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Figure 1　

Management of PDF files

Setting up：

Expand downloaded pubmed_beta.zip and save the pubmed folder with its contents anywhere you want. However, if you are using a language other than English in your OS, save the folder directly below C:\ directory.

Note: This program was tested under Windows XP and 7 but not Windows Vista.

Registration of your PDF files：

Start PubMed-P by double clicking pubmed-P.exe. PubMed-P window (Fig. 1) will show up.

I. Registration of multiple PDF files (batch)

Place your PDF files in the pubmed folder and select “Add pdf files (batch)” from “Add” menu. A sub-window will show up, so click “Start” button. Please wait until the sub-window automatically closes. More than half of recent publications will be registered automatically by executing this function. The ones PubMed-P failed to register will remain in the pubmed folder (rest will be in “cnvd” folder). You can easily (semi-automatically) register the remaining files using the following function.

II. Registration of a single file

Drag & Drop your file on to the list box ② (Fig. 1)

    1) If your file is named PMID.pdf, it will be registered automatically.
    2) Files with any name (other than a sequence of numbers*) may also be registered automatically.
      * PubMed-P recognize any sequence of number as PMID if it is used in a file name, so change the file name if it is not your intension.
    3) If PubMed-P was unable to register your file, a sub-window will pop-up. Text extracted from your file
      may show up in the lower-left text box.

              ( Semi-automatic registration using the subwindow )

              ・　Input keywords that would identify the publication to the upper left text box (horizontal).
                  (You can copy keywords from the text on the sub-window or from PDF file and then paste .
              Also, double clicking words in the extracted text will insert the word into the text box）
              ・　Press “Search” button and search result will show up in the right list box.
              ・　Click on the corresponding publication and press “Select” button.

# PubMed-P will ask you if you want the PDF to be moved to “cnvd” or “pmid” folder. If you do, close PDF file if open and the click OK button.
# PubMed-P retrieves information from PubMed via internet. You may need to set Proxy information (port, ID, and/or pass).

Main functions：

Double-click on a publication in the list ②(Fig. 1) to open the PDF file.

Information (authors, title, abstract, your comment, category) will appear on the PubMed-P window when you click on a paper in the list ②(Fig. 1). With a paper being selected, you can access PDF file, PubMed, and Suppl (supplemental files) by pressing the corresponding button (below the list ②).

You can add your comments to the upper-right text box ③ (Fig. 1). Also, supplemental files on your local computer can be associated with a paper by Drag & Drap-ing a file to the text box ③ (Fig. 1). A paper in the list box ② should be selected to use these functions.

You can set a category name using the lower-right pull-down menu ⑤ (Fig. 1). Category name you entered will be saved in the menu, so you do not need to repeat typing same thing. Important: When you make any changes to comment and category, click “Save” button.

When Pubmed-P is restarted after adding category, the category name will show up under “View” menu, so you can see the list of papers in the category by selecting it.

The list ② can be sorted (descending or ascending order) by author or year using Sort/Author, Year function (menu).

Type your query in the entry box ① and hit “List” button to find a paper you need. Author, title, abstract and comment are the target of the search.

Buttons and Menus:

I. Buttons

Search　keywords typed in the text box ① (Fig. 1)

Prev: Shows previous keywords you typed in the text box.
    List:  Information in the list of your papers (author, title, abstract and comment).
    Text:  Text files in the pubmed/text folder
    PubMed:  PubMed.. of course…
    Google:  Google Scholar

Lower-left buttons will show the information of the selected paper …

    by opening “PDF” file,
    by opening “PubMed” using your default browser,
    by opening “Suppl” files, OR
    “Delete” the information from your list. (PDF file will be moved to pubmed/trash folder)

II. Menus

File/Open pmid folder: You know what I mean…

    /Export to EndNote:
        Information of papers shown in the list on PubMed-P will be converted to MedLine format so that you can
    import using EndNote. The formatted infomation will be saved in pubmed/medline.txt.
        Open EndNote and then select menu, File/Import. Choose the medline.txt in the box next to
    “Choose file”, change Import option to  PubMed(NLM), and click Import button.

    /Check files: See if there are un-registered PDF files in pmid folder.

    /Exit : You know what I mean…

Add/Add pdf files (batch):
        Explained above in the section of main functions.

    /Add suppl. data:
        Select a paper in the list box ② and then use this function to relate any files on your local computer.

Sort/Author (a-z,z-a) : Sort the list ② by names of first authors

    /Year (new,old) : Sort the list ② by Year of publication

View/All...: Select a categry to display on the list ②

Search/List : Author names, title, abstract and comment will be searched by keyword(s) in text box ①

    /Text : See below “Full Text Search” section

    /PubMed : You know what I mean…

    /G-Scholar : You know what I mean…

MyNCBI/Search :
     For example if you type "interleukin" and select this function, you can see papers on interleukin
   published in the past one week. When you search the same key word, papers published between
   the date and the latest search date will be searched.

J-Club/Style1, Style2: See below “Making a list of papers selected on PubMed” section

Help/Readme : Open README.txt or help2.html file

Full text search:

Any text files in "text" folder can be searched with your query. Save your PDF files in text format before using this function.

If you are using Acrobat Reader, select text information by using "Menu bar: Edit/Select All" function and copy-paste on a text editor (ex. Notepad). If you have Adobe Acrobat, use "Menu bar: File/Save as (Text, Accessible)" function. All the text files need to be saved in C:/pubmed/text folder. It would be convenient if you just keep file names as "PMID.txt" .

Type your query in the text box of PubMed-P and select "Menu bar: Search/Text (w)" function. Search result will appear on an IE window (see Example 1).

If your query was found in PMID.txt files, links to PubMed, your file lists and PDF (with Search links）will be added to the search result.

If you are familliar with Regular Expression, more sophisticated search is possible. In this case, use "Menu bar: Search/Text(s)" function. For example, if you enter "statistical analysis(.{1,1000}?)results", description of statistical analysis will be nicely picked up (see Example 2)

（Example 1）
16449960.txt Chamberlin, WM., Naser, SA., , Integrating theories of the etiology of Crohn's Disease On the etiology of Crohn's Disease: Questioning the Hypotheses. PubMed | List | PDF

<1>... in infl ammation”[7]. This hypothesis is challenged by the Ferwerda et al. who show that wild-type NOD2 and Toll-Like Receptors (TLR-2 and TLR-4) are non-redundant recognition systems that act synergistically in response to mycobacterial antigens [8]. Sechi found that over 70% of CD patients with a NOD2 mutation had PCR evidence of a MAP infection. This fi ndings suggests that a specific pathogen may b ...

（Example 2）
12195191.txt Kim, BG., Kim, YS., Kim, JS., Jung, HC., Song, IS., , Diagnostic role of anti-Saccharomyces cerevisiae mannan antibodies combined with antineutrophil cytoplasmic antibodies in patients with inflammatory bowel disease. PubMed | List | PDF

> Statistical Analysis. We used a chi-squared test or Fisher’s exact test for categorical variables. For continuous variables, a two-sample t-test or Wilcoxon’s rank-sum test was used. A P value less than 0.05 was considered statistically significant. SPSS 10.0 for Windows (SPSS Inc., Chicago, IL) was used for both data management and statistical analysis.

Making a list of papers selected on PubMed:

On PubMed website, select papers you want to save and change display format to XML (Fig. 2, 1). Select "File" from "Send to" pull-down menu (Fig. 2, 2) and save "pubmed-result.txt" file in C:/pubmed .

Figure 2

On PubMed-P window, select "Menu bar: J-Club/Style1 or Style 2" (Fig. 1). And then, in the new pop-up window, select HTML file which you want to save the information in the new window popped up. If you use this function for the first time or want to create a new HTML file, type a name in the pop-up window and click "New" button. The list shown below will be automatically created (Fig. 3). If you choose "Style1 or Style 2 (rvs)", info of papers will be sorted in ascending (old->new) order.

If you choose an existing HTML file, the information will be appended.

Figure 3

Style 1

1. Fiot, J., Sanon, S., Azas, N., Mahiou, V., Jansen, O., Angenot, L., Balansard, G., and Ollivier, E. "Phytochemical and pharmacological study of roots and leaves of Guiera senegalensis J.F. Gmel (Combretaceae)."  J Ethnopharmacol,  2006, In press:      [PubMed]

2. Dev, V., Phookan, S., Sharma, VP., Dash, AP., and Anand, SP. "Malaria parasite burden and treatment seeking behavior in ethnic communities of Assam, Northeastern India."  J Infect,  2006, 52: 131-9     [PubMed]

Style 2

1. Fiot, J., Sanon, S., Azas, N., et al.   (2006)  Phytochemical and pharmacological study of roots and leaves of Guiera senegalensis J.F. Gmel (Combretaceae).  J Ethnopharmacol,  In press:      [PubMed]

2. Dev, V., Phookan, S., Sharma, VP., et al.   (2006)  Malaria parasite burden and treatment seeking behavior in ethnic communities of Assam, Northeastern India.  J Infect,  52: 131-9     [PubMed]