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[bioontology-support] The Neli vocab...

Trish Whetzel whetzel at
Mon Feb 16 16:23:02 PST 2009

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?


>-----Original Message-----
>From: Oliver, Helen [mailto:Helen.Oliver.1 at]
>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.
>-----Original Message-----
>From: Trish Whetzel [mailto:whetzel at]
>Sent: 29 January 2009 19:54
>To: Oliver, Helen
>Cc: bioontology-support at
>Subject: RE: The Neli vocab...
>Hi Helen,
>What tool was used to develop the NeLI vocabulary? Regarding the change
>the name, I have reported that as a bug with the "Edit Ontology
>button and for the interim have requested that the name be changed in
>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
>or were the appropriate category selections not present in the list?
>>-----Original Message-----
>>From: Oliver, Helen [mailto:Helen.Oliver.1 at]
>>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
>>I wasn't able to assign categories, either?
>>Thanks in advance,
>>Helen Oliver
>>-----Original Message-----
>>From: Jonquet, Clement Marie [mailto:jonquet at]
>>Sent: 28 January 2009 13:15
>>To: Patty Kostkova; Khaled Khelif; Oliver, Helen
>>Cc: musen at; Trish Whetzel; Olivier.Corby at
>>Subject: RE: The Neli vocab...
>>Dear Neli, Oliver and Khaled,
>>CCs are Pr. Mark Musen, PI of the NCBO project at Stanford and Dr.
>>Whetzel, outreach coordinator.
>>And Dr. Olivier Corby from INRIA (SeaLife).
>>NCBO will be pleased to host the NELI vocabulary in the BioPortal
>>( if possible.
>>BioPortal aims to gather biomedical ontologies in one place and propose
>>services for the community (mappings, annotations, forums &
>>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
>>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]
>>> 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
>>> 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
>>> the
>>> semantic relationships (in particular, is causing (symptom,
>>> 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]
>>> 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
>>> investigation and clinical practice. The Center's mission is to
>>> software and support services for the application of principled
>>> ontologies in biomedical science and clinical care, ranging from
>>> for application developers to software for end-users."
>>> Khaled
>>> -

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