QuickStart

1. System requirments

PubMedMakerIII
Windows98*, WindowsMe, Windows2000, Windows XP, FileMaker Pro 3.0~5.5 (Win)
* If you use Windows95 or WindowsNT, you need to set up WSH: Windows Scripting Host.
　

2. Outline of PubMedMaker

A. Making Reference list for your paper.
1) MEDLINE search at PubMed--You perform a search of the scientific literature in PubMed on the Internet and save the search results as a text file with MEDLINE format.
2) Making FileMaker Pro database--Drag and drop this text file on PubMedMaker icon. FileMaker Pro database is generated in the PubMedMaker folder.
3) Choose literature for citation and making a Reference database--Choose literature which you will cite in your paper and click "Make RefList" button. FileMaker Pro database named "Reference" appears in the PubMedMaker folder.
4) Output Reference list--You set up the style of Reference list in the Reference database to conform to the style of scientific journals. You can out put Reference list file with plain text, rich text (RTF) and HTML (List, Table) in the PubMedMaker folder. Open these files using apporopriate applications, such as, MicrosoftWord, WORDPAD and Internet Explorer.

B. Link to on-line journal.

1) MEDLINE search at PubMed, 2) Making FileMaker Pro database--Same as above.

3) Find literature which have link to on-line journal--You can easily find and choose literature which have link information to on-line journal. Go to List Page in the FileMaker Pro data base. Radio buttons on the right of each record are on if it has links. Click "On-line" button on the foot bar to choose them.

4) Open on-line journal on the internet--Click "Journal" button to open it.
Input Page List Page

C. Automatic management of PDF files of literature.

Set up a PDF folder before making FileMaker Pro database--You have to make "PDF folder" to keep PDF files of literature. To do this, double click PubMedMaker and click PDF folder tab panel. Select present PDF folder or make new one. See Set up a PDF folder.

1) MEDLINE search at PubMed, 2) Making FileMaker Pro database, 3) Find literature which have link to on-line journal, 4) Open on-line journal on the internet--Same as B. Link to on-line journal.

5) Download PDF file of literature--Click "Reprint (PDF) Version of the Article" at on-line journal, and then click "Download". Set the name of PDF file as default, and save it on the desktop.

Input Page List Page

6) Keep PDF file into PDF folder--Click "Keep PDF" button. This button puts away PDF file on the desktop into PDF folder and input PDF name in the PDF name box of FileMaker Pro database.

7) Open PDF file of literature--Click "Open PDF" button. This button open PDF file of literature with Acrobat reader.

There are "Check PDF" button and "Input Stored PDFs" button.

D. Use as reference browser.
1) Addition/delete of literature, 2) Change of appearance, 3) Make a memo, Check reprints/photocopies, Save search words, 4) Perform find in the FileMaker Pro database, 5) Print abstract and print list of literature

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3. Set up PubMedMaker

1) Preferences--Double click PubMedMaker.

Version of FileMaker Pro
--Choose the version of FileMaker Pro that you are using.
making FileMaker files
--Choose one step or two steps. One step: You can make FileMaker Pro database by only one time drag & drop a text file on PubMedMaker icon. Two steps: A converted file (.cvt) is generated at first drag & drop a text file on PubMedMaker icon. FileMaker Pro database is generated by drag & drop a converted file (.cvt) on PubMedMaker icon. See Making of FMP database.
Download files after conversion
--Choose one of three methods. put away in Download files folder: A text file is moved to the Download files folder after conversion, which is automatically made in the PubMedMaker folder. move to Trash: A text file is deleted after conversion. as it is: A text file is left as it is after conversion.
Click "Save" that becomes active if you change the present settings, and click "Quit".

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2) Set up a PDF folder--Click "PDF folder" tab panel of PubMedMaker.

"PDF folder" has a specific structure, in which PDF files are stored. If you use PubMedMaker for the first time, click "New". PubMedMaker makes empty "PDF folder" at any place where you want to set up*. If you have a PDF folder already, click "Select". Choose the "PDF folder" that you are using**.
* Do not put a PDF folder in "My Documents" folder. This is because "Open PDF" command does not work if folder name includes space.

** If PubMedMaker quits abnormally when you choose a "PDF folder", delete "PubMedMaker pdf" file in the Preferences folder. This is because "PubMedMaker pdf" file is broken. Delete it and try again. "PubMedMaker pdf" file is located in PubMedIIIe12\Templates\PubMedMaker pdf.

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4. Use of PubMedMaker

A. Making Reference list for your paper.

1) MEDLINE search at PubMed or NLM Gateway
PubMed: http://www.ncbi.nlm.nih.gov/PubMed/
Search results will be displayed with "Summary" format by default. Choose "MEDLINE" format on pop-up menu, then click "Save". All records are downloaded irrespective of shown records. The records are saved as text file by the default name of "query.fcgi". Input suitable name for literature and click "Save".
NLM Gateway: http://gateway.nlm.nih.gov/gw/Cmd
After search, click "Display Results", "Download or Display". Choose proper provisions on pop-up menu like a below figure. PubMedMaker cannot accept 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".

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2) Making FileMaker Pro database
Making a FileMaker Pro database from a text file--Simply drag & drop a text file on PubMedMaker icon.

one step method
two step method

FileMaker Pro database is generated by only one time drag & drop a text file on PubMedMaker icon.

A converted file (.cvt) is generated at first drag & drop a text file on PubMedMaker icon. FileMaker Pro database is generated by drag & drop a converted file (.cvt) on PubMedMaker icon.

Note: FileMaker Pro database with the same name--If there has already been a FileMaker Pro database with the same name in the PubMedMaker folder, MEDLINE data are added to that database.
　

Conversion of FileMaker Pro database to new version--Simply drag & drop FileMaker Pro database on PubMedMaker icon.

There are three cases that you have to convert FileMaker Pro database.

1) Conversion of old FileMaker Pro database to latest version. You can convert old database generated by PubMedMakerII 3.8 or later.
2) Conversion of FileMaker Pro database for Mac to that for Win.
3) Conversion of FileMaker Pro database 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: You can import currently found records or all records of the database at conversion.

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3) Choose literature for citation and making a Reference database
Choose literature for citation and sort literature

		Choose literature at Input page Check red check box of literature that you are going to cite in your paper, and then click "Checked" button. Literature that you checked are selected and alphabetically sorted by first author's name.
		Choose literature at List page Choose literature by check box--Check red check box and then click "FindX" button. Literature that you checked are selected and alphabetically sorted by first author's name. Choose literature by cite number--Input the cite number in the pink box that you are going to cite in your paper, and then click "FindCite" button. Literature that you input numbers are selected and sorted by the cite number.
		Choose literature by check box and sort them by cite number--First, you roughly choose literature by red check box and "FindX" button. And then input cite numbers in the pink boxes in writing the paper. Second, click "Cite No" sort button. Literature that you input cite numbers are sorted by cite number at start of the list, and those without cite number are sorted by alphabetical order of journal name at end of the list. When you finish to input all cite number, click "FindCite" button.
		Choose literature by check box and perform InputSerialNumber--First, you choose literature by red check box and "FindX" button. Second, perform "InputSerialNumber" on Script menu. Cite numbers are automatically put in the pink boxes. This is applied to Reference list which requirs both alphabetical order of first author's name and cite numbers.
Write Page		If you missed literature in PubMed, you can write such literature at Write Page in the FileMaker Pro database. Click "New" button at first. Second, choose category of literature among Journal, Chapter in Book, and Book. Input data according to the example shown with red letters. There are specific fields used for only Journal, only Chapter in Book, and both for Chapter in Book and Book.

Making a Reference database*

Click "Make RefList" button when you finished to choose literature for citation.
Empty Reference.fp5 or Reference.fp3 is generated if it is not in the PubMedMaker folder. Click MakeRefList button again. The records are exported and imported to Reference database. If Reference database has already had citation data, they are renewed.

* You have to put a FileMaker Pro database in the PubMedMaker folder when you make Reference database.
　

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4) Output Reference list
Reference Set up

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 format to which you are going to contribute.

order settings

Choose the order of Title-Year and delimitors on 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.
　

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

RTF output

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

TXT output

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

List output

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

　

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B. Link to on-line journal.

Input page List page

Indicator for link to on-line journal
Input Page: If the record has a link with on-line journal, the indicator radio button is on. F stands for full text page, S for abstract page.
List Page: The indicators are located at right side of record. Upper radio button indicates a link with full text page, the lower with abstract page.

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

Journal button*
Journal button open on-line journal site of the present record. If indicator is on. Journal button at List page preferentially open full text page.

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

* You can see full text page and download full paper of PDF file if it is free on-line journal. You need a password to access charged journal. Since link icons to on-line journals on PubMed Summary Page can open some charged journals, try "PubMed" button first.
　

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C. Automatic management of PDF files of literature.

Download of PDF files
Go to 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, perform either of below methods.

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

2) To save PDF files by changing web browser settings
Mac:
Open Acrobat Reader and open Preferences on Edit menu. Click "Option", uncheck "Display PDF in Browser" in Web Browser Option.

Buttons for Automatic management of PDF files*

Input page List page

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

Keep PDF button-- This button puts away PDF file on the desktop into PDF folder and input PDF name in the PDF name box of FileMaker Pro database.

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

Open PDF button--This button open PDF file of literature with Acrobat Reader or TextEdit (Mac OS X).

Input Stored PDFs button-- All PDF names are imported to PDF name box if they are found in the PDF folder.

* You have to put a FileMaker Pro database in the PubMedMaker folder when you manage PDF files.
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, all records are shown ("perform find" is canceled).

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D. Use as reference browser

1) Addition/delete of literature

	Add Text button You can add MEDLINE data in the FileMaker Pro database. "Add Text" button imports MEDLINE data from converted files (.cvt) in the PubMedMaker folder. To make converted files (.cvt), you have to set up "making FileMaker files" to two steps in the Preferences. Converted file (.cvt) is deleted after import.
	Add FMP button You can add MEDLINE data in the FileMaker Pro database. "Add FMP" button imports MEDLINE data from other FileMaker Pro database (version II 3.0~III 1.1).
	Delete record button This button deletes current one literature in the database.
	Delete found records button This button deletes all literature currently found in the database.
	Duplicate records delete button You can delete duplicate literature at once. You can choose to be left a firstly or a lastly imported literature of duplicates in the FileMaker Pro database. 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. Window size enlarges automatically.
	Display font button This button toggles Times New Roman and Arial.
	"Smart window" adjusts the window's position and its size. It works in using FileMakerPro 4.0 or later on Mac.

3) Make a memo, Check reprints/photocopies, Save search words

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 is on. With memo list button you can move to memo list page.

You check "get" check box when you get reprints or photocopies of papers. You can find such records by FindGetPaper command on Script menu.

If you want to save search words at PubMed to currently found records, write them in the Word field and click "Save" button at Search Page. "Delete" button erases these words.

4) Perform find in the FileMaker Pro database

You can choose only English literature at Input Page.

This button at Serach Page goes to Find mode of FileMaker Pro. Input key words and put return key. "Return key" performs the find. A search is based on FileMaker Pro's function.

This button at Serach Page goes to Re-Find mode of FileMaker Pro. Previous key words are left. Input key words and put return key. "Return key" performs the find. A search is based on FileMaker Pro's function.

This button at Input Page shows all records to abort the find. "ALL" records button is also in List Page.

5) Print abstract and print list of literature

Before you print, sort literature. Literature are sorted by journal name in alphabetical order (Journal button), first author's name in alphabetical order (Author button), publish date from new to old (Date button) and cite number from 1 to last (Cite No button).

"Abstract" button at Input Page prints Title, Author, Address, Abstract of currently found all literature.

These buttons are in List Page. "Print Abst" button is the same as that in Input Page. Sort literature by Journal button before list print. You can easily find the articles at library since they are sorted by journal name in alphabetical order.

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end of Doc

1) MEDLINE search at PubMed, 2) Making FileMaker Pro database--Same as above.
3) Find literature which have link to on-line journal--You can easily find and choose literature which have link information to on-line journal. Go to List Page in the FileMaker Pro data base. Radio buttons on the right of each record are on if it has links. Click "On-line" button on the foot bar to choose them.

4) Open on-line journal on the internet--Click "Journal" button to open it.	Input Page	List Page

Set up a PDF folder before making FileMaker Pro database--You have to make "PDF folder" to keep PDF files of literature. To do this, double click PubMedMaker and click PDF folder tab panel. Select present PDF folder or make new one. See Set up a PDF folder.
1) MEDLINE search at PubMed, 2) Making FileMaker Pro database, 3) Find literature which have link to on-line journal, 4) Open on-line journal on the internet--Same as B. Link to on-line journal.
5) Download PDF file of literature--Click "Reprint (PDF) Version of the Article" at on-line journal, and then click "Download". Set the name of PDF file as default, and save it on the desktop.
	Input Page	List Page
6) Keep PDF file into PDF folder--Click "Keep PDF" button. This button puts away PDF file on the desktop into PDF folder and input PDF name in the PDF name box of FileMaker Pro database.
7) Open PDF file of literature--Click "Open PDF" button. This button open PDF file of literature with Acrobat reader.
There are "Check PDF" button and "Input Stored PDFs" button.

one step method		two step method

FileMaker Pro database is generated by only one time drag & drop a text file on PubMedMaker icon.		A converted file (.cvt) is generated at first drag & drop a text file on PubMedMaker icon. FileMaker Pro database is generated by drag & drop a converted file (.cvt) on PubMedMaker icon.

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 format to which you are going to contribute.
order settings	Choose the order of Title-Year and delimitors on 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 PubMedMaker folder. Open Reference.RTF by rich text compatible word processor, such as, MicrosoftWord (Mac, Win), AppleWorks (Mac), WORDPAD (Win) or TextEdit (Mac OS X).
TXT output	Click "TXT export" button. Reference.TXT appears in the PubMedMaker folder. Open Reference.TXT by any word processor or text editor.
List output	Click "List export" button. RefList.htm appears in the PubMedMaker 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 PubMedMaker folder. Open RefTable.htm by web browser, such as, Netscape or Internet Explorer, or HTML editor or HTML compatible word processor like MicrosoftWord.

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

Input page	List page
		Check PDF button--"?" icon button inspects "PDF folder". If a PDF file is found in the PDF folder, the name of PDF file is imported to PDF name box of the present literature.
		Keep PDF button-- This button puts away PDF file on the desktop into PDF folder and input PDF name in the PDF name box of FileMaker Pro database.
		Example: The name of PDF file is imported to PDF name box like this.
		Open PDF button--This button open PDF file of literature with Acrobat Reader or TextEdit (Mac OS X).
		Input Stored PDFs button-- All PDF names are imported to PDF name box if they are found in the PDF folder.

	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 is on. With memo list button you can move to memo list page.
	You check "get" check box when you get reprints or photocopies of papers. You can find such records by FindGetPaper command on Script menu.
	If you want to save search words at PubMed to currently found records, write them in the Word field and click "Save" button at Search Page. "Delete" button erases these words.

	You can choose only English literature at Input Page.
	This button at Serach Page goes to Find mode of FileMaker Pro. Input key words and put return key. "Return key" performs the find. A search is based on FileMaker Pro's function.
	This button at Serach Page goes to Re-Find mode of FileMaker Pro. Previous key words are left. Input key words and put return key. "Return key" performs the find. A search is based on FileMaker Pro's function.
	This button at Input Page shows all records to abort the find. "ALL" records button is also in List Page.

	Before you print, sort literature. Literature are sorted by journal name in alphabetical order (Journal button), first author's name in alphabetical order (Author button), publish date from new to old (Date button) and cite number from 1 to last (Cite No button).
	"Abstract" button at Input Page prints Title, Author, Address, Abstract of currently found all literature.
	These buttons are in List Page. "Print Abst" button is the same as that in Input Page. Sort literature by Journal button before list print. You can easily find the articles at library since they are sorted by journal name in alphabetical order.