European PubMed Central Advanced Search

This node re-creates the advanced query interface of European-PubMed Central. The options shown in the query dialog replicate those found on that page. For detailed help see the advanced query page and also the help page

The node uses the RESTful query webservice, documented at http://europepmc.org/RestfulWebService#search . In addition to the query options, a 'Test' button is provided which shows the number of hits and the query as interpreted by the webservice.

The node returns a single column of query results as XML cells - one row per result. The result fields can be accessed using the KNIME XML XPath node. A full list of fields is provided in the SOAP webservices guide

The Flow Variable port gives the query type (idlist, lite, core), hit count, page count, query string, query as parsed by European PubMed Central, and the URL of the first query page. At present, the flow variable output is not available if the node is run in streaming mode.

This node was developed by Vernalis , who have no connection with European PubMed. Problems with the data should be reported directly to European PubMed Central. Vernalis accepts no responsibility for third party data. For further help with the node, contact knime@vernalis.com

Options

ePub Med Central Advanced Query: Query form mirroring that at the Advanced Query form at the European PubMed Central (see above)
General query: Any of the query tags from the European PubMed Central help page can be added here. Also, the query string flow variable output by the node will reproduce the query if used to set this parameter. (Which can then be combined with other query options in the remainder of the form)
Select the query type: idlist (a list of hit IDs), lite (main publication details) or core (extensive details) - see European PubMed Central website for details
Select the sort order: Sort by date or by relevance
Page size: This is the number of hits that will be return by each webservice call. Larger values will require fewer calls, but are more likely to fail (at which point the node will retry at increasing intervals)
Optional email address for EBI Webservices mailing list: If you supply an email address here, it will be added to the EBI ePMC webservices mailing list (see the webstie for details). If you do not wish to be added, leave this field blank. NB Vernalis will NOT see your email address, it will simply be went to the EBI service call. Vernalis will not email you about updates to the node. If you wish to contact Vernalis about the node, please use the contact details below
Test Query: Test the query. The number of hits will be shorn adjacent to the button, and the query as parsed by European PubMed Central will show in the box below
Clear: Clear the Test query boxes. NB Does not clear the query fields!

Input Ports

This node has no input ports

Output Ports

: Single XML column of query results
: Flow variable port has a number of parameters relating to the query added

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Installation

To use this node in KNIME, install the extension Vernalis KNIME Nodes from the below update site following our NodePit Product and Node Installation Guide:

v5.3

A zipped version of the software site can be downloaded here.

Plugin provider: Vernalis Research, UK

Plugin version: 1.36.7.v202405281205

On NodePit since: 2024-07-11

Last update: 2024-11-15

Tags: Streamable

KNIME versions: v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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