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[bioontology-support] NIF Ontology on bioportal has some weirdness

Tom Gillespie tom.h.gillespie at
Thu Oct 13 12:55:55 PDT 2016

Hi Vance,
    The version of nif in bioportal is extremely old and outdated. I'm
trying to get a 3.0 release of NIF out in time for SfN in mid-November. We
are in the process of transitioning our species/taxonomy portion to use
NCBI Taxonomy identifiers from the taxslim
<> provided by obo. You can see
development version of nifstd here: There
are a number of things in flux, and if you have a list of issues that you
are encountering please let me know so that I can fix them, or submit them
to the github bug tracker <>
for nifstd. Thanks!

On Thu, Oct 13, 2016 at 12:10 PM, Maryann Martone <maryann at>

> Hi Vance:
> Thanks for contacting us.  Indeed, it is a mess and we are looking into
> it.  It is an old version, but we always had trouble with the imports
> because of the way it was initially constructed.  Stand by.
> Maryann
> > On Oct 13, 2016, at 10:37 AM, Lemmon, Vance, Ph.D. <
> VLemmon at> wrote:
> >
> > lots of duplications, in fact at species levels there are sometimes 4 of
> one species
> >
> > we were trying to use it with the cedar annotation tool and it is kind
> of a mess
> >
> > <Screen Shot 2016-10-13 at 1.32.57 PM.png><Screen Shot 2016-10-13 at
> 1.34.34 PM.png>
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