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[bioontology-support] NCBO Annotator Behavior Has Changed

Paul R Alexander palexander at
Wed Jul 10 16:56:03 PDT 2013


The last time we updated data in the Annotator was 2013-06-11, so it has been a while.

However, I'm showing a huge drop-off in the number of classes available in GAZ between versions 47282 and 50311 (518195 vs 40151), and in looking at the files we have for the ontology they are different. Version 50311 looks cut off, and I can see from the GAZ sourceforge repo that they haven't updated the file in 14 months, so there must be an error on our end. I've removed the broken versions, but unfortunately, there's no quick fix for re-populating the Annotator data with the good version. My apologies.

You can download the last good version we have here:


On Jul 10, 2013, at 4:25 PM, Patrice Seyed <apseyed at> wrote:

> Hi,
> Just wanted to re-ping, as we're accessing the service for data we're
> generating for a paper due this Friday. Thanks in advance.
> Patrice
> On Tue, Jul 9, 2013 at 3:23 PM, Zach Fry <frydawg524 at> wrote:
>> Hello,
>> I am in the middle of writing a paper using the BioPortal Annotator Service
>> for analysis, and am using the Gazetteer Ontology (Virtual ID 1397), and it
>> seems that over the last week while I was away on vacation, the behavior has
>> changed.
>> When I search for concepts with the Gazetteer Ontology selected, I get the
>> following message bar at the top of the BioPortal webpage (at the bottom of
>> the email). I also have noticed a significant decrease in the number of
>> returned concepts from before.
>> For example: A week ago, when I searched the GAZ ontology for "Crystal
>> Lake", there were 39 unique concepts that were returned, whereas now, only 1
>> concept is returned.
>> Is there anyway that I can have the old version of the ontology made
>> available for me, or I can access an old version of the tool so that I can
>> finish up the research I have been doing?
>> Thanks,
>> Zach Fry
>> Error Message I get:
>> The version of Gazetteer you were attempting to view ($Revision: 1.512 $)
>> has been archived and is no longer available for exploring. You have been
>> redirected to the most recent version ($Revision: 1.512 $).
> -- 
> Patrice Seyed
> DataONE Postdoctoral Fellow, University of New Mexico &
> Tetherless World Constellation, Rensselaer Polytechnic Institute
> Blog:
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> bioontology-support at

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