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Thinkmap for pictorial views of GO?

Bill Bug bbug at speakeasy.org
Fri Jun 7 13:31:33 PDT 2002


Hi All,

Has anyone ever approached the folks at Plumb Design 
(www.plumbdesign.com) regarding the possible use of their Thinkmap 
technology as a presentation/browsing tool for GO.

 From discussions I had with them a few years back when I was developing 
literature database products for the publishers of the Biological 
Abstracts, I know they are very interested the possible applications of 
their technology in the biological sciences.

There are many excellent GO browsers folks have built now, some of which 
have been mentioned in this thread.

The difference with ThinkMap is it excels at visualizing complex webs of 
inter-related terms.  It's really a 'relatedness' browser, as opposed to 
the lexically-based browsers you typically see used for controlled 
vocabularies & thesauri.  I believe ThinkMap can also draw on the 
rules & node/relationship typing you find in rich ontologies to greatly 
enhance the way it visually-guides users through the ontology.

The WordNet Thinkmap demo at the URL listed below gives a spare, but 
interesting demo of this:

http://thesaurus.plumbdesign.com/index.html

It can provide for every ontology/thesaurus visualization need.  
However, Thinkmap might in fact do a very nice job creating the 
pictorial view of GO originally requested in this post by M. Lombardot, 
depending on the exact use he intends to make of them.

Thinkmap might also provide a very usable, GO-mediated front-end to the 
sequence databases into which GO has been mapped.

Cheers,
Bill Bug

Bill Bug
Senior Analyst/Ontological Engineer
Computer Vision Laboratory for Vertebrate Brain Mapping
MCP/Hahnemann University
2900  Queen Lane
Philadelphia, PA, 19129



On Friday, June 7, 2002, at 02:27 PM, David Hill wrote:

From: David Hill <dph at informatics.jax.org>
Date: Fri Jun 07, 2002  02:27:45 PM US/Eastern
To: "Yockey, Courtland" <courtland.yockey at astrazeneca.com>, Thierry 
Lombardot <tlombard at mpi-bremen.de>, go-friends at genome.Stanford.EDU
Subject: Re: Pictorial representation of Gene Ontologies

Yes, currently the ontologies have over 11000 nodes and over14000 
relationships.



At 02:15 PM 6/7/2002 -0400, Yockey, Courtland wrote:
Thierry,

I agree with Chris about the size of a pictorial representation of the
entire 3 Ontologies together.  I would recommend something more along the
lines of showing a GO SLIM tree or a tree that has been sliced at a
particular level, maybe the 2nd level below the main Ontology branch 
points.
Is what you are trying to portray in the figure the overall structure of 
the
GO?  Perhaps you could clarify this.

Courtland

===================
Courtland E. Yockey
AstraZeneca Pharmaceuticals LP
Informatics Scientist
Enabling Science & Technology - Informatics
1800 Concord Pike, FRC CRDL202
Wilmington, DE  19850
phone = 302-886-5151
fax = 302-886-4803
e-mail = courtland.yockey at astrazeneca.com



-----Original Message-----
From: Chris Mungall [mailto:cjm at fruitfly.org]
Sent: Friday, June 07, 2002 2:05 PM
To: Thierry Lombardot
Cc: go-friends at genome.Stanford.EDU
Subject: Re: GOFriends e-mail archive



This is possible in AmiGO for small subsets of GO, but the pictorial 
graph
representations rapidly get enormous as you add more GO terms.

You can also get pie chart representations in AmiGO, but again this
doesn't scale to the whole ontology.

Really the only way to do this is with the standard tree view, but this
has some limitations in terms of representing multiple parentage in an
intuitive way

On Fri, 7 Jun 2002, Thierry Lombardot wrote:

 > Dear GO-friends,
 > I'm looking for a large picture representing all (or most) GO terms and
 > their relationships, in the form of a printable tree/map for example.
 > Did someone create such a representation of GO with the current status
 > already?
 >
 > Thank you in advance,
 >
 > Thierry Lombardot
 > MPI-Bremen,
 > Germany.
 >
 >
 > --
 > This message is from the GOFriends moderated mailing list.  A list of
public
 > announcements and discussion of the Gene Ontology (GO) project.
 > Problems with the list?           E-mail: owner-
gofriends at geneontology.org
 > Subscribing   send   "subscribe"   to   gofriends-
request at geneontology.org
 > Unsubscribing send   "unsubscribe"  to  gofriends-
request at geneontology.org
 > Web:          http://www.geneontology.org/
 >


--
This message is from the GOFriends moderated mailing list.  A list of 
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Problems with the list?           E-mail: owner-
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--
This message is from the GOFriends moderated mailing list.  A list of 
public
announcements and discussion of the Gene Ontology (GO) project.
Problems with the list?           E-mail: owner-
gofriends at geneontology.org
Subscribing   send   "subscribe"   to   gofriends-
request at geneontology.org
Unsubscribing send   "unsubscribe"  to  gofriends-
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Web:          http://www.geneontology.org/


--
This message is from the GOFriends moderated mailing list.  A list of 
public
announcements and discussion of the Gene Ontology (GO) project.
Problems with the list?           E-mail: owner-
gofriends at geneontology.org
Subscribing   send   "subscribe"   to   gofriends-
request at geneontology.org
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