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[bioontology-support] [BioPortal] Feedback from Kyle Ellrott

Trish Whetzel whetzel at stanford.edu
Tue Jun 5 00:09:08 PDT 2012


Hi Kyle, 

There is not a recommended rate, other than no more than 40 calls from the same IP address. The response of the Annotator varies based on a few factors, the amount of text per web service call, the number of ontologies used for annotation, and whether the semantic expansion steps of expanding the annotations via the ontology is-a hierarchy and/or mappings are included. As more parameters are included or larger amounts of text is submitted the response time may decrease. 

We do have a virtual appliance available for BioPortal, the Annotator and Resource Index. More details (system requirements, ontology loading and annotator population workflow) is available at: http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance

Trish 


On Jun 4, 2012, at 11:16 PM, support at bioontology.org wrote:

> 
> Name: Kyle Ellrott
> 
> Email: kellrott at soe.ucsc.edu
> 
> Location: http://bioportal.bioontology.org/annotator
> 
> Comment:
> I'm curious about large scale Annotator runs. Is there a recommended limit for the rate at which I can submit Annotator jobs? Is is possible to run the Annotator tool locally, on our own research cluster, to apply large scale Annotations, without over taxing your systems?
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Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
http://www.bioontology.org

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