Import options

[martinp]

I am just learning my way around Bookends, and I have some questions about the options for getting data into the program. Perhaps there are routes that I haven't discovered yet; suggestions are welcome.

First, the File > Import References option can import various kinds of text file (BIB or RIS) containing data on a reference, but apparently cannot import a PDF. And I seem to be able to select only one file at a time, which makes importing a somewhat tedious process.

Second, when I import a PDF by dragging it onto the Bibdesk window, it will try to attach to any record that is already selected. Even if there is no record selected, the default option in the dialog that opens is to attach the PDF to an existing record rather than to create a new record, though I can select the option to create a new one. I wonder if there is not a way for Bookends to distinguish these two situations?

Third, some questions about autocompleting a PDF. Other software I have used tries to autocomplete by searching Google Scholar, the Library of Congress and PubMed. Bookends will only search Google Scholar without needing personal access permission. I think I'm finding fewer hits than in the other software.

And when I try to autocomplete a new record for a PDF and the data is not found, rather than having an option to enter the data manually, using data visible in the PDF, I have to click Close, at which point the Inspector opens for me to enter data (rather unintuitive). Now the PDF is visible in the Attachments window, but the Inspector is a separate window that usually is at least partly covering the main window. I cannot drag-&-drop data from the PDF to the Inspector. (And oddly if I command-click on highlighted data in the PDF, Bookends asks me if I want to import a file. If I respond affirmatively it seems to delete the record I was creating. I can't figure this out.) And when I tab from one field to the next in the Inspector, the order is Author, Title, Series Editors... where the layout suggests it would be Author, Series Editors, Title...

In short, I'm finding the process of adding new records rather unintuitive. I'd like to be able to select a bunch of files, both BIB/RIS and PDF, and then move smoothly between autocomplete and manual entry as they are added. It would be nice to have the option to modify BIB/RIS files, as well as modify autoimported data, since much of the information on Google Scholar seems inaccurate or incomplete.

[Jon]

First, the File > Import References option can import various kinds of text file (BIB or RIS) containing data on a reference, but apparently cannot import a PDF. And I seem to be able to select only one file at a time, which makes importing a somewhat tedious process.

Personally, I use drag and drop. And you can drop multiple files at once. But you can't mix import and attach by this method.

Second, when I import a PDF by dragging it onto the Bibdesk window, it will try to attach to any record that is already selected. Even if there is no record selected, the default option in the dialog that opens is to attach the PDF to an existing record rather than to create a new record, though I can select the option to create a new one. I wonder if there is not a way for Bookends to distinguish these two situations?

You mean Bookends, I assume. I'm not sure what you are asking for, though. Assuming there are references in the database, one is always selected. You can check the option thats tell Bookends to create a new reference, as you say. Please contact tech support if there are problems with this.

Third, some questions about autocompleting a PDF. Other software I have used tries to autocomplete by searching Google Scholar, the Library of Congress and PubMed. Bookends will only search Google Scholar without needing personal access permission. I think I'm finding fewer hits than in the other software.

Bookends lets you autocomplete with Google Scholar, JSTOR, PubMed, and Web of Science. They are selectable in the lower right-hand corner of the window. The success of the autocomplete depends entirely on the text you enter (if there is no doi). Hint: less text is usually better.

First, the File > Import References option can import various kinds of text file (BIB or RIS) containing data on a reference, but apparently cannot import a PDF. And I seem to be able to select only one file at a time, which makes importing a somewhat tedious process.

Personally, I use drag and drop. And you can drop multiple files at once.

Second, when I import a PDF by dragging it onto the Bibdesk window, it will try to attach to any record that is already selected. Even if there is no record selected, the default option in the dialog that opens is to attach the PDF to an existing record rather than to create a new record, though I can select the option to create a new one. I wonder if there is not a way for Bookends to distinguish these two situations?

You mean Bookends, I assume. I'm not sure what you mean. Assuming there are references in the database, one is always selected. You can check the box to tell Bookends to create a new reference at any time, as you say. Please contact tech support if there are problems with this.

And when I try to autocomplete a new record for a PDF and the data is not found, rather than having an option to enter the data manually, using data visible in the PDF, I have to click Close, at which point the Inspector opens for me to enter data (rather unintuitive). Now the PDF is visible in the Attachments window, but the Inspector is a separate window that usually is at least partly covering the main window. I cannot drag-&-drop data from the PDF to the Inspector. (And oddly if I command-click on highlighted data in the PDF, Bookends asks me if I want to import a file. If I respond affirmatively it seems to delete the record I was creating. I can't figure this out.) And when I tab from one field to the next in the Inspector, the order is Author, Title, Series Editors... where the layout suggests it would be Author, Series Editors, Title...

I'm not sure if you're referring to the same window that we call the the Attachment Inspector. In any case, the pdf is still visible in the lower pane (assuming you have opened it and selected the "pdf" icon. You can copy and paste from there, if you use WebKit to display the pdf.

In short, I'm finding the process of adding new records rather unintuitive. I'd like to be able to select a bunch of files, both BIB/RIS and PDF, and then move smoothly between autocomplete and manual entry as they are added. It would be nice to have the option to modify BIB/RIS files, as well as modify autoimported data, since much of the information on Google Scholar seems inaccurate or incomplete.

You can select a bunch of files, if you use drag and drop, but you can't mix import and attach this way (interesting idea, though). And GS is indeed often incomplete and/or inaccurate. I'm not sure what you mean by "modify BIB/RIS files", though. You can use the other sources I mentioned for autocomplete.

Jon
Sonny Software

[ozean]

And when I try to autocomplete a new record for a PDF and the data is not found, rather than having an option to enter the data manually, using data visible in the PDF, I have to click Close, at which point the Inspector opens for me to enter data (rather unintuitive).

I have also found myself trying to enter the data at that stage – it just seemed logical for me to be able to this since the information that I have is at hand. If one does not have the attachment view open by default, adding this information later requires several steps, instead of just typing away at that stage.

Of course, the other way works perfectly well – it just requires additional steps and (for me) it felt unnecessary, since I already had all I need in front of me at an earlier stage of the process

[Jon]

What do you suggest? The Autocomplete sheet already has an Action popup menu that lets you copy selected text to the text search boxes. I could add options for copying selected text to the reference itself (e.g. to authors, to title, etc.). Then when you closed the sheet the reference window wouldn't open with the empty reference. If there were multiple authors you'd have to copy one at a time (so Bookends wouldn't string them all together), or perhaps there could be an option to copy "to authors (separated by commas)" and "to authors (separated by semicolons)", or something along those lines.

Would this be helpful?

Jon
Sonny Software

[rickl]

I could add options for copying selected text to the reference itself (e.g. to authors, to title, etc.). Then when you closed the sheet the reference window wouldn't open with the empty reference. If there were multiple authors you'd have to copy one at a time (so Bookends wouldn't string them all together), or perhaps there could be an option to copy "to authors (separated by commas)" and "to authors (separated by semicolons)", or something along those lines.

Would this be helpful?

Yes, it would be most helpful. The details don't matter too much to me, but I think it's important when search fails that there be immediate help for inputting details.

[ozean]

Yes, sounds good

Not so sure about what to do with multiple author names either. I rarely have to search for those for PDFs (social science = single authored papers still abundant - in contrast to edited books etc., which I would search via a library catalogue).

[rickl]

I rarely have to search for those for PDFs

Hi, ozean, it's my understanding that we're talking about text entry rather than search.

[martinp]

Jon,

Thanks for your response, and your suggestions about how to facilitate manual import. I work in a discipline where many of the PDFs that are available are old and scanned, and don't include metadata, so manual import is an evil necessity.

I've just viewed the new video that demonstrates searching and importing. I don't seem to have that nice floating, semi-transparent window with buttons to open an attached PDF that I can see in the video! That would be nice to have, because the keyboard shortcut (shift-command-O) sometimes works for me and sometimes doesn't (I'm not sure why).

One other thought about online searching: would there be a reason not to search PubMed and Google Scholar at the same time (as I think Sente does)?

By the way , I apologize for the misleading mention of BibDesk in my original message, when as you figured out I was referring to Bookends. I tried BibDesk, Sente, Papers and Mendeley (after years suffering with EndNote) before selecting Bookends, and I'm still getting them mixed up.

M

[Jon]

Hi,

I think the window you are referring to is the sheet brought up by Autocomplete Paper (Shift-Command-C). It is in this sheet, BTW, that I added the ability to copy selected text (in the pdf) directly into your database in this version of Bookends (10.6) If I'm mistaken, please send me a screen snap of the window (in the video) you are referring to.

As for searching PubMed and GS at the same time, that is technically possible. But in most cases I think it's pretty clear which is more appropriate. In addition, PubMed returns *much* better data, so if it's there you do not want to download the same paper from Google Scholar.

[martinp]

Jon,

I've upgraded to Bookends 10.6 (a bit slow off the mark there, I grant you), but while shift-command-C starts the autocomplete process, if it fails to find the reference info online I still have to click Close and an empty reference window comes up. I can't see a way to enter information other than by hand. Clearly I'm missing something here!

With regard to Google Scholar and Pub Med, I should have asked whether in *autocompletion* it might sense to search both at once, rather than having to select one or the other.

[Jon]

You select the text you want and then click on the Action menu (Gear icon). You'll have the option to enter the text into the reference.

I know what you meant about PubMed and GS. I was pointing out that you should search PubMed first, because if it is in both locations that's the info you'd want to import.

Jon
Sonny Software