NCBI services transition to API keys

Geneious Prime and earlier versions of Geneious use the NCBI "E-Utilities API" to interface with NCBI Blast and search services.

On December 1st, 2018 NCBI implemented a new system for searching/Blasting that uses a personalised "API key". See the following NCBI announcement for more information.

Geneious R11.1 and Geneious Prime allow you to use your own NCBI API key. See the instructions below on how to obtain and use an API key.

Previously the frequency of requests made by Geneious to the NCBI E-Utilities API were monitored and limited based on IP address. 

Users with an API key will be monitored and limited based on their unique key and will be allowed up to 10 requests to NCBI per second.

NCBI still allows Geneious users without an API key to make up to 3 requests to NCBI per second.  Geneious and Geneious Prime will honour this limit with one exception. If you are searching NCBI then make sure you expand the NCBI search list and select and search individual databases only.  DO NOT select the top NCBI icon as Geneious will then search all 9 databases simultaneously, which will exceed the request limit and cause the search to fail.

Note that an API key may be required if you are on an institutional network shared with other Geneious users.  On an institutional network all Geneious user search requests will appear to come from the same IP address, so the 3 requests per second limit may be exceeded for NCBI searches and/or Blast searches, and all requests may be rejected by NCBI.

 

In Geneious R11.0.5 and earlier a "request limit" error will include: Search Failed message: Server returned HTTP response code: 429 for URL

 

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In Geneious R11.1.3 and later an "request limit" error will report a more informative message:

 

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For users of Geneious R7 and earlier

You should not see this error as NCBI services no longer work in Geneious R7 and earlier - see NCBI transition to HTTPS. You should purchase an upgrade to the latest version of Geneious Prime to access NCBI.

 

For users of Geneious R8.1.9 to R10.2.6

1. Ensure you search individual NCBI databases.

2. Use a VPN service so that your search requests do not come from your institutional IP address.

3. Perform your searches early or late when use of Geneious on your institutional network is not so high.

4. Use Geneious outside of your institutional network.

5. Purchase an upgrade to Geneious Prime 2019 or later and register for your own API key (see below).

 

Using an API key with Geneious R11 and Geneious Prime 2019

If you don't have one already, register for a MyNCBI account at https://www.ncbi.nlm.nih.gov/myncbi/ and login.

To create an API key, go to the “Settings” page of your NCBI account. (after signing in, click on your NCBI username in the upper right corner of any NCBI page.)

You’ll see a new “API Key Management” area. Click the “Create an API Key” button. 

 

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Copy your new 37 character API key, run Geneious R11.1 or Geneious Prime, go menu Tools -> Preferences -> NCBI tab and paste your API key into the field provided.

 

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