Subject: Re: CCL:Data and Knowledge Management Tools for Compuational Chemists

From: khinsen{at}cea.fr
Date: Sat, 29 Jan 2005 09:38:34 +0100

On 28.01.2005, at 11:37, Marc Baaden wrote:

> I am looking for software, tools or general approaches to get hold of  
> the
> wealth of information that accumulates (mostly) electronically. In  
> particular
> emails, text/PDF/XML or similar documents, bookmarks to websites and
> bibliographic references.
>
> The main request would be to be able to "store" information as is  
> without
> having to enter it individually into a curated database. Filtering,  
> indexing
> or cataloging through a script would be ok, though. A powerful search  
> should be possible.

My main tool for information management is DEVONthink (see  
www.devon-technologies.com). It has a very convenient user interface  
for capturing information, can index PDF files, and has a very powerful  
search and classification system.

The one thing it doesn't do is managing citations. You can throw in all  
the raw data (e.g. Pubmed XML) and find it back, but there is no  
specific support for formatting citations according to specific  
journals' requirements, nor for transferring them to whatever word  
processor you use. It's still worth throwing the files in, in  
particular if they contain abstracts.

> Some specific points:
> - concerning bibliographic references, there is a wide variety of  
> formats
>   like Pubmed, email-alerts, quotes on websites, ... sometimes with a  
> comment
>   by the person who sent the reference, sometimes with an URL link, ...
>   I would like to be able to gather all information in a first pass  
> without
>   having to parse the format by hand (eg where are authors, title,  
> etc).

You can do that.

> - concerning bookmarks, it would be nice to also have elimination of  
> duplicates
>   and of dead links

No, not that.

> - taking it one step further, indexing the sites listed in the  
> bookmarks might
>   also be an additional useful step

Yes, that's possible (and very useful).

> In an ideal world, I'd also love to make use of some artificial  
> intelligence
> code (eg Self-organizing maps, textual data mining,..) or some  
> machine-learning
> tools, but my feeling is that those are not (yet) usable by  
> non-experts.

The DEVONthink engine is good enough to be useful, but not good enough  
to replace human intelligence. It can classify new data and suggest  
files that are similar to a given one.

Major limitation: MacOS only.
--
------------------------------------------------------------------------ 
-------
Konrad Hinsen
Laboratoire Leon Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: hinsen{at}llb.saclay.cea.fr
------------------------------------------------------------------------ 
-------