feature list - is there a solution?

[rhaynes99]

Hi folks, I am looking for a reference manager with the following features:

+ ability to do a forward or cited reference search from an article in the database and then import add those articles
+ works with bibtex - automatically generates bibtex cite key
+ ability to search articles while in other applications and paste cite key (from an text editor for example)
+ good pdf download abilities

Papers3 seems to do 2,3 above. Doing 1 is really important, Papers3 does not do this well. And Bookends doesn't really seem set up for it.
4) seems difficult to find as well. The Bookends bookmarklet does not seem to automatically a high % of the pdf available even when doing it from a google scholar page which seems to have links to all the pdfs.

Am I asking for too much? Suggestions? Workflows?

[Jon]

Others will chime in, but I'd point out that

1. Bookends has a Cited In feature in the attachment inspector (but it works with a limited number of articles deposited in Crossref). And if you have access to Web of Science, you can use Bookends Browser to get to the Cited By page and import those (if they have DOIs, of course).

2. Bookends automatically generates BibTeX keys if you turn that on in preferences.

3. Not sure what you want here.

4. Google Scholar is a pretty poor resource. PubMed, WoS, and JSTOR are much better, and Bookends can readily get PDFs from all 3 (if you have access privileges). I much prefer direct Online Search to Bookends Browser for this.

Jon
Sonny Software

[rhaynes99]

Thanks Jon -

as for #3 - working in my editor (atom in my case) I can search papers3 with a keyboard shortcut, after finding the paper I want I can paste the bibtex cite key directly into my document.

RH

[rhaynes99]

Hi folks, can anyone provide links to the best youtube videos/tutorial which illustrate the best approaches to achieve the items in my wish list with bookends ?

[Jon]

For these kinds of questions you'll probably hear only from me. For matters of opinion/usage you'll hear from others.

Tutorials can be accessed via the Help menu. Here'a specific link to the video tutorial I think you want (although all are worth a look).

https://www.youtube.com/watch?v=maiGZ_FTBOI

The User Guide has an entire appendix on BibTeX. In addition, BibTeX-specific features are discussed in the body where appropriate (search for BibTeX).

The tutorials are pretty superficial, by design. In addition, new features are added so often they may not have the latest features. If you have need more in-depth information just ask.

Jon
Sonny Software

[rhaynes99]

BTW: I responded to your question about #3 on my wish list a couple of messages up in this thread. Thanks for your help!

[Cassady]

BTW: I responded to your question about #3 on my wish list a couple of messages up in this thread. Thanks for your help!

There is an Alfred (launcher App) workflow that has recently been popped up in a thread on this forum (you will probably find similar ones over at the Alfred.app forums) - that allows you to invoke Alfred, and trigger a Bookends search *inside* the Alfred window.

Once found, *my* usage takes me into BE, where the Cmd+Y/Cmd+Ctr+Y (for page modifier) shortcut then pastes back into my writing app. This is one step extra to what you want, but works well.

That said, that very same workflow might allow for you to paste the citation straight in without first landing in BE - I vaguely recall something along those lines, but never needed it, so never explored the workflow settings properly. This would them emulate what you need exactly, as far as I can tell.

Lastly, the above obviously applies if you need to do some sort of a search - but presuming you know what source you want to cite, and have used that citation in your text already, then the clipboard manager built into Alfred (and presumably something like Launchbar) works a treat, and is very quick.

Just figured I would mention.

[iandol]

Yes, for #3 the Alfred workflow UI can search for authors (+year) or titles/ keywords and then paste the citation into an editor without ever switching to BE. I can get hundreds of results from a database of thousands of papers in about 0.3seconds, very fast! It can paste using bookends / pandoc / mmd formats.

https://github.com/iandol/bookends-tools
viewtopic.php?f=6&t=4361#p19761

The workflow tools will also allow deeper integration with browsers, for example you can highlight a DOI or PMID in your browser and invoke quickadd directly without copy/paste etc. You can also trigger a quick BibTeX export or named groups again without invoking BE directly. This is all thanks to the fact that BE has a flexible Applescript interface, and Jon is so supportive that he will extend the feature set if he can be convinced of their utility (for example he added an applescript event to create new groups recently).

Regarding forward or reverse citation search, there are many overlapping options, including the Inspector (forward citations), using the OpenURL support (you can integrate WoS, Hubmed, google and others), bookends browser, or applescript (I made a Scopus cited by tool that is included in the Alfred workflow as one example, you select a ref and it will open the Scopus page for you). I wish that BE could have direct support of Scopus / WoS / Crossref for reverse citations directly in the Inspector, but this is blocked by exorbitant access fees of these services (they double dip as the university is already paying them a fee!!!), it is not BE's fault...

And regarding automatic PDF downloading, I think Bookends does very well. Google Scholar has no open API and is a mess to interface with so the fact it can find a PDF does not mean others can easily access that.