MedRefs Medical References Management Database Manual

A Database Application Program, Version 4.4
For use with Microsoft Access 97 and later versions

TABLE OF CONTENTS

System requirements Installation The Initialization File
Starting Access and MedRefs with the MedRefs Workgroup Abbreviations employed by MedRefs The Main Menu
The Miscellaneous Menu Program Modifications Licensure and Authorization for MedRefs use

System Requirements

You must have Access 97 installed, a monitor operating preferably at 1024x768 or higher, Windows NT 4.0 or 98 or higher, and adequate memory.  Please note: I have not updated this program for later versions of Access.

Installation

CAUTION: If you are reinstalling or updating MedRefs, and you already have a file named MedRefsD.MDB located in the MedRefs directory and containing data you wish to keep, rename the old copy of MedRefsD.MDB to another name ending in .MDB before reinstalling MedRefs to prevent data loss.

If MedRefs is obtained by downloading, the files needed will be contained inside a compressed ZIP archive file named medrfs32.exe. This is a self-extracting archive file which can be uncompressed (expanded or "exploded") by placing it in a temporary directory and then running it.

Once the archive file has been expanded, create a directory in which to place the MedRefs files and copy all of the files that were unpacked into that directory (typically this directory would be "C:\MedRefs"). Create a shortcut if you like to start MedRefs in Access. 

In addition to a working installation of Microsoft Access, the following files are needed for MedRefs and should be copied to the directory you have chosen.

File Description
MedRefs.ICO MedRefs Icon file
The optional default MedRefs icon
MedRefs.INI MedRefs Sample Initialization File
Optionally contains the names of default directories provided by the user--these are used to locate downloaded NLM files and to store the list of references generated by MedRefs for uploading. It must be located in the same directory as MedRefs.MDB but revised copies may be placed in other user directories to accompany their personal corresponding data files.

Here are sample INI file contents:
InputPath = X:\MCM\     [The directory MedRefs will first look at to search for a NLM file of citations]
RequestsFileDir = X:\MCM\     [The directory MedRefs will place a request list]
MedRefs.MDB Main MedRefs program file.
MedRefs.MDW MedRefs Workgroup Information File
 (System DB).  
This is a "system database" (Workgroup Information File) for the MedRefs Workgroup.. (You will not ordinarily need this file- but you may use it if you are running Access on your computer in an Access Workgroup for which you do not have permission to logon as "Admin").  It is necessary to logon as Admin in order to modify Medrefs.
MedRefsD.MDB MedRefs initial blank data file
The original or default "data" database file, containing the permanent data table "References" and tables of abbreviations ("INAbbrev" and "TIAbbrev") as well as journal names ("Journals"). This file may be copied by the user to another file name, but the tables contained within it may not be renamed. Be sure the name of the new file copy ends with the ".MDB" extension. You should not delete this file, though you may choose to keep it empty and instead to keep your data in other files.  This file is in Access 97 file format.
MedRefs_Manual.HTML MedRefs Manual stub file in HTML format 
As of 8/2/2004, the most recent program manual is located on the McGoodwin.Net website.  This local "stub" file redirects your browser to the current website file.
ReadMe.TXT Notes regarding MedRefs version updates etc.
Sample_Format1.TXT Sample Medline references to import into MedRefs
A
sample of downloaded Medline references in the old NLM/Medline format (see below) that may be used to test the translating function of MedRefs.  UIs have been replaced with PMIDs.
Sample_Format2.TXT Sample Medline references to import into MedRefs
A
sample of downloaded Medline references in the new (c. 2000) NLM format (see below) that may be used to test the translating function of MedRefs.  UIs have been replaced with PMIDs.
Sample_Format3.txt Sample Medline references to import into MedRefs
A
sample of downloaded Medline references in the 2003 NLM-PubMed format in which consecutive citation numbers are not included but instead single blank lines separate the citations.  UIs have been replaced with PMIDs.
Sample_Format4.txt Sample PubMed references to import into MedRefs
A
sample of downloaded PubMed references in the 2004 PubMed format in which consecutive citation numbers are not included but instead single blank lines characters separate the citations and new citations begin with PMIDs.  Medline UIs are no longer included.
WRKGADM.EXE Access 97 Workgroup Administrator Utility
This utility is provided by Microsoft for joining other workgroups in Access (see MedRefs.MDW above).

 

As of version 4.3, you will also need to have installed the Microsoft Scripting Runtime file scrrun.dll, which is installed with many Microsoft applications and current Windows operating systems and which can be downloaded from Microsoft if needed (search Google for "download microsoft scripting runtime" and select a link on the Microsoft site).

Next, create a shortcut (in the Windows Explorer Start menu or on your desktop) to start your new copy of MedRefs.mdb in Access with a command line (all on one line) resembling the following:

"C:\Access\Office\MSACCESS.EXE"  "C:\MedRefs\MedRefs.MDB" /User Admin /Pwd Admin

    where

C:\Access\Office\MSACCESS.EXE  is the location of your copy of Access

C:\MedRefs\MedRefs.MDB  is the location of your copy of the MedRefs main database file

Be sure to replace the path names listed here with the actual paths found on your computer.

Note: In order to modify Medrefs, you must logon to Access as "Admin". See below regarding joining the Medrefs workgroup if necessary.  It is not possible as best as I can determine to successfully specify the Workgroup Information File on the command line, despite what the Access 97 help file states regarding the /wrkgrp command line parameter.

The Initialization File

Each user may optionally copy MedRefs.INI to his/her own directory and edit it with Notepad to specify his/her preferences (see description of line items for this file in table under Installation).

Starting Access and MedRefs with the MedRefs Workgroup

Use the shortcut provided above, suitably modified to logon to Access as "Admin" with the password if any, and to open MedRefs.mdb at the same time.

The Main Menu

After opening the MedRefs database, the Main Menu is displayed and gives seven choices:

(1) Transfer References From an External File To Temp Table
(2) Show and Edit References in Temp Table
(3) Transfer Tagged References from Temp Table to Permanent Table
(4) Show and Edit References in Permanent Table
(5) Save List of Reference Requests to an External File
(6) Miscellaneous Menu
(7) Quit

The user may also use standard Access menu items when appropriate (such as the Find technique).

(1) Transfer References From an External File To Temp Table

Select this choice after first creating a disk file downloaded from the National Library of Medicine or similar resources. This should be a pure text ("ASCII") file and should not contain formatting imposed by a word processing program. The current version of Medrefs requires PMIDs to be positioned as the beginning field of a citation, which is the form found at PubMed but not currently at the NLM. 

To download and import citations from PubMed, the following are representative settings (as of 9/29/04):
Search: PubMed
For: [the Search String: may combine diagnoses in the Search String, and will end up resembling this: 

("fatigue syndrome, chronic"[MeSH Terms] OR chronic fatigue syndrome[Text Word]) OR ("fibromyalgia"[MeSH Terms] OR fibromyalgia[Text Word]) AND English[Lang] AND ("human"[MeSH Terms] OR "hominidae"[MeSH Terms]) AND ("2004/01/01"[PDAT] : "2004/12/31"[PDAT]) AND English[Lang] AND ("human"[MeSH Terms] OR "hominidae"[MeSH Terms]) AND ("2004/01/01"[PDAT] : "2004/12/31"[PDAT])"

Limits included in the serach field above may be set with "Limits": 
    Limited to: All fields
    Languages: English
    Publication Dates: 2002/01/02 to 2003/08/03
    Subsets: MEDLINE
    Publication Types; Ages; Entrez Dates;  Only Items with Abstracts; Human or Animal; Gender: restricted PRN
When results are displayed, select
   Display: MEDLINE
   Send To: File
   Click on SendTo and provide the downloaded file a name

The following information regarding acceptable sample file formats for  importing has been updated to match the NLM replacement of UIs in favor of PMID unique identifiers.  The file may begin with extraneous material such as the search criteria, though it is probably best to delete this type of information. 

Format 1 (Old NLM/Grateful Med/Ovid/BMJ format): Each data field begins with a 2 or 3 letter abbreviation, then spaces to fill out 4 characters total, then a hyphen at the 5-th position, then another space at the 6th position, and finally the beginning of the entry (e.g., "TI  - 11416540") at the seventh character position. Any continuation lines must be preceded by 6 space characters.  Citations begin with a citation number followed by a PMID line.

Format 2 (A Newer NLM format): Each data field begins with a 2 to 4 letter abbreviation, then a space at the 5th position, a hyphen at the 6th position, then another space at the 7th position, and finally the beginning of the entry (e.g., "PMID - 11416540") at the eighth character position. Any continuation lines must be preceded by 7 space characters. Citations begin with a citation number followed by a PMID line.

Format 3 (A Newer c. 2003 NLM PubMed format): Each data field begins with a 2 to 4 letter abbreviation, then a space at the 5th position, a hyphen at the 6th position, then another space at the 7th position, and finally the beginning of the entry (e.g., "PMID - 11416540") at the eighth character position. Any continuation lines must be preceded by 7 space characters.  Citations are separated by single linefeed characters without citation numbers and begin with the PMID line.

Format 4 (Newest c. 2004 NLM PubMed format): Each data field begins with a 2 to 4 letter abbreviation, then a space at the 5th position, a hyphen at the 6th position, then another space at the 7th position, and finally the beginning of the entry (e.g., "PMID - 11416540") at the eighth character position. Any continuation lines must be preceded by 7 space characters.  Citations are separated by single linefeed characters or blank lines without citation numbers and begin with the PMID line.  The Medline UI is no longer included.

Any valid Medline data fields that are not currently allotted explicit storage fields in the References table will be placed in the Abstract or discarded (which to discard versus retain has been pre-programmed in the routine TransferMedlineToTemp). All imported data is stored in a newly-created table named "Temp" (any old data in a table of that name will be discarded). If you wish to transfer citations to MedRefs from another data format, you must arrange to reformat the data as described above in order to automate the importing process. 

Records that are designated by the NLM as PT=Letter are discarded. If you wish to import such letter records, you must delete these PT lines in the downloaded file. 

(2) Show and Edit References in Temp Table

This choice brings up the "ViewTemp" form, which displays the temporary table ("Temp") made with the data imported from the Medline file. The user may edit the fields, sort the records, and mark as "Tagged" those which he/she wishes to add to the permanent table. Data that exceeded the field lengths provided (such as too-long titles) continue in the Abstract- the user may wish to shorten or abbreviate the title appropriately, reincorporating the material shifted to the Abstract back into the title, etc.

The references may also be sorted by PMID ("UI"), Reverse PMID ("RevUI") , Title ("TI"), Source ("SO"), First Author ("AU"), and Institution ("IN"). These choices display all records in the Temp table.

Clicking on "Tag / Untag" allows the user to toggle the Tagged status of the current reference (only "Tagged" records will be transferred to the permanent References table when this action is requested.)

Clicking on "Untag Dupl" will untag all records in the Temp table which have the same PMID as any record in the Permanent Table. Use this to prevent importing duplicate records into the Permanent table. This feature allows the user to download reference searches with overlapping date criteria without concern that some of the references may have already been incorporated into the Permanent table. MedRefs does not, however, prevent the incorporation of duplicate records into the Permanent table if the user do desires.  You may view records in the Temp table which have corresponding records (same PMID) in the References table by pressing "Dupl".

The "Tagged" button allows the display of only tagged references- only these can be transferred to the permanent table. All records are redisplayed when any of the "Sort By" choices are selected.

The references may also be viewed in DataSheet view (View/Datasheet on menu). The user may apply custom sort and selection filters by using the Records/Edit Filter-Sort menu. Caution is urged in selecting all records, as this could lead to deletion of all records accidentally.

Press "Close" to return to the Main Menu.

(3) Transfer Tagged References from Temp Table to Permanent Table

Selecting this automatically transfers all references that are marked "Tagged" in the Temp table to the Permanent table. Don't perform this action more than once, or the same Temp table records will again be transferred and be duplicated in the permanent References table. The user may easily distinguish in the Permanent table the newly imported references by viewing only the tagged records, provided he/she untagged all references in the Permanent table before importing the new ones (see below).

(4) Show and Edit References in Permanent Table

This choice brings up the "ViewRefs" form, which displays the permanent References table. The newly transferred references are still marked as "Tagged", so pressing the Show Only Tagged button will allow the user to see only the new references (perhaps to make a final decision whether to keep each or to be reassured of a successful transfer). They may be untagged individually or as a group with Untag All References in Permanent Table (a choice on the Miscellaneous Menu.)

The references may also be sorted by PMID ("UI"), Reverse PMID ("RevUI"), Title ("TI"), Source ("SO"), First Author ("AU"), Institution ("IN"), Year of Publication ("YR"), and Reverse Year of Publication ("RevYR"). RevUI and RevYR are useful for showing the most recent articles first. In addition, sorting by RevYR is optimized to allow the identification of duplicate articles that have been entered once with a custom PMID and subsequently with a an official PubMed PMID, as these unintended duplicates will be found close together.

To search for a specific author, click on the author field, then press Ctrl-F and enter appropriate values in the Find dialog box (be sure "Current Field" is checked). Rapid searching may also be done on key words in any of the other text box fields (TI, SO, IN, YR, and Unique ID). Searching in the Abstract (or choosing "All Fields") can also be done, though it will be slower as Abstract is a non-indexed field with long entries.

Pressing Show Only Dupl displays only records with duplicate PMID's within the Permanent table (this allows the user to delete duplicates after combining their data as appropriate). It does not compare the contents of the Permanent table with the Temp table. Pressing Show Only Req displays only records marked "Request"- these are the ones which will be written out to a disk file to create a requests list (see Save List of References to an External File.)

The "Xerox" option group offers the following choices: "None" (no copy of the reference is available or none is desired), "Req" (citation is to be included in a file listing requests for copies), "Req'd" (copy of reference has been requested but not yet received), and "Rec'd (copy has been received.)

If the user is entering a reference de novo, he/she may click on the combo box control next to "Source" to select from a list of Journals. Don't use this if an entry is already present in Source unless you wish to completely replace it.

Double-clicking on "DEL" deletes the current reference after confirming. The user may also delete a record by clicking on the record selector bar on the far left and then pressing <delete>.

Clicking on "Tag / Untag" allows the user to toggle the Tagged status of the current reference.

The counter display show the primary key counter. Its principal value is to make clear to the user that two otherwise identical-appearing records are actually duplicates, so that one may be deleted. The counter does not accurately indicate the actual number of records (this number is correctly shown with the "Navigation Buttons" at the bottom of the form.

The references may also be viewed in DataSheet view (Alt-View...).

The user may apply custom sort and selection filters by using the Alt-Records menu. Caution is urged in selecting all records, as this could lead to deletion of all records accidentally.

Press "Close" to return to the Main Menu.

(5) Save List of Reference Requests to an External File

This creates a text file listing abbreviated versions of the references marked "Request", which may be used to request copies. After creating the file, the user is given the option to mark all these references as Requested ("Req'd" on the form).

(6) Miscellaneous Menu

Starts the miscellaneous menu

(7) Quit

This choice closes the MedRefs database and returns to the Access opening screen. You will be prompted to save any unsaved changes.

The Miscellaneous Menu

The Miscellaneous Menu provides these choices:

(1) Create a New File For Your References
(2) Untag All References in Permanent Table
(3) Select a Different File Containing Your References
(4) Delete All Tagged References in the Permanent Table
(5) Show Name and Path of Currently Attached Data File
(6) Export Tagged References to an External File
(7) Export Categorized References to a Text File
(8) Return to Main Menu

The user may also use certain Access menu items shown in the menu bars when appropriate.

(1) Create a New File For Your References

This allows you to create a new data file for your own references (if you are using MedRefs in a multi-user environment) or for a different subject of interest (e.g., ATRFIBR.MDB or BREASTCA.MDB). You may have as many different MedRefs data files as your disk can hold and any of them can be located on a removable disk. You will be prompted for a name (it must end in ".MDB") and a drive and directory in which to place it. This new file will receive copies of "INAbbrev", "TIAbbrev", and "Journals" as they exist in your currently attached data file, but the "References" table will be empty of references. The new file will then be attached and ready for use.

When you create a new file in a different directory, you might consider placing a copy of MedRefs.INI in that directory and editing it with your preferences for default directories, etc.

(2) Untag All References in Permanent Table

Use this to clear all of the tags in the "References" table. Tags can be useful for performing custom sorts or bulk updates or deletes. You will want this ability to delete all tags after performing such an action, especially to prevent accidental deletions with "Delete All Tagged References in the Permanent Table." It is also desirable to untag all the references in the Permanent table before importing new references so that you can determine at a glance which are new.

(3) Select a Different File Containing Your References

This allows you to switch to another existing MedRefs data file. It can be located on a removable disk if desired.

(4) Delete All Tagged References in the Permanent Table

This allows you to delete all tagged references in the Permanent Table. Be careful with this! You will rarely have occasion to use this option.

(5) Show Name and Path of Currently Attached Data File

This can reassure you exactly where the current data file you are viewing is actually located.

(6) Export Tagged References to an External File

This copies all stored fields for all tagged references to an external file. Unlike "Save List of Reference Requests to an External File", all stored fields are copied to the file in their entirety and copied references and not marked "Requested" or untagged.

(7) Export Categorized References to a Text File

This copies all stored fields for all references to an external text file that meet the following criterion: The Abstract must contain the phrase {Category:xxxxxx}at the very end-- this phrase must be enclosed in curly braces as shown.  The user may replace the characters xxxxxx with whatever characters of he/she chooses to represent a particular category for inclusion.  The list generated will be sorted according to Category, then Author.

(8) Return to Main Menu

You need to return to the Main Menu prior to exiting MedRefs.

 Abbreviations

MedRefs utilizes numerous abbreviations for journal names, titles, and institutions when translating files of citations (the user is not obligated to use these abbreviations, however).

To prevent further use of undesired abbreviations in "INAbbrev" or "TIAbbrev", open your data file (e.g., MedRefsD.MDB) directly from Access and delete the undesired abbreviation records.

If you enter new or modify existing abbreviation records, do so with care, using spaces and quotes as in the existing entries to avoid unwanted substitutions. For instance, use " and " = " & " rather than "and" so that "sand" is not converted to "s&", and " department " = " D " rather than "department" so that Interdepartmental is not converted to "interDal". In substituting abbreviated forms of phrases, MedRefs attempts to preserve the case of first letter of the words in the actual entry (e.g., "Department of Medicine" translates as "D o Med" even though " medicine" is the table listing. MedRefs sorts abbreviation entries so that longer ones sharing the same starting characters are replaced first . For example, the phrase " chronic obstructive pulmonary disease" (if listed) would translate to "COPD" before the word " chronic" had the opportunity to translate to " chr".

NOTE: Any changes made by the user to the tables in any new data file or in MedRefsD.MDB will not be affected by program upgrades, but changes stored in MedRefs.MDB by the user will be lost when the program is upgraded.

Program and Structural Modifications Made by the User

The user should not modify the structure of any of the Tables in MedRefs.MDB or in any MedRefs data file, though he/she may, of course, change the data contained within the data table fields. It is easy for the user to corrupt a data table if it is opened in "Design View" and this should be avoided.  Field sizes in the References table are at the maximum size allowable. 

You may create new Tables in your data file, if you wish, and these will not be affected by program upgrades.

All Reports in MedRefs.MDB may be customized as desired and new Reports may be created in MedRefs.MDB,. All changes and additions you make to MedRefs.MDB will be lost if and when MedRefs.MDB is upgraded to a new version.

The Admin user permissions have been revised as of version 3.6 so that he/she now has permission to modify any of the existing Queries, Macros, Forms, or BASIC Modules in MedRefs.MDB. This means that he/she can easily corrupt this application!  The user may also create new Queries, Forms, and Macros. Any modifications or additions made in MedRefs.MDB will of course be lost if MedRefs.MDB is upgraded to a new version.  

It is necessary to logon as Admin in order to modify Medrefs.  If necessary, use the Workgroup Administrator WRKGADM.EXE to "join" the Medrefs workgroup information file MedRefs.MDW, then logon to Access as Admin.

It is possible to convert medrefs.mdb to run in Access 2000.

Licensure and Authorization for MedRefs use

MedRefs is copyrighted 1994-2004 by Michael C. McGoodwin, M.D. It is intended for medical and scientific use only. All of its available files and documentation may be copied and distributed freely for these purposes without charge, provided that 

  1. They are not resold for profit or used in any way that increases costs to patients, 
  2. Program distribution includes this manual
  3. The name of the author/developer is not modified or deleted from the program or its documentation, and 
  4. The author/developer is explicitly acknowledged in any public or institutional use of the program. 

Copies may be obtained if necessary directly from the author for a small distribution fee. Send all comments and suggestions in writing to the email address below.