[Gmod-schema] online ontology editor

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[Gmod-schema] online ontology editor

Andrew McArthur
Colleagues,

I've developed a first draft ontology for our Chado database using OBO-Edit but now need to open up its development to our larger, international working group.  Do you have a suggestion of an online resource for (password-protected) community development of ontologies?  Alternatively, software we could install on our own web servers?

Much thanks,
Andrew McArthur

------
Andrew G. McArthur, Ph.D.
Bioinformatics Consulting Services
Phone: 905.296.3252, Mobile: 905.745.2794, Fax: 647.439.0829
AIM: [hidden email], Skype: agmcarthur




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Re: [Gmod-schema] online ontology editor

Chris Stoeckert
You might try Web Protege. http://protegewiki.stanford.edu/wiki/WebProtege
Cheers,
Chris

On May 14, 2010, at 11:30 AM, Andrew McArthur wrote:

Colleagues,

I've developed a first draft ontology for our Chado database using OBO-Edit but now need to open up its development to our larger, international working group.  Do you have a suggestion of an online resource for (password-protected) community development of ontologies?  Alternatively, software we could install on our own web servers?

Much thanks,
Andrew McArthur

------
Andrew G. McArthur, Ph.D.
Bioinformatics Consulting Services
Phone: 905.296.3252, Mobile: 905.745.2794, Fax: 647.439.0829
AIM: [hidden email], Skype: agmcarthur



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Re: [Gmod-schema] online ontology editor

Chris Mungall-3
In reply to this post by Andrew McArthur

How about svn/cvs, on for example sourceforge, google code or similar?  
Many groups collaboratively develop this way.

On May 14, 2010, at 8:30 AM, Andrew McArthur wrote:

> Colleagues,
>
> I've developed a first draft ontology for our Chado database using  
> OBO-Edit but now need to open up its development to our larger,  
> international working group.  Do you have a suggestion of an online  
> resource for (password-protected) community development of  
> ontologies?  Alternatively, software we could install on our own web  
> servers?
>
> Much thanks,
> Andrew McArthur
>
> ------
> Andrew G. McArthur, Ph.D.
> Bioinformatics Consulting Services
> Email: [hidden email], Web: http://mcarthurlab.blogspot.com
> Phone: 905.296.3252, Mobile: 905.745.2794, Fax: 647.439.0829
> AIM: [hidden email], Skype: agmcarthur
>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema


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Re: [Gmod-schema] online ontology editor

Robson de Souza
On Fri, May 14, 2010 at 12:11 PM, Chris Mungall <[hidden email]> wrote:
>
> How about svn/cvs, on for example sourceforge, google code or similar?
> Many groups collaboratively develop this way.

How do they handle conflicts? Since ontologies are usually stored in a
single file, is the merging of two different versions of a parent
ontology left to the user, which should use OboEdit or Protege to do
so?
Robson

> On May 14, 2010, at 8:30 AM, Andrew McArthur wrote:
>
>> Colleagues,
>>
>> I've developed a first draft ontology for our Chado database using
>> OBO-Edit but now need to open up its development to our larger,
>> international working group.  Do you have a suggestion of an online
>> resource for (password-protected) community development of
>> ontologies?  Alternatively, software we could install on our own web
>> servers?
>>
>> Much thanks,
>> Andrew McArthur
>>
>> ------
>> Andrew G. McArthur, Ph.D.
>> Bioinformatics Consulting Services
>> Email: [hidden email], Web: http://mcarthurlab.blogspot.com
>> Phone: 905.296.3252, Mobile: 905.745.2794, Fax: 647.439.0829
>> AIM: [hidden email], Skype: agmcarthur
>>
>>
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>

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Re: [Gmod-schema] [Biocurator] online ontology editor

Alan Ruttenberg-2
In reply to this post by Chris Mungall-3

On May 14, 2010, at 12:11 PM, Chris Mungall wrote:

>
> How about svn/cvs, on for example sourceforge, google code or similar?  
> Many groups collaboratively develop this way.

I'd recommend google code over sourceforge - sourceforge has been unreliable on things like making sure email lists work properly and are widely indexed.
Examples:

http://code.google.com/p/information-artifact-ontology
http://code.google.com/p/infectious-disease-ontology

I generally create two google groups for each project one "-discuss" list for discussions, with issues from the tracker posted to that list, and one "-commit" list for people who want to track commits to the project.

If you want help with setup, please contact me.

-Alan


>
> On May 14, 2010, at 8:30 AM, Andrew McArthur wrote:
>
>> Colleagues,
>>
>> I've developed a first draft ontology for our Chado database using  
>> OBO-Edit but now need to open up its development to our larger,  
>> international working group.  Do you have a suggestion of an online  
>> resource for (password-protected) community development of  
>> ontologies?  Alternatively, software we could install on our own web  
>> servers?
>>
>> Much thanks,
>> Andrew McArthur
>>
>> ------
>> Andrew G. McArthur, Ph.D.
>> Bioinformatics Consulting Services
>> Email: [hidden email], Web: http://mcarthurlab.blogspot.com
>> Phone: 905.296.3252, Mobile: 905.745.2794, Fax: 647.439.0829
>> AIM: [hidden email], Skype: agmcarthur
>>
>>
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
> _______________________________________________
> Biocurator mailing list
> [hidden email]
> http://mailman.tairgroup.org/mailman/listinfo/biocurator


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Re: [Gmod-schema] online ontology editor

Andrew McArthur
In reply to this post by Chris Mungall-3
The majority of my contributors are clinicians as we are developing a biomedical ontology.  The easier the web interface the better...

On 2010-05-14, at 12:11 PM, Chris Mungall wrote:


How about svn/cvs, on for example sourceforge, google code or similar? Many groups collaboratively develop this way.

On May 14, 2010, at 8:30 AM, Andrew McArthur wrote:

Colleagues,

I've developed a first draft ontology for our Chado database using OBO-Edit but now need to open up its development to our larger, international working group.  Do you have a suggestion of an online resource for (password-protected) community development of ontologies?  Alternatively, software we could install on our own web servers?

Much thanks,
Andrew McArthur

------
Andrew G. McArthur, Ph.D.
Bioinformatics Consulting Services
Email: [hidden email], Web: http://mcarthurlab.blogspot.com
Phone: 905.296.3252, Mobile: 905.745.2794, Fax: 647.439.0829
AIM: [hidden email], Skype: agmcarthur



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------
Andrew G. McArthur, Ph.D.
Bioinformatics Consulting Services
Phone: 905.296.3252, Mobile: 905.745.2794, Fax: 647.439.0829
AIM: [hidden email], Skype: agmcarthur




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Re: [Gmod-schema] online ontology editor

Fields, Christopher J
In reply to this post by Chris Mungall-3
Or *cough*github*cough*.

chris

On May 14, 2010, at 11:11 AM, Chris Mungall wrote:

>
> How about svn/cvs, on for example sourceforge, google code or similar?  
> Many groups collaboratively develop this way.
>
> On May 14, 2010, at 8:30 AM, Andrew McArthur wrote:
>
>> Colleagues,
>>
>> I've developed a first draft ontology for our Chado database using  
>> OBO-Edit but now need to open up its development to our larger,  
>> international working group.  Do you have a suggestion of an online  
>> resource for (password-protected) community development of  
>> ontologies?  Alternatively, software we could install on our own web  
>> servers?
>>
>> Much thanks,
>> Andrew McArthur
>>
>> ------
>> Andrew G. McArthur, Ph.D.
>> Bioinformatics Consulting Services
>> Email: [hidden email], Web: http://mcarthurlab.blogspot.com
>> Phone: 905.296.3252, Mobile: 905.745.2794, Fax: 647.439.0829
>> AIM: [hidden email], Skype: agmcarthur
>>
>>
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema


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Re: [Gmod-schema] online ontology editor

Robert Buels
In reply to this post by Chris Mungall-3
Chris Mungall wrote:
> How about svn/cvs, on for example sourceforge, google code or similar?  
> Many groups collaboratively develop this way.

Chris, why can't niche ontologies like this just be hosted on
obofoundry.org?

Rob

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Re: [Gmod-schema] online ontology editor

Chris Mungall-3

On May 14, 2010, at 11:41 AM, Robert Buels wrote:

> Chris Mungall wrote:
>> How about svn/cvs, on for example sourceforge, google code or  
>> similar?  Many groups collaboratively develop this way.
>
> Chris, why can't niche ontologies like this just be hosted on  
> obofoundry.org?

We'd be happy to grant a cvs or svn account to the obo sourceforge  
project. Alan makes a convincing case for googlecode. And there's also  
github.

Either way, we can list the ontology amongst the others on  
obofoundry.org -- but this is independent of how the group chooses to  
manage its ontology.

I'd also encourage posting on obo-discuss to make sure the ontology  
doesn't overlap too much with existing efforts.

> Rob
>


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