Organizing PubMed / MEDLINE Research With askSam
By Phil Schnyer, askSam CEO
PubMed, a service of the National Library of Medicine, includes over 14 million bibliographic citations and abstracts in the fields of medicine, nursing, dentistry, veterinary medicine, health care systems, and preclinical sciences. These citations are from MEDLINE and additional life science journals. PubMed includes links to many sites providing full text articles and other related resources.
As with many information sources, PubMed offers an abundance of accurate, authoritative, and up-to-date information, but organizing this information for specific research interests can be a chore. A new askSam template combined with a special PubMed filter for TextPipe offer a powerful and easy way to organize, search, and manage PubMed / MEDLINE information.
With askSam, you can:
Bring the results of your PubMed research into a searchable database.
Search and organize the information you collect on PubMed.
Add your own notes to the PubMed information.
Include full-text of original source material, articles, and reports in your askSam database.
Output sorted lists with an overview of your information.
Search for and delete duplicate PubMed entries.
Work with other researchers and share the information you collect.
Distribute the results of your research with the free askSam Viewer.
askSam gives you a powerful tool to manage your research. The basic steps you'll follow to organize your PubMed information using askSam are:
1. Use PubMed to locate relevant sources.
2. Save the search results from PubMed in MEDLINE format on your computer.
3. Create an askSam database using the PubMed / MEDLINE template.
3. Import the file containing the PubMed sources into your askSam database
(during the import phase you will process the information
using the TextPipe PubMed filter).
In the rest of this article, we'll provide instructions on using askSam with PubMed information.
Getting Information From PubMed / MEDLINE
You can access PubMed on the Internet at:
The PubMed home page lets you enter search requests and displays the results. The results are displayed on the screen in the Summary format. You can click to view the abstract.
There is a checkbox next to each PubMed item retrieved by your search. Check the boxes of each item you wish to download to your computer.
To save the selected items on your computer (so you can import them into askSam), you will need to:
1. Set the display format to MEDLINE. You set the display format in the dropdown menu above your search results.
2. Send the results to a FILE. You set the output type by selecting the dropdown menu next to the SEND TO button. Set this to FILE.
3. Once you've set the output type to file, click on the SEND TO button.
A FILE DOWNLOAD dialog will appear.
4. Choose the SAVE button.
The SAVE AS dialog will appear.
5. Choose the location where you want to save this file, and enter a name for the file. We recommend giving the file you save a .TXT extension (because you will be importing it into askSam as a text file).
The file containing your PubMed research is now saved on your computer, and you can now import it into askSam.
Configuring askSam and TextPipe
We've prepared a special askSam Template for PubMed information, and we've also (with the help of the folks at Crystal Software) created a TextPipe filter to properly format the PubMed information when it's imported into askSam.
There is no charge for the askSam Template and the TextPipe filter, but you will need a copy of askSam 5 and a copy of TextPipe for askSam (you can try this out with trial versions of either product which you can download at http://www.asksam.com/downloads.asp.
askSam PubMed/MEDLINE Template
The askSam Template contains pre-defined reports and stored searches as well as several different views for the search results. The template also contains a NOTES Entry Form that allows you to add your own notes and comments to the PubMed records you organize in askSam.
You can download the askSam PubMed/MEDLINE Template from:
After you download the template, place it in your askSam template folder. By default this directory will be c:\program files\askSam\askSam5\templates.
TextPipe PubMed/MEDLINE Filter
The PubMed/MEDLINE filter for TextPipe converts the MEDLINE tags into askSam fields. You will need to have TextPipe installed to use the filter during the import process.
You can download the TextPipe PubMed/MEDLINE filter from:
After you download the filter, place it in your TextPipe template folder. By default this directory will be C:\Program Files\TextPipe.
Once you've placed the template and filter in the appropriate directories, you're ready to go.
Bringing PubMed / MEDLINE Information into askSam
The askSam Template and TextPipe filter are designed to organize search results saved from PubMed in MEDLINE format. This is a two-character tagged field format displaying all fields of the MEDLINE record.
A downloaded MEDLINE record will look like this:
To bring this into askSam in a useful format, we have created a TextPipe Filter. This filter turns the MEDLINE tags into askSam fields.
The filter also combines multiple authors into a single author field (it also does the same with keywords). For example:
is converted to:
To Import PubMed Information Into askSam
Create a new database using the askSam PubMed/MEDLINE Template.
1. Choose FILE - NEW and select the PubMed template from the list of templates.
2. Choose the CREATE button, enter a name for your askSam database, and choose SAVE.
A new askSam database is created. You can now import your PubMed research into this file. You can put all your PubMed information into a single database, or you can create different databases for different research projects.
To import your information into askSam:
3. Choose FILE - IMPORT.
The IMPORT dialog box will appear.
4. In the Import dialog do the following:
- Set FILES OF TYPE to "Text (*.txt)"
- Set the DOCUMENT DELIMITER to the string ##END OF RECORD##
- Set USE FILTER to the PUBMED MEDLINE filter.
- Select the file you saved from PubMed
- Choose the IMPORT button.
Note: If there is no USE FILTER option in your Import dialog, it means
that TextPipe is not installed on your machine. This option only appears
when askSam detects that TextPipe is installed.
Your file will be imported into askSam. Each MEDLINE record is imported into an individual askSam document.
Once the information is in askSam, you can search, add your own comments, keywords, and information as well as run reports.
Searching PubMed Information in askSam
You can use all of askSam's powerful searches on the information you import from PubMed. You can search from the askSam Search Line, use the Search dialog (ACTIONS - SEARCH), or run the stored searches we've prepared in the template. The stored searches allow you to search for a specific author, keyword, or title.
In addition, we've set up several views for your search results. You can choose to see the results of your searches sorted by Author, Date, or Title. You can select a view from the dropdown menu in the Search Results tool bar.
Note: See the askSam manual for a complete description of askSam's powerful search features.
Adding Notes to Your PubMed Information
You can add your own comments and notes to PubMed record using the NOTES Entry Form in the PubMed MEDLINE template.
To add a note:
1. Go to the PubMed Record where you wish to add the note.
2. Press ALT+1
The NOTES Entry Form is inserted at the top of the record. You can enter your notes in the notes field (which is separate from the PubMed information.
Formatted Reports in the PubMed / MEDLINE Template
We've pre-defined several reports to help you organize your PubMed information. You can run each of the reports to see which one gives you the best overview of your information. You can run a report by clicking on the Hypertext link in the first document of the database, or by choosing TOOLS - REPORTS, selecting the report you wish to run, and choosing the RUN button.
Overview with Titles
Lists Title, Authors, Source information (bibliographic cite), and PubMed Date. The items are sorted so that the most recently published are displayed first.
Sample Output from "Overview with Titles" report
Titles and Abstracts
Lists Title, Authors, Source information (bibliographic cite), the abstract, PubMed date, and PubMed ID number. The items are sorted so that the newest ones are displayed first. Click here to see a screen shot of this report.
Title, Author, Date, Abstract
Same information as the previous report but formatted differently. Click here to see a screen shot of this report.
Search for Author
Lets you search for an author and output the Title, Authors, Source information, and abstract. Click here to see a screen shot of this report.
Search for Keyword
Lets you search for a keyword and output the Title, Authors, Source information, and abstract. Click here to see a screen shot of this report.
Overview w/ Notes
Lists the Title, Authors, Source information, and any notes you've added about the PubMed documents. Click here to see a screen shot of this report.
Only Output Documents with Notes
Lists only documents where you've entered notes about the PubMed information. This reports is a great way to see the information most relevant to your research. The report displays the Title, Authors, Source information, and your notes. Click here to see a screen shot of this report.
More Information and Questions
This article gives you a brief description of how to bring PubMed information into askSam... and how to organize it once it's there. Both askSam and TextPipe are very flexible products. You can customize the TextPipe Filter as well as the askSam Template. Feel free to create your own reports, searches, and more. For more information there are a couple places you can turn:
the askSam reference manual has complete instructions on using askSam.
the forums on the askSam Web site (there's a thread under general discussions about PubMed).
We hope you find askSam useful for organizing your PubMed information and look forward to your feedback.
askSam PubMed/MEDLINE Template
TextPipe PubMed/MEDLINE Filter
askSam Trial Download
TextPipe Trial Download