making direct link to pdf files while import

[dragon]

Thanks for the great software, its updates and support.

I have two questions regarding PMID today. These two are related to each other.

1. Is it possible to import PMID into two different fields? In particular, PMID is imported to "URL" field after the Web address, in default. I wonder if I can also show PMID in one of the user field, in addition to the URL filed. I tried to modify the imort filter without any success.

2. I have the papers in pdf format named like PMID.pdf stored in one folder. Is it possible to make a direct link to the file when I import the references from PubMed? I first thought I might import PMID into keywords field with "•" and ".pdf" attached so that it may get attached, but I can not add a text after PMID, so I didn't try it. I also thought I might use the URL filed, but I want to keep this filed intact so that I can access to the PubMed page instantly. Is there any way to make an direct link may be in one of the user field or wherever?

Well, I use an application called "iPapers" from a Japanese site to collect pdf files and organize the pdf papers. It's still a bit premature, but makes my life a lot easier. This app is to download and organize your pdf files, so it's aim is different than Bookends. Well, but you can guess what I'm thinking. Yes, it would be so great if Bookends have a similar feature.....That's too much to ask now, and I'm looking for a way to direct link the files

[Jon]

1. Is it possible to import PMID into two different fields? In particular, PMID is imported to "URL" field after the Web address, in default. I wonder if I can also show PMID in one of the user field, in addition to the URL filed. I tried to modify the imort filter without any success.

No, it's one tagged item per field.

BUT, you can have both with a little trick. Import to a user field, and set Bookends to make the imported reference a hit on import. Then do a Global Change -> Move, moving the user field AFTER URL (in the Hits only). Now you'll have it in two fields.

2. I have the papers in pdf format named like PMID.pdf stored in one folder. Is it possible to make a direct link to the file when I import the references from PubMed? I first thought I might import PMID into keywords field with "•" and ".pdf" attached so that it may get attached, but I can not add a text after PMID, so I didn't try it. I also thought I might use the URL filed, but I want to keep this filed intact so that I can access to the PubMed page instantly. Is there any way to make an direct link may be in one of the user field or wherever?

You mean you have the pdf already, and you want Bookends to associate the import ref with the pdf file you have? No, I can't think of a way of doing this. The way it is normally done (at least by me) is to import the reference to Bookends, download the pdf to the desktop, and then drop the pdf file on the reference window -- Bookends will offer to file it away for you, and rename it (if you want).

Well, I use an application called "iPapers" from a Japanese site to collect pdf files and organize the pdf papers. It's still a bit premature, but makes my life a lot easier.

I'll take a look at it.

Jon
Sonny Software

[Guest]

Jon,

BUT, you can have both with a little trick. Import to a user field, and set Bookends to make the imported reference a hit on import. Then do a Global Change -> Move, moving the user field AFTER URL (in the Hits only). Now you'll have it in two fields.

Thanks for the tip. It works!

I now have an alias of the folder of pdf files in the dock and can easily find and attach "PMID.pdf" files. It will still be wonderful if Bookends incorporates the function of iPapers, although it may make the database more complicated to look at.

Wonderful application, wonderful support.

[prop]

I think the new Spotlight feature of Tiger should improve my PDF file management significantly. I'll then be able to do rapid, full text searches of my PDFs. Then, I'll have both full-text-searchable papers AND Bookends-searchable references with PDFs attached. It'll be the best of both worlds.

Does iPapers offer something that Bookends with Spotlight doesn't?

[Jon]

I won't reply to that directly (others can, I'll listen). But I have realized that Bookends could offer a cool new way to import/attach references from PubMed (and perhaps other sources). I'll see what's possible (and then tell you all what it is). As for Spotlight...we're all eager to see what that may add...

Jon
Sonny Software

[tom]

No, I can't think of a way of doing this. The way it is normally done (at least by me) is to import the reference to Bookends, download the pdf to the desktop, and then drop the pdf file on the reference window -- Bookends will offer to file it away for you, and rename it (if you want).

Jon
Sonny Software

I do first download the pdf file by double-clicking the ref in the internet search (that provokes "checking for full-text..."; for older refs with only a full text in pdf, I get the pdf directly; for newer refs I have to click once more), then I import the ref into bookend(by drag and drop), followed by a trag and drop of the pdf file...so, it's nearly as easy as in ipapers...

tom

[dragon]

Does iPapers offer something that Bookends with Spotlight doesn't?

Hi prop,

What iPapers does, is
- search PubMed (from iPapers),
- if you have hits on the list, goes to the download page (in iPapers window to the direct link from PubMed)
- press down load will bring the pdf file into the specified folder with the file name "PMID.pdf".

- pdf files collected are also automatically indexed (?) like Sente. Easy to navigate by the journal-year and authour-year.

Now you have a collection of papers with index well organized.

iPapers DOES NOT
- show or keep abstracts (>>> I was wrong, iPapers DOES keep abstracts)
- search the text in the files
- create bibliography.

So, since Bookends does keep the url of PubMed, if we can directly download the pdf files from Bookends with one ore two clicks and allow us to open the file directly from Bookends, then we will have not only the publication information of the papers, but also the papers themselves pretty easily.

tom, yes, you can go to PubMed and download and attach to Bookends. But Bookends now have automate search. If we have iPapers feature in Bookends, then we can do everything in Bookends, never go to PubMed Website.

Well, it's hard to explain what I want to say in words, so I will urge people to try iPapers. It's still a premature application, but the idea is great. I hope the function will be incorporated into Bookends some day. Have created more work for Jon?

[Jon]

tom, yes, you can go to PubMed and download and attach to Bookends. But Bookends now have automate search. If we have iPapers feature in Bookends, then we can do everything in Bookends, never go to PubMed Website.

iPapers actually does go to the PubMed site to fetch the pdf (it just does it in it's own Webkit (like Safari) window. So it doesn't need an independent browser.

I can't see a way to directly download pdfs into Bookends without going to PubMed, because the way PubMed links to them differs with every journal. BUT, do see a shortcut that should cut out a few steps in the process that Bookends uses now, and I think you'll find it very useful. I'll post more about this once I've had a chance to implement it and see if it really make things easier.

Jon
Sonny Software

[prop]

Now we're talking! I think this is a "killer" feature, simply because so many people like to have a library of reprints on their hard drive in case their university proxy server is down, or they don't have instant internet access. I know for myself, this combination of Bookends with easy-to-use PDF integration is very important. I appreciate your efforts into making it even better Jon.

[tom]

tom, yes, you can go to PubMed and download and attach to Bookends. But Bookends now have automate search.

I'm not going to PubMed. I'm doing a (PubMed) search in Bookends. When I double-click a search result I get my pdf file; works also for automated searches....
tom

[casey]

Dear Jon,

Thanks for a wonderful alternative to Endnote and for your excellent responsiveness. I'm still in the testing prior to purchase phase, so please excuse any obvious fixes I may not have discovered yet.

To follow up on some of the points in this discussion:

Looking at Apple's website, it appears that Spotlight will be an extremely powerful search engine, capable of searching metadata and organizing the results. This will allow us to search the text of pdf files, and, I'm guessing, their PMIDs, even if they are not in the filename.

What Spotlight will NOT do (I think-hard to say until it's released), is index your pdf files the way iPapers currently does. This indexing is extremely handy, as it allows you to assign pdfs to multiple groups (a la iTunes and iPhoto). Indexing by import date, combined with iPapers' new drag-and-drop feature is also a fantastic way to incrementally archive your pdf files to CD.

I'm still not sure if adding this "pdf collection manager" function to Bookends would be a good thing (a single killer app for downloading and managing pdfs AND generating bibliographies...swoon) or bad (would make Bookends too bloated).

BUT, I think I may have a reasonable workaround that may satisfy those of us who would like the functions of both Bookends and iPapers: How about offering the option of renaming files as "Author year.pdf" OR "PMID.pdf" when the prompt comes up as a pdf file is attached to a Bookends record? We could then keep PMID.pdf files in an article/attachment directory shared by iPapers and Bookends. It would then be a trivial thing to add these pdfs as records to iPapers through drag-and-drop or Import > New in Article Directory (I'm referring to the iPapers menu.) In any case, I'm really starting to appreciate the logic of naming article pdfs using their PMID, so I think this would be a much appreciated feature, even for those who don't use iPapers.

Obviously, not all articles/attachments will have a PMID, but having that renaming option available would be handy. It also makes sense to search for references in Bookends rather than iPapers, as the former has the ability to save searches and run them automatically.

In any case, I encourage your efforts to find easier, more direct means of downloading and attaching pdfs to Bookends records.

Two other feature requests: It would be really nice if we could see which records have attachments in list view, via an icon or something in the first column. Similarly, it would be extremely handy to have a way of tagging or eliminating hits from PubMed searches that represent records already in the Bookends database. This would eliminate importation of duplicate records.

Thanks,
Casey

[Jon]

BUT, I think I may have a reasonable workaround that may satisfy those of us who would like the functions of both Bookends and iPapers: How about offering the option of renaming files as "Author year.pdf" OR "PMID.pdf" when the prompt comes up as a pdf file is attached to a Bookends record? We could then keep PMID.pdf files in an article/attachment directory shared by iPapers and Bookends. It would then be a trivial thing to add these pdfs as records to iPapers through drag-and-drop or Import > New in Article Directory (I'm referring to the iPapers menu.) In any case, I'm really starting to appreciate the logic of naming article pdfs using their PMID, so I think this would be a much appreciated feature, even for those who don't use iPapers.

Hi casey,

Hm, one problem I see is simply the implementation. Many folks aren't attaching PubMed downloads. And of course Bookends would have to assume the PMID was the last number in the URL field. And it means adding another dohickey to either the Attach dialog or Preferences. None of these issues are impossible to deal with, of course, but I wonder if it is worth it. Why again is naming the file by PMID useful in Bookends? Because you can download with iPapers and then transfer?

Two other feature requests: It would be really nice if we could see which records have attachments in list view, via an icon or something in the first column. Similarly, it would be extremely handy to have a way of tagging or eliminating hits from PubMed searches that represent records already in the Bookends database. This would eliminate importation of duplicate records.

For point one, you can. It's an option in Preferences (Lists tab). It's turned off by default, because it makes drawing the list a bit slower, and if you don't have attachments it's a waste.

For point two, a more general approach would be to screen out duplicates on import (just don't import them). This is something I've toyed with, and may implement. The downside is that it would delay the beginning of the download while data on each ref in the database were collected, and modestly slow down each record imported. And it would probably have to rely on your definition of a duplicate in the Remove Dups dialog (so it would not be completely transparent, without reading a bit of the docs). But, it still sounds like a useful addition.

Thanks for the comments.

Jon
Sonny Software

[casey]

Why again is naming the file by PMID useful in Bookends? Because you can download with iPapers and then transfer?

Nope. It's not really useful to Bookends, but it allows people to organize their refs with a unique ID that corresponds to a universal database (PubMed) and allows us to use iPapers for indexing with a minimum of fuss. My plan would be to download from Bookends (with Safari's help, of course), as the saved (auto) searches make it much more powerful for searching PubMed than iPapers. (plus I'd have the added benefit of immediately importing the record into the Bookends db.) Once the pdf was downloaded into the proper directory, I could then attach it to Bookends AND iPapers through drag-and-drop. (iPapers does this one better, as it can search the download directory for new pdf files (if they are named PMID.pdf) and add them automatically to its database.

(BTW, if you could integrate a browser function for pdf downloads like iPapers, it would prevent us from having yet another open app/window on our desktop.)

One search, one download, minimum # of clicks to attach a pdf file to a biblio record (in Bookends) and to index it (iPapers).

Sorry about overlooking the attachment icon in list view. I found the preference setting right before your reply. (Didn't see it the first time.) You're quick!

Casey

[dragon]

(BTW, if you could integrate a browser function for pdf downloads like iPapers, it would prevent us from having yet another open app/window on our desktop.)

One search, one download, minimum # of clicks to attach a pdf file to a biblio record (in Bookends) and to index it (iPapers).

Hi Jon,

Yes, I think Casey describes what I wanted to do at the begining. We don't need to organize pdf files in Bookends, but it would be very handy if we can DOWNLOAD pdf files from Bookends.

When we do internet search from Bookends, a click of a hit directs to the download page of the paper, if any, in Safari. A click of URL filed in the reference window takes us to the page in PubMed.

So, I guess our (if I'm not misunderstanding) wish is
- A click of a hit in the internet search and URL field of reference window (or another new "download" button) takes us to the download page directly
- by not opening Safari but a window in Bookends (like iPapers), and
- download the pdf file in a specific folder with named as PMID.pdf

The rest of the organizing the pdf files can be handled by iPapers, or whatever.

By the way, thanks for the tip you gave me before how to put PMID info in two different fields using Global Change. It really works. Well, sometimes, I forget to choose Hits List and make a mess but that's my problem.

Anyway, thanks for the great application. Makes my life easier for more than a year. To tell the truth, I once leaned to Sente, but now love and stick to Bookends.

[casey]

So, I guess our (if I'm not misunderstanding) wish is
- A click of a hit in the internet search and URL field of reference window (or another new "download" button) takes us to the download page directly
- by not opening Safari but a window in Bookends (like iPapers), and
- download the pdf file in a specific folder with named as PMID.pdf

The rest of the organizing the pdf files can be handled by iPapers, or whatever...

Anyway, thanks for the great application. Makes my life easier for more than a year. To tell the truth, I once leaned to Sente, but now love and stick to Bookends.

Well put, dragon. I couldn't have said it better myself. (and didn't!)

BTW, I too have been toying with Sente vs. Bookends. While Sente's UI seems slightly more "Mac-like", I'm finding it just doesn't offer all of the features of Bookends. The deal-breaker/maker for me is that Sente does not offer the ability to scan rtf files, which leaves you wedded to Word until they add this feature or come out with plugins for other word processors.

Casey[/quote]