Health and Medical News and Resources

General interest items edited by Janice Flahiff

New Image Search Engine from the National Library of Medicine For Biomedical Articles

From the Web announcement

The Open-i project aims to provide next generation information retrieval services for biomedical articles from the full text collections such as PubMed Central. It is unique in its ability to index both the text and images in the articles. The article retrieval is powered by Essie (the search engine that supports ClinicalTrials.gov).

Open-i lets users retrieve not only the MEDLINE citation information, but also the outcome statements in the article and the most relevant figure from it. Further, it is possible to use the figure as a query component to find other relevant images or other visually similar images. Future stages aim to provide image region-of-interest (ROI) based querying. The initial number of images is projected to be around 600,000 and will scale to millions. The extensive image analysis and indexing and deep text analysis and indexing require distributed computing. At the request of the Board of Scientific Counselors, we intend to make the image computation services available as a NLM service.

Vist our Frequently Asked Questions page for more information and help.openi-large
Related articles

 

December 12, 2012 Posted by | Biomedical Research Resources | , , , , | Leave a comment

MedTerm Search Assist – A database to share biomedical terminology and strategies for comprehensive searches

MedTerm Search Assist

By librarians for librarians — A database to share
biomedical terminology and strategies for comprehensive searches

From a Medlib-L listerv entry dated 15 July 2011

The MedTerm Search Assist http://www.hsls.pitt.edu/terms/> database was developed at the Health Sciences Library System, University of Pittsburgh, for librarians to share terminology, MEDLINE search strategies, and search tips with one another for comprehensive searches such as systematic reviews. Any librarian can add a new term into the database or suggest additions for existing records.

Before being displayed in the database, all submitted terms are reviewed for obvious errors such as misspellings, but are not reviewed for thoroughness, quality, or accuracy.

To contribute or browse the database please visit: www.hsls.pitt.edu/terms http://www.hsls.pitt.edu/terms>.

For comments or questions regarding the database please fill out the available form: http://www.hsls.pitt.edu/terms/contact
<http://www.hsls.pitt.edu/terms/contact> or e-mail the project managers  directly: Ahlam Saleh, saleha@pitt.edu or Melissa Ratajeski, mar@pitt.edu

July 18, 2011 Posted by | Librarian Resources | , , , | 2 Comments

PubMed Mobile Beta & Helpful Links on Searching PubMed for BioMedical Information

From the National Library of Medicine (NLM)  Technical Bulletin article posted March 17 2011

PubMed® Mobile Beta provides a simplified mobile friendly Web interface to access PubMed***. PubMed Mobile includes the same basic search functionality and content as Standard PubMed; that is, all search terms and fields work similarly (see Figure 1).

Screen capture of PubMed Mobile homepage.

Simply enter your search in the search box and click “Search” (see Figure 2).

The inital (Summary) display includes the article title, first author’s name, journal title abbreviation, and year of publication.

Click “Free Full Text” or “Review” on the Summary search results page to filter your results. Click “Next” to go to subsequent search result pages.

Click the article title to display the Abstract format (see Figure 3).

Not all data provided on the Standard PubMed Abstract format are included (for example, MeSH® vocabulary); to see complete data use the link to Standard PubMed.

Related Citations display below the abstract. On the abstract page, click “Previous” or “Next” to navigate to other citation abstracts. Click the “Back to results” link to redisplay the Summary search results (see Figure 4).

A link to Standard PubMed is available at the bottom of all PubMed Mobile pages.

PubMed Mobile does not include specialized search pages, such as Limits and Advanced search, or added features, such as My NCBI, Clipboard, or LinkOut/Outside Tool. To use these and other PubMed features, display your retrieval in Standard PubMed via the link at the bottom of the screen.

By Kathi Canese and Edward WelkerNational Center for Biotechnology Information

***PubMed is the largest indexer of the biomedical literature in the world. It can be rather intimidating to search the first few times because there are many options to refine your search in order to get tailored relevant results. Believe me, it is worth the effort!

If you would like expert personalized PubMed search advice, please do not hesitate to contact (preferably call ahead!) a  reference librarian at your local academic, medical, or public library.

Many academic and medical libraries offer some degree of personalized reference service to the public. These services are largely offered by professionals with a Masters degree in Library Science who have many years experience providing relevant research articles and other resources to a wide variety of health professionals and others. They enjoy teaching both formally and informally.

Please feel free to email me (jmflahiff at yahoo.com) with any questions. I would be happy to work on a question for up to 2 hours and reply within 3 days. No charge.

Here are some PubMed tutorials and guides


Related Articles

March 18, 2011 Posted by | Biomedical Research Resources, Finding Aids/Directories, Librarian Resources, Professional Health Care Resources | , , , , , , , | Leave a comment

PubMed Toxicology Subset Streamlines Biomedical Searches in the Professional Literature

Logo for PubMed, a service of the National Lib...

Image via Wikipedia

From a March 25 2011  NLM-TOX-ENVIRO-HEALTH-L NOTICE

The National Library of Medicine (NLM) PubMed database offers a toxicology subset. This subset is created by NLM’s Specialized Information Services (SIS) to facilitate searching for subjects in the area of toxicology.

Here is how to limit searches to toxicology:

  • Go to Pubmed
  • Click on Limits (above search box), and select Toxicology under Subsets

OR

Click on Advanced Search (above search box) , then Limits while building the search

The toxicology subset can also be placed in a search as “tox [sb]”.   Example:   lead AND tox [sb]

The PubMed database comprises more than 19 million citations for biomedical articles from MEDLINE and life science journals. Citations may include links to full-text articles from PubMed Central or publisher web sites.

Here are some PubMed tutorials and guides

Related Articles

March 16, 2011 Posted by | Biomedical Research Resources, Librarian Resources | , , , , | Leave a comment

PubMed MeSH database changes

The PubMed** interface is being changed section by section.
The MeSH section has been revised. 
Here is a message from the GMRLIST (an email list for the National Network of Libraries of
Medicine-Greater Midwest Region (NN/LM-GMR) members)

Hi Folks,Many of you have noticed the change in the MeSH database interface.
http://www.ncbi.nlm.nih.gov/mesh
NCBI is working to update the entire website – section by section.FYI:The Technical Bulletin article
on this change is at:http://www.nlm.nih.gov/pubs/techbull/jf11/jf11_pm_mesh_db.htmlThe updated brochures “Searching PubMed with MeSH are at:
PDF: http://nnlm.gov/training/resources/meshtri.pdf
Word: http://nnlm.gov/training/resources/meshtri.doc

If you have comments or questions about the new interface, feel free to contact NLM directly –
they welcome your feedback.http://apps.nlm.nih.gov/mainweb/siebel/nlm/index.cfm/


Here is a related posting from MEDLIB-L (a medical librarian listserv)

Here’s what I recvd. from NNLM: There have been some changes to MeSH.
–>Type your search term in the MeSH box.
–>Then click the box(es) on the left to select your term(s).
 –>Then click on the far right: Add to Search Builder Here are some helpful resources
(you have to click CTRL + Click for the URLs to work).

PubMed’s MeSH Database**
Searching with the MeSH Database
<http://www.nlm.nih.gov/bsd/viewlet/mesh/searching/mesh1.html> (3 min., February 2011)
* Combining MeSH Terms Using the MeSH Database
<http://www.nlm.nih.gov/bsd/viewlet/mesh/combining/mesh2.html> (3 min., February 2011)
* Applying Subheadings and Other Features of the MeSH Database
<http://www.nlm.nih.gov/bsd/viewlet/mesh/subheadings/mesh3.html> (3 min., February 2011)
You can also see the MeSH Database section in the tutorial:
http://www.nlm.nih.gov/bsd/disted/pubmedtutorial/020_

**Pubmed is the largest database of biomedical journal articles (some are free full text) in the world.
It is most often best searched using medical subject headings (MeSH).

The above two hyperlinks (PubMed and MeSH) including Help pages and tutorials.
Please do not hesitate to contact a public librarian, academic librarian, or medical librarian for assistance
in searching PubMed or locating medical articles.
In the case of academic or medical settings, call ahead to see what services the library has for the general
public.You just might be pleasantly surprised!

(You may also email me at jmflahiff@yahoo.com…I am willing to give free assistance which would
include about an hour of my time)

February 16, 2011 Posted by | Biomedical Research Resources, Finding Aids/Directories, Librarian Resources, Professional Health Care Resources | , , , , , , , , , , | Leave a comment

NLM Catalog: New Search Features for Journals Cited in Entrez Databases

The National Library of Medicine (NLM) has recently launched a redesigned NLM Catalog that implements new search and display options related to journal searching. The search feature applies to PubMed and other Entrez databases.

According to the NLM Technical Bulletin item (full text here), the search and display options will include the search fields acid-free, broad subject terms, current format status, version currently indexed, endyear, ISO abbreviation, language, start year, and NLM title abbreviations. Nice summary table and screenshots.

 

December 21, 2010 Posted by | Uncategorized | , , , , , , , | Leave a comment

NLM® Catalog and Journals Databases Merge

From the November 19, 2010 NLM Technical Bulletin issue
[Please go to http://www.nlm.nih.gov/pubs/techbull/nd10/nd10_nlm_catalog.html to view the entire article, including the accompanying screenshots]

The National Library of Medicine® (NLM) Catalog will soon be redesigned to provide users with a streamlined interface and enhanced search and display of the 1.4 million bibliographic records in the NLM database. The NLM Catalog will contain detailed MEDLINE indexing information about the journals in PubMed® and other National Center for Biotechnology Information (NCBI) databases. The Journals Database will be retired.

What is new in the NLM Catalog

    Additional searchable fields
    Enhancements to the Limits page
    New Journal display option and expanded Full display
    Additional filters
    Searching for Journals
    Launching PubMed searches from the NLM Catalog
    Effect on EUtilities

Additional searchable fields
New search tags will be added to limit searches to a specific field. Some of the new search tags are: Broad Subject Term(s), Current Format Status, Current Indexing Status, Version Indexed, ISSN, and PubMed Central® Holdings. See the full list of Search Field Descriptions and Tags in the NLM Catalog Help

Enhancements to the Limits page
A new category of Limits will be added called Journal Subsets. Users are able to limit searches to journals referenced in the NCBI databases, only PubMed journals, journals currently (or previously) indexed for MEDLINE®, PubMed Central journals, and PubMed Central forthcoming journals. Users can also limit searches to journals published in electronic-only format.

A new Images Material Type (images from the History of Medicine database) and three new Publication Types, Portraits, Postcards, and Posters, will also be added.

New Journal format display option and expanded Full display
A Journal display will be added to the Display Options in the NLM Catalog. This display includes fields of interest to those searching for information about journals, including MEDLINE indexing information. The Full display will also be expanded to include all available fields where applicable.

Additional filters
The following new filters have been created: Journals in the NCBI databases, Journals Currently Indexed in MEDLINE, and PubMed Only Journals. Users can view all available filters by browsing the index on the Advanced Search page. For more information about changing My NCBI filter preferences, please see the My NCBI Help.

Searching for Journals
The NLM Catalog will contain detailed MEDLINE indexing information about the journals in PubMed and other NCBI databases. Users can limit NLM Catalog searches to journals in the NCBI databases by using the Journals in NCBI Databases link on the NLM Catalog homepage or the Limits page (see Figure 1).

Figure 1: NLM Catalog homepage
Enter a topic, journal title or abbreviation, or ISSN into the search box and click Search. Automatic suggestions will display as you type your search terms (see Figure 2).

Figure 2: Journals referenced in the NCBI Databases
On the Summary display, click the journal title or select Journal or Full from the Display Settings menu to view additional information. Note that the limit is activated and can be changed or removed by clicking the appropriate links (see Figure 3).

Figure 3: Summary Display with Limits Activated
Users can also visit the Limits page to limit a search to various journal subsets. The NLM Catalog will apply an AND Boolean operator when the Journals referenced in the NCBI databases limit is selected with a Journal Subset limit. A notice appears at the top of your search results indicating that limits have been activated.

Launching PubMed searches from the NLM Catalog
To build a PubMed search for journals from the NLM Catalog, run a search using Limits and use the check boxes to select journals. Click “Add to search builder” in the PubMed search builder porlet, and the journal title abbreviation(s) will be sent to the search builder box (see Figure 4). If a book or a non-PubMed journal is sent to the PubMed search builder, an error message will warn the user that the PubMed search builder only retrieves citations for PubMed journals. Continue searching the NLM Catalog and adding journals to the PubMed search builder using the Add to search builder button. The search builder will apply an OR Boolean operator if multiple journals are added to the search box. When you are finished, click Search PubMed to view the citations from the selected journal(s) in PubMed.

Figure 4: Using PubMed search builder
Effect on EUtilities
ESearch URLs for db=journals will automatically map to db=nlmcatalog. ESummary and EFetch will retrieve NLM Catalog XML.

By Sarah Torre
National Center for Biotechnology Information

Torre S. NLM® Catalog and Journals Databases Merge. NLM Tech Bull. 2010 Nov-Dec;(377):e7.

November 20, 2010 Posted by | Finding Aids/Directories, Librarian Resources | , , , | Leave a comment

NLM announces MedlinePlus Connect

From a posting by  GMRLIST – email list for the National Network of Libraries of Medicine-Greater Midwest Region (NN/LM-GMR) members. Written by Samanthi Hewakapuge, MA, MLS, Consumer Health Coordinator

Today NLM [US National Libraries of Medicine) announces MedlinePlus Connect (http://medlineplus.gov/connect), a free service that allows electronic health records (EHR) systems to link users to MedlinePlus (http://medlineplus.gov), an authoritative up-to-date health information resource for patients, families and health care providers. MedlinePlus provides information about conditions and disorders, medications, and health and wellness.

MedlinePlus Connect accepts requests for information on diagnoses (problem codes) and medications. NLM mapped MedlinePlus health topics to two standard diagnostic coding systems used in EHRs: ICD-9-CM and SNOMED CT CORE Problem List Subset.

When an EHR submits a request to MedlinePlus Connect, the service returns the closest matching health topic as a response.  MedlinePlus Connect also links EHR systems to drug information written especially for patients. For medication codes, MedlinePlus Connect accepts RXCUIs and NDCs. The API for using this service conforms to the HL7 Context-Aware Knowledge Retrieval (Infobutton) Knowledge Request URL-Based Implementation specification.

MedlinePlus responds to problem code requests in either English or Spanish. Currently, it supports requests for drug information in English only.  NLM is working on adding laboratory test responses to MedlinePlus Connect. We will also support an XML-based Web service at a future date.

You can find more background and technical information at http://medlineplus.gov/connect. If you are an EHR owner or developer interested in staying up-to-date on technical developments with MedlinePlus Connect, or talking to other organizations that are using it, join the free email list athttp://www.nlm.nih.gov/medlineplus/connect/emaillist.html. To send questions or feedback, use the MedlinePlus Contact Us link athttp://apps.nlm.nih.gov/medlineplus/contact/index.cfm.


 

November 10, 2010 Posted by | Librarian Resources, Professional Health Care Resources | , , , , , , , , , | Leave a comment

More Historical Journal Citations are Now in MEDLINE/PubMed

[Editor Flahiff’s note: I remember when getting citations from 1966 was a big deal!]

From a November 1, 2010 US National Library of Medicine (NLM) Bulletin posting

More historical journal citations are now in MEDLINE®/PubMed® with the addition of over 48,000 citations from the 1946 Current List of Medical Literature (CLML). The National Library of Medicine® (NLM®) has been converting information from older print indexes that were the precursors to Index Medicus. When the original MEDLINE database made its debut in 1971, it contained citations to journal articles published from approximately 1966 forward. The 1946 CLML represents the 20th year going back in time to enhance access to the older biomedical literature. With the addition of the 1946 CLML citations, the OLDMEDLINE subset contains over two million citations.

NLM also continues the work of mapping the original keywords assigned to these older references so that current MeSH® terms (Medical Subject Headings) are added to the records and available for searching in PubMed.

Additional information about the OLDMEDLINE data project is available.

 

 

 

November 9, 2010 Posted by | Finding Aids/Directories, Librarian Resources | , , , , , , | Leave a comment

Authoritative, Current Health Information Available on Mobile Devices

Looking for health information while at the doctor’s office, pharmacy, or elsewhere when all you have is a mobile device?

The following mobile Web sites & resources from the US National Library of Medicine may just provide the information you are looking for.

**MedlinePlus Mobile provides information on over 750 diseases, conditions, and wellness areas. It also provides drug information and links to health news items.

**PubMed® for Handhelds Web site is a website for searching MEDLINE® with the web browser of any mobile device.
MEDLINE® is the largest database of  scholarly biomedical citations/abstracts in the world. Links to the full text of most articles are by subscription only. Check with your local library on how to get full text of articles not available at PubMed®.

**Wireless System for Emergency Responders (WISER)****** is a software program for Palm Powered or Pocket PC devices to assist first responders in hazardous material incidents.

**NCBI Bookshelf downloadable versions of books from the NCBI Bookshelf for any mobile device.
From the National Center for Biotechnology Information.

******March 22 2011 WISER update from the National Library of Medicine (via their NLM-TOX-ENVIRO-HEALTH-L listserv)

The National Library of Medicine (NLM) Wireless Information System for Emergency Responders (WISER) 4.4 is now available. It can be downloaded to the WISER Windows, Pocket PC, and SmartPhone platforms from the WISER Web site.   http://wiser.nlm.nih.gov/

The updated online version, WebWISER, is available at  http://webwiser.nlm.nih.gov/getHomeData.do

Highlights of this version include:

1) A new, interactive Chemical Reactivity capability (WISER for Windows); users can
a) Create their own mix of chemicals.
b) See an overview of the resulting potential hazards
c) Delve into the detailed reaction behind each hazard or gas produced.

2) 19 new substances and mixtures of substances, including Crude Oil and the Corexit 9500 and Corexit 9527 dispersants.

Find more information at http://wiser.nlm.nih.gov/whats_new_4_4.html
WISER for iPhone/iPod touch 1.1 is now available from Apple’s App Store.

All WISER platforms now include:

1) The 19 new substances and mixtures of substances.

2) Data updates based on the latest information from the NLM Hazardous Substances Data Bank (HSDB), the Center for Infectious Disease Research and Policy (CIDRAP), and the U.S. Environmental Protection Agency (EPA) Acute Exposure Guideline Levels (AEGLs).

3) Many usability improvements and fixes.

You can follow the activity of the National Library of Medicine Specialized Information Services Division via Twitter (NLM_SIS). http://twitter.com/NLM_SIS

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May 14, 2010 Posted by | Consumer Health, Professional Health Care Resources | , , , , , , , | Leave a comment