Feedback on POC - DAG-edit help (PR#45)

[Katica Ilic]

Dear Alex,

Sure, I'll be happy to assist you with loading the POC ontology to the
DAG-edit.
I am assuming that you are using the most recent version of this software,
which
is 1.418, rev 2 (to download DAG-edit, including plug-ins, please go to the
SourceForge: http://sourceforge.net/project/showfiles.php?group_id=36855).
People usually have it locally installed on their PCs or Macs, but if you
installed it on Unix, it should be the same. The most recent Plant Structure
Ontology files are still in the GO flat file format (anatomy.ontology, rev
1.29,
and anatomy.definition, rev 1.31).

First, you need to open the DAG-edit, go to the File drop-down menu and click
on
the Load Terms. Then, when the new window opens, chose the appropriate adapter,
in this case it is GO Flat File Adapter. Give the name of the path profile in
the File collection, and then add the File path first for the anatomy.ontology
file by clicking on the 'Add' bar and then selecting the File name path below
(use the Browse option to locate the file). For the definition file, choose the
definition file name (use the Browse option to find the exact location of the
document). In both cases, this should be the full path (starting with C:\).
Once
you make sure that your file paths are correct, click OK, and your ontology
should be loaded and you should see the main DAG-edit window with '+plant
ontology' in the upper left corner.

If you still have problems, let me know, I can send you a few screen shots,
which may better illustrate the loading procedure. I also recommend that you
take a look into DAG-edit User Guide (click on the Help, and choose User
Guide).
Unfortunately, we don't have any additional DAG-edit manual, since this
software
was developed by the Gene Ontology Consortium, and they too use the DAG-edit
User Guide. To report bugs or for any other problem with DAG-edit you can
always
contact it's author, John Day-Richter (john.richter at aya.yale.edu), he would be
happy to help you.

And please, don't hesitate to contact me again if you need additional
assistance.

Good luck and thank you for your interest in Plant Ontologies.

Sincerely,

Katica Ilic, POC Project Coordinator 

> ---------- Forwarded message ----------
> Date: Mon, 29 Nov 2004 09:19:40 -0500
> From: feedback_submission at brie4.plantontology.org
> Reply-To: po-dev at plantontology.org,
feedback_submission at brie4.plantontology.org
> To: po-dev <po-dev at plantontology.org>
> Subject: Feedback on POC
> 
>     *** Feedback from Plant Ontology Live Site ***
> 
> refer_to_url: http://www.plantontology.org/ontology/index.html
> 
> comments: Sorry to ask, this may bee too basic but I have no previous
experience
> with DAG-EDIT. I am trying to load the ontology, do you have a manual or
readme
> about how to load this taxonomy in to DAG-EDIT? How can I load it? I have
> downloaded all of your POC. Well hope not to bother you with this, I know it
is
> not relevant... thanks in advance.
> 
> name: alex
> 
> email: a.garcia at imb.uq.edu.au
> 
> organization: imb
> 
> send_feedback: Send your feedback
> 
> 
Katica Ilic, TAIR Curator,	     E-mail: katica at acoma.stanford.edu	
The Arabidopsis Information Resource	Tel: (650) 325-1521 ext. 253	
Carnegie Institution of Washington	Fax: (650) 325-6857	
Department of Plant Biology	        URL: http://arabidopsis.org/		
260 Panama St.
Stanford, CA 94305, U.S.A.