pubmed.mineR (version 1.0.21)

pubtator3_function: function for text annotation using PubTator

Description

pubtator_function is used to extract specific information from an abstract like Gene, chemical, and diseases etc.

Usage

pubtator3_function(x)

Value

It returns a list object containing Gene, Chemical, Disease and PMID. The corresponding concept id numbers are joined by a '>' character. This is useful for further data mining

Arguments

x

numeric value PMID.

Author

S.Ramachandran, Jyoti Rani

Details

pubtator_function allow users to get information about 'Gene', 'Chemical' and 'Disease' for given PMID. It uses online tool PubTator on R plateform. It also removes redundancy from the output. It takes one PMID at once, for multiple PMIDs user can use lapply() function.

References

Wei, Chih-Hsuan, et al. "PubTator 3.0: an AI-powered literature resource for unlocking biomedical knowledge." Nucleic Acids Research (2024): gkae235.

Wei CH et. al., PubTator: a Web-based text mining tool for assisting Biocuration, Nucleic acids research, 2013, 41 (W1): W518-W522. doi: 10.1093/nar/gkt44

Wei CH et. al., Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts, Database (Oxford), bas041, 2012

Wei CH et. al., PubTator: A PubMed-like interactive curation system for document triage and literature curation, in Proceedings of BioCreative 2012 workshop, Washington DC, USA, 145-150, 2012

Examples

if (FALSE) test = pubtator3_function(17922911)
## here pubtator_function() will extract the information from this given pmid.