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pubmed.mineR (version 1.0.3.1)

Text mining of PubMed Abstracts

Description

Text mining of PubMed Abstracts (text and XML) from http://www.ncbi.nlm.nih.gov/pubmed.

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Version

Install

install.packages('pubmed.mineR')

Monthly Downloads

290

Version

1.0.3.1

License

GPL-3

Maintainer

S Ramachandran

Last Published

February 6th, 2015

Functions in pubmed.mineR (1.0.3.1)

HGNC-class

HGNC Class for package.
HGNC2UniprotID

R Data containing HGNC2UniprotID data mapping.
Yearwise-methods

Yearwise Year wise extraction of Abstracts
Find_conclusion

To find the conclusion from the abstract(s).
SentenceToken

To Tokenize the sentences
contextSearch

For Context Search
Genewise-methods

method to find the abstracts for the given gene.
cleanabs

To clean the result of searchabsL
wordsclusterview

To view the words in cluster
cluster_words

To Find the highest frequency of words within clusters
combineabs-methods

Abstracts Method to Combine Abstracts
subabs-methods

Getting subabstracts
searchabsT

To Search Abstracts
cos_sim_calc

To calculate the cosine similarity between terms.
removeabs-methods

removeabs To remove abstracts of a term from the data.
xmlgene_atomizations

Gene atomization of xml abstracts.
contextSearch-methods

Method for Context Search
common_words_new

R Data containing words which frequently in text
gene_atomization

To Extract Genes from the Abstracts
combineabs

To combine the abstracts
input_for_find_intro_conc_html

fetch the abstracts using E-utilities.
getabs

To get Abstracts for a given term.
cos_sim_calc_boot

Cosine Similarity Calculation by Boot Strapping
Yearwise

To Search abstracts Year wise
Abstracts-class

Class "Abstracts" Absract Class
tdm_for_lsa

create Term Document Matrix for lsa analysis
searchabsL-methods

Searching Abstracts
removeabs

To remove abstracts for the query term.
sendabs

To send abstracts
wordscluster

To cluster the words
getabsT

To get Abstracts for a given term.
getabsT-methods

To Get Abstracts
readabs

To read Abstracts
get_original_term

To get the original terms from the corpus.
word_atomizations

Atomization of words
cleanabs-methods

Methods for Function cleanabs
xmlreadabs

To read the abstracts from the PubMed saved in XML format.
find_intro_conc_html

To find the introduction and conclusion from the abstracts.
ready

To Initiate the Classes.
HGNCdata

R Data containing HGNC data.
uniprotfun

To get information about gene from the UniProt.
pubtator_function

function for text annotation uisng online PubTator
R2S4

S4 Converter
getabs-methods

getabs To Get abstracts for a term
printabs

To prind the total number of abstracts in an S4 object of class Abstracts , its start and end
GeneToEntrez

Data containing Entrez Ids
Genewise

To Search the number of abstracts for Genes
searchabsL

To Search the abstracts of term(s) in a combination mode.
searchabsT-methods

searchabsT Searching abstracts
whichcluster

To fetch the cluster for words
sendabs-methods

To send the Data into a File
subabs

To find sub-abstracts
xmlword_atomizations

Word atomizations of abstracts from xml format.