| 1. Introduction
Pubmed(or MEDLINE) is the most popular database to medicine/biology researchers. RefNavigator provides a powerful search interface to Pubmed. Compared to searching in Pubmed webpage, RefNavigator search is more quick and efficient.
In this article, we will demonstrate the Pubmed search function of RefNavigator by several examples.
2. Basic Pubmed Search
First, let’s start a most basic search. Please start RefNavigator and click the main menu "Online Searches"->"Search Pubmed…":
The following window pops out:
Then we input “zinc infant growth” into “All Fields” and select the restriction of “Has Abstract” as shown above, then click “Search”. RefNavigator will report the following results:
We can see that there are 669 records in total and we set the download number as 100, i.e., download the first 100 records, and click “Search”. RefNavigator will immediately retrieve the first 100 records to local computer and save them in the folder designated in this dialogue box.
The download speed of records depends on your network connection speed. As the communication between RefNavigator and Pubmed is based on plain text, it is usually much faster than Web search. If “Retrieve Full Text Links” option is not checked, it can be quicker, but the retrieved results will not include full text links. You can select it or not based on your demand.
If the “Auto Download Free Papers” option is checked, free papers will be downloaded to local computer. But it will make the downloading process longer. The default folder to save downloaded papers is “d:\PubmedFulltext”, and you can change the folder location in RefNavigator “System settings” dialog box. If you have not downloaded full text here, you can also download them later. Just select the references in list box and click the context menu “Download Full Text”.
3. View Search Results
After records are downloaded, they will be saved into the designated folder and RefNavigator will automatically switch to this folder as follows:
Carefully examining this interface, we can find some interesting functions:
- RefNavigator automatically lists SCI Impact Factor of each record, which helps you quickly locate the most important references;
- There are two icons in front of each reference:
 and  . The former indicates this reference has full text link while the latter indicates this reference has free full text link.
- “Folder Statistics” window in the lower left corner shows the statistics of documents types in current folder. We can see that in these 100 records, there are 13 Reviews, 7 Case Reports, 32 Randomized Controlled Trials, etc. Click tag and the references of such type will appear.
- Click “Group By” drop-down menu of Folder Statistics window, which enables automatic grouping by Author, Year or Journal. It helps you quickly locate the most active author in this research field.
Select “Links” tab in Preview window, and you will see full text links of each reference, including “full text link” and ”free full text link”. Duble click the link and it will open a web browser to the web page.
Select one reference and click context menu "Open URL", and it will show corresponding Pubmed page for this reference. You can also click "URL Preview" tab to preview the page inside RefNavigator:
4. Download Free Full Text
Currently, RefNavigator supports downloading free full text from two websites, Pubmed Central and High Wire Press. Therefore, if free full text links belong to the two websites, you can click the main menu “References”->”Download Full text” to automatically download them:
In this case, six papers are downloaded successfully while one fails. If the full text file has been downloaded successfully, the icon before corresponding record will become  , which indicates a local full text file has been attached to the reference:
You can click context menu "Open Full Text" or "Open Full Text with Note Window" to read the pdf now. If you switch to "Pdf Preview" tab, you can also preview the pdf file inside RefNavigator, as shown in above screen shot.
Notice: the pdf preview tab only shows after you install Adobe Acrobat Reader or Acrobat.
5. Advanced Pubmed Search
The secret to an efficient search on Pubmed is to use MeSH vocabulary. In this section, we will use MeSH vocabulary to make our research more precise.
Click main menu “Online Searches”->”Pubmed Search History” and you will see previous search records:
Select this record and click “Load”, then the previous search conditions appear again:
We move the cursor to the input area of “zinc infant growth”, click “…” button and MeSH Browser pops out:
In this dialog, you can search or browse MeSH vocabulary based on tree model, including its explanation, Qualifiers, Thesaurus and related words. We input “zinc” to search MeSH vocabulary, select “Zinc\Blood” and “Zinc\deficiency”, then click “Send to Pubmed Search Window” and close the dialogue box.
Back to the search interface, we can see that MeSH words have been added: 
This time when you click Search, the search result is limited to only 42 records:
RefNavigator also supports Journal Title limit. If search field is “Journal Title”, click “…” to pop out Pubmed Journal Browser instead of MeSH Browser.
Besides, there are many other filters which can be applied on the search interface, such as publication date, Pubmed update time, various specific database subsets, etc. The above mechanisms will help us find truly related documents.
6. Search Other Online Libraries
Besides Pubmed, you can also search other online libraries via RefNavigator. RefNavigator supports lots of scientific literature websites, including Google Scholar, ACM, IEEE Xplorer, Scidirect, Scirus, Arxiv, etc. Click main menu "Online Searches"->"Search Other Online Libraries..." to start a search:
RefNavigator supports lots of popular websites, including Google Scholar, IEEE, ACM, Scidirect, Scirus, Arxiv, etc. Besides, it supports z39.50 based online libraries such as Librarg of Congress. You can define your own z39.50 connections in main menu "Online Libraries"->"Online Libraries Manager".
7. Pubmed Search Task
Finally, we demonstrate the usage of Pubmed search task. We still use Pubmed Search History to load the latest search, and then click “Save As task…” button as follows:
Input task name in the popped dialogue box:
A new Pubmed search task is created and saved as “\Library\Pubmed Search Tasks\My First task” as follows:
The advantage of Pubmed search task is that you may periodically re-run it to update search results and it will automatically mark new records red, which helps you track latest research results.
7. Conclusion Thank you for your patience to read this document. Hope RefNavigator can help you get more successes in your research career. Enjoy it! For any questions or suggestions, please email to support@RefNavigator.com.
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