Hierarchical organization of keywords

[dtziouris]

Hi,

I routinely assign keywords to articles downloaded in order to have an overview. I have noticed that after a while the list of keywords can get pretty messy. Wouldn't it be a good idea to enable a hierarchical organization of the keywords as used in the MeSH terms? For example assigning the keywords 'pain/fibromyalgia' would allow the user to search for the article either with a broader scope (pain) or a narrower one (fibromyalgia). The keywords list could then be displayed in a tree view. I know I can assign all the keywords without hierarchy, but somehow the resulting keyword list is rather confusing. In this context the user could specify to import the MeSH terms as keywords when searching Pubmed.

I hope all the above make some sense. Happy New Year's Eve to everybody,
Dimitrios

[Jon]

Have you looked at the tag cloud feature? It lets you group together keywords under heading that may never appear in the keyword list. Look up "virtual tags" in the User Guide (Help menu).

Jon
Sonny Software

[dtziouris]

Hi Jon,

thanks for the advice, I wasn't aware that I could use tag cloud this way. However there are two limitations in that approach:
1. You are limited to two hierarchical levels
2. What is more important, you don't have the visual schema of the hierarchy.

I will try to make the last point clearer with an example. Suppose you have articles dealing with electrodermal activity(EDA), some of them in a clinical setting, the others are experimental. The stimuli used are music, pictures and noxious stimuli. Pictures can have either erotic or frightening content. If you consistently assign hierarchical keywords (e.g. EDA/experimental/pictures/fear) you would end up with following organization in the Term List pane:



I think that the benefit in gained overview is worth the extra effort in assigning keywords in hierarchies. But this is only my opinion.

Regards,
Dimitrios

[Jon]

Yes, I see your point. I would note (no pun intended) that this really is pretty far from reference management and belongs somewhere in the category of organize/outline/notebook/etc. software. I can see how it would be useful to some people, of course, but it would add quite a bit of complexity to what is now an automatic (term lists) and rather simple (tags) process. I'd be interested to hear if you or anyone else have suggestions about how to extend the current features without adding such complexity.

Jon
Sonny Software

[macula]

Hierarchical tagging is expertly implemented in DevonThink. You may want to take a look at http://www.organizingcreativity.com/201 ... evonthink/.

I use the DevonThink-Bookends script to bidirectionally link each Bookends item with a unique entity in my DevonThink database. While this workflow is imperfect—there is no automatic synchronization between the two applications, for example—I have found it more than adequate, to the point that I no longer use any of the note-keeping facilities of Bookends, rather relying on the impressive Artificial Intelligence algorithms of DevonThink for searching, tagging, and classification.

In my opinion, it would make more sense to develop a "live-sync" mechanism between Bookends and DevonThink, instead of trying to evolve Bookends into a catch-all über-application that would presume to do everything a researcher might conceivably need. (That said, such a mechanism might be exceedingly difficult to build given Apple's sandboxing restrictions.)

[Jon]

Can you give me a more concrete idea of what you think the interaction between Bookends and DT would be?

Also, I'd note that the Bookends group mechanism would also fulfill this function -- hierarchical, can embed groups within groups, etc. Not useful for thousands of "tags", but for dozens, even a hundred or so, I think it would work (you can even make smart groups that find references that do/don't belong to particular groups).

Jon
Sonny Software

[macula]

A recent thread on this forum (viewtopic.php?f=2&t=3167) broaches the issue. The thread was spun out shortly after the release of the DevonThink-Bookends plugin.

In short, it would be great to have modifications in a Bookends item automatically reflected in the DevonThink file corresponding to that item (and vice-versa). I realize this might sound like science fiction, though.