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pubmed.mineR (version 1.0.11)

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

347

Version

1.0.11

License

GPL-3

Maintainer

S. Ramachandran

Last Published

September 12th, 2017

Functions in pubmed.mineR (1.0.11)

HGNC-class

HGNC Class for package.

HGNC2UniprotID

R Data containing HGNC2UniprotID data mapping.

Find_conclusion

To find the conclusion from the abstract(s).

GeneToEntrez

Data containing Entrez Ids

Abstracts-class

Class "Abstracts" Absract Class

BWI

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

Give_Sentences

To extract sentences from the Abstracts

Give_Sentences_PMC

To fetch the sentence from the PMC full text article

Genewise-methods

method to find the abstracts for the given gene.

Genewise

To Search the number of abstracts for Genes

Yearwise-methods

Yearwise Year wise extraction of Abstracts

Yearwise

To Search abstracts Year wise

gene_atomization

To Extract Genes from the Abstracts

genes_BWI

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

get_PMCIDS

To extract the PMC Ids of the abstracts.

get_PMCtable

To fetch the given PMC article.

head_abbrev

To extract the abbreviated term.

input_for_find_intro_conc_html

fetch the abstracts using E-utilities.

pubtator_result_list_to_table

Function to Convert Pubtator result from list into Table

alias_fn

To Find Alias of the Genes.

altnamesfun

To Get Alternative names of Genes

combineabs

To combine the abstracts

getabs-methods

getabs To Get abstracts for a term

getabs

To get Abstracts for a given term.

previousabs_fn

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

prevsymbol_fn

To Find Previous symbols of genes.

printabs

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

HGNCdata

R Data containing HGNC data.

SentenceToken

To Tokenize the sentences

contextSearch-methods

Method for Context Search

contextSearch

For Context Search

common_words_new

R Data containing words which frequently in text

get_Sequences

To extract the Gene sequence from the NCBI.

get_gene_sentences

To extract the sentences for genes from the corpus.

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

xmlword_atomizations

Word atomizations of abstracts from xml format.

cleanabs-methods

Methods for Function cleanabs

cleanabs

To clean the result of searchabsL

currentabs_fn

To Retrive the Abstracts for year.

find_intro_conc_html

To find the introduction and conclusion from the abstracts.

getabsT

To get Abstracts for a given term.

removeabs

To remove abstracts for the query term.

searchabsL-methods

Searching Abstracts

subabs

To find sub-abstracts

subsetabs-methods

To make subset of Abstracts.

cluster_words

To Find the highest frequency of words within clusters

combineabs-methods

Abstracts Method to Combine Abstracts

cos_sim_calc

To calculate the cosine similarity between terms.

cos_sim_calc_boot

Cosine Similarity Calculation by Boot Strapping

get_original_term

To get the original terms from the corpus.

pubtator_function

function for text annotation uisng online PubTator

uniprotfun

To get information about gene from the UniProt.

whichcluster

To fetch the cluster for words

get_original_term2

To get the original terms from the corpus.

official_fn

To extract the official gene symbol.

pmids_to_abstracts

To Find and match the PMIDs to the abstracts.

ready

To Initiate the Classes.

removeabs-methods

removeabs To remove abstracts of a term from the data.

searchabsT

To Search Abstracts

sendabs-methods

To send the Data into a File

To Get MedLinePlus Summary

get_NMids

To extract NM ids from NCBI.

local_uniprotfun

To Get Information from Uniprot.

names_fn

To extract the gene names from HGNC.

searchabsL

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

searchabsT-methods

searchabsT Searching abstracts

subsetabs

To make subsets of large corpus.

tdm_for_lsa

create Term Document Matrix for lsa analysis

wordsclusterview

To view the words in cluster

xmlgene_atomizations

Gene atomization of xml abstracts.