Sonny Software

When Pubmed references get imported into Bookends, the name that appears is the abbreviated name, such as "New Eng J Med", instead of its full name "New England Journal of Medicine". However, the long list of all journals together with their full names is available on the Web as a text file. Many of them are already in the journal glossary in Bookends but many others are not. My question is, Is it possible to import the list of journals directly from a file without having to enter them manually?

Thanks,

frank

You can...there are such text files available for EndNote, for example. The problem is, though, that if you have many thousands of entries it does take time for Bookends to process them prior to a scan, and that is a pain. Since the vast majority of journals are ones you will never cite, we created Concise Medline, which contains most of the major ones. But if you want to create your own out of existing text files, you can (they are just tab-delimited text files).

Jon
Sonny Software

I tried use a tab delimited list in txt format as journal glossary. It is placed in the right folder and glossaries created in BE work. But those made as txt does not, they do not appear in the list of glossaries. I tried divers encodings, but this seems not to help. I assume you use utf-8?
May be you have a hint?

The text *must* be UTF-8. If it isn't, the glossary won't work. You can make sure it is by opening it in TextEdit and saving is explicitly as UTF-8.

Jon
Sonny Software

Jon wrote:The text *must* be UTF-8. If it isn't, the glossary won't work. You can make sure it is by opening it in TextEdit and saving is explicitly as UTF-8.

Jon
Sonny Software

I tried this with a text file. But also to no avail.
Then I duplicated my custom glossary, opened it in TextEdit, and, without any modifications, saved it again. After this it was not visible in my glossary menu in BE any more.
Open and save prefs in TextEdit are set to UTF-8.

Matthias

The save no doubt changed the metadata, which is a bad thing. The file type must be

BEPG

(Creator should be BERB).

You can inspect/edit these with FileType, a free download available on VersionTracker.

Jon
Sonny Software

I have the same problem. Concise Medline is nearly useless for my purposes (among other things, it doesn’t contain any psychology journals). I am moving from Sente and had a perfect “Journal Dictionary” (= journal glossary) there, which I used and edited for many years. I see it is a file with .pkl extension. Is it possible to convert it or import it into Bookends?
Thank you
Olivia

I found a .pkl file and examined it -- it's structured binary file, and NSDictionary type, containing lots of human-unreadable data, such as

streamtypedÅËÑ@ÑÑÑODJournalDictionaryÑÑNSObjectÖíÑÑÑNSMutableSetÑÑNSSetîÑIWíÑÑÑNSMutableDictionaryÑÑNSDictionaryîÑiíÑÑÑNSStringîÑ+NameÜíÑúúOncology reportsÜíÑúúISSNÜíÑúú 1791-2431ÜíÑúúAbbrÜíÑúú Oncol RepÜÜíÑôöíõíÑúúCellular reprogrammingÜíûíÑúú 2152-4998Üí†íÑúúCell ReprogramÜÜíÑôöíõíÑúúHuman pathologyÜíûíÑúú 1532-8392Üí†íÑúú
Hum PatholÜÜíÑôöíõíÑúúPloS oneÜíûíÑúú 1932-6203Üí†íÑúúPLoS OneÜÜíÑôöíõíÑúúOncoimmunologyÜíûíÑúú 2162-4011Üí†íÑúúOncoimmunologyÜÜíÑôöíõíÑúúScienceÜíûíÑúú 0036-8075Üí†í≥ÜíÑôöíõíÑúúNatureÜíûíÑúú 0028-0836Üí†í∂ÜíÑôöíõíÑúú Archives of disease in childhoodÜíûíÑúú 1468-2044Üí†íÑúúArch Dis ChildÜÜíÑôöí†íÑúúSemin Cardiothorac Vasc AnesthÜíõíÑúú2Seminars in cardiothoracic and vascular anesthesiaÜíûíÑúú 1940-5596ÜÜíÑôöíõíÑúúCell death & diseaseÜíûíÑúú 2041-4889Üí†íÑúúCell Death DisÜÜíÑôöíõíÑúúStem cell research & therapyÜíûíÑúú 1757-6512Üí†íÑúúStem Cell Res TherÜÜíÑôöíõíÑúúRetinal cases & brief reportsÜíûíÑúú 1937-1578Üí†íÑúúRetin Cases Brief RepÜÜíÑôöíõíÑúúDevelopmental cellÜíûíÑúú 1878-1551Üí†íÑúúDev

So no, it can't be used by Bookends. If you can export it from Sente as a tab-delimited file perhaps something could be done with that.

Jon
Sonny Software

Thanks for your prompt replies. I had already tried exporting the file from Sente (or copying its content) but nothing can be done.

Perhaps you could provide a larger list of journals cited in PubMed so that users can delete what they don’t need (faster than adding each title by hand). That might be feasible if we had the option of selecting multiple titles at once--so that we can delete whole sections of the list at once, rather than having to delete one title at the time.

Thanks,
Olivia

The problem with adding substantially more titles is that it slows down scanning when there are many thousands. If you send a list of journals covered by PubMed that are not in the list and that you use, please send them to me (with both the full and abbreviated PubMed names). If they aren't covered by PubMed the don't belong in Concise Medline, though. Perhaps a separate psychology glossary would be warranted. Do you happen to have (or can locate) an EndNote journal list? Those can be converted to a Bookends-compatible glossary without a lot of trouble.

Jon
Sonny Software

Yes, the journals I use are all covered by PubMed. Sente’s default journal dictionary seemed good enough as a starting point—I added titles over the years but not too many. My copy currently contains 909 journals.

I have no idea how the Sente default dictionary was created, though (that is, which the criteria for inclusion were). For the same reason, I wouldn’t know what an appropriate EndNote journal list should contain; as you say, a complete list of the journals covered by PubMed is quite impractical. I could try to extract some info from my Sente .pkl file (by finding and deleting the weird text in a copy opened in TextEdit).

I believe that a separate psychology glossary would not be a good idea—at least in my case: I mostly write interdisciplinary papers, therefore I cite psychology and medicine/biology articles in the same paper.

Thank you,
Olivia

If you can send the journals that are not covered, with both full and Medline abbreviation form, I can add them to the Concise Medline we distribute. I assume you're dealing with just a few dozen journals here, not hundreds.

Jon
Sonny Software

Thanks Jon, I will do that.

Here are some I've added/fixed in Concise Medline (mostly neuroscience):

Annu. Rev. Vis. Sci. Annual Review of Visual Science
Cereb. Cortex Cerebral Cortex
Eur. J. Neurosci. European Journal of Neuroscience
Exp. Br. Res. Experimental Brain Research
Front. Mol. Neurosci. Frontiers In Molecular Neuroscience (no periods in original)
J. Comp. Neurol. Journal of Comparative Neurology
J. Opt. Soc. Am. A Journal of the Optical Society of America A
J. Vis. Journal of Vision
Nature Comm. Nature Communications
Nat. Rev. Neurosci. Nature Reviews Neuroscience (full title has a period where it shouldn't)
Trends Cog. Sci. Trends in Cognitive Sciences
Vis. Res. Vision Research

Thanks, I'll update our distribution with these.

Jon
Sonny Software