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[bioontology-support] Help with BioPortal 2.0

Trish Whetzel whetzel at stanford.edu
Sun Dec 14 19:16:55 PST 2008


Hi Calixto,

Just wanted to check-in to see how things are going with your installation
of BioPortal. Also, were you able to track down the reason for an
independent knowledge management system using the LexBIG stack and do you
know if this work is also part of the Cardiovascular Research Grid? I have
seen some references from the OSU BMI department to a BioPortal, but am not
sure if it is the same BioPortal.

Cheers,
Trish 


>-----Original Message-----
>From: Natasha Noy [mailto:noy at stanford.edu]
>Sent: Monday, October 20, 2008 5:57 PM
>To: Calixto Melean
>Cc: Benjamin Dai; Mark Musen; Trish Whetzel
>Subject: Re: Help with BioPortal 2.0
>
>Thank you, Calixto. We'll be interested to find out the answer. It
>seems that we would be able  to help you much more if we were
>operating with one installation of Bioportal.
>
>By the way, one of the features that we plan to roll out in the near
>future, is the ability to restrict BioPortal display only to a certain
>set of ontologies (e.g., only CTSA ontologies, only OBO Foundry
>ontologies, etc.) So, you can send your users to this custiomized
>filtered display. Perhaps that would help streamline things on your
>end. And CTSA could benefit from linkages with other BioPortal
>ontologies, the OBR resource, etc. Just a thought...
>
>Natasha
>
>
>On Oct 20, 2008, at 5:48 PM, Calixto Melean wrote:
>
>> Natasha,
>>
>> Our ontologies will be made public in fact. OSU will stand up a CTSA
>> grid
>> leveraging NCI's caGrid/caCORE technologies. One of the requirements
>> is to
>> create an independent knowledge management system using the LexBIG
>> stack. I
>> would have to get back to you as to why this is the case, as opposed
>> to use
>> an existing terminology repository such as NCBO's. I don't currently
>> know
>> the answer to that question. I will ask.
>>
>> Thanks,
>>
>> Calixto
>>
>>
>> On 10/20/08 8:19 PM, "Natasha Noy" <noy at stanford.edu> wrote:
>>
>>> Calixto,
>>>
>>> I am wondering if it would be feasible for you to transform the
>>> ontologies to the BioPortal maintained at Stanford, since we also use
>>> the LexGrid backend. Or did you not want to make them public at this
>>> point?
>>>
>>> Natasha
>>>
>>>
>>> On Oct 20, 2008, at 4:49 PM, Calixto Melean wrote:
>>>
>>>> Natasha,
>>>>
>>>> The only reason why we are deploying BioPortal local is because we
>>>> have
>>>> manage our own LexGrid server which is loaded with ontologies and
>>>> terminologies used by knowledge engineers in our department
>>>> (Biomedical
>>>> informatics).
>>>>
>>>> Hope this answers your question.
>>>>
>>>> Thanks for your help,
>>>>
>>>> Calixto
>>>>
>>>>
>>>> On 10/20/08 3:25 PM, "Natasha Noy" <noy at stanford.edu> wrote:
>>>>
>>>>> Dear Calixto,
>>>>>
>>>>> Thank you very much for your interest in BioPortal and apologies
>>>>> for
>>>>> some snags in replying. I am glad to hear that you have found a
>>>>> workaround. Benjamin (copied on this message) will help you in
>>>>> identifying where exactly  the latest code is.
>>>>>
>>>>> That said, I was wondering about the trade-off of the decision in
>>>>> having your own copy of BioPortal versus using the BioPortal at
>>>>> NCBO.
>>>>> It might be easier for us to address support requests and the copy
>>>>> that we maintain. May I ask you what were your considerations in
>>>>> deciding to have your own copy? It would help us understand what
>>>>> requirements we are not addressing currently on the BIoPortal side.
>>>>>
>>>>> Thank you very much ,
>>>>>
>>>>> Natasha
>>>>>
>>>>>
>>>>> On Oct 20, 2008, at 6:49 AM, Calixto Melean wrote:
>>>>>
>>>>>> Dr. Noy,
>>>>>>
>>>>>> I posted our main issue to the tracker. Since it is kind of
>>>>>> obvious,
>>>>>> I was wondering if it is possible that I don't have the current
>>>>>> stable version of the code. We are getting the code from the SVN
>>>>>> repository as follows:
>>>>>>
>>>>>> svn checkout https://bmir-gforge.stanford.edu/svn/bioportalui
>>>>>>
>>>>>> There appear to be several distributions under the main folder
>>>>>> (1005, 1006, etc). We have faced the same problem with all of
>>>>>> them.
>>>>>> Perhaps the official working code is kept somewhere else? I'd
>>>>>> appreciate any info on this.
>>>>>>
>>>>>> This is the link to the issue.
>>>>>> https://bmir-
>gforge.stanford.edu/gf/project/bioportal_core/tracker/?action=
>>>>>> Tr
>>>>>> ackerItemEdit&tracker_item_id=777
>>>>>>
>>>>>> I've explained there what I think the problem is.
>>>>>>
>>>>>> Thanks very much,
>>>>>>
>>>>>> Calixto Meleana
>>>>>>
>>>>>>
>>>>>> On 10/19/08 9:28 PM, "Mark Musen" <musen at stanford.edu> wrote:
>>>>>>
>>>>>>> Hi Calixto,
>>>>>>>
>>>>>>> Dr. Natasha Noy (copied on this message) is the product manager
>>>>>>> for
>>>>>>> BioPortal and can help you with your questions.  Natasha can
>>>>>>> point
>>>>>>> you to appropriate members of the development team, if necessary.
>>>>>>>
>>>>>>> Thanks for your interest in our work.  I'd be grateful if you
>>>>>>> could
>>>>>>> let us know what your plans are for the BioPortal software.
>>>>>>>
>>>>>>> Regards,
>>>>>>>
>>>>>>> Mark Musen
>>>>>>>
>>>>>>>
>>>>>>> On Oct 15, 2008, at 12:31 PM, Calixto Melean wrote:
>>>>>>>
>>>>>>>> Mr. Musen,
>>>>>>>>
>>>>>>>> My name is Calixto Melean. I work for the biomedical informatics
>>>>>>>> department at OSU. We have deployed a local copy of the
>>>>>>>> BioPortal
>>>>>>>> 2.0 tool for research purposes and have run into a couple of
>>>>>>>> issues that we would like to ask about. We were wondering if you
>>>>>>>> could kindly provide a point of contact (technical) for us so
>>>>>>>> that
>>>>>>>> we can forward our question to the appropriate resource. The
>>>>>>>> Gforge site that hosts the project has a discussion area,
>>>>>>>> however,
>>>>>>>> it does not appear to be monitored. We have also tried
>>>>>>>> <support at bioontology.org
>>>>>>>>> several weeks ago and received no response.
>>>>>>>>
>>>>>>>> I would greatly appreciate your help with this matter.
>>>>>>>>
>>>>>>>> Thank you very much.
>>>>>>>>
>>>>>>>>
>>>>>>>> ------
>>>>>>>> Please note that my primary email address has changed to
>>>>>>>> calixto.melean at osumc.edu
>>>>>>>> .  Please update your contact information.
>>>>>>>> ------
>>>>>>>>
>>>>>>>> --
>>>>>>>> Calixto Melean
>>>>>>>>
>>>>>>>> Software Engineer
>>>>>>>> Software Research Institute
>>>>>>>> Department of Biomedical Informatics
>>>>>>>>
>>>>>>>> Ohio State University, Columbus, OH
>>>>>>>> Phone: (614) 293-9596
>>>>>>>>
>>>>>>>> <image.jpg>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> ------
>>>>>> Please note that my primary email address has changed to
>>>>>> calixto.melean at osumc.edu
>>>>>> .  Please update your contact information.
>>>>>> ------
>>>>>>
>>>>>> --
>>>>>> Calixto Melean
>>>>>>
>>>>>> Software Engineer
>>>>>> Software Research Institute
>>>>>> Department of Biomedical Informatics
>>>>>>
>>>>>> Ohio State University, Columbus, OH
>>>>>> Phone: (614) 293-9596
>>>>>>
>>>>>> <image.jpg>
>>>>>
>>>>
>>>> ------
>>>> Please note that my primary email address has changed to
>>>> calixto.melean at osumc.edu.  Please update your contact information.
>>>> ------
>>>>
>>>> --
>>>> Calixto Melean
>>>>
>>>> Software Engineer
>>>> Software Research Institute
>>>> Department of Biomedical Informatics
>>>>
>>>> Ohio State University, Columbus, OH
>>>> Phone: (614) 293-9596
>>>>
>>>>
>>>>
>>>>
>>>
>>
>> ------
>> Please note that my primary email address has changed to
>> calixto.melean at osumc.edu.  Please update your contact information.
>> ------
>>
>> --
>> Calixto Melean
>>
>> Software Engineer
>> Software Research Institute
>> Department of Biomedical Informatics
>>
>> Ohio State University, Columbus, OH
>> Phone: (614) 293-9596
>>
>>
>>
>>





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