Almost Everything About HubMed

Jack Yensen

Citation:

Yensen, J.A.P. (June, 2005). Editorial: Almost Everything About HubMed. Online Journal of Nursing Informatics (OJNI), 9, (2) [Online]. Available at http://ojni.org/9_2/hubmed.htm

 

I have heard from many colleagues and graduate students about their problems in finding literature resources for their needs and interests and then of trying to maintain current awareness around those resources. This prompted me to write an editorial on HubMed. HubMed is found at http://www.hubmed.org and is a parallel search engine to PubMed, or as some people have said “HubMed is like PubMed on steroids.” Any search strategies you use in PubMed may be used in HubMed and once you have the core skills for efficient searching of PubMed, HubMed offers many options that are not found in the original PubMed.

This editorial outlines the complete functionality of HubMed and describes how to exploit HubMed to maximum advantage for the person seeking information from the peer reviewed literature that is indexed by PubMed.

Here is a concept map for the article :

 

Getting Started

Firstly, open the main window of HubMed and enter a search term. In this article I have used the search term 'total hip arthoplasty.' This would appear as follows:

After clicking the Search button, we see the search yield window:

Menu Bar

On the top right hand side of the search yield window, we see a menu bar comprising several buttons:

Pressing the HubMed button will return you to the opening search window. Pressing the Help button will give a brief Help window:

Clipboard

If an abstract or some other article property is copied to the clipboard, we can see the clipboard contents by pressing the Clipboard button. Here is an example:

History

During searches, if one or more full text links are followed, the History cache will display the links followed during a current session. Here is an example:

Biologging

If you have a free account at biologging.com, it is possible to add abstracts, citations, full text or other article properties to your personal blog and then add your own comments about each blog entry. Here is an example:

Once the user has logged in, blog entries can be made based upon current searches:

Feeds

One of the more significant functions of HubMed is the ability to capture RSS feeds for a given search. Here is an example:

Inserting the resultant RSS feed into a web based or client side feed aggregator is an excellent way to stay current with newly emerging literature for the search term used in your original search, since this is tantamount to having an automagically and dynamically updating search on the topic of interest. (1)

Before leaving the general search yield page, it is of interest to note that we can Select all or Select none of the 20 results per page and Display checked abstracts, as in:

or Toggle extracts for each of the 20 article citations:

Individual Item Links

If we click on any individual article title, we see a new window for that article with a set of new options, following the Abstract:

Abstract

Clicking the Abstract link will show an abstract (if one exists) for the individual title. It is already displayed in the screen above. Clicking the PubMed link will repeat the search in PubMed.

Full Text

Clicking the Full text link will send the user to the full text (or whatever exists) for that title:

SFX Service

Clicking the SFX service link will send the user to the context sensitive SFX link server, a service of the Ex Libris Group:

From here it is possible to order full text articles, request inter-library loan, run a web search on the title keywords, using one of a variety of different search engines, or download the record in a format suitable for import into a bibliographic database management software like EndNote, ProCite or Reference Manager.

LF+

Clicking the LF+ link will direct the user to Linkfinder Plus with the citation data. If any full text links or other extended services are found, they will be displayed.

GS

Clicking the GS link will drive a search in Google Scholar for the title keywords. This is very useful, as it will often find related or other relevant articles:

Order

Clicking on the Order link will connect with Infotrieve and allow the user with an Infotrieve account to download the full text of the article.

Clip

Clicking the Clip link will add the currently selected titles to the Clipboard (for cutting and pasting elsewhere) and change the Clip link to Clip added.

Citation

Clicking the Citation link will trigger a download prompt for the bibliographic record for the selected titles in RIS format (Reference Manager Import Specification) suitable for import into many bibliographic database managers.

BibTex

This will generate the citation as a bibliography file for later use in LaTex (2):

@Article{best,
author = "Best, JT.",
title = "{Revision total hip and total knee arthroplasty}",
abstract = "{For thousands of patients with advanced degenerative joint disease, total joint arthroplasty provides improved function, decreased pain, and the opportunity to resume a more active lifestyle (). Although hip and knee replacements are both successful interventions for degenerative joint conditions, complications may arise that require revision of the original surgery. In 1999, approximately 25,000 revisions of knee replacements (ICD Code 81.22) and 30,000 revisions of hip replacements (ICD Code 81.53) were performed in the United States (). Approximately 10,000 revision total hip arthroplasty procedures were performed on Medicare patients in 2000. The total cost of revision surgery, including the 10,000 total knee revision procedures performed on this same patient population during that year, exceeds $3 billion ().Descriptions of the risk factors and indications for revision total hip and total knee arthroplasty are included in this article. Nursing interventions and patient education specific to these patient populations are outlined, and a discussion of complications following revision total joint arthroplasty is included.}",
journal = "Orthop Nurs",
year = "2005",
volume = "24",
number = "3",
pages = "174-179",
month = "May-Jun",
pmid = "15928524",
url = "http://www.hubmed.org/display.cgi?uids=15928524"
}

Related

This will search HubMed for related articles and is exactly the same function as found in PubMed.


TouchGraph

This link will invoke the HubMed Graphical browser using Java:

Scopus

This link will connect Scopus subscribers to the Scopus database for an extended and refined search of the titles from the HubMed search.

References

Clicking on References will allow a prompt screen for a Trackback entry for the title.

Tags

If the user has a HubMed account and has the ability to add tags to any given record, clicking the Tags key will allow this.

Rank Relations

Clicking this button will compute a weighted ranking of abstracts related to (max 20) all checked articles.

New Search

This text box allows the user to start an entirely new search.

Refine Search

The Refine search text box allows the user to check or uncheck options boxes to further drill down in the search yield:

Scirus

This link will cause a Scirus search on the search terms used originally, but the search will occur in the Scirus journal database and the web, where the results may be ranked by relevance or date:

CrossRef

This link will send the search query to search full text articles on CrossRef partner sites, via Google and is very useful:

PMC

This link will send the search string to PubMed Central and yield relevant or related full text articles. This is extremely useful where there are limited library resources and where time is big constraint:

XplorMed

The XplorMed server allows you to explore a set of abstracts derived from a PubMed or HubMed search. The system reveals the main associations between the words in groups of abstracts. Then, you can select a subset of your abstracts based on selected groups of related words and repeat your analysis on them. It (XplorMed) is recommended for cases where you do not know exactly what you are expecting to find. I do not always have any luck with the regular link to the XplorMed engine at http://coot.embl-heidelberg.de/xplormed/class_set1_simple.pl, whereas I find the Canadian mirror site behaves more reliably. It is at http://www.ogic.ca/projects/xplormed/class_set1_simple.pl

Here is a search on 'orthopaedic pain management' although the search could be any search string:

at the bottom of this screen there is a second step button which will compute the associations between words from each of the retrieved sets of abstracts and this will often lead to interesting relationships:

Here is the result of the clicking on the highest associations link, in this case Patient:

In the next step, we can rank abstracts based upon word chain linkages. Here I have chosen Patient, pain and Patient, surgery:

This yields the results:

and then I can explore specifically associated articles or their citations, which may not have occurred to me to do with a regular PubMed version of the search.

Graph

If I am interested in the momentum or history of published topics, I can choose the Graph link. This will generate either an SVG or PNG graphic showing the numbers of articles on the search term that have been published over the last few years. Here is an example for nursing terminology and it seems to take off after nursing informatics was recognized as a specialty:

Tricks

If you see the plus sign + in any HubMed window, clicking on it will reveal the button interface:

References

(1) Yensen, J.A.P. (2005, May) Leveraging RSS Feeds to Support Current Awareness. Computers, Informatics, Nursing. 23(3), 164-167.

(2) Harvard Condensed Matter Theory Group.  How to use Bibtex. Retrieved from http://cmtw.harvard.edu/Documentation/TeX/Bibtex/Example.html June 14th, 2005