taskSavannah Administration - Tasks: task #5605, Submission of General Formal...


task #5605: Submission of General Formal Ontology

Submitted by:  Robert Hoehndorf <leechuck>
Submitted on:  Fri 26 May 2006 02:25:54 PM UTC  
Should Start On:  Fri 26 May 2006 12:00:00 AM UTC Should be Finished on:  Mon 05 Jun 2006 12:00:00 AM UTC
Category:  Project Approval Priority:  5 - Normal
Status:  Done Privacy:  Public
Percent Complete:  100% Assigned to:  Patrick Camus <tizzef>
Open/Closed:  Closed Effort:  0.00

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Thu 22 Jun 2006 09:40:00 AM UTC, comment #5: 

Hi Robert, :)

I have approved your project.  You will receive an automated e-mail containing detailed information about the approval.


Patrick Camus <tizzef>
Project MemberIn charge of this item.
Thu 22 Jun 2006 09:32:10 AM UTC, comment #4: 

Hi Patrick,

Sure. Savannah should become the only CVS for GFO, the primary site for developing and publishing GFO. GFO currently uses the bioinformatics.org CVS because there was no other public CVS we could use and I have write access to both CVS. GFO is an ontology which is not biology-specific, and the developers of GFO will not get write-access to the bioonto bioinformatics.org-CVS.
Currently, all changes to GFO are sent to me and I commit them to the CVS.
The CVS on bioinformatics.org will primarily be used for software which is related to ontologies (most of the time not GFO) and biology. GFO (and, to some extent, the core-ontology GFO-Bio which is hosted on bioinformatics.org as well) are developed independently and we want to use Savannah for this purpose.


Robert Hoehndorf <leechuck>
Thu 22 Jun 2006 09:16:27 AM UTC, comment #3: 

Hi Robert,

Please could you tell me in which way you plan to use the Savannah services as you already have an CVS repository ??


Patrick Camus <tizzef>
Project MemberIn charge of this item.
Tue 20 Jun 2006 08:09:28 AM UTC, comment #2: 


sorry for the wrong URL. The code is at the moment on http://www.onto-med.de/ontologies/gfo.owl.

Or, CVS from :pserver:anonymous@bioinformatics.org:/cvsroot, module bioonto/gfo.


Robert Hoehndorf <leechuck>
Thu 15 Jun 2006 09:53:30 AM UTC, comment #1: 


I'm evaluating the project you submitted for approval in Savannah.

Sorry for the long delay, I'll try more reactive in an near futur.

Please can you provide me a new URL for the first draft of your code, the one you provide us doesn't work (http://www.onto-med.de/gfo.owl).


Patrick Camus <tizzef>
Project MemberIn charge of this item.
Fri 26 May 2006 02:25:54 PM UTC, original submission:  

A new project has been registered at Savannah
The project account will remain inactive until a site admin approve or discard the registration.


While this item will be useful to track the registration process, approving or discarding the registration must be done using the specific "Group Administration" page, accessible only to site administrators, effectively logged as site administrators (superuser):


######### REGISTRATION DETAILS #########

Full Name:
  General Formal Ontology

System Group Name:

  non-GNU software & documentation

  Modified BSD License

  The project will develop a machine processable version of the General Formal Ontology (GFO).

The first step is the development of an OWL version of the GFO. A first draft of the OWL file can be found on http://www.onto-med.de/gfo.owl.
It is written in the description logic sub-dialect of OWL, which has many limitations, but is decidable (using a DL-reasoner such as FaCT++, http://owl.man.ac.uk/factplusplus) and can be used for conceptual modelling.
After the OWL version has been tested, a full version in first order logic (using Common Logic, http://cl.tamu.edu) will be developed.

The OWL-DL version of the GFO will form the basis for the creation of a biomedical core ontology based on GFO. This core ontology will be used by at least two open source projects: http://onto.eva.mpg.de/gene_functions.html and the BOWiki project on http://onto.eva.mpg.de/projects.html
For both projects, no source code has been produced, yet, and work has been concentrated on theoretical issues. However, both would be hosted here together with this project.

Other Software Required:
  No requirements, but the following are recommended:
FaCT++ for reasoning (http://owl.man.ac.uk/factplusplus)

Some OWL-Viewer/-Editor. There are famous ones such as Protege, SWOOP or OilEd, which are all written in Java (due to the lack of non-java OWL-libraries, I am sure), and probably require a Sun JRE. Better are web-based collaborative OWL-editors such as pOWL (http://powl.sf.net).
One of the software projects which will use this ontology is a collaborative ontology editing environment (and will be based on PHP and FaCT++).

Other Comments:
  I know that this project is not strictly speaking a software development project nor a project developing documentation, but rather a project to develop a formal specifaction of an ontology.
However, while software describes an algorithm and can be interpreted to solve a problem, an ontology describes a domain (or all of reality) and needs to be interpreted (by a reasoner such as FaCT++) to solve a problem. It is therefore like a library.
Or, more briefly: Please don't reject this project because it does not only develop software or documentation. :)

Robert Hoehndorf <leechuck>


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Follow 11 latest changes.

Date Changed by Updated Field Previous Value => Replaced by
2006-06-22 tizzef StatusWait reply => Done
    Percent Complete90% => 100%
    Open/ClosedOpen => Closed
2006-06-22 tizzef StatusIn Progress => Wait reply
    Percent Complete20% => 90%
2006-06-20 tizzef StatusWait reply => In Progress
2006-06-15 tizzef StatusIn Progress => Wait reply
    Percent Complete10% => 20%
2006-06-06 tizzef StatusNone => In Progress
    Assigned toNone => tizzef
    Percent Complete0% => 10%

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