Journal abbreviations and articles downloaded from PubMed

Reference Manager Reference Manager General
1

Does anyone have any tips on how they keep their journal abbreviations sorted when using RefMan with pubmed?

I found that I couldn’t define styles to use either full length or abbreviated journal names. I managed to solve that by activating ‘term manager’, tidying up all the abbreviations that were in use by downloading the list of medical journals (using the ‘copy preriodicals’ function of term manager). I then replaced all my old ones using the ‘Global edit’ function in term manager. So now my database is perfect, and the term manger contains 2 versions of each journal name (full & Standard abbreviation)

ie. 

American Journal of Hematology
Am.J.Hematol.

Because both are entered in the ‘synonyms’ of ‘Term manager’ it means I can display the bibliography as either full journal names or abbreviated versions.  Which is great.

The problem I have is that whenever I download an article from pubmed (using the send to text file option), The abbreviations pub med uses are different, and not recognised as the same…

ie.

Am J Hematol.

So the new articles i download are not automatically recognised by term manager and can not be displayed as ‘full journal name’ as pub med uses different terms.

I realise I could add in the PubMed definition to one of the user defined fields of term manager, butI’d rather find a way to make reference manager compatible with pubmed. Does anyone know of a ready made database of medical jorunal terms I could upload?

Cheers,

J

1 Like
2

Hi,

The problem comes from a little file situated in the Reference Manager main folder and called “PERDICT.dat”. This file contains a list of abbriged terms of journal titles supposed not to have a dot. In fact, when you import a reference from PubMed, RefMan scans this file with the words of the journal abbreviation and, if a word is not retrieved in the list, it put a dot at the end of the word. The problem is that this term list is not adapted for the abbriged names of the PubMed Journals and a lot of terms are not present. The worst is that the journal form with dots is not recognized by the term list!

Like you, I wanted RefMan not to put all those “.” et the end of the terms when I import references from PubMed so I’ve tried to replace the PERDICT.dat list with all the terms found on the whole list of PubMed Journals and finally I could solved this problem last year with the follow steps :

  1. download the PubMed journal list in txt ( ftp://ftp.ncbi.nih.gov/pubmed/J_Medline.txt )

  2. edit the list with Word to extract only the journal titles and Medline abbreviations

  3. cut the phrases to obtain a list of all the single words contained in those titles

  4. edit the list with Excel to remove the duplicate words

  5. sort alphabetically and save the final list in txt format

  6. rename the file “PERDICT.dat” located at the Reference Manager root folder (for me the path is “C:\Program Files\Reference Manager 12\PERDICT.dat”) in something like “PERDICT.dat.old”

  7. place a copy of the list made from PubMed in the Reference Manager main folder ("C:\Program Files\Reference Manager 12) and rename the txt file with “PERDICT.dat”

If you want to skip the steps 1-5, I can send you a copy of this PERDICT.dat list of terms “PubMed compatible” (13’900 words and 121 Kb) that works fine now for me.

Hope that helps

Pablo Iriarte

CHUV Lausanne

2 Likes
3

Thanks for that Pablo,

I’ll have a go at following your suggestions myself, as I think it owuld help me learn a little more about RefMan. If I can’t amanage it myself I’ll be back to ask you for that list!

Many thanks,

J

4

mind to send me the PERDICT.dat?

wastrel@gmail.com.

Thanks!

5

Could you please send me the PERDICT.dat?

mohamedwahba12@gmail.com.

Thanks!

6

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