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07_​Pubmed_​Author_​Network_​Analysis

PubMed Network Analysis

Prerequisites to run the workflow with other data than in the example:
1. Generate a suitable query on PubMed webpage (http://www.ncbi.nlm.nih.gov/pubmed) , e.g.
(("nonalcoholic"[all fields] OR "non-alcoholic"[all fields] OR "non alcoholic"[all fields]) AND "steatohepatitis"[all fields]) OR (("fat"[all fields] OR "liver"[all fields] OR "hepatic"[all fields]) AND NASH[Title/Abstract])
2. Download hits from PubMed webpage ("Sent to" > "File" > "Format CSV") as CSV file
3. The downloaded CSV file is input for the FileReader node (delimiter = ","; "allow short line"; "read column header") in this workflow.

This workflow finds the most important authors for a new drug indication via network mining approaches and based on a set of PubMed articles that includes relevant terms ofthis new indication. A network with authors as nodes and publications as edges is generated. The number of common publications is used as an edge weight. Authors are connectedwith their documents.Specify the maximumnumber of authors perdocument to consider.- split columns - author namesto upper case- build author setminimum 2(connected with at least 2authors)Read CSVdownloaded from PubMedusing the KNIMEnetwork viewer Create Network Prepare PubMed File Node Degree Filter File Reader InteractiveTable (local) Visualize NetworkComponents This workflow finds the most important authors for a new drug indication via network mining approaches and based on a set of PubMed articles that includes relevant terms ofthis new indication. A network with authors as nodes and publications as edges is generated. The number of common publications is used as an edge weight. Authors are connectedwith their documents.Specify the maximumnumber of authors perdocument to consider.- split columns - author namesto upper case- build author setminimum 2(connected with at least 2authors)Read CSVdownloaded from PubMedusing the KNIMEnetwork viewerCreate Network Prepare PubMed File Node Degree Filter File Reader InteractiveTable (local) Visualize NetworkComponents

Nodes

Extensions

Links

Download

To use this workflow in KNIME, download it from the below URL and open it in KNIME:

Download Workflow
On NodePit since: 2020-12-23
Last update: 2024-04-17
Created with KNIME version: v4.1.0
Tags: PubMedNetwork Mining

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