QuickStart

1. System requirments
2. Set up of PubMedMakerIII
3. Download of MEDLINE data
4. Management of files

5. Use as reference browser
6. Direct link with on-line and PDF files
7. Paper selection and Reference list

Note: Figures and explanations for Mac version are applied to this manual. You cannot see extensions under Windows system.

1. System requirments

You need below system requirments to use PubMedMakerIII.
Windows*: Windows98, WindowsMe, Windows2000, FileMaker Pro 3.0~5.5 (Win)
Macintosh: Macintosh PowerPC, Free memory of 14~18MB, Mac OS 8.5~9.2, FileMaker Pro 3.0~5.5 (Mac)
* If you use Windows95 or WindowsNT, you need to set up WSH: Windows Scripting Host.

go to index

2. Set up of PubMedMakerIII

1) Preferences--Double click PubMedMakerIII.

Version of FileMaker Pro--Select the version of FileMaker Pro that you are using.
making FileMaker files--One step method makes FileMaker File only by drag & drop a Download file on PubMedMakerIII. Two step method makes a convert file (.cvt) at first drag & drop, then makes FileMaker File by second drag & drop convert file (.cvt) on PubMedMakerIII. See Making a FileMaker file.
Download files after conversion--as it is: Download file is left as it is after conversion. put away in Download files folder: Download file is kept in the Download files folder after conversion, which is automatically made in PubMedMakerIII folder. move to Trash: Download file is deleted after conversion.
Click "Save" that becomes active if you change the present settings, and click "Quit".

2) Selection of PDF folder--Click "PDF folder" tab panel of PubMedMakerIII.

If you use PubMedMaker for the first time, click "New". Set a PDF folder at any place where you want*. If you are a user of PubMedMakerII and have a PDF folder already, click "Select". Select the PDF folder that you are using. FileMaker files made with PubMedMakerIII refer to this folder in managing PDF files**. All users must set it up before using PubMedMakerIII even if you will not need PDF files of full text paper.
* Windows users: Do not put a PDF folder in MyDocuments folder (joint folder).

go to index

3. Download of MEDLINE data from PubMed or NLM Gateway

1) PubMed: http://www.ncbi.nlm.nih.gov/PubMed/
Search results will be displayed with "Summary" format by default. Select "MEDLINE" format from pop-up menu, then click "Save". All found records are downloaded irrespective of shown records. The records are saved as text file by the default name of "query.fcgi" or "result.txt". Input suitable name for literature and click "Save".

2)NLM Gateway: http://gateway.nlm.nih.gov/gw/Cmd
After search, click "Display Results", "Download or Display". Select proper provisions like a below figure from pop-up menu. PubMedMakerIII cannot read a text file downloaded with other settings. Set item number to fetch to more than that of search result. The records are saved as text file by the default name of "Cmd". Input suitable name for literature and click "Save".

go to index

4. Management of files

1) Making a FileMaker file--Just drag & drop download text file on PubMedMakerIII.

one step method
two step method

One step method makes FileMaker File only by drag & drop a Download file on PubMedMakerIII.

Two step method makes a convert file (.cvt) at first drag & drop, then makes FileMaker File by second drag & drop convert file (.cvt) on PubMedMakerIII.

Note1: PubMedMakerIII accepts a download file located at any place. You do not need to put it in the PubMedMakerIII folder. But a FileMaker file always appears in the PubMedMakerIII folder.
Note2: FileMaker file with the same name--When you are going to make a FileMaker file, that has the same name with a file in the PubMedMakerIII folder, the data is added to that file. You can also cancel to make a file and remake with using other name.
2) Conversion of FileMaker file--Just drag & drop FileMaker file on PubMedMakerIII.

There are three cases that you have to convert FileMaker file.

1) Conversion of old FileMaker file to new version.
2) Conversion of FileMaker file for Mac to that for Win.
3) Conversion of FileMaker file for Win to that for Mac.

Note1: Converted file has extension of (M).fp5 or (M).fp3 in case of Mac, and (W).fp5 or (W).fp3 in case of Win.
Note2: PubMedMakerIII accepts a FileMaker file located at any place. You do not need to put it in the PubMedMakerIII folder.
Note3: You can import currently found records or all records of original file at conversion.

Note: A FileMaker file functions at any place. But you have to put a FileMaker file in the PubMedMakerIII folder when you perform "Add Text" button, manage PDF files and make a Reference list.

go to index

5. Use as reference browser

1) Addition/delete of records

Add Text button
In the two step method, converted files (.cvt) are made in the PubMedMakerIII folder. You can import records of a converted file (.cvt) to FileMaker file by using "Add Text" button. Converted file is deleted after import.

Add FMP button
In the one step method, download data always become FileMaker file. You can import records of other FileMaker file by using "Add FMP" button. In this case original FileMaker file is left as it is.

Delete record button
This button deletes current one record.

Delete found records button
This button deletes all records currently selected.

Duplicate records delete button
You can delete duplicate records at once. You can choose to be left a firstly or a lastly imported record of duplicates in the FileMaker file.
Note: Duplicate search is performed by using PMID number.

2) Change of appearance

Line space button
If you use 640x480 dot monitor, "line space button" appears. You can widen or reduce the line space of Abstract field.

Font size button
If you use more than 800x600 dot monitor, you can choose 12 or 14 point font. If you choose14 point font at Input page, same font size is used at List Page.

Display font button
This button toggles Times and Geneva (Mac), or Times New Roman and Arial (Win).

3) make a memo

With memo button (pencil icon) memo area appears in the abstract field, you can make a memo in memo area. Click memo button again, memo area hides out. If the record has a memo, the indicator of light blue circle becomes closed from open. With memo list button you can move to memo list page.

go to index

6. Direct link with on-line web site and management of PDF files

1) Direct link with on-line web site

Input page List page

PubMed button*
PubMed button directly open PubMed Summary Page** of the present record.

Journal button*
Journal button directly open on-line journal site of the present record. If the record has a link with on-line journal, the indicator of gray circle becomes closed. F stands for full text page, S for abstract page. Journal button at List page preferentially open full text page.

The indicators at List page are located at right side of record. Upper circle indicates a link with full text page, the lower with abstract page. If the record has a link with on-line journal, the indicator of gray circle becomes closed.

On-line button
You can find literature linking to on-line journal with On-line button.

* You can see full text page and download full paper of PDF file from free on-line journals. You need a password to access charged journals. But you can access some charged on-line journals without password through journal link icon of PubMed Summary Page when you are using Internet Explorer. Therefore, try PubMed button at first, resulting in access to many full text page of on-line journals.
2) Download of PDF files

Access full text page of on-line journal. Click "Reprint (PDF) Version of the Article", and then click "Download"*. Set the name of PDF file as default, and save it on the desktop.

* If a PDF file is displayed on the web browser instead of downloading it, make below settings.

1) To save PDF files without changing web browser settings
Click "Downlod" icon with right button of the mouse and choose "Download/Save Object to File..." from pop-up menu.

2) To save PDF files by changing web browser settings
Double click Adobe Acrobat Reader. Open Preferences from Edit menu, click "Option". Uncheck "Display PDF in Browser" in Web Browser Options (Acrobat Reader 5.0).

3) Automatic management of PDF files*

Input page List page

Check PDF button--"?" icon button inspects the current PDF folder. If a putative PDF file is found in the PDF folder, the name of PDF file is imported to PDF name box of the present record.

Keep PDF button--This button puts away PDF file downloaded on the desktop in the current PDF folder, and import its name to PDF name box of the present record.

Example: The name of PDF file is imported to PDF name box like this.

Open PDF button--This button opens PDF file when the name is displayed in PDF name box of the present record.

Input Stored PDFs button--Just after you make a FileMaker file, click this button. All PDF names are imported to PDF name box if they are found in the current PDF folder.

* You have to put a FileMaker file in the PubMedMakerIII folder when you manage PDF files.
Windows users: It takes a time to complete Check PDF and Keep PDF commands. Please wait until two dialogs appear. Do not click "OK" button before the second dialog appears. After you perform these commands of PDF management, all records are shown ("perform find" is canceled).

go to index

7. Paper selection and Reference list

1) Paper selection and sort

Paper selection at Input page
Click "Checked" button after checking red check box of the papers that you need. The papers that you checked are selected and alphabetically sorted by first author.

Paper selection at List page
1) Paper selection by check box--Check red check box and then click "FindX" button. This selection is applied to Reference list in alphabetical order of first author.
2) Paper selection by cite number--Input the cite number in the pink box of the papers that you are going to cite in your paper, and then click "FindCite" button. This selection is applied to Reference list in order of cite number.

Paper selection by check box and sort by cite number--First, you select papers roughly by selection with red check box that you may cite in your paper, and input cite numbers in writing the paper. Second, click "Cite No" sort button. The papers that you input cite number are sorted by cite number at the start, and those without cite number are sorted by alphabetical order of journal name at the end. This is convenient for making references with try & error. Click "FindCite" button when you finished.

Paper selection by check box and InputSerialNumber--First, you select the papers by selection with red check box that you are going to cite in your paper. Second, perform "InputSerialNumber" from Script menu. Cite numbers are automatically put in the pink boxes. This method is applied to Reference list which requirs both alphabetical order of first author and cite numbers.

2) Making Reference.fp5/.fp3

Click "Make RefList" button when you finished to select papers for citation*. Empty Reference.fp5/.fp3 is generated if it is not in the PubMedMakerIII folder. Click MakeRefList button again. The records cited are exported and imported to Reference.fp5/.fp3. If Reference.fp5/.fp3 has already had citation data, they are renewed.

* You have to put a FileMaker file in the PubMedMakerIII folder when you make Reference.fp5/.fp3.

3) Reference Set up--Please follow "instractions to authors" of the journal to which you are going to contribute.

radio buttons

Check one in each category of Author, Space of initials (if all authors), Journal*, Year, Page, and Cite No, according to the journal's roles to which you are going to contribute.

order settings

Select order of Title-Year and delimitors from pop-up menu, according to the journal's roles to which you are going to contribute.
Note: Delimitors of upper group have space after the characters. Those of lower group do not have space.

style settings

With rich text/HTML option you can set bold/plain/et al italic of Authors and bold/italic/bold-italic/plain of other items. You can also specify the font and No<space>Author/No<tab>Author from pop-up menu. Frame Thick is thickness of frame used in Table output of HTML.

* Note: Period of Journal name meets only major English journals. Please verify the export file.

4) Export of Reference list--Click "Ref export" button to go to Reference Page.

RTF output

Click "RTF export" button. Reference.RTF appears in the PubMedMakerIII folder. Open Reference.RTF by rich text compatible word processor, such as, MicrosoftWord (Mac, Win), AppleWorks (Mac), WORDPAD (Win).

TXT output

Click "TXT export" button. Reference.TXT appears in the PubMedMakerIII folder. Open Reference.TXT by any word processor or text editor.

List output

Click "List export" button. RefList.htm appears in the PubMedMakerIII folder. Open RefList.htm by web browser, such as, Netscape or Internet Explorer, or HTML editor or HTML compatible word processor like MicrosoftWord.

Table output

Click "Table export" button. RefTable.htm appears in the PubMedMakerIII folder. Open RefTable.htm by web browser, such as, Netscape or Internet Explorer, or HTML editor or HTML compatible word processor like MicrosoftWord.

go to index

end of Doc

	Add Text button In the two step method, converted files (.cvt) are made in the PubMedMakerIII folder. You can import records of a converted file (.cvt) to FileMaker file by using "Add Text" button. Converted file is deleted after import.
	Add FMP button In the one step method, download data always become FileMaker file. You can import records of other FileMaker file by using "Add FMP" button. In this case original FileMaker file is left as it is.
	Delete record button This button deletes current one record.
	Delete found records button This button deletes all records currently selected.
	Duplicate records delete button You can delete duplicate records at once. You can choose to be left a firstly or a lastly imported record of duplicates in the FileMaker file. Note: Duplicate search is performed by using PMID number.

one step method		two step method

One step method makes FileMaker File only by drag & drop a Download file on PubMedMakerIII.		Two step method makes a convert file (.cvt) at first drag & drop, then makes FileMaker File by second drag & drop convert file (.cvt) on PubMedMakerIII.

	Line space button If you use 640x480 dot monitor, "line space button" appears. You can widen or reduce the line space of Abstract field.
	Font size button If you use more than 800x600 dot monitor, you can choose 12 or 14 point font. If you choose14 point font at Input page, same font size is used at List Page.
	Display font button This button toggles Times and Geneva (Mac), or Times New Roman and Arial (Win).

Input page	List page
		PubMed button* PubMed button directly open PubMed Summary Page** of the present record.
		Journal button* Journal button directly open on-line journal site of the present record. If the record has a link with on-line journal, the indicator of gray circle becomes closed. F stands for full text page, S for abstract page. Journal button at List page preferentially open full text page.
		The indicators at List page are located at right side of record. Upper circle indicates a link with full text page, the lower with abstract page. If the record has a link with on-line journal, the indicator of gray circle becomes closed.
		On-line button You can find literature linking to on-line journal with On-line button.

Input page	List page
		Check PDF button--"?" icon button inspects the current PDF folder. If a putative PDF file is found in the PDF folder, the name of PDF file is imported to PDF name box of the present record.
		Keep PDF button--This button puts away PDF file downloaded on the desktop in the current PDF folder, and import its name to PDF name box of the present record.
		Example: The name of PDF file is imported to PDF name box like this.
		Open PDF button--This button opens PDF file when the name is displayed in PDF name box of the present record.
		Input Stored PDFs button--Just after you make a FileMaker file, click this button. All PDF names are imported to PDF name box if they are found in the current PDF folder.

		Paper selection at Input page Click "Checked" button after checking red check box of the papers that you need. The papers that you checked are selected and alphabetically sorted by first author.
		Paper selection at List page 1) Paper selection by check box--Check red check box and then click "FindX" button. This selection is applied to Reference list in alphabetical order of first author. 2) Paper selection by cite number--Input the cite number in the pink box of the papers that you are going to cite in your paper, and then click "FindCite" button. This selection is applied to Reference list in order of cite number.
		Paper selection by check box and sort by cite number--First, you select papers roughly by selection with red check box that you may cite in your paper, and input cite numbers in writing the paper. Second, click "Cite No" sort button. The papers that you input cite number are sorted by cite number at the start, and those without cite number are sorted by alphabetical order of journal name at the end. This is convenient for making references with try & error. Click "FindCite" button when you finished.
		Paper selection by check box and InputSerialNumber--First, you select the papers by selection with red check box that you are going to cite in your paper. Second, perform "InputSerialNumber" from Script menu. Cite numbers are automatically put in the pink boxes. This method is applied to Reference list which requirs both alphabetical order of first author and cite numbers.

radio buttons	Check one in each category of Author, Space of initials (if all authors), Journal*, Year, Page, and Cite No, according to the journal's roles to which you are going to contribute.
order settings	Select order of Title-Year and delimitors from pop-up menu, according to the journal's roles to which you are going to contribute. Note: Delimitors of upper group have space after the characters. Those of lower group do not have space.
style settings	With rich text/HTML option you can set bold/plain/et al italic of Authors and bold/italic/*bold-italic*/plain of other items. You can also specify the font and No<space>Author/No<tab>Author from pop-up menu. Frame Thick is thickness of frame used in Table output of HTML.

RTF output	Click "RTF export" button. Reference.RTF appears in the PubMedMakerIII folder. Open Reference.RTF by rich text compatible word processor, such as, MicrosoftWord (Mac, Win), AppleWorks (Mac), WORDPAD (Win).
TXT output	Click "TXT export" button. Reference.TXT appears in the PubMedMakerIII folder. Open Reference.TXT by any word processor or text editor.
List output	Click "List export" button. RefList.htm appears in the PubMedMakerIII folder. Open RefList.htm by web browser, such as, Netscape or Internet Explorer, or HTML editor or HTML compatible word processor like MicrosoftWord.
Table output	Click "Table export" button. RefTable.htm appears in the PubMedMakerIII folder. Open RefTable.htm by web browser, such as, Netscape or Internet Explorer, or HTML editor or HTML compatible word processor like MicrosoftWord.