Jan's Search Tips

Cochrane Library Update

2007-04-29T16:55:00.000-07:00

The Cochrane Database of Methodology Reviews (Methods Reviews) has merged into the Cochrane Database of Systematic Reviews (Cochrane Reviews) with the publication of Issue 2, 2007, of The Cochrane Library on 18th April.

Why is this being done? All Cochrane reviews will now be in a single database, paving the way for further types of reviews (diagnostic test accuracy reviews and overviews of reviews, previously known as umbrella reviews) to be introduced in the future. Other benefits of the merge are the inclusion of methodology reviews in MEDLINE (both PubMed and Ovid MEDLINE) and having them indexed by ISI/Thomson Scientific for the Science Citation Index.

PubMed: 17 Million and Growing

2007-04-29T16:54:00.000-07:00

On April 20, 2007, the number of citations in PubMed surpassed 17 million.

LactMed Expanded

2007-04-14T09:35:00.000-07:00

The Drugs and Lactation Database (LactMed) has added fifty-one substances, including fourteen topical antibacterial and antifungal agents, thirteen X-ray and eight MRI contrast agents, eight acne/skin care agents, and eight other drugs. Thirty-six records have been updated.

LactMed is part of the NLM Toxicology Data Network (TOXNET®). It is a peer-reviewed and fully referenced database of drugs to which breastfeeding mothers may be exposed. LactMed includes information on the levels of such substances in breast milk and infant blood, and the possible adverse effects in the nursing infant. It provides statements of the American Academy of Pediatrics concerning a drug’s compatibility with breastfeeding and suggested therapeutic alternatives to those drugs where appropriate.

For more information:
LactMed 3/2007

MeSH: the Web Site

2007-04-08T06:54:00.000-07:00

You're searching MEDLINE (whatever flavor!) and you're finding little or nothing on your topic - or you're finding ten thousand...

And none of your finely honed searching shortcuts is working for you..

What are you going to do?
Go back to MEDLINE searching fundamentals. I'm talking about the Medical Subject Headings (MeSH), which are one of the building blocks for a good search. A good understanding of how they are organized, how they work, how they are applied to the medical literature not only forms the basis of those 'searching shortcuts' but it is where you should turn when your 'shortcuts' fail...back to the fundamentals.

MeSH: the Web Site is jam-packed full of information, including video tutorials. It covers the tree structures, the principles of indexing, searching tips for PubMed, the MeSH database, tips for chemical searches, and MORE!

Take a look!

For more information:
The Basics of Medical Subject Headings

New Look for TOXNET search results page

2007-04-01T13:07:00.000-07:00

The "Search All (TOXNET) Databases" results page has a new look. References from the National Library of Medicine's TOXLINE® (Toxicology Literature Online) and DART® (Developmental and Reproductive Toxicology) are displayed first, followed by records from the other TOXNET resources (Chemical, Toxicological, and Environmental Health data).

For each resource, the database abbreviation, full name, and number of records found are displayed; click on any one to go to its results page.

For more information:
TOXNET
NLM Technical Bulletin

Ovid MEDLINE Tutorial

2007-03-11T13:12:00.000-07:00

Find it! An Ovid MEDLINE Tutorial

This tutorial is a step-by-step guide for using Ovid MEDLINE. You will learn how to correctly formulate your clinical question, perform searches in Ovid MEDLINE using MeSH terms, save your searches, export your search results to EndNote and RefWorks, and a lot more! This tutorial also includes video demos.

This excellent tutorial was created by my colleague Lei Wang, a very talented Instructional Design Librarian at the Cushing/Whitney Medical Library, Yale School of Medicine.

Give it a try!

PubMed® Subject Subset Strategies Updated for 2007

2007-03-04T16:06:00.000-08:00

NLM announced that the following subject subset strategies have been recently revised: AIDS, Bioethics, Cancer, Complementary Medicine, Systematic Reviews, and Toxicology.

All PubMed subject subset strategies are reviewed at least once a year to see if modifications are necessary. Modifications may include revisions due to changes in MeSH vocabulary, adding or deleting terms, and changing parts of a strategy to try to optimize retrieval. The History of Medicine subset was revised in October 2006.

RxNorm and RxNav...from NLM

2007-02-18T17:54:00.000-08:00

Try out the updated Web-based browser RxNav which allows you to search RxNorm, the NLM database of standard names for clinical drugs that references the names of approximately 17,000 clinical drugs from several sources. RxNav displays graphically links from clinical drugs, both branded and generic, to their active ingredients (e.g., Ibuprofen), drug components (e.g., Ibuprofen 200 MG) and drug forms (e.g., Ibuprofen Oral Tablet). It also associates generic with brand names (e.g., Ibuprofen / Advil).

Every aspect of the RxNorm database can be queried through RxNav, including the names and codes of drugs and components in the drug resources referenced by RxNorm. Spelling suggestions are offered when no exact match is found in RxNorm for a given input term. RxNav accesses the RxNorm server at NLM, which is updated monthly.

For more information:
about RxNorm
about RxNav

Journals recently accepted for MEDLINE

2007-02-11T14:50:00.000-08:00

A new web page on the National Library of Medicine (NLM) web site now lists the journals accepted for MEDLINE indexing. The LSTRC (Literature Selection Technical Review Committee) meets three times per year to decide on which journals meet NLM criteria. This page will be updated after each meeting (February, June, and October)

This new resource includes the full journal title, the journal title abbreviation, NLM Unique Identifier, first issue to be indexed, ISSN (print or electronic or both), and language of the journal. Links from the full journal title take you to fuller bibliographic information about the journal in the NLM Catalog.

Take a look at the list!

New Bioethics Information Resources page

2007-02-04T18:42:00.000-08:00

NLM announced a new consolidated Bioethics Information Resources Web page. This new easy-to-use electronic resource can assist you, whether you're a specialist in the field or researcher or clinician or the general public, in finding the bioethics information you need by searching NLM databases as well as linking to other Federal government and outside resources.

Take a look!

Is MEDLINE enough?

2007-01-30T00:20:00.000-08:00

Recently, several people have asked me about which databases are important to search. I usually ask what the purpose of their search is - couple of 'good' recent articles, a more comprehensive search or a 'no stone unturned' exhaustive search?

If you are looking for a couple of good articles then MEDLINE is probably enough. A more comprehensive search should take you beyond MEDLINE to EMBASE, SCOPUS, Science Citation Index, Google Scholar and depending on your topic, an appropriate specialty database, such as CINAHL or PsycINFO. An exhaustive search will include all of the above plus multiple specialty databases, citation analysis, grey literature, web searching and hand searching the top journals in the discipline.

If you're having trouble deciding which databases you should search for your question or project, consult with your librarian.

More about TRIP!

2006-05-18T06:06:00.000-07:00

Searching TRIP is amazingly simple on the surface but it has some very interesting things going on behind the scenes (more about that later).

I typed 'adhd' in the search box:

Here's what the Category Results looks like:

As with other web-based search engines, click on the appropriate category to browse the individual items.
Try your topic!

TRIP Database - new at CWML!

2006-05-17T06:21:00.000-07:00

TRIP (Turning Research into Practice) Database is a new acquisition at the Medical Library.

TRIP is "the Internet's leading resource for Evidence-Based Medicine - allowing users to easily and rapidly identify the highest quality evidence from a wide range of sources."

Jon Brassey and Dr. Chris Price, founders of this database, realized as they were attempting to answer clinical questions in a clinically relevant time frame, that having to consult multiple resources and multiple web pages to find the 'best evidence' was counterproductive. They decided that if all the content were searchable at one website it would significantly improve the search time. Thus, TRIP was born.

Since then it has grown significantly in terms of ease of use, coverage and popularity. The aims of the TRIP Database have remained the same since 1997 - allow health professionals to easily find the highest-quality material available on the web. The TRIP Database is produced by TRIP Database Ltd.

Just the Facts:
You can find TRIP Database alphabetically under the 'All Resources A-Z' link (hint: click on the Major Resources link in the left-hand scan column of the Library's home page)

Scirus: for scientific information only

2006-05-15T06:04:00.000-07:00

Scirus is a science-specific search engine covering over 250 million science-specific web pages and it is freely available!

This search engine, introduced by Elsevier in 2001, has grown considerably in the past five years. It searches web information, preprint servers, digital archives, repositories and patent and journal databases. Scirus goes deeper than the first two levels of a Web site and can find peer-reviewed articles such as PDF and PostScript files.

Scirus has both a basic and an advanced search mode. With the advanced search menu, you can focus your search by date, information type, file format, content source and subject area.

If you're a Scopus searcher, perhaps you've noticed the Web tab on the results screen. These results are coming directly from Scirus.

Give Scirus a try!

PubMed Central: new journals participating

2006-05-04T06:34:00.000-07:00

The NLM Technical Bulletin has announced that the following journals are now participating in PubMed Central. See the Technical Bulletin for the details about each journal.

Algorithms for Molecular Biology
Implementation Science
International Breastfeeding Journal
Journal of Biomedical Discovery and Collaboration
Journal of Cardiothoracic Surgery
Journal of Occupational Medicine and Toxicology
Orphranet Journal of Rare Diseases
Radiation Oncology
Substance Abuse Treatment, Prevention and Policy
Nuclear Receptor Signalling
Journal of Zhejiang University. Science
Journal of Zhejiang University. Science B.
Beilstein Journal of Organic Chemistry
Biology Direct
Trials
Journal of the Royal Society of Medicine
EMBO Reports
Health Services Research

Database Highlight: African HealthLine

2006-05-01T23:44:00.000-07:00

African HealthLine is a collection of bibliographic databases on African health issues. This unique collection of sources including many from Africa covers all aspects of African health issues. These are the 12 databases that comprise this collection:

African Index Medicus (AIM)
The database of HealthLink Worldwide
The Medicines Information Centre Reference Database of the University of Cape Town
Community Health Information Database (CHID)
SAMED
AIDS Consortium Resource Centre Database
African Subset of "MEDLINE"
African Health subset of "WATERLIT"
African Health Subset of the "Index to South African Periodicals" (ISAP)
African Health Subset of the "South African Index to Theses and Dissertations"
The Bibliography of Filariasis
African Laboratory for Natural Products Database (ALNAP Database)

Just the Facts:
African HealthLine is published by NISC South Africa
Updated quarterly
Part of BiblioLine

LactMed: new database on drugs and lactation

2006-04-24T21:05:00.000-07:00

LactMed: A New Database on Drugs and Lactation from the National Library of Medicine

LactMed, a free online database with information on drugs and lactation, is one of the newest additions to the National Library of Medicine’s (NLM) TOXNET system, a Web-based collection of resources covering toxicology, chemical safety, and environmental health.

Geared to the healthcare practitioner and nursing mother, LactMed contains over 450 drug records. It includes information such as maternal levels in breast milk, infant levels in blood, potential effects in breastfeeding infants and on lactation itself, the American Academy of Pediatrics category indicating the level of compatibility of the drug with breastfeeding, and alternate drugs to consider. References are included, as is nomenclature information, such as the drug’s Chemical Abstract Service’s (CAS) Registry number and its broad drug class.

LactMed was developed by pharmacist who is an expert in this subject area. Three other recognized authorities serve as the database’s scientific review panel. Ancillary resources, such as a glossary of terms related to drugs and lactation, and breastfeeding links are also offered.

LactMed can be searched together with TOXNET’s other databases in a multi-database environment, to obtain other relevant information about drugs. As a work in progress, LactMed will continue to expand with additional drugs and be enhanced with other substances, such as industrial chemicals and radiation.

Notice for PubMed saved searches...

2006-04-17T06:27:00.000-07:00

My NCBI Saved Searches and RSS feeds that were created using a date selected from the old PubMed® Limits screen should be recreated as these old limits are no longer working. Recreate your searches using date limits from the new Limits screen (and delete the old searches). Searchers are reminded that updates are, by definition, citations for recent publications that are new to PubMed and will not include citations for articles published before September 1997. Therefore, date limits are not recommended for strategies used to create My NCBI updates or RSS feeds.

For more information, see the NLM Technical Bulletin.

New Search and Display options in the Journals Database

2006-04-13T06:23:00.000-07:00

The default displays for Entrez PubMed, Journals, MeSH, and the NLM Catalog for search results that retrieve a single item will change from the Summary display to an expanded view. The view will change to Abstract for PubMed, Full for Journals and MeSH, and Expanded for the NLM Catalog.

To check this out in PubMed, here's two titles that you can try on the query line:

killer pop machines
does pizza protect against cancer

Notice that PubMed goes right to the abstract display instead of the normal summary display.

Last author option added to PubMed

2006-04-12T07:28:00.000-07:00

The 'Last Author' feature appears in two places:
Sort By Menu Selection
Single Citation Matcher option

You can also search for 'last author' from the query line by following this syntax:
varmus h [lastau]

For more information, see the NLM Technical Bulletin.

Tutorial on evaluating Internet Health Information

2006-04-11T03:10:00.000-07:00

MedlinePlus now features a tutorial on the topic of teaching people how to evaluate information for accuracy and authority. Evaluating Internet Health Information is slide show (approximately 16 minutes long) which runs automatically but also can be paused and stepped through slide-by-slide.

Take a look!

For more information, see the NLM Technical Bulletin.

Skill Kit: Truncation in PubMed

2006-04-10T07:40:00.000-07:00

If you need to brush up on truncation in PubMed, then this skill kit from the National Library of Medicine will do the trick.

It highlights how truncation works and provides examples. Especially important is a discussion of when to utilize truncation and when not to.

In case you ever used the search tag [ab] ...

2006-04-05T04:32:00.000-07:00

The [ab] search tag has been discontinued in PubMed. But don't worry! To search titles and abstracts (plus other fields), use [tw] or [textword]. To search only the Title and Abstract fields, use [tiab] or [title/abstract].

Check out the PubMed Help Search Field Descriptions and Tags for information about other ways to use 'field qualification' or 'search tags'.

For more information, see the NLM Technical Bulletin.

MeSH Video

2006-04-04T07:29:00.000-07:00

The National Library of Medicine has produced a video on MeSH. Branching out: the MeSH Vocabulary is 12 minute introduction to the Medical Subject Headings - the development, structure and use of this remarkable controlled vocabulary.

If you're a MEDLINE user and have wondered about ways to make your searches more efficient and effective, take a look at this video.

For more information, see the NLM Technical Bulletin.

Library 101 at the Cushing/Whitney Medical Library

2006-04-03T12:55:00.000-07:00

This very cool online tutorial teaches some basic library research skills and gives an introduction to the services available at the Cushing / Whitney Medical Library. You will learn how to locate journal articles (online or print), how to locate books (online or print), how to order materials from other libraries, and more! This tutorial also includes 11 video demos.

Check it out!

MEDLINE citation counts by year of publication

2006-04-01T17:30:00.000-08:00

This is a really interesting chart that gives citation counts in MEDLINE by:

Total citations by year
Number of citations published in the US by year
Percentage of citations published in the US by year

Take a look!

Searching for Meeting Abstracts

2006-02-21T06:52:00.000-08:00

For those of you who are interested in locating meeting abstracts, always a difficult task, try the NLM Gateway.

Over 98% of the Meeting Abstracts in the NLM Gateway now include the conference name in the record. All of the meeting abstracts from a particular conference can be retrieved by searching the conference name. Use the new field qualifier [CN] (which will also search the Corporate Author in Meeting Abstracts, PubMed, and NLM Catalog).

For detailed information on the exact steps, see the Gateway FAQ: How do I search for abstracts from a particular professional conference?

From the NLM Technical Bulletin, Jan-Feb 2006, Technical Notes:  NLM Gateway Enhances Search and Display of Meeting Abstracts.

Using PubMed to scan Journal TOC

2006-02-20T16:19:00.000-08:00

Many researchers and clinicians keep up to date by skimming the contents of their favorite journals. The PubMed® Single Citation Matcher has a fill-in-the-blank form that can be used as a quick way to find the citations included in PubMed for a particular issue of a journal.

For step by step instructions, see:
Skill Kit: Retrieving Citations from a Journal Issue in PubMed®. NLM Tech Bull. 2005 Nov-Dec;(347):e14.

Citation Tracker from Scopus

2006-02-17T09:45:00.000-08:00

At the end of January, Scopus added a new feature that is just...well, just plain cool!

They're calling it 'Citation Tracker'.

Citation Tracker lets you look at citation counts for a particular author's works and presents a Citation Overview table by article title and year. Check it out!

Here's a few tips, though. And I do this so you won't do what I did, which is spend 10 minutes looking for the 'Citation Tracker' tab.

Start off at the main page for Scopus.
Click on author search (it's the last tab, after Basic Search and Advanced Search).
Put in an author's name (follow the instructions for the appropriate syntax).
Click on Search.
Check the appropriate box for your author and then click 'Citation Overview'.

Here's a picture of what the citation overview table looks like.

Subject Subset Strategies updated

2006-02-15T20:56:00.000-08:00

The following PubMed subject subset strategies were recently revised:

Bioethics
Cancer
Complementary Medicine
Space Life Sciences
Toxicology

And lest you forgot, the Systematic Reviews subset was revised in December 2005.

For more detailed information see the subset strategies page.

For you history buffs...

2006-02-13T05:12:00.000-08:00

In the fall of 2005, the National Library of Medicine began an OLDMEDLINE Other Term-to-MeSH mapping project. OLDMEDLINE Other Terms are the original subject headings assigned to the citations when they appeared in the print indexes. This project maps those terms to current MeSH vocabulary and will be updated each year during year end processing. NLM estimates that approximately 92% of the OLDMEDLINE citations now have at least one MeSH term. All current MeSH headings added to these records have been added as major MeSH headings. Additional work on this project will continue.

For more information about the MeSH Mapping Project and about searching OLDMEDLINE citations using MeSH, see the OLDMEDLINE description.

PubMed grows and grows...

2006-02-12T16:10:00.000-08:00

On December 29, 2005, the number of citations in PubMed surpassed 16 million.

PubMed clipboard contents indicator

2006-02-07T06:23:00.000-08:00

You may have noticed that PubMed now has an asterisk indicator for the clipboard tab. This lets you know that you've collected items and posted them to the clipboard. A simple mouseover will even tell you how many items you have. Very helpful!!

For more information, see the NLM Technical Bulletin.

Federated Searching: What's that all about?

2006-02-06T06:49:00.000-08:00

If you've never heard of 'federated searching' then you're not alone! And that's not the only phrase that's used to describe this method of searching -- it can be referred to as: cross database searching, metasearching, broadcast searching.

Here's a simple explanation by way of a scenario:

You need to know what the experts are thinking about a current issue outside your area of expertise. You might have an inkling of where to search but not really. What you need is a tool that will guide your selection of appropriate resources based on your topic and then allow you to search across those selected multiple databases via a single search interface. Results should be presented either in chronological order, by database, or combined in a single merged list. Then you should be able to get right to the full-text of the article or book that you think is going to answer your question - right then and there.

What makes 'federated searching' different from using Google, Google Scholar or any web search engine is that instead of world wide web pages, you're searching across the resources of a University library - a myriad of unique, authoritative databases and resources from every discipline.

The Yale University Library is experimenting with just such a federated search tool and we'd appreciate any feedback you can give us.

Here's where you can try this out:
From the Yale University Library's Database and Article Searching page, click on Quick Start or Multi-Database Searching.

Please let me know what you think!

I'm back....

2006-02-05T14:42:00.000-08:00

Even though writing a blog is a great learning experience and the scope of 'Search Tips' is extremely pertinent to what I do, it's a lot of work. And after the holidays, I just couldn't get up the gumption to resume... but I'm back now.

Interesting things are happening in the 'searching/finding' world and I'll try to keep you up to date!

Year end processing for PubMed

2005-12-22T18:06:00.000-08:00

I just wanted to briefly explain what happens at the end of the year when it seems like PubMed doesn't get updated for weeks. In reality, much work is going on.

All of the changes that have been discussed during the year need to be incorporated into MEDLINE database - changes in the Medical Subject Headings (MeSH) for 2006 are particularly important.

In November, National Library of Medicine makes the announcement of the schedule for year end processing. This announcement details when the final update file for the year will be distributed for MEDLINE, PubMed-not-MEDLINE, and OLDMEDLINE. Until the next year's baseline files are ready, only the In Data Review and In Process files will be updated. NLM will also announce what days during this time period that no updates will occur.

Lastly, NLM will announce the expected date when the processing will be complete and provides links to documentation describing the important changes to Medical Subject Headings.

As a matter of fact for the year 2005, this update was completed on December 12, 2005.

When the process is complete, the announcement is made in the "Entrez PubMed' section of the blue scan column under 'New/Noteworthy' section'.

This year's announcement appeared in several places including the Bibliographic Services Division.

Systematic Reviews strategy updated

2005-12-21T06:06:00.000-08:00

The systematic reviews subset strategy has been updated to reflect changes made to the Medical Subject Headings for 2006.

PubMed
This subset can be found on the Clinical Queries page (under PubMed Services on the blue scan column). The strategy is designed to "retrieve citations identified as systematic reviews, meta-analyses, reviews of clinical trials, evidence-based medicine, consensus development conferences, guidelines, and citations to articles from journals specializing in review studies of value to clinicians."

Besides the clinical queries page, you can use field qualification to apply this subset. Here's the syntax:

osteogenesis imperfecta AND systematic [sb]

Ovid MEDLINE
As far as I know, this has not been updated in Ovid MEDLINE yet. I'll keep you posted!

More details, including the search strategy itself, can be found on the Bibliographic Services Division web site.

Printer friendly option added to PubMed

2005-12-19T15:00:00.000-08:00

Have you noticed the new 'printer' choice from the 'Send to' menu on the search results screen?

You simply conduct your search, make your selections and then choose 'printer' from the 'Send to' drop-down. A print page will pop up with two choices at the top:
Print this page
Close this window

Couldn't be simpler...

For more information see the NLM Technical Bulletin

New from the MeSH Database

2005-12-02T05:45:00.000-08:00

Check this out!

From the MeSH database, you can now select and retrieve PubMed citations where the heading has been designated as a major topic of the article. It is no longer necessary to go to the Full display and create a search using the Send to Search box feature if you simply want to search the term as a major topic.

How do you do this?

From the PubMed Services scan column on the left, click on MeSH Database.
Type a single concept on the query line (for example, osteogenesis imperfecta)
Use the Links Menu (to the extreme right of the subject heading) to choose PubMed - Major Topic

The search will be executed and the next screen will be the PubMed results screen.

Did you also notice that you could make other choices from that handy links menu?

a straight PubMed search
a PubMed - Major Topic search
a Clinical Queries search
a NLM MeSH Browser search

See the NLM Technical Bulletin for more information

Personalizing Scopus

2005-12-01T06:22:00.000-08:00

Here are some reasons to personalize Scopus:

Saved searches: this feature allows you to save whatever search you're working on - very helpful when you don't want to lose what you've already done or you have created a base search on your topic that you know you'll be adding to. This saves you from having to type the keywords in over and over.

Alerts: you can turn a saved search into an alert - determine how frequently you want Scopus to run the search and notify you via email of new articles on your topic. Choose 'Alert Me' from an individual article and Scopus will notify you when that article has been cited by someone else.

Lists: My List allows you to choose and create a collection of documents from any results page. This can be used to export or print all at once, instead of having to print multiple times from several results pages. You can also save a collection of documents for processing at a later date.

Personalizing Scopus is very simple. Create your personal profile by clicking on the 'register' link in the upper right corner of any page in Scopus. Choose a username and password (Note: your ScienceDirect username and password will also work on Scopus and vice versa)

Now, when you are logged in to Scopus, you can click on the 'My Profile' link to access or modify your saved searches, alerts and lists.

Scopus: Refining Results

2005-11-30T05:50:00.000-08:00

In previous posts, I've described the product, talked about basic searching and the results screen. Now, it's time to look at the totally unique way Scopus has devised to refine the results of a search.

Notice the box above the results - it says 'Refine Results'. Look at this box to find out:

Which journals publish most frequently on this topic
Which authors are working on this topic
Distribution of articles per year

You can use these lists to identify potential journals for article submission. If you're working on a systematic review, this would be a great first pass at building a list of journals to hand-search. And the same holds true for the author list - if you're working on a project, this is a good test to see if you are familiar with the key people in the field. You can also identify a potential co-author to collaborate with on future research. That's pretty cool!

Notice that you have the choice to 'limit to' or 'exclude'. Use the check boxes to select one or more journals, authors, or dates and then limit to only those selected or exclude those selected.

FYI
Scopus is available from the Medical Library's Major Resources list.

Wow! New NCBI search toolbar

2005-11-28T04:18:00.000-08:00

This cool toolbar is an optional addition to your Web browser (Internet Explorer or Firefox) that expedites searching the NCBI's resources. It sits right below other browser toolbars.

The toolbar highlights search results and provides shortcuts to NCBI resources.

Check out these features:

searching with the search box
searching with the right mouse button
highlighting search results
shortcuts to NCBI resources

The NCBI Search Toolbar is now available for download from: http://www.ncbi.nlm.nih.gov/projects/toolbar/

For detailed information, see the NLM Technical Bulletin.

Journal Search Links in PubMed

2005-11-22T22:50:00.000-08:00

This new feature is really quite handy.

Check it out by doing a search in PubMed - try: killer pop machines! Click on the author link to display the citation. Notice that the journal title is now a link. Click on it and a menu box with three choices appears. You can choose to search for the journal in PubMed or in the Journals database which is very useful. But, the last choice 'Add to Search' adds a search for the journal to the current search strategy -- this can be extremely helpful especially when you want to limit your topical search to a specific journal.

See the NLM Technical Bulletin for more information.

Scopus: Results Screen

2005-11-21T06:20:00.000-08:00

In two previous posts, I've described what Scopus is and how to conduct a basic search. Now it's time to take a moment to appreciate the Scopus results screen.

I'll admit - when I first started using Scopus the results screen seemed incredibly busy but after just a few searches I realized that it is very easy to read. And because it's a familiar table format, it takes only a glance to find the bit of information that you are looking for.

Here's some interesting things to try out:

Click on the column header to resort the results (column headers are Date, Document (sort by relevance), Author, Source Title, Cited By)
Click on the Abstract + Refs link to look at the article abstract and the cited references. Notice that the cited references are all linked as well.
Click on the YaleLinks to link to the full-text.
Click on the Cited By number to look at the articles that have cited that particular article.
Notice that you can print, export, email and add to list.

Play around with the results screen - more about refining results later.

New PubMed filter

2005-11-09T06:13:00.000-08:00

A new PubMed filter was just added to the My NCBI Filters feature. The new filter, English & Humans, groups search results that match both English language and the MeSH heading Humans. The new filter combines two existing filters, English and Humans (which will remain available individually). This combination is especially helpful if you had to make decisions to keep within the five filters allowed by My NCBI.

Select this new filter from the My NCBI PubMed Quick Pick menu.

Scopus: Basic Searching

2005-11-08T04:20:00.000-08:00

Basic searching in Scopus couldn't be easier. As a matter of fact, the designers wanted the interface to be 'google-like'. You start out by typing your keywords into the query box. You only need to remember a few rules and the example under the first query box gives you clues.

It doesn't matter if you type your entire search string in the first box or use both boxes - you can enter one or more search terms in one or both of the text entry boxes.
The default operator is 'and'. For example, type: cost analysis. The system will intrepret this as: cost and analysis.
To search for a phrase, enclose the phrase in quotation marks: "cost analysis"
You can use the following Boolean operators: and, or , and not
You can select the fields you want searched by using the drop-down box. The default is to search article title, abstract, keywords.
Other limits are listed below the text entry boxes. Available limits are: date range, document type, and subject areas.

Try a few searches. Let me know what you think!

In-depth MEDLINE/PubMed field descriptions

2005-11-01T07:17:00.000-08:00

The Bibliographic Services Division of the National Library of Medicine has produced a web page of MEDLINE/PubMed Data Element Descriptions . This document contains detailed descriptive information about each field within each MEDLINE/PubMed record - including the historical development of the particular field. I find this invaluable when I'm trying to search a specific field and get bizarre results. Sometimes the explanation is simply that, during the time period I'm looking at, it wasn't possible to search that way. For example, check out the history of the author field.

The Bibliographic Services Division advises that this information is supplemental and should be used in conjunction with PubMed Help. As a matter of fact, you should use the Search Field Tags section of PubMed Help for instructions and tips for field searching.

SCOPUS

2005-10-31T06:01:00.000-08:00

Have you tried the Scopus database yet?

This database, created by Elsevier, is quite unique in that is based on a user centered design process involving more 300 researchers and librarians. A team of five full-time designers and a cognitive psychologist used observation and feedback from user tests to develop the interface. Each feature is based on exactly what users asked for.

But, what is it?

It's a full-text indexing and abstracting database. Scopus contains the contents of EMBASE, MEDLINE and Compendex - as a matter of fact the database indexes and abstracts over 14, 000 scholarly journals in the scientific, medical, technical and social science literature including over 400 open access journals. It also integrates Scirus, a web search engine focused on scientific web pages including patent information.

Scopus makes it easier for a researcher to:

Find new articles in a familiar subject field
Find articles by a specific author
Access information that can help evaluate an author
Stay up-to-date
Gain an overview or understanding of a new subject field

Scopus is updated daily.

Over the next couple of posts, I'm going to highlight some of the features of Scopus.

Just the facts:
Scopus is available from the Medical Library's Major Resource list.
To read more about the application of user-centered design (UCD) to Scopus development, see Scopus White Pater Series, Number One

Searching the Canary Database

2005-10-24T07:55:00.000-07:00

In case you haven't tried the Canary Database (see post from October 10), you should definitely take a look at some of the features. Besides the added value of the curated documents, there are some cool things that the database designers have added to enhance the searching experience.

For example, do a quick search on anthrax by typing 'anthrax' in the search box at the top of the screen and click on 'go'. Looks and feels like Google, huh?

The results screen lists 43 records. And, right before the record listing, plots the % hits by year from 1965 to 2005 - giving you a instant feel for the distribution of articles over time. The next cool thing is the linkages bars, which are clickable. The bars indicate the linkages for:
Cause and effect analysis
Interspecies susceptibility data
Shared exposures with humans
Shared outcomes with humans
Gene sequence date

Another feature is the 'Find similar (show/hide)' box to the right of the screen. This allows you to quickly perform Boolean 'and' or 'or' searches within the search set or to redirect the search completely. It also helps to visualize the composition of the articles.

Give this database a try!

ISIHighlyCited.com

2005-10-19T07:33:00.000-07:00

Don't forget that this web-based resource is freely available for anyone to search.

ISIHighlyCited.com produced by Thomson ISI identifies the most cited and influential scientific authors.

If you know who you're looking for, start off with the search option to 'Find a Specific Researcher'. But, by choosing browse you can search by category (21 broad subject categories in life sciences, medicine, physical sciences, engineering and social sciences), by an alphbetic list of names, by institution, and by country.

Give it a try!

Search links added to PubMed displays

2005-10-17T07:32:00.000-07:00

The following fields on PubMed's Citation format are now "search links" to PubMed, MeSH®, and other Entrez databases:

MeSH Terms (headings, publication types, and substances),
Grant Support
Secondary Source ID
Personal Name as Subject

In addition ClinicalTrials.gov identifier numbers (under Secondary Source ID) will link directly to the trial on the ClinicalTrials.gov Web site.

Publication Types and Personal Name as Subject search links will also be available as search links on the Abstract display.

I think that you'll find these links quite handy as you're searching!

For detailed information, see the NLM Technical Bulletin

New Feature for Old MEDLINE

2005-10-14T07:38:00.000-07:00

NLM® is embarking on a project to map the OLDMEDLINE subject headings, found in the PubMed® Other Term [OT] field, to current MeSH®. The original subject headings will be retained in the OT field. NLM expects to have a large percentage of this project completed for the new 2006 PubMed system in mid-December 2005.

See the NLM Technical Bulletin for more details.

PubMed Subject Searching Avoids Conflicts with Journal Titles

2005-10-11T07:31:00.000-07:00

Maybe you've never noticed this before but upon occasion, when you type in terms expecting to do a subject search you get bizarre results - PubMed maps what you've typed to a Journal search. This usually happens when you type something like 'brain development'. The way PubMed treats this is to first look in the MeSH translation table and if there is not a match, it then goes to the Journals Translation table - where it will find a match 'Brain Dev[Journal]'. Probably not what you expected!

NLM is adding to the exceptions table (which now contains heart failure, pediatric surgery, and treatment review) so that other subjects won't be treated as journals by default.

See the NLM Technical Bulletin for all the details.

Canary Database

2005-10-10T07:33:00.000-07:00

Check out the Canary Database - Animals as Sentinels of Human Environmental Health Hazards. This database is produced by Yale University Occupational and Environmental Medicine at the Yale School of Medicine.

The database contains studies in the biomedical literature that explore the use of wildlife, domestic, and companion animals as "sentinels" for the effects of chemical, biological, and physical hazards in the environment that may be a risk to human health.

This compilation of curated peer-reviewed research articles related to the use of animals as sentinels of human health hazards also contains information added by trained curators in addition to bibliographic records from MEDLINE and other well-known databases.

For each study, curators add information about animal species, exposures, health effects, location, and whether the study includes data providing evidence linking animal sentinel events to human health risk in the following ways:

Exposure-effect relationships in the animal
Shared exposures between human and non-human animals
Interspecies susceptibility
Linkage between animal and human health outcomes
Gene sequence information

Use the Canary Database to:

Find out whether a cause and effect relationship between an environmental hazard and a health outcome has been studied in animal populations
Find out what is known about a particular disease reservoir for an infectious agent
Find out how investigators have used different study methodologies
Identify knowledge gaps related to animal sentinel health events

The project team is labelling it 'Public Beta' right now and encourages comments.

TOXNET TRI 2003 released

2005-10-08T16:12:00.000-07:00

The 2003 Toxics Release Inventory (TRI) was released on TOXNET® on June 13, 2005. The new release (1987-2003) contains 1,461,916 records.

The EPA's TRI provides information on the releases of over 600 specific chemicals into the environment as reported annually by industrial facilities around the United States.

NLM's TOXNET® is a group of databases on hazardous chemicals, environmental health, and toxic releases.

New version of the PubMed Tutorial available

2005-09-20T06:24:00.000-07:00

The National Library of Medicine is pleased to release a new version of the PubMed Tutorial. As always, the tutorial is available from the PubMed sidebar.

This new version incorporates changes to PubMed through February 2005 including the My NCBI feature.

New Ovid Features

2005-09-19T06:25:00.000-07:00

I hope you've noticed that Ovid has spruced up its interface - it happened the second week of July!

The main menu screen has a clean updated look and some of the menu choices have been placed in different locations on the screen.

This is always hard for anyone who was so used to the old interface that you barely had to look at the screen and still could click on the correct button.

Several new features have been added to this newly spruced up interface:

Find A Citation
Find Similar
Find Citing Articles

Find a Citation is a great addition to the Ovid interface and works much the same as PubMed's Citation Matcher. It allows you to plug known information about an article into a form - and you can plug as few as one or two items. The system will return every article in the database that matches that data -- a great way to attempt the location of an article based on what little you might remember about that article. It is also useful when trying to pull up a citation quickly.

Now, this is my opinion and it's really for those folks at Yale who are using this interface to search MEDLINE and other databases, but I think that the other two features should be used with caution.

Find Citing Articles looks for citing articles in Journals@Ovid only. And while there are many journals in Journals@Ovid, it is not an accurate picture of who is really citing the article. There are other resources (Web of Science, Scopus) available that will simply do a better job for you.

Finding Similar is using an alogorithm based on words in the title to find similar articles. Every time that I've tried this, it's been disappointing. I usually get one or two 'similar' articles but I know there's more.

So, enjoy the new look and Find a Citation but be cautious with Find Citing Articles and Find Similar.

Database Highlight: Global Health and Global Health Archive

2005-09-18T12:15:00.000-07:00

Global Health brings together the resources of two internationally renowned databases - the Public Health and Tropical Medicine (PHTM) database, previously produced by the Bureau of Hygiene and Tropical Diseases (BHTD), and the human health and diseases information extracted from CAB ABSTRACTS.

Dating back to 1973, together they provide a unique resource which offers a substantially deeper subject coverage of information related to human health and communicable diseases than many other sources currently available.

Global Health provides an alternative, complementary point of reference with a broad analysis of foreign language journals, books, research reports, patents and standards, dissertations, conference proceedings, annual reports, public health, developing country information, and other difficult to obtain material.

The Global Health database covers the following aspects of human health and disease:

communicable diseases (including HIV/AIDS)
tropical diseases, i.e, diseases in the tropics (including field and experimental studies)
parasitic diseases and parasitology - medical entomology
human nutrition (including food composition, food poisoning, effects of diet on health, nutritional disorders, and experimental aspects)
community and public health (including chronic diseases, occupational health, health status indicators, the impact of agriculture on health, and cancer epidemiology)
medicinal and poisonous plants (including pharmacology, tissue culture, animal studies, plant composition, allergens, and toxins)

Over 16,000 serial sources from more than 130 countries are scanned regularly for inclusion in the Global Health database, to produce approximately 25,000 new entries per year. Nearly all records have informative English abstracts prepared by scientists and linguists.

Global Health Archive is a "unique electronic map of humankind's global scientific heritage."

800,000 records from 1910 to 1973, equivalent to 300 volumes of research, provide a unique resource which offers a substantially deeper subject coverage of information related to human health and communicable diseases than many other sources currently available.

Global Health Archive is presented as a searchable modern database fully compatible with other databases, indexed by our subject specialists, placing obsolete terms in their modern context.

The Global Health Archive database covers the following aspects of human health and disease:

public health
tropical and communicable diseases
nutrition
helminthology
entomology
mycology

For More Information:
Click on Major Resources from the Library's home page. Part of the Ovid family of databases.
Ovid Field Guide
Serials Cited

New Version of TOXMAP Available

2005-09-07T07:17:00.000-07:00

A new version of TOXMAP was released July 25, 2005.

TOXMAP 2.4 contains the following new features:

2003 Toxics Release Inventory Data (TRI)
Chemical Spell Checker: Chemical names are often hard to spell; TOXMAP now locates 'near matches'
TRI chemical list page, with links to National Library of Medicine chemical information resources
Updated and expanded FAQs

TOXMAP is an interactive web site from the National Library of Medicine that shows the amount and location of reported toxic chemicals released into the environment on maps of the United States. TOXMAP allows users to visually explore information about releases of toxic chemicals by industrial facilities around the United States as reported annually to the Environmental Protection Agency (EPA). It also integrates the map display with access to relevant bibliographic references and other data on these chemicals, providing a map-based portal to these resources.

[From the NLM Technical Bulletin]

Healthy People 2010 added to PubMed Special Queries

2005-08-31T07:19:00.000-07:00

A link to the search interface providing searches for published literature related to the Healthy People 2010 focus areas of the HP2010 Information Access Project was added to the Special Queries resource page available from PubMed's blue sidebar.

The National Library of Medicine® and the Public Health Foundation staff have worked together to develop pre-formulated search strategies for selected Healthy People 2010 focus areas. The purpose of these searches is to make information and evidence-based strategies related to the Healthy People 2010 objectives easier to find. Select a focus area and see a list of specialized searches for the objectives. The "PubMed search" icons on the focus area page search PubMed.

Healthy People 2010 is a set of health objectives for the Nation to achieve over the first decade of the new century. It can be used by many different people, States, communities, professional organizations, and others to help them develop programs to improve health.

Ovid troubles...

2005-08-29T07:36:00.000-07:00

If you're having trouble with the new Ovid search interface in any way, shape, or form, it might be that you need to upgrade your Web browser...especially if you are a Mac user. I know this for a fact because I am a Mac user.

We've put together a page that should help you figure out whether it's your web browser that's the culprit.

Database Highlight: IDDB

2005-08-25T07:09:00.000-07:00

Investigational Drugs Database (IDDB) provides validated, integrated and evaluated information about the R&D portfolios of more than 17,000 companies and institutes involved in drug development including:

• Information about more than 92,000 therapeutic patents, with optional links to the full text of the original patent.

• Pipeline status of more than 21,000 investigational drugs, with comprehensive drug reports, development histories, bibliographies and expert commentary on the most promising candidates.

• Over 68,000 chemical structures, fully substructure searchable for easy identification.

• Approximately 400 meeting reports a year, from about 300 selected scientific conferences, with extensive first-time disclosure of investigational drugs.

• A growing bibliography of more than 492,000 references, gathered from a diverse range of scientific and commercial publications, with links to abstracts of full text where available

FYI
IDDB is available from a single workstation in the Medical Library. Contact Judy Spak or Daniel Dollar to arrange a time for using this resource in the library.

Only those affiliated with Yale University and the Yale-New Haven Medical Center have access to this unique database.

ClinicalTrials.gov Identifier to be Added to MEDLINE/PubMed Data

2005-08-24T06:14:00.000-07:00

NLM will be including the ClinicalTrials.gov identifier number in MEDLINE records, when that information appears in the original publication. NLM states that this will be added 'about July 2005'. I have been on the lookout for this addition but still can only find two citations with the ClinicalTrials.gov identified. Still it will be very handy once it is consistently applied.

The reason for this is based the recommendation from the International Committee of Medical Journal Editors on the topic of registering clinical trials before publication of the results and that the clinical trial registration number be included at the end of the article abstract.

The data will also appear in PubMed in the Secondary Source ID list in the Citation display, in the SI field of the MEDLINE tagged display, and in the DataBankList elements of the XML display.

An example in the Citation format display would be:

Secondary Source ID:

ClinicalTrials.gov/NCT00000161

If there are multiple ClinicalTrials.gov numbers mentioned in one journal article, all will be added to the MEDLINE record.

In PubMed, the data will be searchable using the [si] search tag; each of the pieces or the entire string is searchable, e.g.:

nct00000161 [si]

clinicaltrials.gov [si]

clinicaltrials.gov/nct00000161 [si]

Use "clinicaltrials.gov [si]" to retrieve all citations to articles listing trial registration in ClinicalTrials.gov regardless of which particular trial is involved.

For More Information:
Tybaert S, Knecht LS. ClinicalTrials.gov Identifier to be Added to MEDLINE^®/PubMed^® Data. NLM Tech Bull. 2005 May-Jun;(344):e13.

PubMed Citation Status Tag

2005-08-18T05:43:00.000-07:00

All citations in PubMed with the status tag [PubMed] have had the bibliographic data (e.g.: authors, article title, source information, abstract) reviewed for accuracy. The coverage of this status tag has now been expanded from two to three types of citations.

The newest addition is:

A citation for an article in a journal that is not indexed for MEDLINE. These are typically citations to articles from journals that deposit their full text articles in PubMed Central®, but have not yet been recommended for indexing in MEDLINE

The other two types are:

A citation for an article in a journal from which NLM regularly indexes articles, but this article is on a topic considered outside the scope of MEDLINE®
A citation for an article from issues of journals published prior to their selection for MEDLINE indexing and submitted to NLM since late 2003

To search for citations with the [PubMed] citation status tag use: pubmednotmedline [sb]

New NLM Mobile link in PubMed

2005-08-17T06:38:00.000-07:00

This is for all you PDA (Palm OS or Pocket PC) users...

Check out the new link, NLM Mobile, on PubMed's blue sidebar. It's under 'Related Resources'.
The NLM Mobile link provides access to a directory of PubMed tools that are appropriate for mobile devices. These include Palm Powered^™ and Pocket PC handheld computers as well as newer smartphones and Blackberry^™ devices.

Database Highlight: ClinicalTrials.gov

2005-08-15T06:23:00.000-07:00

ClinicalTrials.gov provides regularly updated information about federally and privately supported clinical research in human volunteers. The main purpose is to link patients to medical research.

ClinicalTrials.gov gives information about a trial's purpose, who may participate, locations, and phone numbers for more details. The information provided on ClinicalTrials.gov should be used in conjunction with advice from health care professionals.

ClinicalTrials.gov is a service of the US National Institutes of Health and developed by the National Library of Medicine.

Search Filters: things to think about

2005-08-11T07:19:00.000-07:00

Search filters are:

Fast, easy to use, and good when focusing on ‘best evidence’ or looking for articles emphasizing therapy, etiology, prognosis and diagnosis
Not great for all types of searches; very focused on clinical information and, not all search topics lend themselves to this approach
Not good for comprehensive searches – sometimes there is way too much information and sometimes way too little
great to analyze for potential subject headings, subheadings, and textwords to use in creating your own search filters. They can also be translated for use in other databases.

Saved Searches in PsycINFO

2005-08-09T08:21:00.000-07:00

Ah, this one is not at all easy and convenient. To whet your appetite before I tell you how this works, here's a list of the saved searches that the experts at the American Psychological Association (creators of PsycINFO) provide:

Achievement Measures
APA Journals
Attitude Measures
Developing Nations
Intelligence Measures
Language Disorders
Learning Disorders
Mental Health Personnel
Neuropsychological Assessment
Neurotransmitters
Nonprojective Personality Measures
Psychiatric Patients
Perceptual Measures
Projective Personality Measures
Racial/Ethnic Populations
Rehabilitation
Substance Abuse
"Talking" therapies
Tests, Measures, Scales
Tomography

So, now I give you the bad news! PsycINFO provides these as text files and therefore each of them must be transcribed line-by-line into Ovid PsycINFO. Save this as a Permanent Saved Search. When you conduct a topical search and you want to apply a filter, click on the Run Saved Searches button. Select and run the appropriate saved search. Then, using AND, combine the result of your topical search with the final set number of the saved search.

FYI
PsycINFO Saved Searches

Clinical Queries in Ovid

2005-08-05T07:31:00.000-07:00

The clinical queries in Ovid are exactly the same ones in PubMed but they have been translated into the appropriate Ovid syntax.

How you get to them is what's different.

After choosing to search MEDLINE via the Ovid search interface, conduct your topic search. When that's complete to your satisfaction, click on the Limit button (Hint: it's the target icon). Scroll until you see 'Clinical Queries' box. This box contains three possible filters for each category (i.e., therapy (sensitivity), therapy (specificity), therapy (optimized)). The categories are therapy, diagnosis, etiology, prognosis, clinical prediction guides, costs, economics, reviews, and qualitative reviews. Select the appropriate filter and then click on the red 'Limit A Search' button. The results will be posted to the Search History box on the main search page.

Now a word about the 'optimized' category - which is a category that PubMed doesn't offer. Brian Haynes describes this category as "search strategies that best balance sensitivity and specificity".

As with everything in life, practicing and experimenting with these clinical queries will help you determine when it's best to use them and when it's not.

For more information:

Finding the gold in MEDLINE: clinical queries. Haynes, RB Wilczynski, N. ACP Journal Club 142(1): A8, Jan/Feb, 2005

Clinical Queries in PubMed

2005-08-03T06:30:00.000-07:00

You can find the PubMed Clinical Queries page under PubMed Services in the blue scan column on the left. But if you want a list of all the topic-specific PubMed queries provided by the National Library of Medicine (NLM) Bibliographic Services Division, check out the Special Queries (appears in the same blue scan column right under Clinical Queries).

The clinical queries page allows you to do three types of searches: search by clinical study category, find systematic reviews, or medical genetics searches.

Health services research study categories include appropriateness, process assessment, outcomes assessment, costs, economics, and qualitative research. Click on Special Queries to get to the health services research filters.

The best way for you to get a feel for how these work is to give it a try!

For more information about the construction of PubMed search filters:

Summary of Enhancements for Clinical Queries for MEDLINE for studies
Related Resources for Searching for Systematic Reviews
Filter Table
Finding the gold in MEDLINE: clinical queries. Haynes, RB Wilczynski, N. ACP Journal Club 142(1): A8, Jan/Feb, 2005
Health Services Research Study Design Definitions

Hedges, clinical queries, search filters

2005-08-01T06:19:00.000-07:00

If you haven't used hedges, clinical queries or search filters, then you're missing a powerful searchers' tool.

These predefined search strategies are mostly available in databases based on controlled vocabularies but not always. MEDLINE (both PubMed and Ovid), PsycINFO, and to some degree, CINAHL all provide some form of search filters - and of course, each database refers to them by a different name.

Whatever the name (and henceforth my term is 'search filters'), they compensate for indexing inconsistencies, the vagaries of the English language, and different levels of search skill competence.

In MEDLINE, these search filters focus on levels of evidence (RCTs, systematic reviews, etc.), clinical queries (therapy, etiology, diagnosis, prognosis) , or health services research (costs, economics, outcomes assessment). In PsycINFO, filters cover such areas as: achievment measures, attitude measures, neuropsychological assessment, "talking" therapies and more.

How does it work?

Conduct your topical search.
Find and run the search filter.
Using AND, combine the result of your topical search with the final set number of the search filter.

Tune in again for the gory details (PubMed, Ovid, PsycINFO and CINAHL)!

Expanded Years for Science Citation Index

2005-07-29T06:56:00.000-07:00

The Science Citation Index (from the Web of Science) is now online from 1900 to the present. You can search for early 20th Century articles written by such notables as Albert Einstein, Alexander Fleming and Marie Curie and retrieve article citation data. This added coverage is from 262 journals published between 1900 to 1944 and a full journal list is available.

FYI
Web of Science is listed under Major Resources on the Library's home page.

Web of Science: Results Analysis

2005-07-26T07:30:00.000-07:00

Have you explored the Results Analysis feature in the Web of Science?

The results analysis extracts data values from a field you select and then produces a report showing the values in ranked order.

For example, suppose you search Web of Science for articles about conjunctivitis in children. You could use this feature to generate a list of authors who published articles on that subject. The authors who published the largest number of articles would be at the top of the list.

Some of the other ways to analyze the results are by: institution, country/territory, document type, institution name, language, publication year, source title, and subject category.

To perform a results analysis, click the Analyze button on any Summary Results page to go to the Results Analysis page.

Check it out!

PubMed search terms highlighted

2005-07-25T07:10:00.000-07:00

Well, this is pretty cool.

On July 19, PubMed added a highlighting feature that will help you find just where your search terms are. Search terms will be highlighted in pale yellow in the Summary, Abstract, and Citation display formats.

Highlighted terms will include your search terms as well as terms that have been added by PubMed to enhance your search. Check out the 'Details' tab to see how PubMed translated your terms.

Highlighting must be turned on in My NCBI and is only active when you are signed into My NCBI. Register/Sign in to My NCBI and click on User Preferences on the My NCBI sidebar. The default will be "Off." Selecting a color and clicking OK activates this feature.

For more information about this see the NLM Technical Bulletin. All the details and more...

Web of Science: cited reference searching

2005-07-21T08:38:00.000-07:00

For my example, I want to see who has cited the following article since it was published in 1994:

Tinetti ME, Baker DI, McAvay G, Claus EB, Garrett P, Gottschalk M, Koch ML, Trainor K, Horwitz RI. A multifactorial intervention to reduce the risk of falling among elderly people living in the community. N Engl J Med. 1994, 331(13):821-7.

From the Major Resources scan column on the Library's web page, click on "Web of Science". Click on 'Cited Reference Searching'.

In the Cited Author box, enter the author's last name and initials:
tinetti m* [* is the truncation symbol]

In the Cited Year box, enter the year:
1994

Click on the SEARCH button.

The next screen displays all of the works by tinetti m* in 1994 sorted alphabetically by cited work. We're looking for the article in the New England Journal of Medicine and you can see that articles in that journal begin about halfway down the page.

Here's a segment of what that looks like:

I've highlighted the article with a red box. Notice the 627 in the 'Times Cited' column and that other entries above and below this one seem to be for the same citation. Looking closely you'll see that the problem is mostly with different page numbers. This usually means that some authors could be a tad more careful in typing or proofreading their bibliographies.

Click on 'View Record' (on the far right) to view the full record details including the bibliographic information, abstract, author addresses and more. But the most important bits on the full record screen are the 'cited references' and the 'times cited' links.

The 'Cited References' are the references that ME Tinetti cited in this article -- in other words, her reference list for this article. The 'Times Cited' are the articles that have cited this one in their reference lists since it was published in 1994.

Give this a try with an article that you know and love. Explore some of the other links!

Tips
If you're wondering why I didn't enter the journal title in the 'Cited Work' box, it's because it's too time consuming to find the 'right' journal abbreviation. I always start with the author and the year - if the author is prolific in that year then I begrudgingly use the tools to find the 'right' abbreviation for the journal. MEDLINE users know the New England Journal of Medicine as N Engl J Med but in the WoS, it's New Engl J Med. A painful lesson...

More about comparisons

2005-07-20T08:34:00.000-07:00

A comment on yesterday's entry asked "So, is there overlap between the databases? Is scopus the best, based on this? Or does web of science and google have uniques hits?"

This is a great question - one that I had myself immediately after I did this test (along with lots of other questions!). But, I can't answer it definitively...yet. Because of this little test, several colleagues and I are going to take a look at the resulting sets of cited references and do some in-depth comparisons. I'll report back when that's completed.

That said, however, I think that looking at what the three databases cover just in terms of types of materials, dates covered, total number of items indexed/covered then a clearer picture emerges of how and where the differences might occur. This chart takes information directly from each product's web site and gives only a superficial look at what's really under the hood. Notice that Google Scholar is not at all forthcoming about the depth and breadth of what material they are covering.

It may be that you won't be able to select a 'best' resource for cited reference searching and that depending on your discipline and the purpose for your cited reference search, you might end up using multiple resources to get the best result.

Cited reference searching: comparisons

2005-07-19T07:25:00.000-07:00

I thought it would be interesting to look at how Google Scholar, the Web of Science, and SCOPUS fared in head-to-head competition in cited reference searching. For an explanation of cited reference searching see Cited Reference Searching (July 6).

I chose four articles by Yale School of Medicine authors and using each of the three databases, looked at the 'times cited' or 'cited by' fields. I compared the numbers in the chart below.

If you're wondering what that number in parentheses on the Web of Science line is for, it simply indicates how many people cited the article incorrectly... in most cases the page number was slightly off.

FYI
Here's the deets for the four articles:

Inzucchi SE. Oral antihyperglycemic therapy for type 2 diabetes: scientific review. JAMA. 2002, 287(3):360-372.

Kazdin AE, Weisz JR. Identifying and developing empirically supported child and adolescent treatments. J Consult Clin Psychol. 1998, 27(2):217-36.

Mellman I, Steinman RM. Dendritic cells: specialized and regulated antigen processing machines. Cell. 2001, 106(3):255-8.

Tinetti ME, Baker DI, McAvay G, Claus EB, Garrett P, Gottschalk M, Koch ML, Trainor K, Horwitz RI. A multifactorial intervention to reduce the risk of falling among elderly people living in the community. N Engl J Med. 1994, 331(13):821-7.

Search Tips Blog is back!

2005-07-18T07:20:00.000-07:00

That is, the blogger herself is back.

I've been on vacation on and off for the last six weeks but I'm back now and ready to 'tip' away...

Thanks to Judy Spak, who both guest blogged and entry-posted while I was away!

Image Resources for Teaching

2005-07-07T07:38:00.000-07:00

Judy Spak, Curriculum Support Librarian, has created a great new resource page which includes commercial biomedical image databases (restricted access), Yale image resources, and a compilation of general image directories and databases.

FYI
Image Resources for Teaching

Cited Reference Searching

2005-07-06T08:36:00.000-07:00

Cited reference searching is different than subject searching in that this technique allows you follow the evolution of a topic forward and backward in time. Here's how it works...

You've started your search for information and have located an article written in 1995 that seems to be almost perfect but it's a tad old. Wouldn't it be helpful if you could identify articles that have cited this wonderful article since it was written in 1995? Using the technique 0f cited reference searching, you can accomplish this fairly simply.

The logic behind cited reference searching is that an author cites articles that are related to his.

Some of the reasons why an author might cite another article are that it might:

provide part of the context in which the current paper is being written or is another aspect of the same topic
represent an earlier stage in research or thinking which is explored further in the current paper
provide a technique or procedure used in the current study
state something that the author of the current paper would like to refute

In other words, you can watch a topic evolve...not to mention that you can check out how many times your own articles have been cited.

There are many resources that provide cited reference searching but the gold standards are Science Citation Index, Social Science Citation Index, and the Arts and Humanities Citation Index from the Web of Science.

CINAHL and PsycINFO are two other databases that have been adding cited references to each article record for several years (more about that in future posts!). SCOPUS, a new product for our library, offers cited reference analysis and Google Scholar allows a form of cited reference searching.

Watch for some comparisons in upcoming posts!

New! Journal Citation Reports 2004 data

2005-07-05T05:54:00.000-07:00

Thomson Scientific just announced that the 2004 data is now available for Journal Citation Reports.

Enhancements include more category level analysis: much of the same statistical information available for individual journals is now available for journal categories, for data from 2003 forward. This provides a view of coverage, citation behavior and relationships across an entire subject. Cited Category and Citing Category lists show the most frequently cited journals in the subject. This information helps put a journal's impact factor into context.

FYI
See previous post on JCR.

Database Highlight: PIER

2005-06-30T05:59:00.000-07:00

PIER (Physicians' Information and Education Resource), produced by the American College of Physicians - American Society of Internal Medicine, is a web-based information support tool specifically designed to deliver rapidly accessible, comprehensive, up-to-date, and evidence-based guidance to clinicians. The information, written by experts and peer-reviewed, is presented in a standard structure that mirrors questions and decisions that physicians routinely address when caring for patients.

Content is organized around five modules: diseases; screening and prevention; complementary and alternative medicine; ethical and legal issues; and procedures. Each section begins with a few succinct evidence-based guidance statements - and clicking on a guidance statement brings up a specific recommendation and its supporting rationale, evidence, and comments. All recommendation statements have letter grades that alert the user to the strength of supporting evidence.

The Medical Library subscribes to PIER through the Stat!Ref service.

Give it a try! It's really easy to use.

FYI
Available from the All Major Resources A-Z list. Click on Stat!Ref.

MEDLINE Database on Tap

2005-06-28T05:22:00.000-07:00

MEDLINE Database on Tap (aka MD on Tap or MDoT) is a Web application which targets mobile health care professionals by facilitating access to medical information at the point of care. MDoT provides a way to search the National Library of Medicine's MEDLINE, read abstracts from a set of 120 core clinical journals, and access the ClinicalTrials.gov database. To use it, you need a PDA with Palm 4.0 OS or higher and a wireless Internet connection. An equivalent Pocket PC client is underdevelopment.

The client is available for PDAs and smartphones with Palm operating systems and a wireless connection to the Internet. You can download the newest version from http://mdot.nlm.nih.gov/proj/mdot/downloadPalm.php.

With this newest version, there are two cool new features:

When the Auto Spell Check option is selected, ambiguous search terms are replaced with those terms suggested by an internal NLM e-spell utility for the actual search. The actual terms used are shown at the bottom of the Search tab.
As an alternative to the default PubMed search engine, you can select Essie, an experimental probabilistic search engine developed at the Lister Hill National Center for Biomedical Communications. Essie ranks results by relevance, then by date. These options can be combined with any (or all!) of the other search options. Also, a big, friendly “Go” button has replaced the magnifying glass as the icon to tap to execute your search.

Check out the screenshots.
Download the program and give it a try!

PubMed RSS feeds

2005-06-27T05:14:00.000-07:00

RSS feeds are available from PubMed. To add a PubMed search to your RSS feeds, run a search in PubMed and choose RSS Feed from the Send To pull-down menu.

For detailed instructions see the NLM Technical Bulletin .

Entrez: The Life Sciences Search Engine

2005-06-17T09:26:00.000-07:00

In my previous post, I discussed the rich linking environment in Entrez. What makes this resource even more impressive is the search gateway page that NCBI has created to search across all of Entrez's inter-connected nodes with one query.

The gateway is a wonderful place to start a search of the Entrez system. For example, I saw a recent Yale Medicine article on zebrafish and I’d like a summary of related information on that topic.

Try typing in zebrafish on the query line and the system searches across all of Entrez's nodes. Sometimes there are hundreds or thousands of results from a particular database and sometimes there are no relevant results returned. This makes sense, since not all nodes may contain data on a particular topic.

As always, NCBI provides excellent Help for this resource, including mouse-over synopses of the nodes and their scope. Entrez even searches for relevant NCBI and other outside websites and resources, including the National Library of Medicine's on-line catalog. Another nice feature of the gateway is that it uses MeSH (Medical Subject Headings) to search PubMed.

The Entrez gateway is a great place to start researching a topic, but it has its limitations. To perform a thorough search of a specific aspect of your topic, such as genomic information or nucleotide sequences, it's always best to use the search screens for the individual nodes.

Take the Entrez gateway out for a spin at www.ncbi.nlm.nih.gov/gquery/gquery.fcgi
You'll be amazed at the power of this search engine.

Tip: The Entrez gateway is called different things, depending on which Entrez node you are searching. If you are in PubMed, the link to the gateway is called All Databases. In other nodes, it's called Entrez.

Posted by Judy Spak, guest blogger.

ISI Essential Science Indicators

2005-06-16T10:01:00.000-07:00

Essential Science Indicators (ESI) provides internet access to a compilation of essential science performance statistics and science trends data derived from ISI's databases. The chief indicators of output, or productivity, are journal article publication counts. For influence and impact measures, ESI employs both total citation counts and cites per paper scores. The former reveals gross influence while the latter shows weighted influence, also called impact.

Types of data featured in ESI include most cited author rankings, institutional (university, corporate, government research lab) rankings, national rankings, and journal rankings. Another unique feature is the listing of research areas called Research Fronts, algorithmically derived topics reflecting research intensive and breakthrough areas of current science. An editorial feature called Special Topics gives special attention to selected areas of research.

Highly cited papers and hot papers have been selected for ESI based on percentile rankings specific to fields of science and specific time periods. While highly cited papers are chosen from the most recent 10 years of data, hot papers focus on very recent papers (from the past two years) that show an unusual rate of citation in the current period. Both highly cited and hot papers are searchable by a variety of attributes.

FYI

It is important to recognize that the data in ESI are limited to ISI-indexed journal articles only. No books, book chapters, or articles published in journals not indexed by ISI are taken into account here, either in terms of publication or citation counts.
Data is updated every two to four months.
Check out the HELP (and I'd put a link in here but for the fact that the page consists of frames! UGH!)
ESI is a part of the ISI Web of Knowledge.

Journal Citation Reports

2005-06-15T09:30:00.000-07:00

If you've ever wondered about how to choose the 'best' journal in a discipline to submit your article to, Journal Citation Reports is the resource for you.

This comprehensive and unique resource tool allows you to evaluate and compare journals using citation data drawn from over 7,000 scholarly and technical journals from more than 3,300 publishers in over 60 countries. It is the only source of citation data on journals, and includes virtually all specialties in the areas of science, technology, and social sciences. Journal Citation Reports can show you the:

Most frequently cited journals in a field
Highest impact journals in a field
Hottest journals in a field
Leading journals in a field
Most published articles in a field

FYI
JCR is available from the Medical Library's home page - look for Journal Citation Reports under Major Resources.
If you're new to this resource, check out the tutorial and if you really need detailed information, check out the HELP
JCR is part of the ISI Web of Knowledge.

Introducing Entrez

2005-06-14T10:44:00.000-07:00

Most people are familiar with PubMed, but I wonder how many know about the extremely rich databases, that along with PubMed, make up the Entrez system.

Created by the National Center for Biotechnology Information (NCBI) in 1991, Entrez began as a system that contained three "nodes", one for published articles (MEDLINE, later called PubMed), a nucleotide database and a protein database. Today, Entrez is made up of more than 20 nodes or databases. Each node represents specific data objects of the same type, e.g., protein sequences.

What makes Entrez such a robust search system is that it integrates the biomedical literature, DNA and protein sequence databases, 3D protein structure and protein domain data, population study datasets, expression data, assemblies of complete genomes, and taxonomic information into a tightly interlinked system. THIS IS VERY POWERFUL STUFF! These links allow you to search in one of the nodes or databases and link to related information in the other databases.

The image above is a thumbnail of an interactive graphic that demonstrates the rich linking between the Entrez nodes. Check it out on the Model of Entrez Databases page . Place your mouse on one of the nodes and it will show the various links to other databases, including how many records are linked from each resource. Very cool.

For a more in-depth description of the Entrez search and retrieval system, visit the Entrez information pages from NCBI.

Posted by Judy Spak, guest blogger. Stay tuned for more Entrez posts coming soon.

Searching for Guidelines

2005-06-13T02:56:00.000-07:00

Searching for practice guidelines is much easier when you use the National Guideline Clearinghouse.

This comprehensive database of evidence-based clinical practice guidelines and related documents is an initiative of the Agency for Health Care Research and Quality (AHRQ), U.S. Department of Health and Human Services.

The mission of NGC is to "provide physicians, nurses, and other health professionals, health care providers, health plans, integrated delivery systems, purchasers and others an accessible mechanism for obtaining objective, detailed information on clinical practice guidelines and to further their dissemination, implementation and use."

Key Features

Search
There are three ways to search NGC. The first is the basic search box that appears on every page; the second is the detailed search allows you to create very specific search queries based on various attributes such as target population; and the third, frequently requested searches, is designed to assist NGC users in finding guidelines related to frequently requested search topics.
Browse
This handy feature allows users to scan for guidelines available on the NGC site by disease/condition, treatment/intervention, or developing organization.
Compare
This unique feature provides you with the ability to generate side-by-side comparisons for any combination of two or more guidelines. You can also look at syntheses of selected guidelines that cover similar topic areas.
Resources
NGC has compiled a lengthy list of resources including annotated bibliographies, discussion list, FAQs, patient resources, PDA downloads, guideline archives, etc.

Keep this resource in mind when you are looking for clinical guidelines...it will save you time.

Field Guide to MEDLINE

2005-06-10T11:50:00.000-07:00

Here's a handy book that I recommend to anyone who wants to build their searching skills. It covers an overview of content, basic tools and search strategies in the second chapter and then in the third and fourth chapter applies the techniques to PubMed and Ovid. So chapter 3 covers PubMed and chapter 4 covers Ovid. There are ample screen shots to illustrate each technique.

And even though both of these interfaces are changing and might not look exactly like they did when this book was produced in 2003, the theory and techniques will not change.

Borrow it from your local library...I'm sure you'll find it useful.

Stave, Christopher D. Field Guide to MEDLINE: Making Searching Simple. Philadelphia: Lippincott Williams & Wilkins, 2003.

Database Highlight: images.MD

2005-06-09T08:04:00.000-07:00

images.MD compiles over 50,000 high-quality images spanning all of internal medicine, all derived from Current Medicine’s series of illustrated atlases. Each image is accompanied by detailed text written by over 2,000 contributing experts.

The images include: histology, pathology, radiographs, original artworks, graphs, tables, or just the state-of-the-art commentary. Detailed references accompany each image. Most importantly, because the Yale Medical Library subscribes to images.MD, you're provided with unlimited personal use of the images in your collections, plus the tools and online workspace to help you use them effectively.

This database of images provides both a basic and advanced search feature as well as an easily browsed index. The My Slides feature lets you create and manage slidesets.

Check it out! You can find images.MD on the Medical Library's homepage under the eResources scan column.

Selecting keywords for your journal article

2005-06-08T06:07:00.000-07:00

The National Library of Medicine offers some general suggestions for authors as they select keywords for their articles. Use their database to help you locate appropriate vocabulary.

And don't forget that your friendly Medical Librarian can also give you assistance in choosing appropriate keywords for your journal article!

Using subheadings in MEDLINE

2005-06-07T04:18:00.000-07:00

Many MEDLINE searchers utilize subheadings when they want to hone in on a specific aspect of a topic. There are 83 of these topical subheadings and when used in conjunction with a MeSH term, you can really fine-tune your results.

Here are some examples of frequently used subheadings: adverse effects, complications, diet therapy, drug therapy, diagnosis, etiology, epidemiology, therapy, psychology, nursing, etc.

I use subheadings frequently when I'm doing a clinical search. For example, if my search question has to do with how effective pharmacotherapy is in improving cognitive symptoms in patients with dementia, then linking the subheading 'drug therapy' to the subject heading 'dementia' will produce a set of citations that is specifically about the treatment of dementia with drugs. Then I would continue to search for the other concepts in my search question.

FYI
Don't forget the MeSH website. Check it out!

Indexing articles for MEDLINE

2005-06-06T06:34:00.000-07:00

If you've ever wondered how articles are indexed and who does the indexing for MEDLINE, here's a few details.

Altogether, about 100 indexers perform the indexing for the National Library of Medicine (NLM) and they are all trained by NLM. Indexers have at least a Bachelor's degree in life sciences, attend a two-week formal training class at NLM, and undergo continuous review for a year. The required production rate is 4 articles per hour.
Indexers work in an online environment which provides extensive validation and 'reminder' programs to enhance consistency and accuracy.
The sequence is: understand the subject content of the article, apply MeSH terms to cover all topics substantively discussed, apply 10-12 MeSH terms per article, indicate major points of the article with an asterisk, apply the subheadings, apply check tags (organism, age, gender, etc.)
Authors frequently want to know how to select keywords for their articles, but NLM doesn't use author-assigned keywords in MEDLINE. Only keywords assigned from the Medical Subject Headings (MeSH) are used. NLM finds that authors frequently choose MeSH terms that are too broad - NLM policy is to select the most specific subject heading possible. A tip for authors from NLM is to use their preferred keywords in the title or abstract where they will be retrievable via textword searching.

For more information:
FAQs about Indexing

Clinical Prediction Guides Added to PubMed Clinical Queries

2005-06-03T05:50:00.000-07:00

Check out the Clinical Queries page under PubMed Services on the left scan column.

A new clinical study category has been added - Clinical Prediction Guides.

Clinical Prediction Guides pertain to the prediction of some aspect of a disease or condition and have been advocated as a mechanism for enhancing clinical judgement. Clinical prediction studies develop or validate rules, guides, indexes, equations, scales, scores or models to predict a diagnosis, prognosis, risk (etiology), therapeutic response, therapeutic drug level or clinical outcome.

An example of a clinical prediction guide is the Modified Mid America Heart Institute Coronary Care Unit scoring system - a new comprehensive prognostic index for Coronary Care Unit patients. Med Sci Monit. 2005 Feb 25;11(3):CR95-99

Database Hightlight: Clinical Evidence

2005-06-01T06:28:00.000-07:00

When you're looking for evidence on the effects of common clinical interventions, consider using Clinical Evidence.

Clinical Evidence summarizes the current state of knowledge and uncertainty about the prevention and treatment of clinical conditions, based on thorough searches and appraisal of the literature. It is neither a textbook of medicine nor a set of guidelines. It describes the best available evidence from systematic reviews, RCTs and observational studies where appropriate, and if there is no good evidence it says so.

The contents are driven by questions rather than by the availability of research evidence. Rather than start with the evidence and summarise what is there, they identify important clinical questions, and then search for and summarise the best available evidence to answer them.

The summaries in Clinical Evidence result from a rigorous process aimed at ensuring that they are both reliable and relevant to clinical practice. You can check out this process by looking at their search strategies and their critical appraisal criteria (under the 'About Us' tab on the Clinical Evidence web site)

Clinical Evidence is available from the Major Resources A-Z list on the Cushing/Whitney Medical Library's home page. And the print version is available in the Medical Library Information Room (Ref 18 RA427 C45)

The Facts
Published by BMJ Publishing Group
Updated continuously, with full literature searches in each topic every 12 months
Available in electronic and print (full-text and Concise)
Web version updated monthly; print version updated twice yearly

Full author name searching enhanced: PubMed

2005-05-31T06:29:00.000-07:00

You can now search full author names in PubMed!

The National Library of Medicine has included full author names in MEDLINE records since 2002 - except until now the full author field has only been a display field - you could never search the field.

Just type the full author name on the query line: julia s wong

Some tips:

You can use the Single Citation Matcher but not the new first author name search feature.
Searching by full author name limits to citations to articles published from 2002 forward, and to journals that publish using the full names of authors.
You can type the name in natural (julia s wong) or inverted order (wong julia s).
You can browse full author names in the Full Author Name index available on the Preview/Index screen. Select Full Author Name on the fields pull-down menu, enter a last name in the box, and click on Index.

Give it a try!

For more details, see the NLM Technical Bulletin
http://www.nlm.nih.gov/pubs/techbull/mj05/mj05_full_author.html

Related Records: Web of Science

2005-05-25T08:35:00.000-07:00

Try out the 'Related Records' feature from any of the Web of Science databases - Science Citation Index, Social Science Citation Index, and the Arts & Humanities Citation Index.

Once you click on the related records link for a particular article, the Summary page displays a list of articles whose cited reference lists include at least one of the sources cited by the original article (the original articles title always appears at the top of the page -- just to help keep you oriented). Articles that share the largest number of sources with the original article are listed first.

Related Records searching assumes that articles citing the same works have a subject relationship, regardless of whether their titles, abstracts, or keywords contain the same terms. The more cited references two articles share, the closer this subject relationship is.

You can use this feature to find "more like this" articles. For example:

1. After searching on the topic otitis media AND diagnosis, you find the article by K. Blomgren titled " Current challenges in diagnosis of acute otitis media".
2. Click on the Cited References to examine the article's cited reference list.
3. Most of the 49 cited references look relevant so you click on Find Related Records.
4. The Related Records - Summary page displays articles whose reference lists include at least on of the articles cited by the Blomgren article.

The articles that share the greatest number of references with the original article appear at the top of the list.

You can also click on the related records link for any individual article as well.

To view the references shared by the two Related Records, click the link in the Shared Refs column. The number in this column is the number of references shared by the two Related Records. The number in the Cited Refs column is the total number of references in the record's cited reference list.

Give it a try!