I thought this would be a good time to answer some of the common questions I have been hearing while reviewing the recent changes.

1. Where can I set the limits?

You can now access the limits by a NEW link on the homepage just above the search box, this will open a newly created separate page.
• A date range menu has been added.
• The choices have been reorganized by order of popularity.
• The Text Options has been moved to the bottom left of the page.
• Clear limits with the reset button and then run a new search.

Note: there are new publication types in the list, Webcasts and Research Support, American Recovery and Reinvestment Act.

2. How do I print in the new design?

Printing can be done in a couple of ways. When viewing your results you can use your browsers print function (file—print) or Ctrl P to print what you see on the screen. This will take out the PubMed header but include the full text icons that are associated with a citation.
OR
Choose your items, by clicking the boxes to the left of the citation, and use the display settings: select Summary (Text) or Abstract (text) to eliminate the web related content. The Summary (Text) option will change the format of the citation slightly by putting the author names first, offering that arrangement for those who prefer it.

3. How do I see the MeSH terms and other supplemental data?

Below the citation, if “indexed for MEDLINE”, will be a plus sign followed by the available components: Publication Types, MeSH Terms, Substances, click on this to expand/open the information to display all pertinent information.

4. Where do my Clipboard items display?

After selecting Send To:
• an icon will display on the results page on the right hand side.
• the number 0 will be assigned to clipboard items in the history section.
• NEW: A Clipboard link will show on the PubMed homepage in the list under the PubMed Tools heading

5. What choices do I have for E-mailing formats?

• Summary-Send your citation in the summary format if you want a hyperlink that the recipient can use to go to PubMed where the fulltext and other PubMed features will display.
• Abstract-Send in Abstract form to include the icons connected to full text along with the MeSH terms, Publications Types and other Supplemental Data that is part of the indexed record.
• Abstract (text) Send in the Abstract (text) form to have an easy to print version, this will not include hyperlinks, icons or MeSH and other supplemental data.
• Medline, XML and PMID List are also options.
• NEW: Recently a feature has been added to allow for large sets of citations to be sent in batches. The size limit has been 200 per e-mail but this new option will allow the user to select a starting point. For instance, if the first 200 have been sent the next group should start at 201.
A description is in the NLM Technical Bulletin: http://www.nlm.nih.gov/pubs/techbull/jf10/jf10_pm_batch_email.html

The Advanced Search Page has been trimmed down. The former box that contained multiple search menus and the Limits section has been removed.

• In their place is the NEWSearch Builder where you can use the drop down menu to select the field you want to search and use the Boolean operator buttons to combine and build your search.The Index to fields and field values has been streamlined into this section as well allowing for multiple selection of terms: choose the field from the drop down menu, type in your term, click the index button to the right of the search box, select multiple choices from the list by using the Ctrl function and add to the search box.

• Instructions have also been added to the Search Builder and History sections. They are viewable by clicking on the text at the bottom of the box/section.

Read about all the changes including changes to PubMed and many other NLM Resources in the latest NLM Technical Bulletin article. http://www.nlm.nih.gov/pubs/techbull/current_issue.html

The newly redesigned PubMed Interface is live now.

NLM has several articles in the NLM Technical Bulletin that cover the changes.
In these postings you will find answers to questions about printing, the location of the content formerly found in the tabs, how to display the MeSH terms assigned to an indexed article and other questions you may have.

PubMed Redesign : a complete overview of the redesign with images.

Linkout in the PubMed Redesign : explains where the icons display when viewing results in different formats and the format for URL’s.

PubMed Now Using the Redesigned Interface : note that there were some changes made from the preview version including Details displaying with the search results.

The recorded webcast along with answers to questions asked during the 2009 PubMed Redesign sessions (held on October 6th and 7th) has also been posted: Webcast: 2009 PubMed Redesign

In addition there are some added features to MyNCBI:
MyNCBI: MyBibliography and Other Citations Enhanced

I will be hosting brief sessions via Adobe Connect throughout the month to review some of the changes. Currently there are two scheduled: Tuesday, November 3rd at 10a.m. and Monday November 9th at 2 p.m.

Are you curious about new NCBI resources? Want to stay informed about changes and updates? The NCBI newsletter, NCBI News, is where you can learn about new developments at NCBI. It is published electronically on a monthly basis. Each issue has a section for a Featured Resource, New Databases and Tools, GenBank News, Updates and Enhancements and Announce Lists and RSS Feeds.

Recent topics include the new database Biosystems, 2009 H1N1 Influenza Sequences, updates to PubChem, BLAST and the new discovery components in PubMed.  Check out the February, March and June issues to read about the Discovery Initiative and the related discovery components: Sensors, Database Ads and Analysis Tools. These components display with search results in the literature databases such as PubMed and sequence databases such as Entrez Protein.

The newsletter can be downloaded as a .pdf document or viewed in NCBI Bookshelf, where you can easily search for a specific topic. Here’s the direct link to the latest issue (August 2009): NCBI News-August 2009

In addition to the newsletter NCBI offers additional options to stay informed about changes and developments:

• Choose from a list of topic specific e-mail list-servs: http://www.ncbi.nlm.nih.gov/Sitemap/Summary/email_lists.html
• Subscribe to NCBI-Announce (the latest issue of NCBI is announced here): http://www.ncbi.nlm.nih.gov/About/news/announce_submit.html
• Subscribe to RSS feeds, available for NCBI Announce and others: http://www.ncbi.nlm.nih.gov/feed/
• View a brief summary of What’s New: http://www.ncbi.nlm.nih.gov/About/whatsnew.html

The NLM Technical Bulletin also posts news, updates and changes to NLM resources that may not be included in NCBI. It is managed by the Medlars Management Section and contains frequent posts about PubMed: Chronological list of PubMed postings.

If you were unable to attend the PubMed Redesign Presentation online webinar, or if you would like to listen to the class again, a recording of this class is now available here: https://webmeeting.nih.gov/p93606971/

The session was held on Wednesday, August 26, 2009 from 2:00 – 3:00 pm

David Gillikin, Chief of NLM’s Bibliographic Services Division, reviews the draft design for the new search results page along with some explanations of coming changes in PubMed.

A question and answer session follows the presentation. This webinar is a repeat of the presentation at the NLM Online Users’ Meeting at the Medical Library Association’s annual conference in May.

This free, online class was conducted using Adobe Connect. The recording provides the session in its entirety with audio and the PowerPoint presentation.

The recording runs for approximately 49 minutes.

Over recent years, we’ve received a fair number of technical support calls from NER members. At first glance, it would seem logical to categorize support calls by the NLM resource.  A more instructive approach, however, would probably be to take a closer view of the broader technical issues. When PubMed and DOCLINE users encounter errors, many immediately assume that the problem is centralized in Bethesda (i.e., NLM) when in fact, the problem often lies with local network or local desktop issues.

To reduce the incidence of “local” issues in the future, users may want to consider the following:

1. When accessing NLM applications (such as PubMed, DOCLINE, etc.), make sure your workstation is set up to accept “cookies”.

2. If there’s an unexpected occurrence in the display of screens while in PubMed or DOCLINE, make sure that workstation cache has been cleared.

[ NOTE: When clearing workstation cache, do not delete those "cookies" needed by DOCLINE.]

3. After clearing cache, if the technical problem recurs, write down the steps you took and report your problem either to the NER or to NLM Customer Service.

More information related to enabling cookies or clearing cache may be found below:

Enabling cookies (using Internet Explorer):

http://www.timeanddate.com/cookiesie.html

Enabling cookies (using Firefox):

http://www.timeanddate.com/custom/cookiesmozilla.html

Clearing cache:

http://www.nlm.nih.gov/services/doc_clearcache.html

Several useful definitions on the subject:

CACHE

Cache is a temporary storage area on a user’s computer where frequently accessed data is rapid ready for immediate use so that re-computing original data is not required.  Cache should be refreshed routinely.

Clearing cache on your web browser may improve web page downloading time and overall performance while accessing databases on the web.

COOKIES

A “cookie” is information sent by a website server to the user’s workstation while they are connected to that site. Cookies store information about user interactions that may be needed later for the system to perform a function.

Most browsers allow users to decide whether or not to accept cookies, as well as the time frame in which to maintain them. Some websites may become unusable when a user decides to reject cookies.

Example: the automatic login functionality found  in ILL management systems depend on the use of cookies and will not work if cookies are disabled.

CONNECTIVITY

Connectivity involves the transport of data between two points (from server to workstation, server to server, etc.)

To increase your computer’s connectivity to the web, remember to:

1. Clear workstation cache from time to time. This will enhance your workstation’s performance with web-based applications (like PubMed and DOCLINE); and
2. Maintain cookies on your computer, so that your computer is instantly recognized by NLM.

NN/LM Middle Atlantic Region (MAR), New England Region(NER), and Southeast Atlantic Region (SE/A) will present a live webinar on the upcoming National Library of Medicine PubMed page redesign. David Gillikin, Chief of NLM’s Bibliographic Services, will review the draft design for the new search results page and abstract view in PubMed. This webinar is a repeat of the presentation at the NLM Online Users’ Meeting at the Medical Library Association’s annual conference in May.

IMPORTANT: This webinar is free and open to NN/LM members in the MAR, NER, and SE/A regions only. Because participation is limited, we ask that you do not forward this message to individuals outside the MAR, NER, and SE/A areas. This webinar will be offered separately in other regions.

No pre-registration is required. Participation will be open on a first come, first served basis.
***Admission to the session will close 5 minutes after the start time of 2:00pm***

Meeting Name: PubMed Redesign MAR, NER, SEA
When: Wednesday, 08/26/2009, 2:00-3:00 pm

To join the meeting: Log in early(up to 15 minutes before the class start time) by using this link: https://webmeeting.nih.gov/pubmedredesignmarnersea/

Note: This will get you to the visual portion of the presentation.

To get the audio: After joining the meeting, a pop up window will ask for your phone number. This will allow the system to call you.
If you need to manually dial into the meeting: Call 1-877-239-6389, Pass-Code: 265688

TEST YOUR CONNECTION AHEAD OF TIME: If you have never attended an Adobe Connect Pro meeting before, please test your connection prior to the webinar: https://webmeeting.nih.gov/common/help/en/support/meeting_test.htm

In the latest NLM Technical Bulletin posting is a full description of recent changes to MyNCBI. These changes include the ability to share your individual saved collection(s) by changing your settings to public. If you want to keep them private no change is needed. You can also create your own customized filters. A full explanation is given in the May 29^th posting.

http://www.nlm.nih.gov/pubs/techbull/mj09/mj09_pm_myncbi_collections.html

If you’re interested in more information about MyNCBI go to the section in the online PubMed Help Book. This is a complete overview from setting up your account to managing your settings and data.

http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helppubmed&part=pubmedhelp#pubmedhelp.My_NCBI

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.

Click to view Image 1
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.

Click to view image

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

Click to view image

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

Click to view image

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.