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[bioontology-support] [bioontology-curator] Bioportal login issues

Ray Fergerson ray.fergerson at
Tue Mar 18 12:03:25 PDT 2014

Very strange. We don't require the acronyms for projects to be all upper
case. In any case, project creation now appears to work.




From: Samson Tu [mailto:swt at] 
Sent: Monday, March 17, 2014 10:58 PM
To: Ray Fergerson
Cc: Samson Tu; sridevi polavaram; BioPortal Curators;
bioontology-support at
Subject: Re: [bioontology-support] [bioontology-curator] Bioportal login




I had some email exchanges with Sridevi over the weekend. It appears to be
another example of acronyms having to be all-cap letters. He was able to
create his project after changing the acronym.


With best regards,


On Mar 17, 2014, at 3:51 PM, Ray Fergerson <ray.fergerson at>



We will check into the project creation problem but this should not
prevent you from uploading your ontology. Creating an ontology has nothing
to do with creating a project. Just go to the Browse page and hit the big
"create an ontology" button.




From: sridevi polavaram [ <mailto:spolavar at>
mailto:spolavar at] 
Sent: Saturday, March 15, 2014 3:11 AM
To: Ray Fergerson; BioPortal Curators;
<mailto:bioontology-support at>
bioontology-support at
Subject: Re: [bioontology-curator] Bioportal login issues


Hi Ray,

 Thanks for the response. I have switched to IE. But, i still see some
weird behavior for the requests i am making to the bioportal server.

I have created a new account by name  <>
NeuroMorpho.Org, it gave me error message saying that Bioportal has been
notified of it, but then, i did see in the dash board that my account has
been logged in anyways! This is just FYI, but right now my account seem to
be working fine. However, i cannot create a new project. I have tried to
enter the following information four times and it failed all the time. I
saw the same error message, but this time, it was true.

Name: Neuronal Morphologies and Metadata Classification System

Acronym: NMOSp

Institution: George Mason University

Contacts:  <mailto:spolavar at> spolavar at

Homepage:  <> NeuroMorpho.Org
Description: This is species taxonomy for the data curated in
<> NeuroMorpho.Org. The existing ontologies are
re-used as needed as the new metadata information for species and strains
is deposited in  <> NeuroMorpho.Org database. This
species hierarchy consists of 56% of NCBI taxonomy and 39% of Rat strain
ontology. The remaining 5% mostly consists of new concepts and few others
from NIFSTD and MESH.

Ontologies used: NCBITAXON, RS, NIFSTD, MESH

Can i please request you to upload this information and create a new
project form me. After my project is created, i want to upload my obo
ontology file (attached). Once you set this up, I would like to test the
new widget system asap.

FYI. I have many more ontologies that i want to upload subsequently, all
of them are related to  <> NeuroMorpho.Org.
Hopefully, i should be able to manage uploading and editing them by

Thank you,





On Thu, Mar 13, 2014 at 6:00 PM, Ray Fergerson <
<mailto:ray.fergerson at> ray.fergerson at> wrote:

I suggest clearing your cache and trying again. The registration page
should have an image of text for you to enter. I am also using Firefox and
it works for me. Perhaps this is removed because you are blocking images
(or ads?).


It sounds like you are still using the old system, which is about to be
shutdown. If by ontology id you mean something like "1234" then this is
the old system. The ids for ontologies on the new system are acronyms.
There are new widgets which work with the next system.




From: bioontology-curator [mailto:
<mailto:bioontology-curator-bounces at>
bioontology-curator-bounces at] On Behalf Of sridevi
Sent: Wednesday, March 12, 2014 12:42 PM
To: BioPortal Curators
Subject: [bioontology-curator] Bioportal login issues


Dear Curator,

 I had setup my account in Biportal and have been managing two resources
on it. Here are the acronyms that are listed in bioportal:

(a) NCBI_NMOsp_1_2_2

(b) H1_NMOABA_4_1

These two are currently setup as view to NCBI taxonomy and ABA ontologies.

Mainly, I have been using the auto completion web service using the
ontology IDs. But now, i am having a couple of issues with the system.

1. first of all i am not able to login with my existing user account, so i
tried to create a new login for which i get an error! (see attachment)

2. I don't see ontology IDs for these resources. Can i still be able to
use the auto completion widget?

Please let me know if you can resolve these issues as i am trying to
upload latest versions to the Bioportal.

Thank you,


Lab IT Supervisor/Neuroscience PhD candidate
Computational Neuroanatomy Group
Krasnow Institute for Advanced Study
George Mason University
 <mailto:spolavar at> spolavar at
Phone:  <tel:703-993-4376> 703-993-4376 (O)



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Samson Tu                                                     email:
swt at

Senior Research Scientist                               web:

Center for Biomedical Informatics Research    phone: 1-650-725-3391

Stanford University                                          fax:



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