pubmed.mineR: Text Mining of PubMed Abstracts

Text mining of PubMed Abstracts (text and XML) from http://www.ncbi.nlm.nih.gov/pubmed.

Author
Jyoti Rani, S.Ramachandran, Ab Rauf Shah
Date of publication
2016-02-18 06:51:38
Maintainer
S. Ramachandran <ramu@igib.in>
License
GPL-3
Version
1.0.5

View on CRAN

Man pages

Abstracts-class
Class '"Abstracts"' Absract Class
alias_fn
To Find Alias of the Genes.
altnamesfun
To Get Alternative names of Genes
BWI
To Get the Buzz Word Index of terms form the Abstracts.
cleanabs
To clean the result of searchabsL
cleanabs-methods
Methods for Function 'cleanabs'
cluster_words
To Find the highest frequency of words within clusters
combineabs
To combine the abstracts
combineabs-methods
'Abstracts' Method to Combine Abstracts
common_words_new
R Data containing words which frequently in text
contextSearch
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
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.
gene_atomization
To Extract Genes from the Abstracts
genes_BWI
Function to get the Buzz Word Index of Genes from the...
GeneToEntrez
Data containing Entrez Ids
Genewise
To Search the number of abstracts for Genes
Genewise-methods
method to find the abstracts for the given gene.
getabs
To get Abstracts for a given term.
getabs-methods
'getabs' To Get abstracts for a term
getabsT
To get Abstracts for a given term.
getabsT-methods
To Get Abstracts
get_gene_sentences
To extract the sentences for genes from the corpus.
get_NMids
To extract NM ids from NCBI.
get_original_term
To get the original terms from the corpus.
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.
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.
HGNC2UniprotID
R Data containing HGNC2UniprotID data mapping.
HGNC-class
HGNC Class for package.
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 gene names from HGNC.
official_fn
To extract the official gene symbol.
pmids_to_abstracts
To Find and match the PMIDs to the abstracts.
previousabs_fn
To Retrive the Abstracts from the large corpus for given...
prevsymbol_fn
To Find Previous symbols of genes.
printabs
To prind the total number of abstracts in an S4 object of...
pubtator_function
function for text annotation uisng online PubTator
pubtator_result_list_to_table
Function to Convert Pubtator result from list into Table
readabs
To read Abstracts
ready
To Initiate the Classes.
removeabs
To remove abstracts for the query term.
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-methods
Searching Abstracts
searchabsT
To Search Abstracts
searchabsT-methods
'searchabsT' Searching abstracts
sendabs
To send abstracts
sendabs-methods
To send the Data into a File
SentenceToken
To Tokenize the sentences
subabs
To find sub-abstracts
subabs-methods
Getting subabstracts
subsetabs
To make subsets of large corpus.
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
word_atomizations
Atomization of words
wordscluster
To cluster the words
wordsclusterview
To view the words in cluster
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-methods
'Yearwise' Year wise extraction of Abstracts

Files in this package

pubmed.mineR
pubmed.mineR/inst
pubmed.mineR/inst/CITATION
pubmed.mineR/NAMESPACE
pubmed.mineR/data
pubmed.mineR/data/HGNC2UniprotID.rda
pubmed.mineR/data/common_words_new.rda
pubmed.mineR/data/HGNCdata.rda
pubmed.mineR/data/datalist
pubmed.mineR/data/GeneToEntrez.rda
pubmed.mineR/R
pubmed.mineR/R/whichcluster.R
pubmed.mineR/R/get_original_term.R
pubmed.mineR/R/uniprotfun.R
pubmed.mineR/R/gethgnc.R
pubmed.mineR/R/Genewise.R
pubmed.mineR/R/get_PMCtable.R
pubmed.mineR/R/Abstracts-class.R
pubmed.mineR/R/wordscluster.R
pubmed.mineR/R/get_NMids.R
pubmed.mineR/R/Give_Sentences.R
pubmed.mineR/R/head_abbrev.R
pubmed.mineR/R/pubtator_function.R
pubmed.mineR/R/searchabsL.R
pubmed.mineR/R/xmlgene_atomizations.R
pubmed.mineR/R/wordsclusterview.R
pubmed.mineR/R/local_uniprotfun.R
pubmed.mineR/R/pmids_to_abstracts.R
pubmed.mineR/R/xmlreadabs.R
pubmed.mineR/R/tdm_for_lsa.R
pubmed.mineR/R/input_for_find_intro_conc_html.R
pubmed.mineR/R/searchabsT.R
pubmed.mineR/R/official_fn.R
pubmed.mineR/R/cleanabs.R
pubmed.mineR/R/previousabs_fn.R
pubmed.mineR/R/Find_conclusion.R
pubmed.mineR/R/xmlword_atomizations.R
pubmed.mineR/R/getabs.R
pubmed.mineR/R/removeabs.R
pubmed.mineR/R/Yearwise.R
pubmed.mineR/R/altnamesfun.R
pubmed.mineR/R/subabs.R
pubmed.mineR/R/ready.R
pubmed.mineR/R/printabs.R
pubmed.mineR/R/get_Sequences.R
pubmed.mineR/R/getabsT.R
pubmed.mineR/R/SentenceToken.R
pubmed.mineR/R/gene_atomization.R
pubmed.mineR/R/BWI.R
pubmed.mineR/R/Give_Sentences_PMC.R
pubmed.mineR/R/pubtator_result_list_to_table.R
pubmed.mineR/R/genes_BWI.R
pubmed.mineR/R/cluster_words.R
pubmed.mineR/R/names_fn.R
pubmed.mineR/R/get_gene_sentences.R
pubmed.mineR/R/alias_fn.R
pubmed.mineR/R/currentabs_fn.R
pubmed.mineR/R/cos_sim_calc_boot.R
pubmed.mineR/R/prevsymbol_fn.R
pubmed.mineR/R/combineabs.R
pubmed.mineR/R/word_atomizations.R
pubmed.mineR/R/subsetabs.R
pubmed.mineR/R/get_PMCIDS.R
pubmed.mineR/R/HGNC-class.R
pubmed.mineR/R/contextSearch.R
pubmed.mineR/R/find_intro_conc_html.R
pubmed.mineR/R/get_original_term2.R
pubmed.mineR/R/cos_sim_calc.R
pubmed.mineR/R/sendabs.R
pubmed.mineR/R/readabs.R
pubmed.mineR/MD5
pubmed.mineR/DESCRIPTION
pubmed.mineR/man
pubmed.mineR/man/getabsT-methods.Rd
pubmed.mineR/man/searchabsT-methods.Rd
pubmed.mineR/man/Genewise-methods.Rd
pubmed.mineR/man/combineabs.Rd
pubmed.mineR/man/subabs.Rd
pubmed.mineR/man/ready.Rd
pubmed.mineR/man/readabs.Rd
pubmed.mineR/man/pubtator_result_list_to_table.Rd
pubmed.mineR/man/wordsclusterview.Rd
pubmed.mineR/man/Yearwise-methods.Rd
pubmed.mineR/man/local_uniprotfun.Rd
pubmed.mineR/man/subsetabs-methods.Rd
pubmed.mineR/man/sendabs.Rd
pubmed.mineR/man/BWI.Rd
pubmed.mineR/man/get_gene_sentences.Rd
pubmed.mineR/man/gene_atomization.Rd
pubmed.mineR/man/cleanabs.Rd
pubmed.mineR/man/genes_BWI.Rd
pubmed.mineR/man/get_original_term2.Rd
pubmed.mineR/man/Give_Sentences_PMC.Rd
pubmed.mineR/man/get_Sequences.Rd
pubmed.mineR/man/removeabs-methods.Rd
pubmed.mineR/man/GeneToEntrez.Rd
pubmed.mineR/man/getabs.Rd
pubmed.mineR/man/uniprotfun.Rd
pubmed.mineR/man/Find_conclusion.Rd
pubmed.mineR/man/getabsT.Rd
pubmed.mineR/man/pubtator_function.Rd
pubmed.mineR/man/contextSearch-methods.Rd
pubmed.mineR/man/Yearwise.Rd
pubmed.mineR/man/xmlgene_atomizations.Rd
pubmed.mineR/man/cluster_words.Rd
pubmed.mineR/man/subabs-methods.Rd
pubmed.mineR/man/alias_fn.Rd
pubmed.mineR/man/cleanabs-methods.Rd
pubmed.mineR/man/Genewise.Rd
pubmed.mineR/man/get_PMCtable.Rd
pubmed.mineR/man/Abstracts-class.Rd
pubmed.mineR/man/pmids_to_abstracts.Rd
pubmed.mineR/man/cos_sim_calc_boot.Rd
pubmed.mineR/man/wordscluster.Rd
pubmed.mineR/man/cos_sim_calc.Rd
pubmed.mineR/man/HGNC2UniprotID.Rd
pubmed.mineR/man/get_NMids.Rd
pubmed.mineR/man/head_abbrev.Rd
pubmed.mineR/man/get_original_term.Rd
pubmed.mineR/man/searchabsL-methods.Rd
pubmed.mineR/man/searchabsT.Rd
pubmed.mineR/man/find_intro_conc_html.Rd
pubmed.mineR/man/altnamesfun.Rd
pubmed.mineR/man/HGNCdata.Rd
pubmed.mineR/man/xmlreadabs.Rd
pubmed.mineR/man/whichcluster.Rd
pubmed.mineR/man/previousabs_fn.Rd
pubmed.mineR/man/prevsymbol_fn.Rd
pubmed.mineR/man/sendabs-methods.Rd
pubmed.mineR/man/tdm_for_lsa.Rd
pubmed.mineR/man/xmlword_atomizations.Rd
pubmed.mineR/man/searchabsL.Rd
pubmed.mineR/man/get_PMCIDS.Rd
pubmed.mineR/man/official_fn.Rd
pubmed.mineR/man/contextSearch.Rd
pubmed.mineR/man/subsetabs.Rd
pubmed.mineR/man/HGNC-class.Rd
pubmed.mineR/man/word_atomizations.Rd
pubmed.mineR/man/Give_Sentences.Rd
pubmed.mineR/man/currentabs_fn.Rd
pubmed.mineR/man/getabs-methods.Rd
pubmed.mineR/man/removeabs.Rd
pubmed.mineR/man/SentenceToken.Rd
pubmed.mineR/man/input_for_find_intro_conc_html.Rd
pubmed.mineR/man/common_words_new.Rd
pubmed.mineR/man/names_fn.Rd
pubmed.mineR/man/combineabs-methods.Rd
pubmed.mineR/man/printabs.Rd