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pubmed.mineR (version 1.0.15)

Text Mining of PubMed Abstracts

Description

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

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Install

install.packages('pubmed.mineR')

Monthly Downloads

290

Version

1.0.15

License

GPL-3

Maintainer

S. Ramachandran

Last Published

May 6th, 2019

Functions in pubmed.mineR (1.0.15)

Genewise-methods

method to find the abstracts for the given gene.

Yearwise

To Search abstracts Year wise

combineabs-methods

Abstracts Method to Combine Abstracts

combineabs

To combine the abstracts

names_fn

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

official_fn

To extract the sentences containing official gene symbol from abstracts.

Genewise

To Search the number of abstracts for Genes

subabs-methods

Getting subabstracts

Find_conclusion

To find the conclusion from the abstract(s).

subabs

To find sub-abstracts

alias_fn

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

To Get Alternative names of Genes

GeneToEntrez

Data containing Entrez Ids

cleanabs-methods

Methods for Function cleanabs

get_Sequences

To extract the Gene sequence from the NCBI.

get_PMCtable

To fetch the given PMC article tables. Deprecated

getabs

To get Abstracts for a given term.

cleanabs

To clean the result of searchabsL

getabsT-methods

To Get Abstracts

common_words_new

R Data containing words which frequently in text

prevsymbol_fn

To extract the sentences containing Previous symbols of HGNC genes.

contextSearch-methods

Method for Context Search

printabs

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

searchabsT

To Search Abstracts

sendabs-methods

To send the Data into a File

get_gene_sentences

To extract the sentences for genes from the corpus.

HGNC-class

HGNC Class for package.

HGNC2UniprotID

R Data containing HGNC2UniprotID data mapping.

get_original_term

To get the original terms from the corpus. deprecated

pmids_to_abstracts

To Find and match the PMIDs to the abstracts.

HGNCdata

R Data containing HGNC data.

SentenceToken

To Tokenize the sentences

find_intro_conc_html

To find the introduction and conclusion from the abstracts.

previousabs_fn

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

removeabs

To remove abstracts for the query term.

gene_atomization

To Extract Genes from the Abstracts

get_original_term2

To get the original terms from the corpus.

getabs-methods

getabs To Get abstracts for a term

getabsT

To get Abstracts for a given term.

searchabsL-methods

Searching Abstracts

head_abbrev

To extract the abbreviated term.

ready

To Initiate the Classes.

subsetabs-methods

To make subset of Abstracts.

subsetabs

To make subsets of large corpus.

whichcluster

To fetch the cluster for words

removeabs-methods

removeabs To remove abstracts of a term from the data.

searchabsL

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

word_associations

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

searchabsT-methods

searchabsT Searching abstracts

Abstracts-class

Class "Abstracts" Abstract Class

wordsclusterview

To view the words in cluster

xmlgene_atomizations

Gene atomization of xml abstracts.

BWI

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

cluster_words

To Find the highest frequency of words within clusters

co_occurrence_fn

Extracts sentences with co-occurrence of two sets of terms

contextSearch

For Context Search

cos_sim_calc

To calculate the cosine similarity between terms.

get_NMids

To extract NM ids from NCBI.

cos_sim_calc_boot

Cosine Similarity Calculation by Boot Strapping

currentabs_fn

To Retrive the Abstracts for year.

genes_BWI

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

get_MedlinePlus

To Get MedLinePlus Summary

input_for_find_intro_conc_html

fetch the abstracts using E-utilities.

get_PMCIDS

To extract the PMC Ids of the abstracts.

To Get Information from Uniprot.

pubtator_function

function for text annotation using PubTator

sendabs

To send abstracts

pubtator_result_list_to_table

Function to Convert Pubtator result from list into Table

xmlreadabs

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

space_quasher

Removes extra spaces between words.

tdm_for_lsa

create Term Document Matrix for lsa analysis

uniprotfun

To get information about gene from the UniProt.

xmlword_atomizations

Word atomizations of abstracts from xml format.

Give_Sentences

To extract sentences from the Abstracts

Give_Sentences_PMC

To fetch the sentence from the PMC full text article

Yearwise-methods

Yearwise Year wise extraction of Abstracts