What’s New and Different in PubMed? Lots!

PubMed has made many changes over the past few months. Here’s a summary of some…and more are coming!

Citation Sensor

Citation Sensor is a new PubMed feature that matches searches with citations. It recognizes combinations of search terms that are characteristic of citation searching, e.g., volume/issue numbers, author names, journal titles, and publication dates, which it then matches to citations.

If your search invokes the Citation Sensor, you will see a yellow area above the retrieval with links to one or more citations for your consideration:

More information at http://www.nlm.nih.gov/pubs/techbull/mj08/mj08_pubmed_atm_cite_sensor.html.

Drug Sensor

When a drug name is used in a search, a Drug Sensor may display excerpts of information from other resources. The Drug Sensor currently highlights a publication which is new on the PubMed Bookshelf: PubMed Clinical Q&A, a collection of evidence-based medicine summaries based on published systematic reviews. These summaries can be used to learn more about current treatment practices and the level of evidence that supports them.

drug sensor preview

Each PubMed Clinical Q&A summary highlights the key questions identified in the systematic review, gives a brief answer, and links back to the source of the evidence in the results section of the original full-length review. More information at http://www.nlm.nih.gov/pubs/techbull/ja08/ja08_drug_sensor.html.

Gene Sensor

The Gene Sensor is released to detect searches that include the symbol for a gene found in the Gene database. Gene Sensor checks the query entered in the search box and if it detects the symbol for a gene found in the Gene database, a “Gene Information” box displays above the search results with links to organism-specific information and the full report in Gene.

gene sensor preview


Advanced Search

Advanced Search is now the place to go to use features such as field searching and limits. In the near future the tabs for Limits, Preview/Index, History, Clipboard, and Details will be removed from the basic PubMed pages. History, Limits, Index of Fields, and a link to Details are available from the Advanced Search screen. A link for the Clipboard appears to the right of the search box on the PubMed screen when the Clipboard has content. More information at http://www.nlm.nih.gov/pubs/techbull/nd08/nd08_pm_adv_search_evolves.html.

My NCBI Redesign

My NCBI now has a homepage that, upon signing in, displays a summary of and links to the contents of the account, i.e., the preferences and filters selected and saved searches, collections and bibliography. The Table of Contents sidebar also provides links to the account’s contents.

my ncbi preview

Title Sort

PubMed’s Sort feature has a new option, Sort by Title. The order of sorting for the article title is: numbers (0-9), letters (A-Z). The order of sorting ignores A, An, The, and special characters at the beginning of the title.

title sort preview


The Abstract and Citation displays now include the PubMed Central ID (PMCID). The NIH Public Access Policy has become mandatory, requiring NIH grantees to submit a copy of their accepted, peer-reviewed article to PubMed Central (PMC). This requirement, and others, are explained at the NIH Public Access Policy Web site. An additional requirement is that researchers must provide the PMCID for articles when citing an article in grant applications, proposals, and progress reports. Details on this requirement are found within the Public Access Frequently Asked Questions.

Authors who need the PMC IDs (PMCID) of their publications to fulfill NIH Public Access Policy requirements can now find this on the PubMed Abstract, AbstractPlus, Citation, and MEDLINE formats. More information at http://www.nlm.nih.gov/pubs/techbull/ma08/ma08_pmcid.html.

pmcid preview

Patient Drug Information Links

Links to drug information on the AbstractPlus display to MedMaster Patient Drug Information are now available for all PubMed users. The links are generated using the drug name searches that are expanded based on regular PubMed mapping, e.g., albuterol will map to “albuterol”[MeSH Terms] OR albuterol[Text Word] and the citations retrieved will include a drug link to MedMaster for albuterol.

drug info preview

Details at http://www.nlm.nih.gov/pubs/techbull/so07/so07_patient_drug_info.html.

Summary Display Update

The Summary display has been improved to enable easier scanning of article titles. PubMed search results (Summary format) have until now displayed the citation with the author names first, followed by the title of the article and the source data. Author names – no matter how many – served as the link to the AbstractPlus format. To improve the look of the Web page as well as to make it easier to scan titles, the positions of author names and the title of the article have been reversed. The article title now displays on top and serves as the link to the AbstractPlus format. Author names appear under the title and the rest of the citation remains the same.

summary preview

Details at http://www.nlm.nih.gov/pubs/techbull/nd08/nd08_pm_new_summary.html.

Get up to speed on Web of Knowledge

ISI’s Web of Knowledge is the platform for several licensed databases available to the UC Berkeley community:

Did you know …

… You can search more than one WoK database at the same time?

… You can save searches and have them automatically re-run periodically?

… You can set up email notification whenever someone cites a particular article or author?

Web of Knowledge provides short online tutorials on these and other topics on their Training Opportunities web page. Check it out!

California County Scorecard of Children’s Well-Being

This scorecard tracks 26 indicators by county of the well-being of California’s children. You can view results by county or by indicator. The data here comes in large part by analysis of 3 surveys: the U.S. Census Bureau’s 2006 American Community Survey, California Health Interview Survey and California Healthy Kids Survey. This resource is linked from our Statistical/Data Resources web page at:


January 14th Richmond Instruction Session: Toxicological Resources

* Need to find literature on pesticides, drugs/pharmaceuticals, or poisons?
* Want to explore relationships between job tasks, exposure to toxic agents, and health effects?
* Want to know the potential toxic effects of the ingredients in common household products, from shampoo to white out?
* Interested in information on the releases of toxic chemicals in your neighborhood?

If you answered yes to any of these questions, then please come to the Sheldon Margen Public Health Library’s Toxicology Resources class!

Topics covered will include:
1.  Using bibliographic databases such as PubMed, TOXLINE, and others to find journal articles on toxic substances
2.  How to manipulate, save, or download your search results
3.  Job-related potential toxic exposures and their health effects
4.  How to find out what’s in common household products
5.  How to learn about toxic releases into the environment 

Class: Toxicology Resources
When: Tuesday, January 14, 2009, 10 – 11 AM
Where: Richmond Campus, Building C, Room 136

This class is intended for CDPH staff who are unfamiliar with toxicological resources, or who desire a refresher on finding basic toxicological information. It is also intended for those who are curious about the toxics in household products and in the environment.

If you wish to attend, please RSVP by Friday, January 9th to Judy Bolstad at
jbolstad@library.berkeley.edu, or (510) 642-2510. 

Feel free to send some examples of real life questions you frequently get or need answers to. We’ll try and incorporate some of these into the class. These one-hour training sessions are free to CDPH employees. Please obtain your supervisor’s approval to attend. Hope to see you there!

County-Level Mapping of Interactive Birth Data Now Available from CDC’s VitalStats

VitalStats is a collection of vital statistics products from CDC’s National Center for Health Statistics. It includes tables, data files, and reports that allow users to access and examine vital statistics and population data interactively. Previously, users could only map state-level data, but with the release of the new mapping feature, users can map to the county-level. Within a map, users can zoom, drill, pan, select, or view selections as charts and tables. The data can also be printed, saved or exported to Excel. For more information, please see:


A pdf quick guide to VitalStats may also be downloaded at:

From Exposure to Illness: Community Health Studies and Environmental Contamination

The Environmental Health Investigations Branch of the California Department of Public Health has created an online guide for those who want to study the link between environmental exposure to chemicals and the health effects experienced by a community by conducting a health study. The information gives the basics about health studies, discusses when a health study is appropriate, and offers examples and alternatives to health studies. Check out this guide, which is linked from our Toxicology/Occupational Health Resources page at: