| pubtator_function {pubmed.mineR} | R Documentation |
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
pubtator_function(x)
Arguments
x |
numeric value PMID. |
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.
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
Author(s)
S.Ramachandran, Jyoti Rani
References
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
## Not run: test = pubtator_function(17922911)
## here pubtator_function() will extract the information from this given pmid.