Text Mining of PubMed Abstracts

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Documentation for package ‘pubmed.mineR’ version 1.0.20

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Abstracts-class Class '"Abstracts"' Abstract Class
additional_info To extract sentences with nultiple keywords from Abstracts
alias_fn To extract sentences containing Alias of the Human Genes from Pubmed abstracts.
altnamesfun To Get Alternative names of Genes
BWI To obtain the Buzz Word Index of terms from the Abstracts.
cleanabs To clean the result of searchabsL
cleanabs-method Methods for Function 'cleanabs'
cleanabs-methods Methods for Function 'cleanabs'
cluster_words To Find the highest frequency of words within clusters
combineabs To combine the abstracts
combineabs-method 'Abstracts' Method to Combine Abstracts
combineabs-methods 'Abstracts' Method to Combine Abstracts
common_words_new R Data containing words which frequently in text
contextSearch For Context Search
contextSearch-method Method for Context Search
contextSearch-methods Method for Context Search
cos_sim_calc To calculate the cosine similarity between terms.
cos_sim_calc_boot Cosine Similarity Calculation by Boot Strapping
co_occurrence_advance Extracts multiple sentence with co-occurrence of two sets of terms)
co_occurrence_fn Extracts sentences with co-occurrence of two sets of terms
currentabs_fn To Retrive the Abstracts for year.
Find_conclusion To find the conclusion from the abstract(s).
find_intro_conc_html To find the introduction and conclusion from the abstracts.
genes_BWI Function to obtain the Buzz Word Index of Genes from the abstracts.
GeneToEntrez Data containing Entrez Ids
Genewise To Search the number of abstracts for Genes
Genewise-method method to find the abstracts for the given gene.
Genewise-methods method to find the abstracts for the given gene.
gene_atomization To Extract Genes from the Abstracts
getabs To get Abstracts for a given term.
getabs-method 'getabs' To Get abstracts for a term
getabs-methods 'getabs' To Get abstracts for a term
getabsT To get Abstracts for a given term.
getabsT-method To Get Abstracts
getabsT-methods To Get Abstracts
get_DOIs function for extracting Digital Object Identifier (DOIs) of papers
get_gene_sentences To extract the sentences for genes from the corpus.
get_MedlinePlus To Get MedLinePlus Summary
get_NMids To extract NM ids from NCBI.
get_original_term To get the original terms from the corpus. deprecated
get_original_term2 To get the original terms from the corpus.
get_PMCIDS To extract the PMC Ids of the abstracts.
get_PMCtable To fetch the given PMC article tables. Deprecated
get_Sequences To extract the Gene sequence from the NCBI.
Give_Sentences To extract sentences from the Abstracts
Give_Sentences_PMC To fetch the sentence from the PMC full text article
head_abbrev To extract the abbreviated term.
HGNC-class HGNC Class for package.
HGNC2UniprotID R Data containing HGNC2UniprotID data mapping.
HGNCdata R Data containing HGNC data.
input_for_find_intro_conc_html fetch the abstracts using E-utilities.
local_uniprotfun To Get Information from Uniprot.
names_fn To extract the sentences in asbtracts containing gene names from HGNC.
new_xmlreadabs To read the abstracts from the PubMed saved in XML format.
official_fn To extract the sentences containing official gene symbol from abstracts.
pmids_to_abstracts To Find and match the PMIDs to the abstracts.
previousabs_fn To Retrieve the Abstracts from the large corpus for given years.
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
pubtator_function function for text annotation using PubTator
pubtator_function_JSON function for text annotation using PubTator
pubtator_result_list_to_table Function to Convert Pubtator result from list into Table
readabs To read Abstracts
readabsnew To read Abstracts
ready To Initiate the Classes.
removeabs To remove abstracts for the query term.
removeabs-method 'removeabs' To remove abstracts of a term from the data.
removeabs-methods 'removeabs' To remove abstracts of a term from the data.
searchabsL To Search the abstracts of term(s) in a combination mode.
searchabsL-method Searching Abstracts
searchabsL-methods Searching Abstracts
searchabsT To Search Abstracts
searchabsT-method 'searchabsT' Searching abstracts
searchabsT-methods 'searchabsT' Searching abstracts
sendabs To send abstracts
sendabs-method To send the Data into a File
sendabs-methods To send the Data into a File
SentenceToken To Tokenize the sentences
space_quasher Removes extra spaces between words.
subabs To find sub-abstracts
subabs-method Getting subabstracts
subabs-methods Getting subabstracts
subsetabs To make subsets of large corpus.
subsetabs-method To make subset of Abstracts.
subsetabs-methods To make subset of Abstracts.
tdm_for_lsa create Term Document Matrix for lsa analysis
uniprotfun To get information about gene from the UniProt.Deprecated.
whichcluster To fetch the cluster for words
wordscluster To cluster the words
wordsclusterview To view the words in cluster
word_associations Extracts the words associated (to the left and to the right) with a given word
word_atomizations Atomization of words
xmlgene_atomizations Gene atomization of xml abstracts.Deprecated.
xmlgene_atomizations_new Gene atomization of xml abstracts.
xmlreadabs To read the abstracts from the PubMed saved in XML format.
xmlword_atomizations Word atomizations of abstracts from xml format.
Yearwise To Search abstracts Year wise
Yearwise-method 'Yearwise' Year wise extraction of Abstracts
Yearwise-methods 'Yearwise' Year wise extraction of Abstracts