[Papyrus-L] Saga of a Papyrus data conversion

[Derek B. Cornish]

Jim -

Thanks very much - from a relatively new Papyrus user - for your detailed
description of converting to Ref Manager. I am sure it will be helpful, not
only for Ref Manager users, but others contemplating moving to a Windows
program.

In fact I did just that after having accumulated a small collection of
references in Papyrus - many of which I had imported into Papyrus from text
files using the excellent intructions for building filters. I am now using
Biblioscape, although I must say I find it somewhat fragile and
temperamental, constantly requiring index rebuilding. Partly because of
these problems I have been considering returning to Papyrus, which I was
quite reluctant to leave. I was very interested in your comment:

> First, until very recently I used Papyrus on the most modern versions of
Windows XP, and it should work fine, providing you do a few tweaks to the
"Command Prompt".

What tweaks did you use, and do they solve all the XP problems mentioned
from time to time on this mailing-list? I still use a number of DOS programs
on XP, not because I am some sort of information technology dinosaur, but
simply because they work better for me than their Windows equivalents. Some
DOS programs in question are: Quicken (UK v6 with UK and US accounts),
Grandview outliner, Lotus Agenda, and PC-Write - all used with TameDOS
[http://www.tamedos.com/] to improve their functioning in an XP DOS window.

Derek

> -----Original Message-----
> From: papyrus-l-bounces at ResearchSoftwareDesign.com 
> [mailto:papyrus-l-bounces at ResearchSoftwareDesign.com] On 
> Behalf Of Jim Mallet
> Sent: Saturday, October 28, 2006 3:07 PM
> To: Papyrus Discussion List
> Subject: [Papyrus-L] Saga of a Papyrus data conversion
> 
>  
> [sending again, since first time didn't work] I sympathize 
> with both these queries (Bill Lindsay and Florin Curta).  I 
> thought some of you might find my own experiences helpful.
> 
> After many years of using Papyrus, I too felt I ought to make 
> the change.
> 
> First, until very recently I used Papyrus on the most modern 
> versions of Windows XP, and it should work fine, providing 
> you do a few tweaks to the "Command Prompt".  Bill Lindsay's 
> *.BIB file must have got corrupted somehow.  Are you sure it 
> still works on your Windows 98?  If you have a network card, 
> perhaps you can make a local network with your two computers
> -- we used to run Win98 and Win 2000/XP on the same network 
> OK; then you would just copy between the two computers -- get 
> a geek to help if you don't know how to do that.
> 
> For my new software, I ended up using another Thompson-ISI 
> programme, Ref Manager, rather than EndNote, because I heard 
> it was more customizable.  I still don't know whether this is 
> actually true.  They were all bought up by Thompson-ISI, so 
> it's a monopoly now, which is a pity.
> 
> Theoretically, it is simple to transfer the data, you output 
> the file using a RIS format from Papyrus, and then import it 
> into the new database using Ref Manager's RIS filter.
> 
> But in practice, you lose a lot of formatting if you import 
> from Papyrus using the standard filter.  Particularly italics 
> (which are commonly found in titles of papers, and are 
> important in biology for scientific names), and special 
> characters such as accented letters in foreign languages, 
> which Papyrus was quite good at handling using Extended ASCII 
> characters.  The italics highlighting is specific to Ref 
> Manager, but the special characters are a problem because 
> whereas Papyrus and old fashioned pre-Windows programmes used 
> extended ASCII text codes, the newer Windows programmes use 
> different ANSI text codes for special characters.
> 
> To solve most of the problems, I needed to edit the RIS text 
> file using a text editor (n.b. beware use of MS Word and 
> other Windows programmes, which will often create line breaks 
> where you don't want them). For a text editor, I strongly 
> recommend TextPad, available as a fully functional trial 
> version on the internet.
> 
> Eventually, I found there was a way that I could tell 
> Reference Manager where the italics were. I was simply able 
> to replace the italics on and off codes, which Papyrus 
> helpfully put into the output file, into the Ref Manager 
> preferred import codes, which you can set up.
> 
> I had to scan through the large text file of the resultant 
> literature data to find examples of the special characters 
> which showed up as strange characters in the text file.  
> Although I often couldn't see these codes properly in the 
> text editor, I could highlight them and paste them into the 
> "Find" part of a "Find and Replace" dialog of TextPad, and 
> replace them with the correct special character (again placed 
> in the "Replace" box by pasting from a text file).  After a 
> few tentative attempts, I found it worked, and so I replaced 
> all examples of weird characters I found globally.  Since I 
> didn't know all the special characters I had used, I merely 
> searched through replacing most things, i.e. most of the 
> French, Spanish and German accents.  I think I got most of them.
> 
> Then I had a problem that Ref Manager thought that every 
> single one of my journal names were the abbreviations, and 
> not the full journal names that Papyrus had given it.  In 
> fact, I had lost all the abbreviations!
> 
> To sort this out, I talked with the people at Ref Manager who 
> helped me a bit.  Ref Manager, like Papyrus, contains a 
> databased list of periodicals with several abbreviations 
> allowed for each, which it treats as synonyms if there is an 
> exact match.  So what I did in the end was export a list of 
> journals with abbreviations from Papyrus, edit them into the 
> appropriate format as a text file (I had to make sure all the 
> special characters were correctly replaced in this new file as well).
> 
> I then started a new Ref Manager database with no data in it, 
> and imported the journal list according to the instructions 
> given me by the Ref Manager help personnel.
> 
> Then, into this new file, I imported the literature records 
> from the existing database that I had converted from the RIS 
> file (i.e. this was now in another Reference Manager 
> database).  Then since the new Ref Manager in every case 
> recognized the full journal title as a synonym of the 
> journals it already knew about (both the literature records 
> and the periodical titles were of course from the same 
> original Papyrus database), the synonym was correct.  Now it 
> knows all the journal abbreviations too.
> 
> As you can see, this was all quite tricky and took a certain 
> amount of knowledge about how to manipulate text files, plus 
> a lot of manual search and replace work.  But I think it was 
> quicker to do this than to all the retyping it would have 
> required if I hadn't done the automated editing of the RIS file.
> 
> Finally, I have all of my data, journals and abbreviations, 
> and keywords etc.  When I say all my data, this is all the 
> approx 11000 major papers I have ever made notes on, ever 
> since I was an undergraduate (I am 50 now).  I started with a 
> card index, and when a Professor in the USA managed to get a 
> work-study student to type it all into Papyrus.  It's kind of 
> nice to have everything I have ever read as an academic!  And 
> it's in a useful format for literature citation.  I have now 
> successfully written articles with complex, numerical 
> references, and which allow automatic citations using Ref 
> Manager's MS-Word add-in.  Updating numerically cited 
> reference lists (as in Science or Nature) was very hard to do 
> in Papyrus, so it probably is labour saving to make the change.
> 
> But I still miss Papyrus!  I found it a lot easier to use 
> than Ref Manager, even though Papyrus wasn't windowed, and I 
> can no longer cut and paste a simple abbreviated reference, 
> which was possible in Papyrus, of course. I could then pop 
> the pasted reference into an email and send it to a friend, 
> or print it out for a student.  Papyrus had an amazing number 
> of clever, labour-saving attributes which today's literature 
> database software still don't match.
> 
> Hope this helps
> 
> Sincerely, Jim Mallet
> 
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