Apologies for crossposting
Contents for July/August Bulletin at
http://www.nlm.nih.gov/pubs/techbull/ja02/ja02_issue_cover.html listed
below.
I was particularly interested in the updated training manuals
(http://www.nlm.nih.gov/pubs/web_based.html), and the PubMed usage stats
graph (http://www.ncbi.nlm.nih.gov/About/tools/restable_stat_pubmed.html),
but there is loads of info on all sorts of things in this one...
Fiona
Fiona McLean, British Library
[log in to unmask]
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National Library of Medicine
Technical Bulletin 327 - July -August 2002
New table G classification numbers added
The following are additions to Table G of the NLM Classification , 5th
edition 1994, rev 1999, since the publication of this tool in September
2000:-
* Section IV. Americas, add - DA9--Aruba
* Section VIII. Middle East and Asia, add - JU5--United Arab
Emirates
* Section X. Islands of the Pacific and Indian Oceans, add -
LE1-- East Timor
New Clinical Alert issued
The National Heart, Lung and Blood Institute of the National Institutes of
Health has stopped a major clinical trial on the risks and benefits of
combined estrogen and progestin in healthy menopausal women due to an
increased risk of invasive breast cancer. Although there were noteworthy
benefits of estrogen plus progestin, including fewer cases of hip fractures
and colon cancer, on the balance the harm was greater than the benefit. The
study, which was scheduled to run until 2005, was stopped after an average
follow-up of 5.2years.
NCBI announces new Entrez Programming Utilities
The National Center for Biotechnology Information (NCBI) has developed a new
set of Entrez Utilities. The new Entrez Utilities [EU] consolidate the
original utilities currently in use. A link to these new utilities can be
found on the PubMed sidebar, labelled "E-Utilities".
Utility users should begin using the new EU now and revise any existing
URL's that were created using the original utilities (eg PmFetch,
PmNeighbor). URL's created using the original utilities will continue to
work until December 2002 by which time your transition to the new utilities
will be complete. If you have not done so already, please subscribe to the
EU Announcement Mailing List to keep up to date with developments. To
subscribe send an email message with "subscribe" in the subject area to :-
[log in to unmask]
Reminder: Linking to PubMed
Manually constructed URL's created for the old PubMed system (ie
http://www.ncbi.nih.gov/htbin-post/Entrez/query?db=m...) will not work after
December 2002 . All old URL's must be changed to follow the specifications
outlined in the Linking to PubMed and other Entrez databases documentation.
Educational Clearinghouse Database: A service of the National Training
Center and Clearinghouse
The NTCC Home page is accessible at http://www.nnlm.gov/mar/online
There are two ways to get to the clearinghouse database from the NTCC Home
page. For those familiar with Web searching and NLM materials, go directly
to the clearinghouse database by clicking on the Educational Clearinghouse
Database link. For those people who are not familiar with NLM materials
click on the Documentation link on the NTCC Home page. This page explains
the purpose and objectives of the clearinghouse database and provides
definitions concerning the type of information found in the database.
Using the Clearinghouse database
It is possible to browse or search to find educational material. Browse by
Content, Format, Audience or Title. Searching can be done by Content,
Format, Audience and/or Keywords. Content, Format and Audience search terms
are predefined and can be selected from the pull-down menus.
Search results can be provided either as a brief description or full
database record.
UMLS moves to quarterly releases
New releases to the UMLS (Unified Medical Language System) have been issued
annually since 1990. Beginning in 2002 the UMLS will be released quarterly.
Following releases in January and May there will be two more releases this
year - one in August and the other in October. PubMed, NLM Gateway and
Clinical Trials.gov all utilize the UMLS to enhance searching and all are
updated following each UMLS release.
PubMed Search Statistics
In response to user requests for PubMed statistics the National Center for
Biotechnology Information (NCBI) has released a PubMed Searches graph. This
new graph is available from the Overview on the PubMed sidebar as well as
from the Databases and Tools section of the About NCBI web page. The new
graph provides statistical information for PubMed searches from January 1997
to the present.
New Search Engine on NLM Web Site
The National Library of Medicine has released a new search engine on its web
site. This new search engine is a concept-based information retrieval
system which not only searches keywords, but concepts and topics are also
automatically extracted from data thus allowing related concepts to be
retrieved at the same time.
Search results are listed and navigated via a series of folders - National
Library of Medicine, Health Information - MEDLINEplus, Profiles in Science,
and Exhibits. This structure allows users to choose a concept and to move
conveniently among folders. The library plans to expand implementation of
the new search engine site by site, starting with the soon-to-be-released
Spanish MEDLINEplus and MEDLINEplus.
To find out more see the Search FAQ at http://www.nlm.nih.gov/searchfaq.html
UI List - New display format in PubMed
PubMed's Display pull-down menu has a new option, UI List. This format
displays the same information as the Brief format, ie Authors, the first
30characters of the Title and the PMID (PubMed Unique Identifier). However,
if you use the Save or Text function with UI List you will get a list
containing only PMIDs.
August 2002 PubMed, NLM Gateway and Clinical Trials.gov training manuals
available
The August 2002 editions of the training manuals are now available for
downloading from the NLM web site: PubMed, NLM Gateway, Clinical Trials.gov
and TOXNET. The workbooks were updated to reflect the changes to all, bar
TOXNET, since October 2001. The manuals are available for downloading in
Portable Document Format (PDF) and Microsoft (MS) Word formats. They are
broken down into sections so you can choose areas of interest. These
materials correspond to the NLM's National Training Center and Clearinghouse
training courses described at http://nnlm.gov/mar/online/description.html
Migration of Monographic Citations to Locatorplus: Merge Project
At the end of June, 30,933 monographic and audiovisual records previously in
the ELHILL databases HISTLINE, SPACELINE and/or BIOETHICSLINE were matched
with their source records, now in Locatorplus. These Locatorplus records
were then marked to show that they may be of interest to users searching for
materials in the specialized subject areas of history of medicine, space
life sciences or bioethics.
In the case of records previously in BIOETHICSLINE, unique keywords assigned
by the Kennedy Institute of Ethics (KIE), Medical Subject Headings (MeSH),
and related data from each BIOETHICSLINE record were also merged into the
matching Locatorplus record.
An additional 21,921 Locatorplus records were updated with the two marker
fields below to indicate that they had previously appeared in HISTLINE.
035 $a(DNLM)HISTLINE
998 $aHISREL $b19991201
An additional 6,544 Locatorplus records were updated with the two marker
fields shown below to indicate that they previously appeared in SPACELINE
035 $a(DNLM)NASA
998 $aNASREL $b19991201
An additional 2,656Locatorplus records were updated with the two marker
fields shown below to indicate that they previously appeared in
BIOETHICSLINE
035 $a(DNLM)KIE:#######
(where ####### represents the previously assigned Unique
Identifier (UI) used in BIOETHICSLINE)
998 $aKIEREL $bYYYYMMDD
(where YYYYMMDD represents the Date of Entry (DA) of the
record in BIOETHICSLINE)
Certain unique BIOETHICSLINE data were also merged into the Locatorplus
records and appear in the MARC 21 fields according to the following:-
BIOETHICSLINE Element
Locatorplus Field (in MARC 21 format)
Name
Call Number (CA)
090
Abstract (AB)
520
Keyword Identifier (KWI)
600 or 610 or 611 or 630 or 651
MeSH Heading (MH)
650 or 651
Publication Type (PT)
655 or 659
Keyword Description (KWD); Subject Caption (SC); 690
Keyword Identifier (KWI) that are not appropriate for
A more specific 6XX field in Locatorplus
KIE Subject Headings (SJ)
960
This completed conversion project marks the final phase in the
reorganization of the monographic data from the specialized databases into
Locatorplus.
PubMed's LinkOut-Serhold interface
The PubMed LinkOut for Libraries program has been expanded to include print
holdings. Libraries that store their print holdings information in the
National Library of Medicine's SERHOLD database can now display this
information in LinkOut.
For libraries already participating in LinkOut, select the LinkOut-SERHOLD
interface function from the sidebar of the submission utility to print
holdings information. For more information see
http://www.ncbi.nlm.nih.gov/entrez/linkout/doc/liblinkout.html#serhold
If you are not currently participating in LinkOut and do not have a User
Name and Password for the submission utility email [log in to unmask]
for information. Enter "LinkOut Registration Request" in the Subject box.
The body of the message should include the following information:-
* Library name
* Contact person
* Email address
* Phone number
* Address
Requests will be processed on a first-come first-served basis up to 10
requests per day.
URLF and URLS data to be deleted from PubMed
The URLF and URLS fields have been removed from the MEDLINE format in PubMed
and will be removed from the XML format at the end of the year. These
fields held links to full text and summaries at providers' websites,
however, the data was often incomplete and not updated. The Entrez Utility
, Elink, can be used to obtain LinkOut URL's.
Update: Expanded Clinical Trials.gov search capabilities
This article describes briefly the new capabilities, added in May 2002, to
help refine searching. The Help Page also provides information on these
features.
At present, ClinicalTrials.gov contains more than 6,500 clinical studies in
approximately 69,000 locations worldwide sponsored by the federal
government, pharmaceutical industry and private non-profit sources.
The number of clinical trials in the system has substantially increased
since the finalisation of the Food and Drug Administration's (FDA's)
Guidance for industry: Information program on Clinical Trials.gov for
serious or life threatening disease and conditions. The guidance document
requires all investigational new drug holders to register clinical trials.
The website which can be accessed at http://clinicaltrials.gov/ provides
patients, family members, health care professionals and members of the
public with easy access to clinical trials on a wide range of diseases and
conditions.
Finding studies
Three mechanisms are available for finding clinical study protocol records -
Basic search, Focused search, and Browse.
Synonym expansion
When using either the Basic or Focused search the system automatically
includes words or phrases that are synonymous with the search terms.
Spell checking
Alternative words may be used if a search term is not found in the database
- eg if a query produces choices, clicking on the circle to the left of a
word automatically reruns the search with word substitution.
Viewing the results
On the search results page the query used to obtain these results is shown
at the top of the page. Underneath, retrieved studies are listed in brief
format.
To view multiple studies, click on the checkboxes of the studies you wish to
view and click on the "Displayed Selected Studies" button.
UPDATE
Search within results
Users often wish to modify or limit their results after an initial search.
Use the Search Within Results button at the top of the Search Results page
to limit the retrieval set. Click on the "Tips" link on the Search Within
Results page for brief definitions of the fields that may be used to limit a
search.
Search Operators
ClinicalTrials.gov supports the use of Boolean Operators, Phrase searching,
and Field Specification in all search text boxes: Basic Search, Focused
Search, Search Within Results and Modify Your Search under Query Details.
Boolean Operators
Boolean queries may be constructed using AND/OR/NOT and need to be in upper
case letters. Angle brackets, previously required, should not be used.
Parentheses may be used to nest clauses.
Phrase searching
Quotes limit search to a specific phrase. When no quotes are used,
ClinicalTrials.gov searches for both the phrase and "relaxed" forms of the
phrase. Relaxed forms of the union (ANDing) of all combinations of words
found in the original query, while maintaining word order in the search
strategy.
Studies found by the relaxed forms are ranked on the Search Results page
according to the degree of relaxation: "more relaxed" forms (more AND's) are
ranked lower than those forms closer to the original phrase.
The relaxation strategy is the underlying mechanism for generating Query
Suggestions (see "Alternative Search Formulations for Natural Language
Searches" later in this article.
Field Specification
Field specification is used to specify the part of the study to be searched.
These fields correspond to the limits in Search Within Results. All
characters need to be in upper case letters. Each field specified must be
enclosed in square brackets.
Query Details: Modify your search and Query Suggestions
Users sometimes wish to reformulate their search strategies and/or see terms
used after synonym expansion and "relaxed forms". After submitting a
search, use the Query Details button at the top of the Search Results page
to edit a search or view synonyms used.
Alternative Search Formulations for Natural Languages Searches
Some end users use natural language searches. To assist them in
reformulating their searches, ClinicalTrials.gov provides suggestions for
alternative combinations of search terms based on the initial search.
PubMed citatations linked to ClinicalTrials.gov studies via LinkOut
For ClinicalTrials.gov study records that have links to PubMed citations,
there are now reciprocal links back to the ClinicalTrials.gov study records
from the PubMed citations via the LinkOut display.
Links to Search Requests
A syntax is available for creating "canned searches" in ClinicalTrials.gov.
Librarians, web developers and other information professionals may find this
mechanism useful for directing end users to particular sets of study records
through single links.
Simple Queries
The syntax for performing simple queries, searches involving a single field
and term, can easily be generated using URL's.
URL's may also be used to link specific studies by referencing the
NLM-assigned unique NCT number: http://clinicaltrials.gov/show/NCT00004451
ClinicalTrials.gov web pages may also be linked eg
http://clinicaltrials.gov/info/resources links to the Resources page, which
provides background information and general resources about clinical trials.
Complex Queries
The syntax for performing complex queries requires familiarity with search
operators described previously and standard URL encoding. Any search that
can be created at the ClinicalTrials.gov interface (eg Basic and Focused
Search) may be encoded in a single link, using the template:
http://clinicaltrials.gov/search/term={URL-ENCODED QUERY}. A left-and
right-square bracket must enclose specific fields to be searched. The URL
encoding for these characters is listed, in addition to the URL encoding for
double quotes which can be used to limit a search to a specific phrase. Any
spaces in the URL are encoded with the plus sign"+".
Links Pull-down menu on PubMed citations
The PubMed display has recently been revised to consolidate some links into
a Links pull-down.
The Links pull-down menu has been created to support new ways of using the
ever growing number of links between records in the Entrez databases. All
links, except for Related Articles, will be included in the new pull-down
menu which is available on the first 50 records per page.
In addition to putting the links users are familiar with in this pull-down,
NLM will be adding new links:
* Cited in Books - this PubMed record is cited in the bibliography of
an online Book. Clicking this link will take you to the section(s) of the
book where it was cited.
* Cited in PMC - this PubMed record is cited by a full text article in
PubMed Central. The link takes you to the article(s) in PMC where it is
cited.
The full list of Links in Entrez is available.
Fiona McLean
Health Care Information Officer
British Library
96 Euston Road
London NW1 2DB
Email: [log in to unmask]
Phone: 020 7412 7489
Fax: 020 7412 7954
Webpages: http://www.bl.uk/health
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