pubtator_function: function for text annotation using PubTator
In pubmed.mineR: Text Mining of PubMed Abstracts
Description
Usage
Arguments
Details
Value
Author(s)
References
Examples
Description
pubtator_function is used to extract specific information from an abstract like Gene, chemical, and diseases etc.
Usage
1
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
1
2
## Not run: test = pubtator_function(17922911)
## here pubtator_function() will extract the information from this given pmid.
Example output
pubmed.mineR documentation built on Nov. 26, 2021, 5:11 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Details Value Author(s) References Examples
Description
pubtator_function is used to extract specific information from an abstract like Gene, chemical, and diseases etc.
Usage
1 |
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
1 2 | ## Not run: test = pubtator_function(17922911)
## here pubtator_function() will extract the information from this given pmid.
|
Example output
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.