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pubmed.mineR (version 1.0.1)

Text mining of PubMed Abstracts.

Description

An R package for text mining of PubMed Abstracts (http://www.ncbi.nlm.nih.gov/pubmed). The algorithms are designed for two formats (text and XML) from PubMed

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Version

Install

install.packages('pubmed.mineR')

Monthly Downloads

355

Version

1.0.1

License

GPL-3

Maintainer

S Ramachandran

Last Published

March 18th, 2014

Functions in pubmed.mineR (1.0.1)

Yearwise-methods

Yearwise Year wise extraction of Abstracts

To get Abstracts for a given term.

Find_conclusion

To find the conclusion from the abstract(s).

To get the information of pathways for Genes

R Data containing HGNC data.

HGNC Class for package.

create Term Document Matrix for lsa analysis

common_words_new

R Data containing words which frequently in text

To combine the abstracts

searchabsL-methods

Searching Abstracts

sendabs-methods

To send the Data into a File

cleanabs-methods

Methods for Function cleanabs

To Search the number of abstracts for Genes

gene_atomization

To Extract Genes from the Abstracts

To send abstracts

To calculate the cosine similarity between terms.

To Find the highest frequency of words within clusters

removeabs-methods

removeabs To remove abstracts of a term from the data.

For Context Search

To Initiate the Classes.

To cluster the words

find_intro_conc_html

To find the introduction and conclusion from the abstracts.

To fetch the cluster for words

getabsT-methods

To Get Abstracts

get_original_term

To get the original terms from the corpus.

Getting subabstracts

To get Abstracts for a given term.

searchabsT-methods

searchabsT Searching abstracts

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

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

To read Abstracts

word_atomizations

Atomization of words

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

contextSearch-methods

Method for Context Search

xmlgene_atomizations

Gene atomization of xml abstracts.

To Tokenize the sentences

input_for_find_intro_conc_html

fetch the abstracts using E-utilities.

To get information about gene from the UniProt.

Data containing Entrez Ids

combineabs-methods

Abstracts Method to Combine Abstracts

To Search abstracts Year wise

Genewise-methods

method to find the abstracts for the given gene.

To clean the result of searchabsL

To remove abstracts for the query term.

R Data containing HGNC2UniprotID data mapping.

To get the Links of the pathways for given genes

To Search Abstracts

xmlword_atomizations

Word atomizations of abstracts from xml format.

Abstracts-class

Class "Abstracts" Absract Class

cos_sim_calc_boot

Cosine Similarity Calculation by Boot Strapping

To find sub-abstracts

wordsclusterview

To view the words in cluster

getabs To Get abstracts for a term

pubtator_function

function for text annotation uisng online PubTator

To Retrive the Abstracts for year.

To Find Previous symbols of genes.

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

local_uniprotfun

To Get Information from Uniprot.

To extract the PMC Ids of the abstracts.

To Get Alternative names of Genes

get_original_term2

To get the original terms from the corpus.

To extract the official gene symbol.

Function to get the Buzz Word Index of Genes from the abstracts.

To fetch the given PMC article.

To extract sentences from the Abstracts

To extract the Gene sequence from the NCBI.

To Retrive the Abstracts from the large corpus for given years.

subsetabs-methods

To make subset of Abstracts.

get_gene_sentences

To extract the sentences for genes from the corpus.

To make subsets of large corpus.

To extract the abbreviated term.

To retreive information from DAVID.

pubtator_result_list_to_table

Function to Convert Pubtator result from list into Table

To extract the gene names from HGNC.

Give_Sentences_PMC

To fetch the sentence from the PMC full text article

To Find Alias of the Genes.

pmids_to_abstracts

To Find and match the PMIDs to the abstracts.

To extract NM ids from NCBI.