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re: st: manuals

From   David Airey <>
Subject   re: st: manuals
Date   Wed, 17 Dec 2003 08:07:34 -0600

R. Allan Reese                       Email:

There was discussion some months back about making the manuals available
as files. I liked the manuals when I first met Stata (v3) but have
concluded at v8 that the hyperlink structure has perhaps gone too far for
a paper-bound (in literal and metaphorical senses) format.
Cross-referencing is fine, but my recollection is that human readers can
hold in short-term memory at most three layers of recursion. The Graphics
manual is particularly tedious in making one look for an object, then
object_options, object_style etc. And the ordering is unnatural. Do you
look under the letter, graph_letter or what? See under "a" for added_text
(not t!), or "m" for labelling points then "t" for textbox_options.

Rather than end with a moan, I'll grit my teeth and, via this pokey
white-on-black window on a 17in VDU, send Season's Greetings to all.
I recently went to a genomics conference in Tennessee and saw an amazing product by a private firm hired to help pharmaceutical companies keep and make sense of disparate sources of data they generate. Most of the time, these companies don't know what each part is actually doing. It's not so much the content that makes this product interesting as the interface to the private and public bioinformatics databases. The interface has a central window, surrounded by 8 others, extensible if you have more LCDs tied in. Anyway, a query in the central window shows up other database links in the 8 surround windows. My point here is that the extensive and layered cross referencing of commands in Stata, especially graphics commands and options, and this lends itself to not only a hyperlinked environment, but a more complex visual display of these links. The consistent structure of the graphics sub options lends itself to having each option type as its own database, and commands can be related to these. The same kind of interface could then be set up and would facilitate faster and more effective browsing of Stata's powerful controls. Below is the abstract to this fascinating new tool in case Stata wishes to investigate it. It is certainly from the future.

12:05 PM
KDT: Supporting Intelligent Browsing of Disparate Bio-medical Data.
Edy S. Liongosari
Edy S. Liongosari

Abstract: KDT is a tool that utilizes a knowledge modeling approach to intelligently extract and integrate a large set of disconnected bio-medical information. From thirteen publicly available sources of almost 100GB of raw data, the tool identifies over 2.5 million bio-medical entities with two billion relationships among those entities. Through an extensive use of user definable rules, the entities and relationships are cleansed, analyzed and integrated to form a single unified knowledge web. The rules also allow KDT users to customize what entities and relationships to display on the screen, how to derive and prioritize the relationships. This allows KDT to go beyond simply showing a web page of links pertinent to a particular subject. It allows its users to see how the entities are linked together at different levels of certainty. It uncovers hidden linkages by intelligently traversing the integrated knowledge web and deriving additional relationships. It also highlights certain unusual links that might be worth exploring. KDT’s a unique web-enabled user interface allows users to navigate through a large knowledge web with ease and view a large set of relationships at once. In this talk, I will describe and demonstrate KDT’s capabilities, its current status, how it is used in Pharmaceutical companies as well as our collaboration with INIA West.

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