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I'm using Carrot2-Workbench 3.16.3.0 for PubMed queries.

Mostly, I run into the "payload" and "api key" problem. I have a private PubMed key. But, neither the Workbench nor the online version allows me to enter it.

Is there any easy way to use it, or is it hard-coded in the source?

Zardaloop
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Uwe Baumert
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  • Carrot2 uses PubMed's [ESearch](https://dataguide.nlm.nih.gov/eutilities/utilities.html#esearch) utility -- would your private PubMed key be compatible with that API or it's for a different PubMed API? – Stanislaw Osinski May 28 '20 at 08:06
  • I've used my API key together with R packages that make use of PubMed's ESearch utilities. So, yes I suppose so. I generated it after logging into MyNCBI. – Uwe Baumert May 28 '20 at 17:27
  • The lack of the api_key parameter in ESearch API documentation confused me a bit, hence the question. I implemented the API support in the on-line demo (see the answer below). – Stanislaw Osinski May 29 '20 at 11:30

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Previous versions did not support PubMed API keys, the latest on-line version does, it's under the "options" button:

PubMed API key in Carrot2 search demo

Stanislaw Osinski
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  • Thank you very much. I appreciate your quick feedback very much and will give it a try. Do you intend to include this feature also in a future version of the carrot2-Workbench? – Uwe Baumert May 29 '20 at 11:36
  • In the upcoming 4.0.0 release, we'll be phasing out the desktop-based Workbench and replacing it with a browser-based counterpart, which you will be able to run locally or access on-line. The previous versions will remain available for download, but we most likely won't be adding new features to them. – Stanislaw Osinski May 30 '20 at 18:30
  • Thank you very much for clarification. The current online version has a limit of 350 for max results, that the desktop-based Workbench does not have. Will the upcoming 4.0.0 release also have a max result limit. I think, that with a personal API key this might be not necessary. – Uwe Baumert Jun 01 '20 at 11:27
  • What is the maximum number of results you're processing? – Stanislaw Osinski Jun 01 '20 at 12:07
  • The current project consists of up to ca. 650 references. – Uwe Baumert Jun 04 '20 at 08:13
  • I've just increased the PubMed limit in the on-line version to 1000 results. – Stanislaw Osinski Jun 09 '20 at 14:03
  • Thank you very much! I appreciate your work! Works perfectly. – Uwe Baumert Jun 11 '20 at 11:26