OBI browser and SVN access

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OBI browser and SVN access

Melanie Courtot-2
Hi all,

Allen, in Oliver's group, has been working on developing a version of  
the VO browser (http://www.violinet.org/vaccineontology/vobrowser/)  
for OBI.
He has a first prototype (available at http://ontobrowser.hegroup.org/index.php)
, and offered to commit the code under our SVN so that others may  
participate.

In order to do so he needs to be added to the OBI project on  
Sourceforge (http://sourceforge.net/project/memberlist.php?group_id=177891 
), and unless anybody objects, I will grant him access on Wednesday  
morning PST.

Thanks,
Melanie

---
Mélanie Courtot
TFL- BCCRC
675 West 10th Avenue
Vancouver, BC
V5Z 1L3, Canada





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Re: OBI browser and SVN access

Helen Parkinson
Hi

how would Allen like feedback on this tool? Is there any documentation
of functionality?

thanks

Helen

Melanie Courtot wrote:

> Hi all,
>
> Allen, in Oliver's group, has been working on developing a version of  
> the VO browser (http://www.violinet.org/vaccineontology/vobrowser/)  
> for OBI.
> He has a first prototype (available at http://ontobrowser.hegroup.org/index.php)
> , and offered to commit the code under our SVN so that others may  
> participate.
>
> In order to do so he needs to be added to the OBI project on  
> Sourceforge (http://sourceforge.net/project/memberlist.php?group_id=177891 
> ), and unless anybody objects, I will grant him access on Wednesday  
> morning PST.
>
> Thanks,
> Melanie
>
> ---
> Mélanie Courtot
> TFL- BCCRC
> 675 West 10th Avenue
> Vancouver, BC
> V5Z 1L3, Canada
>
>
>
>
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry® Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9-12, 2009. Register now!
> http://p.sf.net/sfu/devconf
> _______________________________________________
> Obi-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/obi-devel
>  

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Re: OBI browser and SVN access

Frank Gibson
Is this a generic browser that can support OWL ontologies?  If it already exists, which it appears to do looking at the VO site, I am not sure if it would make sense to duplicate the source code in the OBI repository. Would it not make more sense just to implement via its own repo, assuming that exists?

Frank

On Mon, Oct 5, 2009 at 8:47 PM, Helen Parkinson <[hidden email]> wrote:
Hi

how would Allen like feedback on this tool? Is there any documentation
of functionality?

thanks

Helen

Melanie Courtot wrote:
> Hi all,
>
> Allen, in Oliver's group, has been working on developing a version of
> the VO browser (http://www.violinet.org/vaccineontology/vobrowser/)
> for OBI.
> He has a first prototype (available at http://ontobrowser.hegroup.org/index.php)
> , and offered to commit the code under our SVN so that others may
> participate.
>
> In order to do so he needs to be added to the OBI project on
> Sourceforge (http://sourceforge.net/project/memberlist.php?group_id=177891
> ), and unless anybody objects, I will grant him access on Wednesday
> morning PST.
>
> Thanks,
> Melanie
>
> ---
> Mélanie Courtot
> TFL- BCCRC
> 675 West 10th Avenue
> Vancouver, BC
> V5Z 1L3, Canada
>
>
>
>
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9&#45;12, 2009. Register now&#33;
> http://p.sf.net/sfu/devconf
> _______________________________________________
> Obi-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/obi-devel
>

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http://peanutbutter.wordpress.com/

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Re: OBI browser and SVN access

He, Oliver
In reply to this post by Helen Parkinson
Hi Helen,
 
For now you can probably email Allen and/or me for feedback. We will probably set up some sourceforge site, so we can talk later using some email mailing list. 
 
Thanks!
--Oliver

>>> Helen Parkinson <[hidden email]> 10/5/2009 3:47 PM >>>
Hi

how would Allen like feedback on this tool? Is there any documentation
of functionality?

thanks

Helen

Melanie Courtot wrote:

> Hi all,
>
> Allen, in Oliver's group, has been working on developing a version of 
> the VO browser (http://www.violinet.org/vaccineontology/vobrowser/) 
> for OBI.
> He has a first prototype (available at http://ontobrowser.hegroup.org/index.php)
> , and offered to commit the code under our SVN so that others may 
> participate.
>
> In order to do so he needs to be added to the OBI project on 
> Sourceforge (http://sourceforge.net/project/memberlist.php?group_id=177891
> ), and unless anybody objects, I will grant him access on Wednesday 
> morning PST.
>
> Thanks,
> Melanie
>
> ---
> Mélanie Courtot
> TFL- BCCRC
> 675 West 10th Avenue
> Vancouver, BC
> V5Z 1L3, Canada
>
>
>
>
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9&#45;12, 2009. Register now&#33;
> http://p.sf.net/sfu/devconf
> _______________________________________________
> Obi-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/obi-devel
>  

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ahead of the curve. Join us from November 9&#45;12, 2009. Register now&#33;
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Re: OBI browser and SVN access

He, Oliver
In reply to this post by Frank Gibson
Hi Frank,
 
This is based on the VOBrowser we developed, and we plan to make it more generic for OBI and other OWL ontologies. However, there will be an OBI version that is customized for OBI use. Alan, Jie, Melanie, Helen, and James may also want to improve it by coding or providing feedbacks. In this case, it would help to have it stored in OBI repository. Thanks,
 
--Oliver   

>>> Frank Gibson <[hidden email]> 10/5/2009 4:24 PM >>>
Is this a generic browser that can support OWL ontologies? If it already exists, which it appears to do looking at the VO site, I am not sure if it would make sense to duplicate the source code in the OBI repository. Would it not make more sense just to implement via its own repo, assuming that exists?

Frank

On Mon, Oct 5, 2009 at 8:47 PM, Helen Parkinson <[hidden email]> wrote:
Hi

how would Allen like feedback on this tool? Is there any documentation
of functionality?

thanks

Helen

Melanie Courtot wrote:

> Hi all,
>
> Allen, in Oliver's group, has been working on developing a version of
> the VO browser (http://www.violinet.org/vaccineontology/vobrowser/)
> for OBI.
> He has a first prototype (available at http://ontobrowser.hegroup.org/index.php)
> , and offered to commit the code under our SVN so that others may
> participate.
>
> In order to do so he needs to be added to the OBI project on
> Sourceforge (http://sourceforge.net/project/memberlist.php?group_id=177891
> ), and unless anybody objects, I will grant him access on Wednesday
> morning PST.
>
> Thanks,
> Melanie
>
> ---
> Mélanie Courtot
> TFL- BCCRC
> 675 West 10th Avenue
> Vancouver, BC
> V5Z 1L3, Canada
>
>
>
>
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9&#45;12, 2009. Register now&#33;
> http://p.sf.net/sfu/devconf
> _______________________________________________
> Obi-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/obi-devel
>

------------------------------------------------------------------------------
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is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay
ahead of the curve. Join us from November 9&#45;12, 2009. Register now&#33;
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http://peanutbutter.wordpress.com/

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Re: OBI browser and SVN access

Philippe Rocca-Serra
Hi Oliver,

This sounds great. Do you plan to provide a web service access ?
Our isacreator tool currently accesses NCBO bioportal and EBI OLS but it
is always good to be able to have more options.
a soap service allowing query by term or accession and browsing
hierarchy would be a very nice feature!

Thanks

Philippe

Yongqun He wrote:

> Hi Frank,
>  
> This is based on the VOBrowser we developed, and we plan to make it
> more generic for OBI and other OWL ontologies. However, there will be
> an OBI version that is customized for OBI use. Alan, Jie, Melanie,
> Helen, and James may also want to improve it by coding
> or providing feedbacks. In this case, it would help to have it stored
> in OBI repository. Thanks,
>  
> --Oliver  
>
> >>> Frank Gibson <[hidden email]> 10/5/2009 4:24 PM >>>
> Is this a generic browser that can support OWL ontologies? If it
> already exists, which it appears to do looking at the VO site, I am
> not sure if it would make sense to duplicate the source code in the
> OBI repository. Would it not make more sense just to implement via its
> own repo, assuming that exists?
>
> Frank
>
> On Mon, Oct 5, 2009 at 8:47 PM, Helen Parkinson <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hi
>
>     how would Allen like feedback on this tool? Is there any documentation
>     of functionality?
>
>     thanks
>
>     Helen
>
>     Melanie Courtot wrote:
>     > Hi all,
>     >
>     > Allen, in Oliver's group, has been working on developing a
>     version of
>     > the VO browser (http://www.violinet.org/vaccineontology/vobrowser/)
>     > for OBI.
>     > He has a first prototype (available at
>     http://ontobrowser.hegroup.org/index.php)
>     > , and offered to commit the code under our SVN so that others may
>     > participate.
>     >
>     > In order to do so he needs to be added to the OBI project on
>     > Sourceforge
>     (http://sourceforge.net/project/memberlist.php?group_id=177891
>     > ), and unless anybody objects, I will grant him access on Wednesday
>     > morning PST.
>     >
>     > Thanks,
>     > Melanie
>     >
>     > ---
>     > Mélanie Courtot
>     > TFL- BCCRC
>     > 675 West 10th Avenue
>     > Vancouver, BC
>     > V5Z 1L3, Canada
>     >
>     >
>     >
>     >
>     >
>     >
>     ------------------------------------------------------------------------------
>     > Come build with us! The BlackBerry&reg; Developer Conference in
>     SF, CA
>     > is the only developer event you need to attend this year.
>     Jumpstart your
>     > developing skills, take BlackBerry mobile applications to market
>     and stay
>     > ahead of the curve. Join us from November 9&#45;12, 2009.
>     Register now&#33;
>     > http://p.sf.net/sfu/devconf
>     > _______________________________________________
>     > Obi-devel mailing list
>     > [hidden email]
>     <mailto:[hidden email]>
>     > https://lists.sourceforge.net/lists/listinfo/obi-devel
>     >
>
>     ------------------------------------------------------------------------------
>     Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
>     is the only developer event you need to attend this year.
>     Jumpstart your
>     developing skills, take BlackBerry mobile applications to market
>     and stay
>     ahead of the curve. Join us from November 9&#45;12, 2009. Register
>     now&#33;
>     http://p.sf.net/sfu/devconf
>     _______________________________________________
>     Obi-devel mailing list
>     [hidden email]
>     <mailto:[hidden email]>
>     https://lists.sourceforge.net/lists/listinfo/obi-devel
>
>
>
>
> --
> Frank Gibson, PhD
> http://peanutbutter.wordpress.com/
>
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should
> not be used for urgent or sensitive issues
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9&#45;12, 2009. Register now&#33;
> http://p.sf.net/sfu/devconf
> ------------------------------------------------------------------------
>
> _______________________________________________
> Obi-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/obi-devel
>  


--
Philippe Rocca-Serra, PhD

Technical Coordinator
www.ebi.ac.uk/net-project

The European Bioinformatics Institute   email:  [hidden email]
EMBL Outstation - Hinxton               direct: +44 (0)1223 492 553
Wellcome Trust Genome Campus            fax: +44 (0)1223 492 620
Cambridge CB10 1SD, UK                  room: A3-141
--


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Re: OBI browser and SVN access

He, Oliver
Hi Philippe,
 
Our strategy is simple: we store an ontology in a Virtuoso RDF database, and then use PHP and SPARQL programming to access the rdf database and make sparql queries. Therefore, I am sorry to say that our tool (we name OntoBee) cannot support SOAP. Basically, OntoBee will provide an VOBrowser like ontology browsing feature:
and will also include a SPARQL script web interface like the following:
 
and it will also provide some limited features for ontology development, for example, checking terms that have the same names. We may eventually provide support to Java programming, and thus more features using Java tools like OWL API and Jena.   
 
Oliver


>>> Philippe Rocca-Serra <[hidden email]> 10/6/2009 4:56 PM >>>
Hi Oliver,

This sounds great. Do you plan to provide a web service access ?
Our isacreator tool currently accesses NCBO bioportal and EBI OLS but it
is always good to be able to have more options.
a soap service allowing query by term or accession and browsing
hierarchy would be a very nice feature!

Thanks

Philippe

Yongqun He wrote:

> Hi Frank,

> This is based on the VOBrowser we developed, and we plan to make it
> more generic for OBI and other OWL ontologies. However, there will be
> an OBI version that is customized for OBI use. Alan, Jie, Melanie,
> Helen, and James may also want to improve it by coding
> or providing feedbacks. In this case, it would help to have it stored
> in OBI repository. Thanks,

> --Oliver  
>
> >>> Frank Gibson <[hidden email]> 10/5/2009 4:24 PM >>>
> Is this a generic browser that can support OWL ontologies? If it
> already exists, which it appears to do looking at the VO site, I am
> not sure if it would make sense to duplicate the source code in the
> OBI repository. Would it not make more sense just to implement via its
> own repo, assuming that exists?
>
> Frank
>
> On Mon, Oct 5, 2009 at 8:47 PM, Helen Parkinson <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hi
>
>     how would Allen like feedback on this tool? Is there any documentation
>     of functionality?
>
>     thanks
>
>     Helen
>
>     Melanie Courtot wrote:
>     > Hi all,
>     >
>     > Allen, in Oliver's group, has been working on developing a
>     version of
>     > the VO browser (http://www.violinet.org/vaccineontology/vobrowser/)
>     > for OBI.
>     > He has a first prototype (available at
>     http://ontobrowser.hegroup.org/index.php)
>     > , and offered to commit the code under our SVN so that others may
>     > participate.
>     >
>     > In order to do so he needs to be added to the OBI project on
>     > Sourceforge
>     (http://sourceforge.net/project/memberlist.php?group_id=177891
>     > ), and unless anybody objects, I will grant him access on Wednesday
>     > morning PST.
>     >
>     > Thanks,
>     > Melanie
>     >
>     > ---
>     > Mélanie Courtot
>     > TFL- BCCRC
>     > 675 West 10th Avenue
>     > Vancouver, BC
>     > V5Z 1L3, Canada
>     >
>     >
>     >
>     >
>     >
>     >
>     ------------------------------------------------------------------------------
>     > Come build with us! The BlackBerry&reg; Developer Conference in
>     SF, CA
>     > is the only developer event you need to attend this year.
>     Jumpstart your
>     > developing skills, take BlackBerry mobile applications to market
>     and stay
>     > ahead of the curve. Join us from November 9&#45;12, 2009.
>     Register now&#33;
>     > http://p.sf.net/sfu/devconf
>     > _______________________________________________
>     > Obi-devel mailing list
>     > [hidden email]
>     <mailto:[hidden email]>
>     > https://lists.sourceforge.net/lists/listinfo/obi-devel
>     >
>
>     ------------------------------------------------------------------------------
>     Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
>     is the only developer event you need to attend this year.
>     Jumpstart your
>     developing skills, take BlackBerry mobile applications to market
>     and stay
>     ahead of the curve. Join us from November 9&#45;12, 2009. Register
>     now&#33;
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>     Obi-devel mailing list
>     [hidden email]
>     <mailto:[hidden email]>
>     https://lists.sourceforge.net/lists/listinfo/obi-devel
>
>
>
>
> --
> Frank Gibson, PhD
> http://peanutbutter.wordpress.com/
>
> **********************************************************
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> not be used for urgent or sensitive issues
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9&#45;12, 2009. Register now&#33;
> http://p.sf.net/sfu/devconf
> ------------------------------------------------------------------------
>
> _______________________________________________
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>  


--
Philippe Rocca-Serra, PhD

Technical Coordinator
www.ebi.ac.uk/net-project

The European Bioinformatics Institute   email:  [hidden email]
EMBL Outstation - Hinxton               direct: +44 (0)1223 492 553
Wellcome Trust Genome Campus            fax: +44 (0)1223 492 620
Cambridge CB10 1SD, UK                  room: A3-141
--


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Re: OBI browser and SVN access

Alan Ruttenberg-2
In reply to this post by Philippe Rocca-Serra
Sparql is a web service much simpler than soap. Why not give it a go.  
That's what Allen uses on the backend.

-Alan

On Oct 6, 2009, at 4:56 PM, Philippe Rocca-Serra <[hidden email]>  
wrote:

> Hi Oliver,
>
> This sounds great. Do you plan to provide a web service access ?
> Our isacreator tool currently accesses NCBO bioportal and EBI OLS  
> but it
> is always good to be able to have more options.
> a soap service allowing query by term or accession and browsing
> hierarchy would be a very nice feature!
>
> Thanks
>
> Philippe
>
> Yongqun He wrote:
>> Hi Frank,
>>
>> This is based on the VOBrowser we developed, and we plan to make it
>> more generic for OBI and other OWL ontologies. However, there will be
>> an OBI version that is customized for OBI use. Alan, Jie, Melanie,
>> Helen, and James may also want to improve it by coding
>> or providing feedbacks. In this case, it would help to have it stored
>> in OBI repository. Thanks,
>>
>> --Oliver
>>
>>>>> Frank Gibson <[hidden email]> 10/5/2009 4:24 PM >>>
>> Is this a generic browser that can support OWL ontologies? If it
>> already exists, which it appears to do looking at the VO site, I am
>> not sure if it would make sense to duplicate the source code in the
>> OBI repository. Would it not make more sense just to implement via  
>> its
>> own repo, assuming that exists?
>>
>> Frank
>>
>> On Mon, Oct 5, 2009 at 8:47 PM, Helen Parkinson <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>>    Hi
>>
>>    how would Allen like feedback on this tool? Is there any  
>> documentation
>>    of functionality?
>>
>>    thanks
>>
>>    Helen
>>
>>    Melanie Courtot wrote:
>>> Hi all,
>>>
>>> Allen, in Oliver's group, has been working on developing a
>>    version of
>>> the VO browser (http://www.violinet.org/vaccineontology/vobrowser/)
>>> for OBI.
>>> He has a first prototype (available at
>>    http://ontobrowser.hegroup.org/index.php)
>>> , and offered to commit the code under our SVN so that others may
>>> participate.
>>>
>>> In order to do so he needs to be added to the OBI project on
>>> Sourceforge
>>    (http://sourceforge.net/project/memberlist.php?group_id=177891
>>> ), and unless anybody objects, I will grant him access on Wednesday
>>> morning PST.
>>>
>>> Thanks,
>>> Melanie
>>>
>>> ---
>>> Mélanie Courtot
>>> TFL- BCCRC
>>> 675 West 10th Avenue
>>> Vancouver, BC
>>> V5Z 1L3, Canada
>>>
>>>
>>>
>>>
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Re: OBI browser and SVN access

Frank Gibson
In reply to this post by He, Oliver


On Tue, Oct 6, 2009 at 8:03 PM, Yongqun He <[hidden email]> wrote:
Hi Frank,
 
This is based on the VOBrowser we developed, and we plan to make it more generic for OBI and other OWL ontologies. However, there will be an OBI version that is customized for OBI use. Alan, Jie, Melanie, Helen, and James may also want to improve it by coding or providing feedbacks. In this case, it would help to have it stored in OBI repository. Thanks,

So this is your decision to make, and I have no objections in principle to putting it in OBI SVN. However, if it is a generic browser my reccommendation would be to set up you own repository, probably your own sourceforge/google/github project and ask people from OBI to contribute. The source code should remain in one place and the developers move, not the other way around. This is your project to manage as you see fit, however, this would be my recommendation.

Frank



 
 
--Oliver   

>>> Frank Gibson <[hidden email]> 10/5/2009 4:24 PM >>>

Is this a generic browser that can support OWL ontologies? If it already exists, which it appears to do looking at the VO site, I am not sure if it would make sense to duplicate the source code in the OBI repository. Would it not make more sense just to implement via its own repo, assuming that exists?

Frank

On Mon, Oct 5, 2009 at 8:47 PM, Helen Parkinson <[hidden email]> wrote:
Hi

how would Allen like feedback on this tool? Is there any documentation
of functionality?

thanks

Helen

Melanie Courtot wrote:
> Hi all,
>
> Allen, in Oliver's group, has been working on developing a version of
> the VO browser (http://www.violinet.org/vaccineontology/vobrowser/)
> for OBI.
> He has a first prototype (available at http://ontobrowser.hegroup.org/index.php)
> , and offered to commit the code under our SVN so that others may
> participate.
>
> In order to do so he needs to be added to the OBI project on
> Sourceforge (http://sourceforge.net/project/memberlist.php?group_id=177891
> ), and unless anybody objects, I will grant him access on Wednesday
> morning PST.
>
> Thanks,
> Melanie
>
> ---
> Mélanie Courtot
> TFL- BCCRC
> 675 West 10th Avenue
> Vancouver, BC
> V5Z 1L3, Canada
>
>
>
>
>
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**********************************************************
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