# Text Mining of PubMed Abstracts

## Documentation for package ‘pubmed.mineR’ version 1.0.16

- DESCRIPTION file.

## Help Pages

Abstracts-class | Class '"Abstracts"' Abstract Class
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_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.
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_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.
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.
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