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[bioontology-support] Posting large amounts of text into Annotator

John Graybeal jgraybeal at stanford.edu
Fri Apr 3 13:06:09 PDT 2020


Vivian,

The Annotator API is what we mean when we say Annotator Web Service.

The HTTP 414 error is a function of HTTP limits on URL size enforced by various services. (See for example http://ncbo-support.2288202.n4.nabble.com/bioontology-support-JAVA-IOException-code-414-URL-too-long-with-get-call-td4652615.html.)

Try using a POST instead of a GET URI. (Reference this previous support message: http://ncbo-support.2288202.n4.nabble.com/bioontology-support-Annotating-large-texts-tp4652649p4652661.html). I'm sorry, I don't think we have explicit examples, but this is a common way of communicating over HTTP, so lots of web documentation.

You reach a practical limit of 60 seconds before a timeout occurs on your request, so especially during busy times you will haeve to keep your request sizes lower. (Limiting the number of ontologies that you request annotation against is another way to minimize the computation time.)

If you have a lot of large pieces of text, you will need to install the virtual appliance (free), or ask us to set up a dedicated server (contact us).

John




On Apr 3, 2020, at 12:05 PM, Vivian Zhu <vivianzhu88 at gmail.com<mailto:vivianzhu88 at gmail.com>> wrote:

Dear Mr. Graybeal,

I was wondering how I could annotate large amounts of text (500 words or more) with the Annotator.

The Annotator website tells me that I can use the Annotator Web Service to annotate large pieces of text. However, when I click the link to the web service, I am redirected to the Annotator API.

The API says that I can post text using "/annotator?text={input text}", but this only works if I input small pieces of text. When I input large pieces of text, I get an HTTP 414 error saying that my URI request is too large. How can I solve this issue?

Thank you!
Vivian

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360



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