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[bioontology-support] [BioPortal] Feedback from Chris

Ray Fergerson ray.fergerson at stanford.edu
Fri May 24 17:52:43 PDT 2013


Sorry for the long delay. This appears to be working now, but is slow.
This particular term has a property with hundreds of class values. Terms
like this result is unreliable performance in the current system,
particularly for UMLS ontologies. This is one of the problems that should
be fixed with our new backend. 

 

Ray

 

From: bioontology-support-bounces at lists.stanford.edu
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of chris
k
Sent: Thursday, April 25, 2013 8:41 AM
To: Trish Whetzel; support at bioontology.org
Subject: Re: [bioontology-support] [BioPortal] Feedback from Chris

 

Hello Trish,

Thank you for your reply. I understand that the speed of the response is
much slower with larger pagesize. 
For most cases, I get the expected response within a certain time period.
My problem is that in some cases there is no response at all, independent
of how long I wait.

Currently, I can give you some examples in which I get no response, for
meddra (1422):

Pagesize = 1, pagenum = 69255
Pagesize = 10, pagenum = 6924
Pagesize = 300, pagenum = 231
Pagesize = 1000, pagenum = 70

respectively using:

http://rest.bioontology.org/bioportal/virtual/ontology/1422/all?pagesize=1
<http://rest.bioontology.org/bioportal/virtual/ontology/1422/all?pagesize=
1&pagenum=69255&apikey=%3cYourAPIKey> &pagenum=69255&apikey=<YourAPIKey>
http://rest.bioontology.org/bioportal/virtual/ontology/1422/all?pagesize=1
0
<http://rest.bioontology.org/bioportal/virtual/ontology/1422/all?pagesize=
10&pagenum=6924&apikey=%3cYourAPIKey> &pagenum=6924&apikey=<YourAPIKey>
http://rest.bioontology.org/bioportal/virtual/ontology/1422/all?pagesize=3
00
<http://rest.bioontology.org/bioportal/virtual/ontology/1422/all?pagesize=
300&pagenum=231&apikey=%3cYourAPIKey> &pagenum=231&apikey=<YourAPIKey>
http://rest.bioontology.org/bioportal/virtual/ontology/1422/all?pagesize=1
000
<http://rest.bioontology.org/bioportal/virtual/ontology/1422/all?pagesize=
1000&pagenum=70&apikey=%3cYourAPIKey> &pagenum=70&apikey=<YourAPIKey>

Thanks,
Chris

  _____  

Subject: Re: [bioontology-support] [BioPortal] Feedback from Chris
From: whetzel at stanford.edu
Date: Thu, 25 Apr 2013 09:00:29 -0400
CC: krirage18 at hotmail.com
To: support at bioontology.org

Hi Chris, 

 

I have been able to get to the last page of the results of the "Get All
Terms" call for MedDRA. However, the speed of the response is determined
by how much data is returned, therefore with a larger pagesize of 1,000
the response is slower than with a pagesize of 10. What is the smallest
pagesize you've tried?

 

Trish 

 

 

On Apr 24, 2013, at 4:12 PM, support at bioontology.org wrote:

 


Name: Chris

Email: krirage18 at hotmail.com

Location: http://bioportal.bioontology.org/

Comment:
Hi,

I am trying to get all MedDra terms through REST services but I cannot
fetch the last page. I am using PAGESIZE=1000 and I am trying to get the
content of page 70/70 (which should contain 389 terms) but I get no
response. The previous 69 pages load successfully.

To replicate error (no response actually, there is no error message):
http://rest.bioontology.org/bioportal/virtual/ontology/1422/all?pagesize=1
000&pagenum=70&apikey=<YourAPIKey>

I use the ontocat application apikey. I have also tried with
smaller/larger PAGESIZE but I still cannot get all terms. Thank you in
advance for any help!

Regards,
Chris
_______________________________________________
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bioontology-support at lists.stanford.edu
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

 

Trish Whetzel, PhD

Outreach Coordinator

The National Center for Biomedical Ontology

Ph: 650-721-2378

http://www.bioontology.org

 

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