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[bioontology-support] Loading NIF1.0 in BioPortal

Trish Whetzel whetzel at
Mon Mar 23 22:12:09 PDT 2009

It appears that the previous issue with the Pathway ontology was not a
fluke. I did the update in the afternoon and the ontology was explorable,
however both on the Home page and the metadata page the status is now listed
as parsing. This was loaded as admin (as was the Pathway ontology) so it is
not the case that the ontology author has uploaded a new version. This
ontology is from a collaborator so it would be nice to resolve this problem
quickly (at least from my point of view). 










From: Nick Griffith [mailto:ngriff at] 
Sent: Monday, March 23, 2009 12:47 PM
To: Trish Whetzel
Cc: 'Natasha Noy'
Subject: Re: Loading NIF1.0 in BioPortal


i think the pathway thing was just a fluke.. editing shouldnt mess with
anything else.. if it happens again then we know its a bigger bug, but try
to edit the metadata for this guy to see if it happens again



On Mar 23, 2009, at 12:26 PM, Trish Whetzel wrote:

Hi Nick,


Not sure what is on your plate these days, can you give me an estimate of
when these updates can be made for the metadata for NIF? I have not tried to
update using the web form since last I did that for the Pathway ontology, it
became not 'explorable' afterwards.






From: Fahim Imam [mailto:smtifahim at] 
Sent: Friday, March 20, 2009 5:47 PM
To: Trish Whetzel
Subject: Re: Loading NIF1.0 in BioPortal


Hi Trish,
I can see that the updated version of NIFSTD has been loaded in BioPortal
yesterday. Thanks a lot for that. Here is the complete info for the
BioPortal's MetaData tab that needs to be updated as soon as possible.   

.    Ontology Name: NIFSTD
.    Ontology Id:1084
.    Format: OWL
.    Categories: Anatomy, Cell, Subcellular, Molecule, Function,
Dysfunction, Organism 
.    Contact Email: smtifahim at
.    Contact(s): Fahim Imam
.    Home Page:
.    Documentation Page: 
.    Publications Page:
.    Description: The NIFSTD ontology is composed of a collection of OWL
modules with separate modules covering major domains of neuroscience:
anatomy, cell, subcellular, molecule, organism, function and dysfunction.
Each of these modules can be imported separately.  The list of these OWL
modules with their URLs and other technical details about NIFSTD can be
found at
The current state and progress of NIFSTD ontology can be found in our
project wiki page

Please let me know if you have any concerns.

Best regards,

On Thu, Mar 19, 2009 at 6:42 PM, Fahim Imam <smtifahim at> wrote:

Hi Trish,
Yes, keep it as 1.0. Tomorrow, I'll send you the list of categories for
NIFSTD and the info for description field that you can add under the Meta
data tab. 


On Thu, Mar 19, 2009 at 3:58 PM, Trish Whetzel <whetzel at> wrote:

Sure, should the file still be listed as version 1.0? The categories can be
updated after re-loading.





Nick Griffith




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