We have been notified that the tabs containing Limits, Preview/Index, History, Clipboard and Details will be going away. We don’t know when but it could be soon. The Advanced Search page is where you will find all of these functions now. In addition, a link to the Clipboard will display on the homepage, next to the search box, after selections have been sent to it.

This posting summarizes what you will find on the Advanced Search page. There are new sections in addition to the areas that cover the content of the tabs.

The familiar sections:

• The History section is at the top of the page just below the single search box. The default shows five searches but this can be expanded by clicking the MORE HISTORY button or reduced back to the first five by using the LESS HISTORY button. If items have been sent to the Clipboard then the last item on the list, numbered zero and highlighted in green, will connect to the Clipboard.
• The Limits section is mostly the same. The various groupings have been reorganized a bit and the dates section as not been included at this time. The journal and author component is covered in the multiple search box section.
• The Preview/Index section is at the bottom of the page. It is now called Index of Fields and Field Values. You can still make multiple selections there by using the shift or control keys.

The new sections:

• The section titled Search by Author, Journal, Publication Date and more contains multiple search boxes. The default is set to the fields listed previousl but these can be changed by using the drop down menus. The author and journal fields have the auto-complete feature. Additional citation related search boxes can be displayed by selecting the Add More Citation Search Fields found below the three search boxes.

This section is meant to replace the single citation matcher that is now found in the blue sidebar on the homepage. Also in this section are links to the alphabetical indexes. They are located next to the individual search boxes. Note that in this area you can only select one term/phrase at a time.

• The Queries section, found at the bottom of the page, contains links to Clinical (Clinical Queries) and Topic Specific (Special Queries) pages, as well as the MeSH and Journal databases.

The Advanced Search page does have it’s own URL http://www.ncbi.nlm.nih.gov/pubmed/advanced. Changes and improvements continue on a regular basis. The NLM Technical Bulletin will keep you up to date on the changes.

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Single search box and history sections

Click to view Image 2
Index of fields and field values and queries sections

PubMed is constantly changing. To keep you informed I am going to post brief overviews on a regular basis. This first posting will cover the 3 display formats that are typically used when viewing search results: Summary, Abstract and Abstractplus.

What’s different in each PubMed display?

Display formats vary based on added features…

Summary display-this is the default display and where most of the new features are occurring. There are many experimental “discovery tools” being tested. A user may see a new box displayed to the right of their results one day but not another.
Here’s a quick overview of what is available now:

First the format of the citation has changed.  

• The title of the article now displays on top and is the link to open the abstract or abstractplus display.
  The option to have the author(s) display first is still available by using the drop-down menu to convert to text format or for saving to a file.
• The icons that indicated whether there was an abstract, full text or availability in PubMed Central are no longer available. Instead it is noted at the end of the citation if an abstract is not available; otherwise it can be assumed that there is one.
• PubMed Central availability is noted below the citation. The limits section in Advanced Search or preferences in MyNCBI can be used to filter your results for free full text. This is not clearly indicated in the summary format but icons to the supplier are shown in the abstract and abstrcatplus displays

New features:

• Recent Activity-a box displayed to the right of the results shows your search history in PubMed as well as other databases from NCBI, currently these include PubMed Central, Gene and OMIM

• Drug Sensor-a new resource from the PubMed Bookshelf titled, PubMed Clinical Q&A will display in a box on the right side of the page if content connected to the drug term is available. This resource is in process. It is a growing collection of evidence based medicine summaries (more on this in a future posting).

• Citation Sensor-

• Identifies components of a citation in your search terms and make suggestions for possible matches
• Displays in a yellow highlighted box at the top of the full results page

• Gene Sensor-currently displaying to 50% of the users, this will be located in the same area as the Citation Sensor-it will provide a link to a record(s) in Entrez Gene where terms from your search have identified information there.

MORE TO COME: additional boxes will randomly display to the right of the citation. Some of these, “Results found in article titles” and “Also Try”, are displaying to a limited amount of users now.

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Abstract display-this format has not changed much. It is the most basic display with the abstract included-here library and publisher icons show at the top of the citation, related articles are identified with a link.

• Related Articles link is to the right of the citation
• Library and publisher icons are at the top of the citation

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AbstractPlus display- this adds more content than the plain abstract page. The related articles feature is visible in a box to the right of the citation and results for consumer drug information are displayed here.

• Related articles with related reviews box-this is where the first five related articles are displayed in a box to the right of the citation, two review articles within that set are marked with the word highlighted in red. The results can be expanded by clicking on the appropriate link below the box.
• Patient Drug Information (AHFS Consumer Medication Information)-This is drug information intended for the consumer, the information comes from the same source used in MedlinePlus
• Library holdings, publisher icons-Icons linking to available full text are displayed, in abstractplus library icons are displayed below the citation and publisher icons are to the right above the boxes

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Submitted by Lauri Fennell

Catching up:

Well I think this could become a theme. Just when you think you are all caught up you realize while you were doing that more changes occured! Not to mention getting back from MLA always requires some catch up.

PubMed has made lots of changes lately. I imagine you may have noticed a few. Luckily I am not too far behind. Most of these changes are published in the May-June Technical Bulletin but let me summarize some of them for you. They were highlighted at the NLM booth at MLA, too. You can still view the presentations by going to the NLM Distance Education page! The one titled “Pubmed Review” runs for 25 minutes and covers the topics below and more. http://www.nlm.nih.gov/bsd/dist_edu.html

Advanced Search Feature:
Have you tried the Advanced Search feature? The link to it is located next to the search box on the Pubmed homepage. It is currently in beta. The folks at NLM look forward to your comments and feedback. Use the Write the Help Desk at the bottom of the Pubmed page if you want to share your thoughts.

The screen has a similar look to the Limits page and includes a limits section.

You will notice that some of the new changes are based on the fact that people use Pubmed frequently to find specific citations rather than performing subject searches. The default selections for the search boxes are Author, Journal and Publication date. Which, I assume is to guide those who are looking for citations. These choices can easily be changed by using the “drop down” list.

Some of the features I like are the icons to the right of the search boxes that open the index, the new capability to lock or unlock your limits (there’s an icon for this in each of the limits selections) and ever since they introduced this I have appreciated the auto-complete feature when searching for authors or journal titles.

Here’s the link to the May-June issue of the Technical Bulletin where you can get more detail:
http://www.nlm.nih.gov/pubs/techbull/mj08/mj08_advanced_search.html

New Automatic Term Mapping (ATM):
Have you ever been frustrated when you searched for a citation and the journal name was treated as a MeSH term? Well, NLM is trying to help with that. Many people search without using field tags to direct their searches and the new ATM will help them get more relevant results. In fact there will be many more results in general, meaning the new advanced search feature will come in very handy.

ATM will now continue to search for the term in other fields even if it identifies the word or words as a MeSH term. The new ATM will translate words entered in the search box by continuing to search beyond an identified MeSH term using [All Fields] to offer other possibilities. Multiple words will be separated then ANDed together and then continue on to be searched as a phrase.

This change will allow a word to be considered as a journal name as well as a subject term thus avoiding the confusion when they are the same. Some of the common examples are Cell, Circulation, and the example given in the video is Gene Therapy. Occasionally even and author name may have been interpreted as subject term.

Examples: both of these phrases are journal names

“gene therapy”[MeSH Terms] OR (”gene”[All Fields] AND “therapy”[All Fields]) OR “gene therapy”[All Fields]

“drug therapy”[Subheading] OR (”drug”[All Fields] AND “therapy”[All Fields]) OR “drug therapy”[All Fields] OR “drug therapy”[MeSH Terms] OR (”drug”[All Fields] AND “therapy”[All Fields])

Don’t forget, using ATM will include those citations that are not indexed for Medline, such as in process citations. Searching with terms that limit to Medline indexing will exclude those.

Examples and more explanation can also be found in this section of the Technical Bulletin:
http://www.nlm.nih.gov/pubs/techbull/mj08/mj08_pubmed_atm_cite_sensor.html

Or by watching the recording mentioned above.

Citation Sensor:
This is a new feature that aims to recognize if you are looking for a particular article rather than a set of results. The nice thing about it is it that it pulls out citations by grouping them at the top of the results page. Thereby, giving you the option to choose a citation, if that is what you are looking for, but still giving you additional results if you were looking for something more.

A description is included within the article on ATM.
http://www.nlm.nih.gov/pubs/techbull/mj08/mj08_pubmed_atm_cite_sensor.html

Coming Soon… just so we can try to keep up

Related Reviews:
As with all the changes introduce in Pubmed, this feature will appear randomly at first. If you are one who gets to see it please send your comments.
This feature will be seen in the AbstractPlus view. The purpose is to pull Review articles out of the Related Articles results and group them separately. The relevancy ranking will still be applied.
More on this at: http://www.nlm.nih.gov/pubs/techbull/mj08/mj08_related_reviews.html

My Bibliography:
This will be introduced in MyNCBI soon. Along with the ability to separate collections as well as saved searches in MyNCBI this new feature will allow you to create a bibliography and receive alerts if you choose to.

Collaborators:
Also worthy to note is the addition of collaborators in a citation. If available, collaborators (investigators) will be shown below the author list.

Submitted by Lauri Fennell

NLM Drug Information Portal

I have only begun to explore this one. The format is easy to follow. One section I looked at is in the News and Features section called Inside the Medicine Cabinet. This section highlights one particular drug, giving current uses, development history, chemical structures and much more.

http://druginfo.nlm.nih.gov/drugportal/drugportal.jsp

Read more:
http://www.nlm.nih.gov/pubs/techbull/jf08/jf08_sis_drug_portal.html

NLM Gateway has a new design

NLM Gateway will soon have a new sleek look, shown below.
http://gateway.nlm.nih.gov/gw/Cmd

All the same functions still exist with new enhancements to the page.
Read more: http://www.nlm.nih.gov/pubs/techbull/jf08/jf08_gateway_redesign.html

Submitted by Lauri Fennell

I am new to this role at the NN/LM NER, so I have been doing some catch up. The NLM Technical Bulletin is full of great information. It includes many interesting updates related to Pubmed. I thought maybe you have some catching up to do, too?

Here are some of the highlights:

Diacritics in PubMed® Displays and Searching
Since late April 2007 “…diacritical marks have been displayed in author names and affiliation (first author’s address) on the AbstractPlus, Abstract, and Citation displays…”

Read more:
http://www.nlm.nih.gov/pubs/techbull/nd07/nd07_diacritics.html

PubMed® Subject Subset Strategies Updated for 2008
When using the limits feature you have the option of choosing topic subsets. These subsets are reviewed annually. The following subset strategy was recently revised:

Bioethics, Cancer, Complementary Medicine, and Systematic Reviews

A description of the strategy can be found from the Pubmed Subset Strategies page: http://www.nlm.nih.gov/bsd/pubmed_subsets.html

You can take advantage of these pre-formulated strategies from the limits page

PubMed Central®, the collection continues to grow…
http://www.nlm.nih.gov/pubs/techbull/jf08/jf08_pmc.html

Patient Drug Information Available from PubMed®
MedMaster drug information added to PubMed AbstractPlus display format.

Note: some of you may have been seeing this since October. The results were displaying randomly at first but are now expected to show up, if relevant, in all Pubmed searches.
Read more: http://www.nlm.nih.gov/pubs/techbull/so07/so07_patient_drug_info.html

Now I’m keeping up

This was recently announced…

PubMed® Alerts: E-mail Notification of Major System Problems
Now you can be notified of major system problems with Pubmed by signing up for e-mail alerts. Read more http://www.nlm.nih.gov/pubs/techbull/ma08/ma08_pubmed_alerts.html

***There is so much more I didn’t include here***

To read the entire NLM Technical Bulletin:
http://www.nlm.nih.gov/pubs/techbull/current_issue.html

Submitted by Lauri Fennell

PubMed is constantly updated with improvements and changes. Besides the Technical Bulletin there are many tutorials and training resources.

I recently watched the recorded version of the Chemicals and Drugs in Pubmed webcast—twice actually. You know how you catch more the second time around? It is definitely true in this case. Did any of you happen to catch it? This search clinic was originally presented on August 23, 2007 (before I was at NN/LM).

It was recorded so it can be viewed at any time. I highly recommend it.

Search Clinic: Chemicals and Drugs in Pubmed
http://www.nlm.nih.gov/bsd/disted/clinics/chem.html

In addition to watching the recorded clinic, you can read the transcript and/or the questions and answers section.

Here are some of the highlights:

First I found it helpful to have the differences of a few of the subheadings used for chemicals and drugs explained, specifically toxicity, poisoning and adverse effects.

Toxicity: studies designed to determine ill effects of a substance (usually animal studies)

Poisoning: life threatening—whether by medication error, accidental or otherwise

Adverse effects: choosing this subheading will include both toxicity and poisoning—includes side effects and complications of accepted doses

Detailed definitions for these terms when used as subheadings can be found by searching for each term in the MeSH database.

Further explanation about substance names, pharmacological action and when to use the MeSH tag was also very helpful.

Substance names: chemicals and drugs are not always indexed with a MeSH heading. Instead they may be indexed under a substance name. If this is the case the substance will be mapped to the MeSH heading appropriate for that substance.

Here’s an example:
When searching in MeSH for zetia (recently in the news) you will get this record:

Ezetimibe is the substance name for Zetia. You find the drug brand names in the list for entry terms. This substance is mapped to Azetidines as a MeSH term. The pharmacological action assigned to it is anticholesteremic agents.

The Questions and Answers section was very helpful. Some questions were answered later with additional NLM staff input.
http://www.nlm.nih.gov/bsd/disted/clinics/qa.html

Some additional items that will become clearer after watching the webcast:

1. Check the details box to see if the chemical/substance name you used is mapped to a MeSH or Substance Name. If it is not, use the preview/index feature to search for the name to see if there are alternatives you can use
2. Using the [pa] versus the [mh] tag: using [pa] searches the full list of substances designated with that pharmacological action. Using [mh] searches for the action as a subject. You can combine it with the specific substance term you are interested in
3. Citations indexed prior to 1996 do not routinely have a pharmacological action tied to them. (from question 11 in Q & A)

Here are a couple additional links that can be helpful when searching for Chemicals and Drugs:

Pharmacological action terms
http://www.nlm.nih.gov/bsd/disted/mesh/paterms.html

Searching chemicals and drugs
http://www.nlm.nih.gov/bsd/disted/mesh/drugsearch.html

From the Technical Bulletin:
PubMed® and the Expansion of Pharmacological Action Terms
http://www.nlm.nih.gov/pubs/techbull/nd07/nd07_pa_update.html