Tools to text mine PubMed


The major goal of bioinformatics is to assist biologists in their basic tasks. One of the redundant and laborious task is to perform literature review of any problem. Usually, this is performed by searching each key term in pubmed and some times these key terms can be hundreds. Secondly, this approach has many limitations because of the server load and interface. My biologists friends frequently request me to text mine the pubmed for there key terms and give them the data in excel sheet. This will help them in having a birds eye view of the literature about their hypothesis and gene of interests. There are many different tools provided by NCBI to text mine pubmed and the best thing about that is they already have the analyzed data present which can be downloaded easily from relevant website. One just have to parse the data from these files. The complete list of tools and software available for this purpose are provided on the following link. The major tools include:

This tool contains all genes and relevant information. If you click on any gene name you will get a list of all genes in which this gene is reported with all the PubMed article till the database was updated (It was early 2018, I have plan to update this database soon). 


Other than these 2 major tools a large list of tools is available at following link to perform personalized tasks but I believe these 2 tools offers all the basic functionality to perform literature review about any gene, disease, drug or variant which is asked very frequently.