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pubmed.mineR (version 1.0.20)
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
756
Version
1.0.20
License
GPL-3
Maintainer
S. Ramachandran
Last Published
April 8th, 2024
Functions in pubmed.mineR (1.0.20)
Search functions
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.
subabs-methods
Getting subabstracts
readabsnew
To read Abstracts
space_quasher
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.