⚠️There's a newer version (1.0.21) of this package.Take me there.

pubmed.mineR (version 1.0.20)

Text Mining of PubMed Abstracts

Description

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

Copy Link

Version

Install

install.packages('pubmed.mineR')

Monthly Downloads

290

Version

1.0.20

License

GPL-3

Maintainer

S. Ramachandran

Last Published

April 8th, 2024

Functions in pubmed.mineR (1.0.20)

SentenceToken

To Tokenize the sentences

cleanabs

To clean the result of searchabsL

co_occurrence_advance

Extracts multiple sentence with co-occurrence of two sets of terms)

cluster_words

To Find the highest frequency of words within clusters

get_Sequences

To extract the Gene sequence from the NCBI.

co_occurrence_fn

Extracts sentences with co-occurrence of two sets of terms

get_DOIs

function for extracting Digital Object Identifier (DOIs) of papers

currentabs_fn

To Retrive the Abstracts for year.

cos_sim_calc_boot

Cosine Similarity Calculation by Boot Strapping

get_original_term

To get the original terms from the corpus. deprecated

get_original_term2

To get the original terms from the corpus.

genes_BWI

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

get_PMCtable

To fetch the given PMC article tables. Deprecated

cleanabs-methods

Methods for Function cleanabs

get_PMCIDS

To extract the PMC Ids of the abstracts.

get_gene_sentences

To extract the sentences for genes from the corpus.

alias_fn

To extract sentences containing Alias of the Human Genes from Pubmed abstracts.

pubtator_result_list_to_table

Function to Convert Pubtator result from list into Table

combineabs-methods

Abstracts Method to Combine Abstracts

find_intro_conc_html

To find the introduction and conclusion from the abstracts.

combineabs

To combine the abstracts

getabs-methods

getabs To Get abstracts for a term

getabs

To get Abstracts for a given term.

searchabsT-methods

searchabsT Searching abstracts

searchabsT

To Search Abstracts

subabs

To find sub-abstracts

subsetabs-methods

To make subset of Abstracts.

readabs

To read Abstracts

common_words_new

R Data containing words which frequently in text

getabsT-methods

To Get Abstracts

Yearwise-methods

Yearwise Year wise extraction of Abstracts

contextSearch-methods

Method for Context Search

removeabs

To remove abstracts for the query term.

removeabs-methods

removeabs To remove abstracts of a term from the data.

word_associations

Extracts the words associated (to the left and to the right) with a given word

head_abbrev

To extract the abbreviated term.

Yearwise

To Search abstracts Year wise

input_for_find_intro_conc_html

fetch the abstracts using E-utilities.

word_atomizations

Atomization of words

local_uniprotfun

To Get Information from Uniprot.

names_fn

To extract the sentences in asbtracts containing gene names from HGNC.

gene_atomization

To Extract Genes from the Abstracts

cos_sim_calc

To calculate the cosine similarity between terms.

contextSearch

For Context Search

getabsT

To get Abstracts for a given term.

prevsymbol_fn

To extract the sentences containing Previous symbols of HGNC genes.

printabs

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

searchabsL-methods

Searching Abstracts

new_xmlreadabs

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

searchabsL

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

Removes extra spaces between words.

ready

To Initiate the Classes.

official_fn

To extract the sentences containing official gene symbol from abstracts.

get_NMids

To extract NM ids from NCBI.

get_MedlinePlus

To Get MedLinePlus Summary

xmlword_atomizations

Word atomizations of abstracts from xml format.

xmlreadabs

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

pmids_to_abstracts

To Find and match the PMIDs to the abstracts.

uniprotfun

To get information about gene from the UniProt.Deprecated.

whichcluster

To fetch the cluster for words

wordscluster

To cluster the words

previousabs_fn

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

pubtator_function

function for text annotation using PubTator

wordsclusterview

To view the words in cluster

sendabs-methods

To send the Data into a File

pubtator_function_JSON

function for text annotation using PubTator

sendabs

To send abstracts

subsetabs

To make subsets of large corpus.

tdm_for_lsa

create Term Document Matrix for lsa analysis

xmlgene_atomizations

Gene atomization of xml abstracts.Deprecated.

xmlgene_atomizations_new

Gene atomization of xml abstracts.

HGNC-class

HGNC Class for package.

GeneToEntrez

Data containing Entrez Ids

Give_Sentences_PMC

To fetch the sentence from the PMC full text article

Genewise-methods

method to find the abstracts for the given gene.

BWI

To obtain the Buzz Word Index of terms from the Abstracts.

Abstracts-class

Class "Abstracts" Abstract Class

Give_Sentences

To extract sentences from the Abstracts

HGNC2UniprotID

R Data containing HGNC2UniprotID data mapping.

Genewise

To Search the number of abstracts for Genes

altnamesfun

To Get Alternative names of Genes

Find_conclusion

To find the conclusion from the abstract(s).

additional_info

To extract sentences with nultiple keywords from Abstracts

HGNCdata

R Data containing HGNC data.