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[bioontology-support] The Neli vocab...

Trish Whetzel whetzel at stanford.edu
Wed Feb 18 23:09:36 PST 2009


Ok, I was not aware of that plugin for Protégé 4.0. Let me know if there are
any problems with your username, I believe that we can easily find that
information in the database and send to you.

Trish


>-----Original Message-----
>From: Oliver, Helen [mailto:Helen.Oliver.1 at city.ac.uk]
>Sent: Tuesday, February 17, 2009 9:14 AM
>To: Trish Whetzel
>Subject: RE: The Neli vocab...
>
>Trish,
>
>You may need the Protégé SKOS plugin, as the vocabulary is written in
>SKOS. The plugin is for use with Protégé 4, not 3:
>
>http://code.google.com/p/skoseditor/
>
>I will try to edit the categories, but I can't remember my user name so
>I can only hope that the admins will email me a reminder.
>
>Thanks & regards,
>
>Helen
>
>
>
>-----Original Message-----
>From: Trish Whetzel [mailto:whetzel at stanford.edu]
>Sent: 17 February 2009 00:23
>To: Oliver, Helen
>Cc: support at bioontology.org
>Subject: RE: The Neli vocab...
>
>Hi Helen,
>
>The ontology name has been changed and we have fixed a bug with the
>'Edit
>Ontology information' button so categories you add should be displayed
>on
>the Home page. However, there is a time delay in refreshing the Home
>page so
>it may ~3 hours before that change is visible on the Home page.
>
>As for displaying the ontology contents in BioPortal, I have not been
>able
>to open the ontology in Protégé, which is used in the backend of
>BioPortal.
>Can you provide some direction on how to open the ontology in Protégé?
>
>Thanks,
>Trish
>
>
>>-----Original Message-----
>>From: Oliver, Helen [mailto:Helen.Oliver.1 at city.ac.uk]
>>Sent: Friday, January 30, 2009 2:25 AM
>>To: Trish Whetzel
>>Subject: RE: The Neli vocab...
>>
>>Hi Trish,
>>
>>It was developed in Protégé, the language was SKOS.
>>
>>I did select the categories and then they didn't appear.
>>
>>Thanks,
>>
>>Helen
>>
>>-----Original Message-----
>>From: Trish Whetzel [mailto:whetzel at stanford.edu]
>>Sent: 29 January 2009 19:54
>>To: Oliver, Helen
>>Cc: bioontology-support at lists.stanford.edu
>>Subject: RE: The Neli vocab...
>>
>>Hi Helen,
>>
>>What tool was used to develop the NeLI vocabulary? Regarding the change
>>of
>>the name, I have reported that as a bug with the "Edit Ontology
>>Information"
>>button and for the interim have requested that the name be changed in
>>the
>>database here by the developers.
>>
>>Was the problem with the categories also related to the Edit ontology
>>button, ie did you make selections for category and then they did not
>>appear
>>or were the appropriate category selections not present in the list?
>>
>>Trish
>>
>>
>>>-----Original Message-----
>>>From: Oliver, Helen [mailto:Helen.Oliver.1 at city.ac.uk]
>>>Sent: Wednesday, January 28, 2009 5:51 AM
>>>To: Trish Whetzel
>>>Subject: FW: The Neli vocab...
>>>
>>>
>>>Dear Trish,
>>>
>>>I just uploaded the NeLI vocabulary, but I notice that there's no list
>>>item for SKOS in the list of formats.
>>>
>>>Also, I tried to amend the name from "National electronic Library for
>>>Infection Vocabulary" to "NeLI Vocabulary", but the change is not
>>>showing.
>>>
>>>I wasn't able to assign categories, either?
>>>
>>>Thanks in advance,
>>>
>>>Helen Oliver
>>>
>>>-----Original Message-----
>>>From: Jonquet, Clement Marie [mailto:jonquet at stanford.edu]
>>>Sent: 28 January 2009 13:15
>>>To: Patty Kostkova; Khaled Khelif; Oliver, Helen
>>>Cc: musen at stanford.edu; Trish Whetzel; Olivier.Corby at sophia.inria.fr
>>>Subject: RE: The Neli vocab...
>>>
>>>Dear Neli, Oliver and Khaled,
>>>
>>>CCs are Pr. Mark Musen, PI of the NCBO project at Stanford and Dr.
>>Trish
>>>Whetzel, outreach coordinator.
>>>And Dr. Olivier Corby from INRIA (SeaLife).
>>>
>>>NCBO will be pleased to host the NELI vocabulary in the BioPortal
>>>(http://bioportal.bioontology.org/) if possible.
>>>BioPortal aims to gather biomedical ontologies in one place and
>propose
>>>services for the community (mappings, annotations, forums &
>>discussion).
>>>
>>>When the vocabulary will be on the portal, it should not take that
>long
>>>for me to process it and include it in our ontology-based services
>>>(hierarchy services, mapping services, path services, annotation
>>>services, etc.)
>>>
>>>The portal is developed in order to enable ontology developers to
>>submit
>>>their ontologies themselves (and update them etc.). Therefore, I
>invite
>>>you Patty and Oliver to do it via the portal URL.
>>>Trish might help you in the process if any difficulties show up...
>that
>>>might append ;)
>>>
>>>Best regards all
>>>Clement Jonquet
>>>
>>>> -----Original Message-----
>>>> From: Patty Kostkova [mailto:patty at soi.city.ac.uk]
>>>> Sent: Tuesday, January 27, 2009 10:34 AM
>>>> To: 'Khaled Khelif'
>>>> Cc: Jonquet, Clement Marie; 'Oliver, Helen'
>>>> Subject: RE: The Neli vocab...
>>>>
>>>> Dear Khaled and Clement,
>>>>
>>>> Many thanks for your interest in the NeLI vocabulary. We are very
>>>> interested
>>>> in sharing this with you to test your semantic annotation engine.
>>>>
>>>> Could you let us know more about the evaluation you would like to
>run
>>>-
>>>> we
>>>> might be in a potion to assist you. If the results are positive
>(like
>>>> they
>>>> were evaluating Meat-annot with INRIA) there might be a potential
>for
>>>a
>>>> shared paper if you're interested.
>>>>
>>>> My colleague Helen Oliver will email you the latest version.
>However,
>>>> please
>>>> treat this strongly as a beta-version as we are still finishing some
>>>of
>>>> the
>>>> semantic relationships (in particular, is causing (symptom,
>>>diseases)).
>>>> Should you require the list of keywords and their definitions in the
>>>> vocabulary, this is more or less finalized for the 1st version 1. In
>>>> the
>>>> future, we will extend the coverage with more public health and
>>>> outbreak
>>>> related concepts.
>>>>
>>>> With best wishes,
>>>> Patty
>>>>
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: Khaled Khelif [mailto:khaled.khelif at sophia.inria.fr]
>>>> Sent: Tuesday, January 27, 2009 3:05 PM
>>>> To: Patty Kostkova
>>>> Cc: Clement JONQUET
>>>> Subject: The Neli vocab...
>>>>
>>>> Hi Patty,
>>>>
>>>> A colleague at Stanford University, Clément Jonquet, working on the
>>>> NCBO
>>>> project*, asked me if he can integrate the Neli Vocabulary in their
>>>> portal, in order to test their workflow (semantic annotations) on
>the
>>>> Neli website.
>>>> Can I give him the version I have? I think that we can compare our
>>>> annotations and imagine some improvments. What do you think?
>>>>
>>>> * "The goal of the NCBO is to aid biomedical researchers in their
>>>> knowledge-intensive work, by providing online tools and Web-based
>>>> resources (such as BioPortal) that enable investigators to access,
>>>> review, and integrate disparate ontologies in all aspects of
>>>biomedical
>>>> investigation and clinical practice. The Center's mission is to
>>create
>>>> software and support services for the application of principled
>>>> ontologies in biomedical science and clinical care, ranging from
>>tools
>>>> for application developers to software for end-users."
>>>> http://bioportal.bioontology.org/
>>>>
>>>>
>>>> Khaled
>>>> -
>>>>
>>
>





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