pubmed.mineR: Text Mining of PubMed Abstracts

Text mining of PubMed Abstracts (text and XML) from <>.

Install the latest version of this package by entering the following in R:
AuthorJyoti Rani, S.Ramachandran, Ab Rauf Shah
Date of publication2017-04-25 05:45:52 UTC
MaintainerS. Ramachandran <>

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Man pages

Abstracts-class: Class '"Abstracts"' Absract Class

alias_fn: To Find Alias of the Genes.

altnamesfun: To Get Alternative names of Genes

BWI: To Get the Buzz Word Index of terms form the Abstracts.

cleanabs: To clean the result of searchabsL

cleanabs-methods: Methods for Function 'cleanabs'

cluster_words: To Find the highest frequency of words within clusters

combineabs: To combine the abstracts

combineabs-methods: 'Abstracts' Method to Combine Abstracts

common_words_new: R Data containing words which frequently in text

contextSearch: For Context Search

contextSearch-methods: Method for Context Search

cos_sim_calc: To calculate the cosine similarity between terms.

cos_sim_calc_boot: Cosine Similarity Calculation by Boot Strapping

currentabs_fn: To Retrive the Abstracts for year.

Find_conclusion: To find the conclusion from the abstract(s).

find_intro_conc_html: To find the introduction and conclusion from the abstracts.

gene_atomization: To Extract Genes from the Abstracts

genes_BWI: Function to get the Buzz Word Index of Genes from the...

GeneToEntrez: Data containing Entrez Ids

Genewise: To Search the number of abstracts for Genes

Genewise-methods: method to find the abstracts for the given gene.

getabs: To get Abstracts for a given term.

getabs-methods: 'getabs' To Get abstracts for a term

getabsT: To get Abstracts for a given term.

getabsT-methods: To Get Abstracts

get_gene_sentences: To extract the sentences for genes from the corpus.

get_MedlinePlus: To Get MedLinePlus Summary

get_NMids: To extract NM ids from NCBI.

get_original_term: To get the original terms from the corpus.

get_original_term2: To get the original terms from the corpus.

get_PMCIDS: To extract the PMC Ids of the abstracts.

get_PMCtable: To fetch the given PMC article.

get_Sequences: To extract the Gene sequence from the NCBI.

Give_Sentences: To extract sentences from the Abstracts

Give_Sentences_PMC: To fetch the sentence from the PMC full text article

head_abbrev: To extract the abbreviated term.

HGNC2UniprotID: R Data containing HGNC2UniprotID data mapping.

HGNC-class: HGNC Class for package.

HGNCdata: R Data containing HGNC data.

input_for_find_intro_conc_html: fetch the abstracts using E-utilities.

local_uniprotfun: To Get Information from Uniprot.

names_fn: To extract the gene names from HGNC.

official_fn: To extract the official gene symbol.

pmids_to_abstracts: To Find and match the PMIDs to the abstracts.

previousabs_fn: To Retrive the Abstracts from the large corpus for given...

prevsymbol_fn: To Find Previous symbols of genes.

printabs: To prind the total number of abstracts in an S4 object of...

pubtator_function: function for text annotation uisng online PubTator

pubtator_result_list_to_table: Function to Convert Pubtator result from list into Table

readabs: To read Abstracts

ready: To Initiate the Classes.

removeabs: To remove abstracts for the query term.

removeabs-methods: 'removeabs' To remove abstracts of a term from the data.

searchabsL: To Search the abstracts of term(s) in a combination mode.

searchabsL-methods: Searching Abstracts

searchabsT: To Search Abstracts

searchabsT-methods: 'searchabsT' Searching abstracts

sendabs: To send abstracts

sendabs-methods: To send the Data into a File

SentenceToken: To Tokenize the sentences

subabs: To find sub-abstracts

subabs-methods: Getting subabstracts

subsetabs: To make subsets of large corpus.

subsetabs-methods: To make subset of Abstracts.

tdm_for_lsa: create Term Document Matrix for lsa analysis

uniprotfun: To get information about gene from the UniProt.

whichcluster: To fetch the cluster for words

word_atomizations: Atomization of words

wordscluster: To cluster the words

wordsclusterview: To view the words in cluster

xmlgene_atomizations: Gene atomization of xml abstracts.

xmlreadabs: To read the abstracts from the PubMed saved in XML format.

xmlword_atomizations: Word atomizations of abstracts from xml format.

Yearwise: To Search abstracts Year wise

Yearwise-methods: 'Yearwise' Year wise extraction of Abstracts


Abstracts-class Man page
alias_fn Man page
altnamesfun Man page
BWI Man page
cleanabs Man page
cleanabs,Abstracts-method Man page
cleanabs-methods Man page
cluster_words Man page
combineabs Man page
combineabs,Abstracts-method Man page
combineabs-methods Man page
common_words_new Man page
contextSearch Man page
contextSearch,Abstracts-method Man page
contextSearch-methods Man page
cos_sim_calc Man page
cos_sim_calc_boot Man page
currentabs_fn Man page
Find_conclusion Man page
find_intro_conc_html Man page
gene_atomization Man page
genes_BWI Man page
GeneToEntrez Man page
Genewise Man page
Genewise,Abstracts-method Man page
Genewise-methods Man page
getabs Man page
getabs,Abstracts-method Man page
getabs-methods Man page
getabsT Man page
getabsT,Abstracts-method Man page
getabsT-methods Man page
get_gene_sentences Man page
get_MedlinePlus Man page
get_NMids Man page
get_original_term Man page
get_original_term2 Man page
get_PMCIDS Man page
get_PMCtable Man page
get_Sequences Man page
Give_Sentences Man page
Give_Sentences_PMC Man page
head_abbrev Man page
HGNC2UniprotID Man page
HGNC-class Man page
HGNCdata Man page
input_for_find_intro_conc_html Man page
local_uniprotfun Man page
names_fn Man page
official_fn Man page
pmids_to_abstracts Man page
previousabs_fn Man page
prevsymbol_fn Man page
printabs Man page
pubtator_function Man page
pubtator_result_list_to_table Man page
readabs Man page
ready Man page
removeabs Man page
removeabs,Abstracts-method Man page
removeabs-methods Man page
searchabsL Man page
searchabsL,Abstracts-method Man page
searchabsL-methods Man page
searchabsT Man page
searchabsT,Abstracts-method Man page
searchabsT-methods Man page
sendabs Man page
sendabs,Abstracts-method Man page
sendabs-methods Man page
SentenceToken Man page
subabs Man page
subabs,Abstracts-method Man page
subabs-methods Man page
subsetabs Man page
subsetabs,Abstracts-method Man page
subsetabs-methods Man page
tdm_for_lsa Man page
uniprotfun Man page
whichcluster Man page
word_atomizations Man page
wordscluster Man page
wordsclusterview Man page
xmlgene_atomizations Man page
xmlreadabs Man page
xmlword_atomizations Man page
Yearwise Man page
Yearwise,Abstracts-method Man page
Yearwise-methods Man page


R/whichcluster.R R/get_original_term.R R/uniprotfun.R R/gethgnc.R R/Genewise.R R/get_PMCtable.R R/Abstracts-class.R R/wordscluster.R R/get_NMids.R R/Give_Sentences.R R/head_abbrev.R R/pubtator_function.R R/searchabsL.R R/xmlgene_atomizations.R R/wordsclusterview.R R/local_uniprotfun.R R/pmids_to_abstracts.R R/get_MedlinePlus.R R/xmlreadabs.R R/tdm_for_lsa.R R/input_for_find_intro_conc_html.R R/searchabsT.R R/official_fn.R R/cleanabs.R R/previousabs_fn.R R/Find_conclusion.R R/xmlword_atomizations.R R/getabs.R R/removeabs.R R/Yearwise.R R/altnamesfun.R R/subabs.R R/ready.R R/printabs.R R/get_Sequences.R R/getabsT.R R/SentenceToken.R R/gene_atomization.R R/BWI.R R/Give_Sentences_PMC.R R/pubtator_result_list_to_table.R R/genes_BWI.R R/cluster_words.R R/names_fn.R R/get_gene_sentences.R R/alias_fn.R R/currentabs_fn.R R/cos_sim_calc_boot.R R/prevsymbol_fn.R R/combineabs.R R/word_atomizations.R R/subsetabs.R R/get_PMCIDS.R R/HGNC-class.R R/contextSearch.R R/find_intro_conc_html.R R/get_original_term2.R R/cos_sim_calc.R R/sendabs.R R/readabs.R
man/getabsT-methods.Rd man/searchabsT-methods.Rd man/Genewise-methods.Rd man/combineabs.Rd man/subabs.Rd man/ready.Rd man/readabs.Rd man/pubtator_result_list_to_table.Rd man/wordsclusterview.Rd man/Yearwise-methods.Rd man/local_uniprotfun.Rd man/subsetabs-methods.Rd man/sendabs.Rd man/BWI.Rd man/get_gene_sentences.Rd man/gene_atomization.Rd man/cleanabs.Rd man/genes_BWI.Rd man/get_original_term2.Rd man/Give_Sentences_PMC.Rd man/get_Sequences.Rd man/removeabs-methods.Rd man/GeneToEntrez.Rd man/getabs.Rd man/uniprotfun.Rd man/Find_conclusion.Rd man/getabsT.Rd man/pubtator_function.Rd man/contextSearch-methods.Rd man/Yearwise.Rd man/xmlgene_atomizations.Rd man/cluster_words.Rd man/subabs-methods.Rd man/alias_fn.Rd man/cleanabs-methods.Rd man/Genewise.Rd man/get_PMCtable.Rd man/Abstracts-class.Rd man/get_MedlinePlus.Rd man/pmids_to_abstracts.Rd man/cos_sim_calc_boot.Rd man/wordscluster.Rd man/cos_sim_calc.Rd man/HGNC2UniprotID.Rd man/get_NMids.Rd man/head_abbrev.Rd man/get_original_term.Rd man/searchabsL-methods.Rd man/searchabsT.Rd man/find_intro_conc_html.Rd man/altnamesfun.Rd man/HGNCdata.Rd man/xmlreadabs.Rd man/whichcluster.Rd man/previousabs_fn.Rd man/prevsymbol_fn.Rd man/sendabs-methods.Rd man/tdm_for_lsa.Rd man/xmlword_atomizations.Rd man/searchabsL.Rd man/get_PMCIDS.Rd man/official_fn.Rd man/contextSearch.Rd man/subsetabs.Rd man/HGNC-class.Rd man/word_atomizations.Rd man/Give_Sentences.Rd man/currentabs_fn.Rd man/getabs-methods.Rd man/removeabs.Rd man/SentenceToken.Rd man/input_for_find_intro_conc_html.Rd man/common_words_new.Rd man/names_fn.Rd man/combineabs-methods.Rd man/printabs.Rd

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