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pubmed.mineR (version 1.0.21)

Text Mining of PubMed Abstracts

Description

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

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Version

Install

install.packages('pubmed.mineR')

Monthly Downloads

481

Version

1.0.21

License

GPL-3

Maintainer

S. Ramachandran

Last Published

September 8th, 2024

Functions in pubmed.mineR (1.0.21)

additional_info

To extract sentences with nultiple keywords from Abstracts

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

cleanabs-methods

Methods for Function cleanabs

get_original_term

To get the original terms from the corpus. deprecated

co_occurrence_advance

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

get_gene_sentences

To extract the sentences for genes from the corpus.

To extract the Gene sequence from the NCBI.

co_occurrence_fn

Extracts sentences with co-occurrence of two sets of terms

getabs To Get abstracts for a term

find_intro_conc_html

To find the introduction and conclusion from the abstracts.

gene_atomization

To Extract Genes from the Abstracts

get_MedlinePlus

To Get MedLinePlus Summary

To Tokenize the sentences

To combine the abstracts

To get Abstracts for a given term.

To Retrive the Abstracts for year.

combineabs-methods

Abstracts Method to Combine Abstracts

getabsT-methods

To Get Abstracts

get_original_term2

To get the original terms from the corpus.

cos_sim_calc_boot

Cosine Similarity Calculation by Boot Strapping

For Context Search

To Find the highest frequency of words within clusters

To extract the abbreviated term.

input_for_find_intro_conc_html

fetch the abstracts using E-utilities.

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

To extract the sentences containing Previous symbols of HGNC genes.

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

To calculate the cosine similarity between terms.

pubtator3_function

function for text annotation using PubTator

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

To extract NM ids from NCBI.

To extract the PMC Ids of the abstracts.

word_associations

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

To fetch the given PMC article tables. Deprecated

To fetch the cluster for words

common_words_new

R Data containing words which frequently in text

To send abstracts

searchabsT-methods

searchabsT Searching abstracts

contextSearch-methods

Method for Context Search

To extract the sentences containing official gene symbol from abstracts.

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

Removes extra spaces between words.

local_uniprotfun

To Get Information from Uniprot.

function for extracting Digital Object Identifier (DOIs) of papers

pubtator_function_JSON

function for text annotation using PubTator

pmids_to_abstracts

To Find and match the PMIDs to the abstracts.

To Search Abstracts

pubtator_function

function for text annotation using PubTator.Deprecated.

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

To get Abstracts for a given term.

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

pubtator_result_list_to_table

Function to Convert Pubtator result from list into Table

xmlword_atomizations

Word atomizations of abstracts from xml format.

Getting subabstracts

To find sub-abstracts

To remove abstracts for the query term.

word_atomizations

Atomization of words

searchabsL-methods

Searching Abstracts

create Term Document Matrix for lsa analysis

To Initiate the Classes.

sendabs-methods

To send the Data into a File

To cluster the words

To make subsets of large corpus.

subsetabs-methods

To make subset of Abstracts.

To read Abstracts

removeabs-methods

removeabs To remove abstracts of a term from the data.

xmlgene_atomizations_new

Gene atomization of xml abstracts.

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

To read Abstracts

To get information about gene from the UniProt.Deprecated.

xmlgene_atomizations

Gene atomization of xml abstracts.Deprecated.

wordsclusterview

To view the words in cluster

Yearwise-methods

Yearwise Year wise extraction of Abstracts

To Search abstracts Year wise

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

Abstracts-class

Class "Abstracts" Abstract Class

To Get Alternative names of Genes

To extract sentences from the Abstracts

R Data containing HGNC data.

Give_Sentences_PMC

To fetch the sentence from the PMC full text article

Genewise-methods

method to find the abstracts for the given gene.

To Search the number of abstracts for Genes

Find_conclusion

To find the conclusion from the abstract(s).

Data containing Entrez Ids

To clean the result of searchabsL

HGNC Class for package.

R Data containing HGNC2UniprotID data mapping.