following is an overview of the additions and changes in 2004 Medical
Subject Headings (MeSH)
Overview of vocabulary
* 666 descriptors were added representing topics with no directly
corresponding descriptors in 2003 MeSH.
* 109 descriptors were replaced with more up-to-date terminology.
* 20 descriptors were deleted
* 484 see references (entry terms) were added.
Case reports
For 2004 this MeSH heading has been deleted and replaced by a Publication
type that characterizes the nature of the publication rather than what it is
about.
New definition for Toxicity subheading
The definition for the subheading/Toxicity has been revised to allow the use
for both experimental and environmental exposure.
The /toxicity subheading definition has been adjusted and is now used with
drugs and chemicals for experimental human and animal studies of their ill
effects. It includes studies to determine the margin of safety or the
reactions accompanying administration at various dose levels. It is used
also for exposure to environmental agents. Poisoning should be considered
for life-threatening exposure to environmental agents.
Expansion of Trees
The MeSH trees were expanded from nine to eleven levels to allow a more
accurate reflection of the hierarchy in elaborated and complex areas.
Organisms-Category B:
Animals: the expansion of the MeSH tree structure has allowed for a
long-awaited revision concerning the heading ANIMALS, the check tag ANIMAL,
and related headings. The old descriptor ANIMALS will be changed to ANIMAL
POPULATION GROUPS. It will retain all indented terms.
The check tag ANIMAL will be changed to a new descriptor ANIMALS. It will
function as both a descriptor and a check tag and will be treed at B1. The
singular word Animal will map to this new plural heading.
The former descriptors B1 INVERTEBRATES and B2 VERTEBRATES will be treed
under ANIMALS. The old B5 ALGAE AND FUNGI will be split into two
descriptors. ALGAE will be at the top of B2 and FUNGI will now be at the top
of B5.
2003 Tree 2004 Tree
B1 Invertebrates B1 Animals
B2 Vertebrates Animal Population Groups
B3 Bacteria Chordata
B4 Viruses Chordata, Nonvertebrate
B5 Algae and Fungi Vertebrates
B6 Plants Invertebrates
B7 Archaea B2 Algae
B3 Bacteria
B4 Viruses
B5 Fungi
B6 Plants
B7 Archaea
Bacteria B3
This subcategory was expanded with 310 new descriptors.
Substances - Category D
Amino Acids, Peptides and Proteins (D12): 246 new descriptors were added.
Proteins and Enzymes: A total of 65 new enzyme classes have been added to
the category of Enzymes. Several new major enzyme categories include: DNA
Repair Enzymes, Metalloexopeptidases, Oxidoreductases Acting on CH-CH Group
Donors, Proprotein Convertases, and Ubiquitin-Protein Ligase Complexes.
Electron Transport Chain Complex Proteins and Photosynthetic Reaction Center
Complex Proteins were added as new descriptors. These two broad categories
bring together the protein components that are part of biological
respiration and photosynthesis. There are also several new descriptor
classes under each heading which represent specific components of these
complexes.
Receptors, G-Protein-Coupled was added as new class to the Cell Surface
Receptors. There are over 100 descriptors now re-treed in this category. In
addition several new specific G-protein-coupled receptor classes have been
added. Receptors, Proteinase-Activated has been added for another class of
cell surface receptors that are activated by proteolytic action.
Angiogenic Proteins: A new descriptor class has been added for proteins that
regulate the proliferation of new blood vessels. Several existing and new
descriptor classes are now treed under this heading.
Complex Mixtures (D20) is a new subtree. It contains descriptors for
heterogeneous materials such as Manure, Soil, and Venoms.
Chemical Actions and Uses (D27) consists of the MeSH descriptors used for
Pharmacological Activity (PA). It has been re-grouped into Pharmacologic
Actions (D27.505), which includes Molecular Mechanisms of Action
(D27.505.519), Physiological Effects of Drugs (D27.505.696), and Therapeutic
Uses (D27.505.954). The other groups are Specialty Uses of Chemicals
(D27.720) and Toxic Actions (D27.888).
The MeSH heading, Antibiotics, has a new preferred heading, Anti-Bacterial
Agents. Antibiotics remains an entry term. The heading was renamed because
the formal meaning of antibiotics is something produced by a living organism
that is used to kill other organisms. According to this formal meaning,
sulfa drugs, quinolones, and other agents commonly used in this way are not
antibiotics. Additionally, semi-synthetic antibiotics that alter what is
produced naturally do not fit this description. Anti-Bacterial Agents more
aptly describe these substances.
In the D27 subtree, descriptors which included chemical structure in the
name were removed. For example, Antibiotics, Aminoglycoside was deleted and
those citations maintained to Anti-Bacterial Agents (formerly Antibiotics)
and to Aminoglycosides. In addition, Noxae (formerly D5) and Specialty Uses
(formerly D26) have been moved to the Chemical Actions and Uses grouping.
The duplicated tree of Anti-Infective Agents (formerly D20) has been
deleted.
Other revised chemical groups include Xanthones and Flavonoids. Many of the
flavones required retreeing to the appropriate area in the restructured
flavonoids section.
Physiology-Category G:
Circulatory and Respiratory Physiology (G9) and Musculoskeletal Physiology
(G11.427) were restructured into two new categories: physiological phenomena
and physiological process, while maintaining the subgroupings of Blood
Physiology, Cardiovascular Physiology, Respiratory Physiology, and
Musculoskeletal Physiology. This was done by creating eight new headings to
make the subgroupings: Blood Physiologic Phenomena, Blood Physiologic
Processes, Cardiovascular Physiologic Phenomena, Cardiovascular Physiologic
Processes, Respiratory Physiologic Phenomena , Respiratory Physiologic
Processes, Musculoskeletal Physiologic Phenomena , and Musculoskeletal
Physiologic Processes.
Ethnic Groups and Geographic Origins-Categories I and M:
The MeSH descriptor Racial Stocks,and its four children (Australoid Race,
Caucasoid Race, Mongoloid Race, and Negroid Race) have been deleted from
MeSH in 2004 along with Blacks and Whites. Race and ethnicity have been used
as categories in biomedical research and clinical medicine. Recent genetic
research indicates that the degree of genetic heterogeneity within groups
and homogeneity across groups make race per se a less compelling predictor.
2004 MeSH Subtree
Persons M1
Population Groups M1.686
Continental Population Groups M1.686.508
African Continental Ancestry Group M1.686.508.100
African Americans M1.686.508.100.100
American Native Continental Ancestry Group M1.686.508.150
Indians, Central American M1.686.508.150.575
Indians, North American M1.686.508.150.600
Indians, South American M1.686.508.150.625
Inuits M1.686.508.150.675
Asian Continental Ancestry Group M1.686.508.200
Asian Americans M1.686.508.200.100
European Continental Ancestry Group M1.686.508.400
Oceanic Ancestry Group M1.686.508.600
Ethnic Groups M1.686.754
African Americans M1.686.754.100
Arabs M1.686.754.167
Gypsies M1.686.754.283
Hispanic Americans M1.686.754.441
Mexican Americans M1.686.754.441.500
Inuits M1.686.754.520
Jews M1.686.754.600
2003 MeSH Subtree
Persons M1
Ethnic Groups M1.194
Aborigines M1.194.025
Arabs M1.194.037
Asian Americans M1.194.050
Blacks M1.194.100
Eskimos M1.194.247
Gypsies M1.194.265
Hispanic Americans M1.194.285
Mexican Americans M1.194.285.500
Indians, Central American M1.194.370
Indians, North American M1.194.403
Indians, South American M1.194.486
Jews M1.194.582
Whites M1.194.980
PubMed
PubMed will use 2004 MeSH in its translation tables and MeSH Database as
well as in the citation data as soon as end-of-year activities are complete.
Additional Information
The following files:
* New Headings with Scope Notes [247KB]
* Replaced Headings [12KB]
* MN (tree number) Changes [534KB]
may be downloaded from Medical Subject Headings - Files Available to
Download <http://www.nlm.nih.gov/mesh/filelist.html>. Scroll down to the
last three links under the 2004 MeSH category on this page. Clicking on any
of these three links takes you to a Memorandum of Understanding. Scroll down
to the bottom and click the "I agree with these conditions" button. Next,
complete the MeSH Registration Form and click the Submit button at the
bottom of the form. Next, verify that your information has been correctly
entered and then click on the Proceed button. Scroll down to the last three
links under the 2004 MeSH category to download the three files.
For more information about 2004 MeSH, please see the MeSH home page at:
<http://www.nlm.nih.gov/mesh/meshhome.html>.
Heading mapped-to Maintenance: for Supplementary Concept Records names of
substance
The Medical Subject Headings (MeSH®) controlled vocabulary contains
Supplementary Concept Records (SCRs) in addition to Main Headings (also
called Descriptors) and Subheadings (also called Qualifiers). SCRs are
typically chemicals that indexers have seen in the biomedical literature
cited in MEDLINE. Such a substance is not a Main Heading, but is established
as an SCR in MeSH so that the preferred form of the substance name can be
controlled and added to MEDLINE citations as part of the regular indexing
process. Other information about the substance may also be listed in the SCR
record in the MeSH Browser such as a corresponding registry number (Chemical
Abstracts Service or Enzyme Commission Nomenclature number) and entry
vocabulary, consisting of synonyms and closely related names (e.g., trade
names and lab numbers) for the substance.
There are over 130,000 SCRs in MeSH. Unlike the Main Headings and
Subheadings that are changed on an annual basis, new SCRs are added and
existing ones edited on a daily basis. The results of this daily maintenance
in the MeSH authority files are passed along to the MEDLINE citations, so
that the updated information is available (Tuesday - Saturday) in the
MEDLINE citation in PubMed where the substance name is searched as [nm] and
the registry number as [rn]. Both entry vocabulary and related registry
numbers are also part of the PubMed translation tables for searching SCRs.
SCR Names of Substance and Registry Numbers were added to the online MEDLINE
citations beginning mid-year 1980.
Each SCR has an associated Main Heading(s), which is its Heading Mapped-to
(HM) in the MeSH Browser. (See Figure 1.) Every time an indexer chooses an
SCR as relevant to an article, the DCMS (Data Creation and Maintenance
System) also adds the SCR's Heading Mapped-to value(s) to the MEDLINE
citation as an MH, along with the asterisk designation if the indexer has
indicated that the SCR is the main point of the article.
What Has Changed:
As science progresses and the MeSH vocabulary is reviewed, these Heading
Mapped-to values may change. Until now, the NLM has not done maintenance to
the MEDLINE citations when the HM changes in the MeSH authority file. As a
result, the literature indexed in MEDLINE may not have a consistent MH
throughout time that corresponds to a particular SCR.
As part of the annual year-end processing cycle this year, NLM performed
maintenance to add the current HM value as an MH for every SCR Name of
Substance in a MEDLINE citation whenever the current value was absent. The
2003 MeSH data was used for this sweep against the entire MEDLINE file. Then
the 2004 MeSH data were examined for specific HM changes since the 2003
MeSH, and those additional changes were also added to the MEDLINE citations
as appropriate.
This HM maintenance is also now part of the SCR updating routine, so these
changes will be reflected in MEDLINE in PubMed throughout the year, not just
annually.
NLM chose to add the current HM value as an MH to the MEDLINE citations
rather than attempt to replace the old value with the current value for two
reasons:
1. It is impossible to tell if the HM value was placed in the
MEDLINE citation originally from the Heading Mapped-to routines, or if the
indexer independently chose that MH for another reason pertinent to that
article, and
2. the HM value may have changed more than once over time
and/or have more than one value at a time, making it difficult to know with
certainty which MH should be replaced.
One situation is of particular note in this new maintenance procedure: the
MH that is added to the MEDLINE citation is the exact string as stored in
the HM element of the MeSH Browser. When an asterisk is part of that string
(see Figure 1), the asterisk is added to the MEDLINE citation, even though
the SCR may not have been a main point of that particular article. The NLM
is investigating the significance and feasibility of altering that
procedure.
NLM expects that these additional, current MH access points will improve
search retrieval for those searchers choosing to use MeSH in their
strategies. Examples 1 and 2 demonstrate the maintenance activity and the
resulting changes in retrieval.
Figure 1 - cadmium acetate SCR record in 2004 MeSH Browser; Heading Mapped
to element
Name of Substance cadmium acetate
Record Type C
Registry Number 543-90-8
Related Number 22429-86-3 (trihydrate)
Related Number 5743-04-4 (dihydrate)
Entry Term cadmium acetate, trihydrate
Entry Term cadmium acetate, dihydrate
Heading Mapped to *Acetates
<http://www.nlm.nih.gov/cgi/mesh/2004/MB_cgi?term=Acetates>
Heading Mapped to *Cadmium
<http://www.nlm.nih.gov/cgi/mesh/2004/MB_cgi?term=Cadmium>
Source Boll Soc Ital Biol Sper 1979;55(4):361
Thesaurus ID Merck Index, 9th ed, #1601
Frequency 49
Note RN given refers to parent cpd
Date of Entry 19810206
Revision Date 20000803
Unique ID C028031
Example 1:
As seen in Figure 1, the SCR cadmium acetate has two Heading Mapped to
values: *Acetates and *Cadmium. In 2003 PubMed:
cadmium acetate [nm] has 49 postings
cadmium acetate [nm] NOT cadmium [mh:noexp] has 0 postings
cadmium acetate [nm] NOT acetates [mh:noexp] has 31 postings
The Heading Mapped-to maintenance added *Acetates as a MeSH Heading to the
31 citations. No action was taken for the *Cadmium value because all 49
citations with the SCR already had that MH present. Evidently at some time
in the past, this SCR had only the one HM value with *Acetates being added
as the second HM value later.
Effective with the 2004 maintained PubMed data, an MH search on either
Acetates or on Cadmium will include all 49 of these citations with cadmium
acetate as a name of substance.
Example 2:
The SCR paldimycin has two Heading Mapped to values in the 2004 MeSH
Browser: Acetylcysteine/analogs & derivatives and Disaccharides. (See Figure
2.)
Figure 2 - paldimycin SCR record in 2004 MeSH Browser; Heading Mapped to
element
Name of Substance paldimycin
Record Type C
Registry Number 102426-96-0
Entry Term U-70138F
Heading Mapped to Acetylcysteine/analogs & derivatives
<http://www.nlm.nih.gov/cgi/mesh/2004/MB_cgi?term=Acetylcysteine>
Heading Mapped to Disaccharides
<http://www.nlm.nih.gov/cgi/mesh/2004/MB_cgi?term=Disaccharides>
Previous Indexing * GLYCOPEPTIDES (87-92)
<http://www.nlm.nih.gov/cgi/mesh/2004/MB_cgi?term=GLYCOPEPTIDES>
Source Antimicrob Agents Chemother 1986;30(5):806
Frequency 12
Note used against Chlamydia infections; a complex of paldimycin A and
paldimycin B; see also paldimycin A and paldimycin B
Date of Entry 19870121
Revision Date 20010322
Unique ID C050461
In 2003 PubMed
paldimycin [nm] has 12 postings
paldimycin [nm] NOT acetylcysteine/aa [mh:noexp] has 12 postings
paldimycin [nm] NOT disaccharides [mh:noexp] has 12 postings
The Heading Mapped-to maintenance added both Acetylcysteine/analogs &
derivatives and Disaccharides to all 12 citations having paldimycin [nm]. In
the past this SCR was probably mapped to Glycopeptides as all 12 citations
have this MH present.
Effective with the 2004 PubMed maintained data, an MH search on either
Acetylcysteine or on Disaccharides will include all 12 of these citations
with paldimycin as a name of substance
Take a Coffee Break
Coffee Break is a collection of short stories and interactive tutorials
about recent biomedical discoveries. These snapshots of science are short
enough to be enjoyed over a cup of coffee but also give a detailed report on
a molecular topic.
Since October 2003, Coffee Break has been available on the Bookshelf
<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Books>. Coffee Break still
includes molecular insights, links to NCBI resources, and tutorials
<http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowSection&rid=cof
feebrk.box.301>, but it is now indexed and searchable. Another innovation is
the new tutorials that are animated using Macromedia Flash(tm). This enables
the reader to take an active part in using NCBI tools to sift through
molecular information. These tutorials can also be downloaded enabling
teachers to use them in the classroom.
The latest Coffee Break features an interactive tutorial
<http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowSection&rid=cof
feebrk.foreword.349> about the hemochromatosis gene, HFE. The reader starts
with a summary about the gene and its disease. To investigate the nature of
the gene, the student can take part in the Flash tutorial.
In the tutorial, NCBI tools are used to investigate a particular transcript
variant of the HFE gene. It is revealed that the transcript contains several
SNPs, or single nucleotide polymorphisms. To assess their importance, the
student can see whether an amino acid is changed as a result of the SNP,
what the nature of this change is, and where the altered amino acid appears
in a 3D simulation of the HFE protein.
Coffee Break shows, in an approachable way, the many resources available at
NCBI and how powerful they become when used in combination. You can read
more about Coffee Break at About Coffee Break
<http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowSection&rid=cof
feebrk>.
MEDLINE data changes - 2004
T
his time of year the NLM Technical Bulletin traditionally includes
information on changes made to MEDLINE during annual National Library of
Medicine (NLM) maintenance known as Year-End Processing. This article
attempts to collect in one place the notable data changes for 2004.
MeSH vocabulary updated for 2004
The MeSH Browser <http://www.nlm.nih.gov/mesh/MBrowser.html> currently
contains 2004 MeSH with a link to 2003 MeSH. Searchers should consult this
Browser to find descriptors of interest and to see these in relationship to
other descriptors. The Browser displays MeSH records, including the scope
notes, annotations, entry vocabulary, history notes, allowable qualifiers
(subheadings), etc. for MeSH headings along with subheading records and
Supplementary Concept Records (SCRs) for substances that are not MeSH
headings. It also provides links to relevant sections of the NLM Indexing
Manual.
It is expected that PubMed's MeSH database and translation tables will be
updated to reflect 2004 MeSH in early December 2003 when end-of-year
activities are complete and the newly maintained MEDLINE is available via
PubMed.
Updated MeSH in MEDLINE citations
MEDLINE citations with updated MeSH should be in PubMed in early December
2003.
New MeSH headings
This year 666 new MeSH Headings were added.
In general, NLM does not retrospectively re-index MEDLINE citations with new
MeSH Headings. Therefore, searching for a new MeSH Term qualified as [mh] or
[majr] effectively limits retrieval to citations indexed after the term was
introduced. An unqualified subject search in PubMed expands a search by
including both MeSH Term and Text Words, and may retrieve relevant citations
indexed before the introduction of a new MeSH Term.
For example, a new MeSH term, Malnutrition, has been introduced for 2004
MeSH. A PubMed query on November 26, 2003 for malnutrition unqualified
yields 129,776 citations, of which 128,769 have already been indexed; none
of these 128,769 citations will have the new MeSH heading added. Searchers
may wish to include headings previously used to index these new concepts in
addition to the text word retrieval that PubMed will automatically add to an
unqualified strategy. For Malnutrition, the previous indexing was Nutrition
Disorders.
Changes to MeSH headings
This year 109 MeSH Headings were replaced with more up-to-date terminology.
During year-end processing, NLM makes the changes in the MeSH headings on
the MEDLINE citations.
For example, this year the old MeSH Heading Progestational Hormones has been
changed to Progestins in 2004 MeSH. The MeSH term Progestational Hormones on
MEDLINE citations indexed from 1966-2003 will all be changed to Progestins.
The old version of the heading has been retained as an entry term to the new
heading, so no adjustments to searching are necessary, unless you want your
text word portion to use the more up-to-date vocabulary.
Another example is the deletion of the MeSH heading Anabolic Steroids from
2004 MeSH. All occurrences of that term in MEDLINE citations will be
replaced by the new MeSH heading, Anabolic Agents. In this case, the old
version of the heading has not been retained as an entry term to the new
heading, so adjustments to searching and stored searches are needed.
Beyond the replaced-by heading changes, year-end processing includes
additional adjustments to MEDLINE citations to reflect the 2004 MeSH
vocabulary and enhance retrieval. These follow-on adjustments are largely
the adding of more MeSH headings or supplementary concept record Names of
Substances (NM) to help refine retrieval. In some cases, the changes clarify
areas where a single concept existed before but it is now represented by 2
or more specific concepts.
Remember that the mapping of "old" headings and/or see references (entry
terms) can also change. For example, Blacks was a 2003 MeSH Heading. Blacks
has become a see reference in 2004 to the new heading African Continental
Ancestry Group. As a result, the search term Blacks will still retrieve
postings, but those hits are not necessarily the exact equivalent of what
was retrieved before. In 2004, the old concept of Blacks is now represented
by the preferred term of African Americans, which is treed under the African
Continental Ancestry Group. (See also Ethnic Groups and Geographic Origins
below.)
Here is a summary list of 2003 MeSH headings that were replaced by another
heading yet the 2003 string maps to yet another heading for 2004.
2003 Heading 2004 Replaced-by-Heading 2003 Heading is a See
Reference or a Redefined 2004 Heading
Animals Animal Population Groups Animals
Blacks African Americans African Ancestry Continental Group
Cytochrome a Cytochrome a Group Cytochromes a
Cytochrome b Cytochrome b Group Cytochromes b
Cytochrome c Cytochrome c Group Cyrochromes c
Mannosidosis alpha-Mannosidosis Mannosidase Deficiency Diseases
Mosses Bryopsida Bryophyta
Pneumocystis carinii Pneumocystis Pneumocystis carinii [redefined MH]
Tonometry Tonometry, Ocular Manometry
In addition to "old" MeSH headings becoming entry terms to a different MeSH
heading, see references can be moved to a different heading as well. For
example, Sphagnum was a see reference to Mosses in 2003, but moved to become
a see reference to Sphagnopsida for 2004.
These types of changes suggest searchers should routinely use the Details
button in PubMed to see how terms are mapped in the new year's vocabulary
and then check the MeSH Browser <http://www.nlm.nih.gov/mesh/MBrowser.html>
for clarification.
Other notable MeSH changes and related impact on searching
Animal to Animals
The 2003 MeSH Heading Animals will be changed to Animal Population Groups
and will retain a second-level position in the MeSH Category B Tree
hierarchy. The MeSH term Animal will be changed to a new heading Animals
with B1 as its tree number.
Age Group MeSH Heading Change
For 2004, one change was made in the Age Groups. Middle Aged replaces Middle
Age; the latter term remains an entry term and the tree structure has not
changed. The Ages pull-down menu in the PubMed Limits function remains the
same. There is no impact for searchers.
MeSH Heading to Publication Type Change: Case Report
The MeSH Heading Case Report will be removed from all MEDLINE citations and
will be replaced with the publication type Case Reports.
Broadened Definition for /toxicity
For 2004, the definition of the /toxicity subheading has been broadened to
include exposure to environmental agents. No changes were made to existing
MEDLINE citations.
Ethnic Groups and Geographic Origins
The MeSH term Racial Stocks and its four children (Australoid Race,
Caucasoid Race, Mongoloid Race, and Negroid Race) have been deleted from
MeSH in 2004. A new heading, Continental Population Groups, has been created
with new indentions that emphasize geography. Ethnic Groups is a sibling to
the new Continental Population Groups.
Indexers will now be indexing to the geographic origins. To accommodate this
change in policy, the following edits were made in MeSH headings on MEDLINE
citations:
2003 Heading 2004 Replaced-by-Heading
Aborigines Oceanic Ancestry Group
Australoid Race Oceanic Ancestry Group
Blacks African Americans
Caucasoid Race European Continental Ancestry Group
Eskimos Inuits
Mongoloid Race Asian Continental Ancestry Group
Negroid Race African Continental Ancestry Group
Racial Stocks Continental Population Groups
Whites European Continental Ancestry Group
Some additional edits were also made. For example, citations that were
indexed to Blacks that were also indexed to countries other than the United
States had the new MeSH heading African Continental Ancestry Group added as
well
Entry Combination Revisions
This year during year-end processing, NLM again replaced certain MeSH
heading/subheading combinations known as Entry Combinations, with the
appropriate precoordinated MeSH heading or other MeSH heading/subheading
combination in MEDLINE citations (e.g., the combination Lymphatic
Vessels/growth & development was changed to Lymphangiogenesis and the
combination Bone Marrow Cells/transplantation was changed to Bone Marrow
Transplantation). Searchers who get zero retrieval on a MeSH
heading/subheading combination may want to check the 2004 MeSH Browser for
that heading to see if that subheading is listed as an Entry Combination and
what the appropriate equivalent is for searching. Here is what the MeSH
Browser looks like for the Bone Marrow Cells example:
MeSH Heading Bone Marrow Cells
Entry Combination transplantation:Bone Marrow Transplantation
<http://www.nlm.nih.gov/cgi/mesh/2004/MB_cgi?term=Bone+Marrow+Transplantatio
n>
Heading Mapped-To (HM) Maintenance
This year NLM performed maintenance to add the current HM value as an MeSH
Heading for every SCR (Supplementary Concept Record) Name of Substance in a
MEDLINE citation, whenever the current value was absent.
EC/RN Numbers [RN] and Name of Substance [NM]
Changes in 2004 MeSH also cover Enzyme Commission (EC) Nomenclature and CAS
Registry Number data, including Substance Name [NM]. These affect not only
the MeSH chemical concepts in Category D, but the Supplementary Concept
Records as well. The corresponding changes were made to MEDLINE citations
during year-end processing.
Supplementary Concept Records (SCRs) Elevated to MeSH Headings
For general information on SCRs elevated to MeSH heading status, see the
article, Changes in the Treatment of Chemical Data in MEDLINE® Citations.
NLM Tech Bull. 2001 Nov-Dec;(323):e7.
</pubs/techbull/nd01/nd01_mesh_chemical.html>
Pharmacological Action (PA) for Supplementary Concept Records:
As a reminder, a new policy, effective August 2002, calls for adding PAs to
new or existing SCRs only if the following three criteria are met:
* there must be more than 20 citations discussing the Pharmacological
Action being exhibited by that drug;
* there must be substantial evidence that the Pharmacological Action
is in effect in humans (i.e., the drug is used clinically); and
* a reasonable proportion of the literature (10%) on that drug
accounts for those effects
Expansion of Trees
MeSH Trees were expanded from 9 to 11 levels this year. There is one
11-level heading:
Sex Chromatin A11.284.430.106.279.345.190.160.180.383.800
An example of a 10-level heading is:
Trypanosoma lewisi B01.500.841.750.443.950.450.868.887.410
Maintenance to Citations Created by the Kennedy Institute of Ethics
Other maintenance is being done to citations created by the Kennedy
Institute of Ethics (KIE) to add the MeSH Headings Human or Animals where
appropriate. Prior to NLM's re-invention of its Data Creation and
Maintenance System (DCMS) in late 2000, it was not KIE practice to index
with these headings. However, now that KIE-created citations are part of
regular MEDLINE processing, KIE follows NLM indexing practice on the use of
these headings to improve retrieval for searches on bioethical topics.
Other changes to MEDLINE data
Deletion of the MEDLINE UI
NLM has completed the transition to using the PMID as the only unique
identifier for MEDLINE and OLDMEDLINE citations. The MEDLINE UI (Unique
Identifier) is no longer exported to PubMed or to licensees, nor is it
searchable or displayable in PubMed effective with the 2004 data reload. A
MEDLINE/PMID Matcher is available at
<http://eutils.ncbi.nlm.nih.gov/entrez/publisher/uidpmid.cgi/> to assist
users who need help in translating from the MEDLINE UI to the PMID.
Identification of Clinical Trials in MEDLINE
For the tenth year, NLM continued to work with the Cochrane Collaboration to
enhance the identification of clinical trials in MEDLINE. During 2003,
"Randomized Controlled Trial" or "Controlled Clinical Trial" Publication
Types, along with their parent Publication Type of Clinical Trial, were
added to over 1,900 MEDLINE citations identified by the Cochrane
Collaboration. The updated MEDLINE citations have been available in PubMed
since late October.
2-way Links for Published Erratum [PT]
Older citations with the publication type Published Erratum [PT] now have a
link back to the citation for the original paper, and that citation links
forward to the citation for the published erratum. Originally, NLM was
making the 2-way links only for errata published since the year 2000; now
over 900 citations with Published Erratum, regardless of the publication
date, have 2-way links. See the Abstract or Citation display for PMID
1952033
<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_u
ids=1952033&dopt=Abstract> as an example.
Remember that most published errata are themselves not indexable items;
rather, NLM annotates the original citation with the "Erratum in:"
information, but there is no citation to which to link. In those cases where
the published erratum had additional substantive information that also
warranted a citation, there are now 2-way links between the erratum notice
and the original paper's citation.
New Status Value: In Data Review
Starting after the new PubMed system comes up in early December, users
viewing the MEDLINE format display may see a new Status value. The new
value, "in data review," will indicate that this citation was released to
PubMed after issue level bibliographic data verification only (meaning that
the journal, date of publication, volume, and issue are all correct). The
citation remains "in data review" for verification of the citation level
elements, notably authors, article title, and abstract. Once the citation
level verification has been completed for every citation in an issue, those
citations are re-released to PubMed carrying a Status value of "in process."
Only publisher-supplied citations will go through this second release as an
in process level citation; citations created via keyboarding or scanning and
optical character recognition at NLM are quality-controlled for all data
elements before being sent to PubMed the first time. This change in
procedure for publisher-supplied citations is being done to shorten the time
before corrections appear in PubMed and are available to licensees. Before,
"in process" citations were released only once after undergoing issue level
data verification and corrections to other data elements were not made
public in PubMed until the citations were completely processed with MeSH
headings assigned. Now these citations will be released a second time after
citation level verification and in advance of full MeSH indexing being
completed.
The summary display of PubMed will use the same PubMed label of [PubMed - in
process] for both the "in data review" and "in process" status values. The
MEDLINE display format shows the citation's actual status value. The value
"in data review" means that NLM has not completed its review of the citation
level data elements. NLM may also make further edits to citations with the
value "in process" as staff continue to review citations while they are
being indexed with MeSH.
Pharmacological action terms identified in MeSH database
The Entrez MeSH database (See link from PubMed's sidebar) now indicates
those terms that are identified by MeSH as Pharmacological action headings
(eg Anti-bacterial agents, Cholinergic agents, Heparin antagonists,
Alkylating agents). These terms are displayed in the database with
[Pharmacological Action] following the term. The corresponding record for
the MeSH heading is displayed first. Depending on the search term(s) used
these records may not be sequential in the display of the retrieval.
Clicking on the Pharmacological Action term displays the full format which
lists the chemicals (Headings and Substance Names) with that action noted by
MeSH.
Use this new MeSH database feature if you are interested in knowing which
chemicals are included in the searches using the [PA] tag eg heparin
antagonists [pa].
UMLS 2003 AC quarterly update
The Unified Medical Language System (UMLS) Metathesaurus was updated, has
recently released and is available for download from the Knowledge Source
Server <http://umlsks.nlm.nih.gov.>. CD-ROMs of the data will be sent to
UMLS licensees who have requested them. Other licensees may request CD-ROMs
by sending e-mail to [log in to unmask] <mail to: [log in to unmask]>.
The PDF version of the UMLS documentation will soon be available on the UMLS
Web site at: <http://www.nlm.nih.gov/research/umls>.
NLM anticipates releasing SNOMED CT® in the 2004AA UMLS Metathesaurus during
the first quarter of 2004. SNOMED CT will be released in the "Rich Data
Format" (MR+). This new format will support source transparency-the
capability to represent the complete information in new and updated
vocabularies. The classic Metathesaurus Relational (MR) format, in which the
UMLS was issued for many years, will continue to be available.
Full archives of BMLA/JMLA available via PubMed Central
The National Center for Biotechnology Information (NCBI) recently released
the full archives of the Bulletin of the Medical Library Association (BMLA)
on the PubMed Central <http://pubmedcentral.gov/> Web site. The BMLA
archives go from v.1 n.1, 1911 through v.89 n.4, 2001. Then the title is
available as Journal of the Medical Library Association (JMLA) from v.90 n.1
2002 -
The archives can be viewed directly at:
BMLA (v.1 1911 - v.89 n.4 2001)
<http://www.pubmedcentral.gov/tocrender.fcgi?action=archive&journal=72>;
JMLA (v.90 n.1 2002 - )
<http://pubmedcentral.gov/tocrender.fcgi?action=archive&journal=93>.
NLM is in the process of scanning the backfiles of all of the titles in
PubMed Central. With the exception of the BMLA, the plan is to release the
archives in increments by decade from most current to earliest. To read more
about the scanning project, see:
<http://www.pubmedcentral.gov/about/scanning.html>.
Two new books added to the NCBI Bookshelf
The National Center for Biotechnology Information (NCBI) has recently added
two books to the Bookshelf <
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Books>:
* Genomes. 2nd ed.
Brown, T. A.
Oxford, UK: BIOS Scientific Publishers, Ltd; 2002.
* Human Molecular Genetics 2. 2nd ed.
Strachan, Tom and Read, Andrew P.
Oxford, UK: BIOS Scientific Publishers Ltd; 1999.
The books in Bookshelf may be searched directly from the Bookshelf site, via
links from the Links pull-down menu from relevant PubMed® citations, or
through the new Entrez <http://www.ncbi.nlm.nih.gov/Entrez/> Global query
feature.
American customer satifaction index evaluation of NLM web sites
Starting October 1, 2003, NLM began surveying five of its Web sites using
the American Customer Satisfaction Index (ACSI).
The sites being surveyed are the main Web site <http://www.nlm.nih.gov>,
MEDLINEplus <http://medlineplus.gov>, MEDLINEplus en español
<http://www.nlm.nih.gov/medlineplus/spanish/medlineplus.html>, TOXNET
<http://toxnet.nlm.nih.gov> and the AIDSinfo <http://aidsinfo.nih.gov/> Web
site.
The NLM survey will be active for 12 months from October 1, 2003 to
September 30, 2004. The sampling rate is low to minimize the number of times
users are asked to take the survey, and the survey does not collect
information identifying any specific user.
Results from MEDLINEplus, MEDLINEplus en español, and the NLM main Web site
are already being tabulated.
If prompted, please take a moment to respond to our survey. Your opinion
will help us make our Web sites better.
Newly maintained MEDLINE now available in PubMed
As of December 3, PubMed's MEDLINE citations, translation tables, and the
MeSH® database have been updated to reflect 2004 MeSH. Now that end-of-year
activities are complete, MEDLINE via PubMed
<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi> may be searched using 2004
MeSH vocabulary.
Also on December 3, NLM resumed the daily (Tuesday-Saturday) updates to
PubMed of MeSH-indexed citations (including the backlog of citations indexed
since November 13 with 2004 MeSH but not yet added to PubMed).
Enhanced functionality plus access to more data in the NLM Gateway's latest
release
A new version of the NLM Gateway was released in mid-December. This release
introduces three new features:-
* Linkout for Journal Citations
* Direct links to full text in PubMed Central on Brief and Expanded
displays on Journal Citations
* British and American spellings - Gateway searches will retrieve the
same citations regardless of whether the English or American spelling is
used.
Access to more data
New to this release of Gateway will be access to two additional
collections:- OMIM (Online Mendelian Inheritance in Man) and HSDB (Hazardous
Substances Date Bank). OMIM is a catalogue of human genes and genetic
disorders that contains textual information and references. HSDB is a
comprehensive, scientifically reviewed, factual database containing records
for over 4500 toxic or potentially toxic chemicals.
Cataloguing news - 2004
LocatorPlus is now using 2004 MeSH
From mid-December the National Library of Medicine adopted the 2004 MeSH
vocabulary for cataloguing and for records being created by collaborating
data producers.
MeSH terms in LocatorPlus were changed to reflect 2004 MeSH, with the
exception of terms on record as having been created by Johns Hopkins
University, Population Information Program.
In general, the cataloguing section applied the changes described, as they
were applied, for citations in MEDLINE. In some instances different
approaches were taken due to the character of the literature and number of
records requiring maintenance in LocatorPlus. Cataloguing applied changes
in the following areas:-
* Publication Types
* Age Groups
* Ethnic Groups and Geographic Origins
* Animal, Animals and Animal Population Groups
* Substances (Category D)
Clarification of the use of the term Adolescent on NLM cataloguing records
This clarification is a reminder that all uses of the subject heading
Adolescence were changed to the term Adolescent in conjunction with last
year's MeSH year-end processing in December 2003. NLM reiterates this
notice to confirm that the age-related terms that are appended as part of
the subject heading string in NLM distributed records always reflect current
MeSH vocabulary.
DOCLINE version 2.0 directs users to full text articles available at
producer sites
This latest version of DOCLINE features links from DOCLINE and Loansome Doc
via PubMed to free full text articles whenever the article requested is
available either in PubMed Central or at the producer site. The highlights
of more than fifty enhancements include:-
* An overhaul to the interface for maintaining a library's institution
record
* Improved searching of institution records
* Ability to request colour copies
* An alert message when users request articles that are free at the
producer's web site
About Open Access publishing in PubMed Central
PubMed Central recently added information about Open Access Publishing at
<http://www.pubmedcentral.gov/about/openaccess.html> This page includes the
definition of Open Access Publishing from the Bethesda statement on the
subject. This page also includes other relevant open access publishing
links including information on the PMC agreement for acceptance of
individual open access articles from journals that do not participate in PMC
on a routine basis.
2004 MeSH information added to MeSH Home Page
The MeSH home page has been updated with the 2004 Introduction to MeSH
including
* New 2004 MeSH Subject Headings, Alphabetic list
* Changed descriptors - 2004
* Deleted descriptors -2004
* New 2004 MeSH headings by Tree subcategory
Ordering information for "Black & White" MeSH is also available. This
publication includes an alphabetic list of MeSH headings and the Tree
structures and is included as part of the January issue of a subscription to
Index Medicus, but may also be ordered individually.
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