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[bioontology-support] [SPAM:####] Re: [POSSIBLE VIRUS:###] Re: ADO (AlzheimerDisease Ontology) in BioPortal

Ashutosh Malhotra ashutosh.malhotra at scai.fraunhofer.de
Tue Jul 23 11:35:22 PDT 2013


Yes, Now everything looks fine!

Thanks a lot for your support!

Regards
Ashutosh

----- Original Message -----
From: "Ray Fergerson" <ray.fergerson at stanford.edu>
To: "Ashutosh Malhotra" <ashutosh.malhotra at scai.fraunhofer.de>
Cc: "Michaela Gündel" <michaela.guendel at scai-extern.fraunhofer.de>, support at bioontology.org
Sent: Tuesday, July 23, 2013 7:40:27 PM
Subject: RE: [bioontology-support] [POSSIBLE VIRUS:###] Re: ADO (Alzheimer	Disease Ontology) in BioPortal

It looks like this latest version is working correctly. I don't know why the 
zip file didn't work but at least it is going now.

Ray

-----Original Message-----
From: Ashutosh Malhotra [mailto:ashutosh.malhotra at scai.fraunhofer.de]
Sent: Tuesday, July 23, 2013 5:31 AM
To: Ray Fergerson
Cc: Michaela Gündel; support at bioontology.org
Subject: Re: [bioontology-support] [POSSIBLE VIRUS:###] Re: ADO (Alzheimer 
Disease Ontology) in BioPortal

Dear Ray Fergerson,
                    I am sorry but the ontology was not again parsed 
properly. Anyway, this time we have merged all files into one and this 
should most likely do the job.For your reference, please find a version 
attached..

Regards
Ashutosh

----- Original Message -----
From: "Ray Fergerson" <ray.fergerson at stanford.edu>
To: "Ashutosh Malhotra" <ashutosh.malhotra at scai.fraunhofer.de>
Cc: "Michaela Gündel" <michaela.guendel at scai-extern.fraunhofer.de>, 
support at bioontology.org
Sent: Monday, July 22, 2013 8:40:03 PM
Subject: RE: [bioontology-support] [POSSIBLE VIRUS:###] Re: ADO (AlzheimerDiseaseOntology) in BioPortal

Ashutosh,

It looks like it parsed. Is it correct?

Note that your zip has an extra level of directory (the files are not at the 
top). In spite of this though it may have worked

Ray

-----Original Message-----
From: bioontology-support-bounces at lists.stanford.edu
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of 
Ashutosh Malhotra
Sent: Monday, July 22, 2013 6:11 AM
To: Ray Fergerson
Cc: Michaela Gündel; support at bioontology.org
Subject: [bioontology-support] [POSSIBLE VIRUS:###] Re: ADO (Alzheimer 
Disease Ontology) in BioPortal


Dear Ray Fergerson,
                    As suggested by you we have followed the route two 
(including imports, in a zip) to remove parsing problem existing with our 
Alzheimer's disease ontology:
http://bioportal.bioontology.org/ontologies/3251

A new version have been submitted to Bioportal, also find it attached to the 
email in case you want to have a look.

Thanks for your suggestions! We hope that the existing issue will be 
resolved soon.

Regards
Ashutosh
----- Original Message -----
From: "Ray Fergerson" <ray.fergerson at stanford.edu>
To: "Michaela Gündel" <michaela.guendel at scai-extern.fraunhofer.de>,
support at bioontology.org
Cc: "Ashutosh Malhotra" <ashutosh.malhotra at scai.fraunhofer.de>
Sent: Friday, July 19, 2013 8:49:39 PM
Subject: RE: [bioontology-support] ADO (Alzheimer Disease Ontology) in 
BioPortal




Michaela,



We to resolve imports, both by following the URL and by loading from the 
local file. There are three imports in your ontology but none of them 
resolve to anything.



http://scai.fraunhofer.de/bridge_AO_BFO



http://scai.fraunhofer.de/bridge_AO_NDDUO



http://scai.fraunhofer.de/synonyms_autoAO



The easiest fix would be to make these URLs resolve.



An alternative is to submit the ontology, including imports, in a zip. To do 
this create a zip:



1) Name of zip is exactly the name of the main ontology file (foo.owl ->
foo.zip)

2) At the top level of the zip include both the main ontology and all
imports

3) Have no additional directories in the zip



Ray









From: bioontology-support-bounces at lists.stanford.edu
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of
Michaela Gündel
Sent: Friday, July 19, 2013 5:11 AM
To: support at bioontology.org
Cc: Ashutosh Malhotra
Subject: [bioontology-support] ADO (Alzheimer Disease Ontology) in BioPortal




Dear BioPortal team,

my colleague has submitted the following ontology:
http://bioportal.bioontology.org/ontologies/3251

The ontology contains owl:imports, which don't seem to be resolved in the
uploaded ontology version. So, my question is, does BioPortal resolve
owl:import statements, and what do we have to do to make it work? Otherwise
we might merge everything into one big file.

Would you please be so kind as to let us know?

Thank you very much!


Cheers
Michi

---
Michaela Gündel, MSc in Life Science Informatics Bonn-Aachen International
Center for Information Technology (B-IT) Fraunhofer Institute for Algorithms
and Scientific Computing (SCAI) Department of Bioinformatics Sankt Augustin,
Germany www.scai.fraunhofer.de

-- 

Ashutosh Malhotra

Fraunhofer Institute for Algorithms -
and Scientific Computing [SCAI]
Dept. of Bioinformatics
Schloss Birlinghoven
53754, Sankt Augustin, Germany
www.ashutoshmalhotra.com



-- 

Ashutosh Malhotra

Fraunhofer Institute for Algorithms -
and Scientific Computing [SCAI]
Dept. of Bioinformatics
Schloss Birlinghoven
53754, Sankt Augustin, Germany
www.ashutoshmalhotra.com



-- 

Ashutosh Malhotra 

Fraunhofer Institute for Algorithms - 
and Scientific Computing [SCAI] 
Dept. of Bioinformatics 
Schloss Birlinghoven 
53754, Sankt Augustin, Germany 
www.ashutoshmalhotra.com 





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