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[bioontology-support] [bioportal-announce] BioPortal 3.9 Released

linforest linforest at 163.com
Fri Jun 22 06:00:42 PDT 2012


Trish,

That's alright. Instead, it is me (and maybe other Chinese users) who should thank you and your colleagues for the BioPortal and related technologies.
Have a nice day!

Regards,
..Lin



At 2012-06-22 20:14:45,"Trish Whetzel" <whetzel at stanford.edu> wrote:

I've submitted a request to enable the FlexViz visualization in cases such as this where BioMixer is blocked. Sorry about the trouble, I was not aware of this situation prior to the release.


Trish 




On Jun 22, 2012, at 2:55 AM, linforest wrote:


Trish,

FlexViz was okay for me in the past, and it also worked for Chinese Characters in the property values (i.e., Chinese synonyms for the preferred names of the concepts in the BioPortal ontologies).
Certainly, it would be great if FlexViz could be triggered as an alternative.

Thank you so much!

Regards,
..Lin

At 2012-06-22 00:27:18,"Trish Whetzel" <whetzel at stanford.edu> wrote:

Hi Lin, 


Thanks for the screenshot. Were you able to use the visualization in the past with FlexViz? If yes, this visualization is still used in the system and perhaps could be triggered if there is an issue with accessing BioMixer as in this case. 


Trish 




On Jun 20, 2012, at 8:50 PM, linforest wrote:


Ray and Trish,

Many thanks for your timely responses.
I understood the cuurent situation.
The attached is the Snapshot.

Regards,
..Lin



At 2012-06-21 02:28:04,"Ray Fergerson" <ray.fergerson at stanford.edu> wrote:


Unfortunately this is currently a generic problem in China. The Google app engine site used by visualization software is blocked by the “Great Firewall of China”.

 

http://www.greatfirewallofchina.org/index.php?siteurl=http%3A%2F%2Fbioportal-integration.bio-mixer.appspot.com

 

It isn’t clear to my why the Google app engine site is blocked but it is.

 

We will eventually move the visualization software to run on the Stanford servers and this should fix this problem. Until then though there is little that you can do (other than petitioning your government!). Sorry.

 

Ray

 

From:bioontology-support-bounces at lists.stanford.edu [mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of Trish Whetzel
Sent: Wednesday, June 20, 2012 7:40 AM
To: linforest
Cc:support at bioontology.org
Subject: Re: [bioontology-support] [bioportal-announce] BioPortal 3.9 Released

 

Hi Lin, 

 

Can you send a screenshot of the page?

 

Thanks,

Trish 

 

 

On Jun 20, 2012, at 6:17 AM, linforest wrote:





Dear BioPortal support,

The Visualization of ontologies is not available due to time-out of the URL bioportal-integration.bio-mixer.appspot.com.
I'm a user from China.

 

Best Regards,
Sincerely,
Lin Zhang

 


At 2012-06-20 08:43:16,"Trish Whetzel" <whetzel at stanford.edu> wrote:



We are pleased to announce the release of BioPortal 3.9. The major new features in this release are:

 

·         We have revised the search interface, both for specifying a search and in the format of the returned results. The new “advanced search” capability allows users to specify more clearly exactly what terms they would like to find. This capability also allows us to choose better (more commonly desired) defaults for the “basic search”. The returned search results are now grouped by ontology and the results are ranked so that terms from “better”  ontologies are returned first. We also show definitions for terms that have them. In general this response format was inspired by the Google search response interface so we hope that it looks familiar. We are specifically soliciting feedback from users on this revision. Please send any comments to support at bioontology.org.  *

 

·         We include the first version of the BioMixer visualization software (available through the “Visualize” links). This software replaces the older FlexViz system. There are a number of technology improvements (i.e. the removal of Flash technology) over the older system and the newer system is more powerful as well (i.e. you can now navigate mappings from the basic interface). More complete versions of BioMixer will be introduced in subsequent releases. Please provide any feedback you can on this new system. *

 

·         We have regenerated all automatically generated mappings in the system. These include lexical mappings, UMLS CUI mappings, identical identifier mappings, and OBO-xref mappings. We have also loaded mappings between selected UMLS ontologies as specified in the UMLS database (MRMAP).

 

*  This item was requested via the User Support mailing list. Thank you for your comments and suggestions!

 

 

Trish Whetzel, PhD

Outreach Coordinator

The National Center for Biomedical Ontology

Ph: 650-721-2378

http://www.bioontology.org

 

"Like" NCBO on Facebook: http://on.fb.me/bioontology

 

Follow NCBO on Twitter: http://twitter.com/#!/bioontology

 

Join in Discussions on LinkedIn: http://linkd.in/ncbo-group

 






 

Trish Whetzel, PhD

Outreach Coordinator

The National Center for Biomedical Ontology

Ph: 650-721-2378

http://www.bioontology.org

 

"Like" NCBO on Facebook: http://on.fb.me/bioontology

 

Follow NCBO on Twitter: http://twitter.com/#!/bioontology

 

Join in Discussions on LinkedIn: http://linkd.in/ncbo-group

 



<Amino Acid - AliphaticAminoAcid - Terms - NCBO BioPortal 2012-06-20 21-11-53.png>







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