RISmed: Download Content from NCBI Databases

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A set of tools to extract bibliographic content from the National Center for Biotechnology Information (NCBI) databases, including PubMed. The name RISmed is a portmanteau of RIS (for Research Information Systems, a common tag format for bibliographic data) and PubMed.

Author
Stephanie Kovalchik [aut, cre]
Date of publication
2016-11-02 18:17:27
Maintainer
Stephanie Kovalchik <s.a.kovalchik@gmail.com>
License
GPL (>= 2)
Version
2.1.6

View on CRAN

Man pages

AbstractText
Extracts 'AbstractText' from 'Medline' object.
AbstractText-methods
~~ Methods for Function 'AbstractText' in Package 'RISmed' ~~
Acronym
Extracts 'Acronym' from 'Medline' object.
Acronym-methods
~~ Methods for Function 'Acronym' in Package 'RISmed' ~~
Affiliation
Extracts 'Affiliation' from 'Medline' object.
Affiliation-methods
~~ Methods for Function 'Affiliation' in Package 'RISmed' ~~
Agency
Extracts 'Agency' from 'Medline' object.
Agency-methods
~~ Methods for Function 'Agency' in Package 'RISmed' ~~
ArticleId
Extracts 'ArticleId' from 'Medline' object.
ArticleId-methods
~~ Methods for Function 'ArticleId' in Package 'RISmed' ~~
ArticleTitle
Extracts 'ArticleTitle' from 'Medline' object.
ArticleTitle-methods
~~ Methods for Function 'ArticleTitle' in Package 'RISmed' ~~
Author
Extracts 'Author' from 'Medline' object.
Author-methods
~~ Methods for Function 'Author' in Package 'RISmed' ~~
Cited
Number of citations
Cited-methods
~~ Methods for Function 'Cited' in Package 'RISmed' ~~
c-methods
Concatenate Medline
CollectiveName
Extracts 'CollectiveName' from 'Medline' object.
CollectiveName-methods
~~ Methods for Function 'CollectiveName' in Package 'RISmed'...
CopyrightInformation
Extracts 'CopyrightInformation' from 'Medline' object.
CopyrightInformation-methods
~~ Methods for Function 'CopyrightInformation' in Package...
count
Count of record results for EUtilsQuery
Country
Extracts 'Country' from 'Medline' object.
Country-methods
~~ Methods for Function 'Country' in Package 'RISmed' ~~
DayAccepted
Extracts 'DayAccepted' from 'Medline' object.
DayAccepted-methods
~~ Methods for Function 'DayAccepted' in Package 'RISmed' ~~
DayEpublish
Extracts 'DayEpublish' from 'Medline' object.
DayEpublish-methods
~~ Methods for Function 'DayEpublish' in Package 'RISmed' ~~
DayPmc
Extracts 'DayPmc' from 'Medline' object.
DayPmc-methods
~~ Methods for Function 'DayPmc' in Package 'RISmed' ~~
DayPpublish
Extracts 'DayPpublish' from 'Medline' object.
DayPpublish-methods
~~ Methods for Function 'DayPpublish' in Package 'RISmed' ~~
DayPubmed
Extracts 'DayPubmed' from 'Medline' object.
DayPubmed-methods
~~ Methods for Function 'DayPubmed' in Package 'RISmed' ~~
DayReceived
Extracts 'DayReceived' from 'Medline' object.
DayReceived-methods
~~ Methods for Function 'DayReceived' in Package 'RISmed' ~~
ELocationID
Extracts 'ELocationID' from 'Medline' object.
ELocationID-methods
~~ Methods for Function 'ELocationID' in Package 'RISmed' ~~
EUtilsGet
Results of an NCBI EUtils query
EUtilsQuery
Construct URL to make NCBI EUtils query
EUtilsSummary
Get summary of NCBI EUtils query
EUtilsSummary-class
Class '"EUtilsSummary"'
GrantID
Extracts 'GrantID' from 'Medline' object.
GrantID-methods
~~ Methods for Function 'GrantID' in Package 'RISmed' ~~
HourAccepted
Extracts 'HourAccepted' from 'Medline' object.
HourAccepted-methods
~~ Methods for Function 'HourAccepted' in Package 'RISmed' ~~
HourEpublish
Extracts 'HourEpublish' from 'Medline' object.
HourEpublish-methods
~~ Methods for Function 'HourEpublish' in Package 'RISmed' ~~
HourPmc
Extracts 'HourPmc' from 'Medline' object.
HourPmc-methods
~~ Methods for Function 'HourPmc' in Package 'RISmed' ~~
HourPpublish
Extracts 'HourPpublish' from 'Medline' object.
HourPpublish-methods
~~ Methods for Function 'HourPpublish' in Package 'RISmed' ~~
HourPubmed
Extracts 'HourPubmed' from 'Medline' object.
HourPubmed-methods
~~ Methods for Function 'HourPubmed' in Package 'RISmed' ~~
HourReceived
Extracts 'HourReceived' from 'Medline' object.
HourReceived-methods
~~ Methods for Function 'HourReceived' in Package 'RISmed' ~~
id
Get ids from EUtilsQuery
ISOAbbreviation
Extracts 'ISOAbbreviation' from 'Medline' object.
ISOAbbreviation-methods
~~ Methods for Function 'ISOAbbreviation' in Package 'RISmed'...
ISSN
Extracts 'ISSN' from 'Medline' object.
ISSNLinking
Extracts 'ISSNLinking' from 'Medline' object.
ISSNLinking-methods
~~ Methods for Function 'ISSNLinking' in Package 'RISmed' ~~
ISSN-methods
~~ Methods for Function 'ISSN' in Package 'RISmed' ~~
Issue
Extracts 'Issue' from 'Medline' object.
Issue-methods
~~ Methods for Function 'Issue' in Package 'RISmed' ~~
Language
Extracts 'Language' from 'Medline' object.
Language-methods
~~ Methods for Function 'Language' in Package 'RISmed' ~~
Medline
Class '"Medline"'
MedlinePgn
Extracts 'MedlinePgn' from 'Medline' object.
MedlinePgn-methods
~~ Methods for Function 'MedlinePgn' in Package 'RISmed' ~~
MedlineTA
Extracts 'MedlineTA' from 'Medline' object.
MedlineTA-methods
~~ Methods for Function 'MedlineTA' in Package 'RISmed' ~~
Mesh
Extracts 'Mesh' headings from 'Medline' object.
Mesh-methods
~~ Methods for Function 'Mesh' in Package 'RISmed' ~~
MinuteAccepted
Extracts 'MinuteAccepted' from 'Medline' object.
MinuteAccepted-methods
~~ Methods for Function 'MinuteAccepted' in Package 'RISmed'...
MinuteEpublish
Extracts 'MinuteEpublish' from 'Medline' object.
MinuteEpublish-methods
~~ Methods for Function 'MinuteEpublish' in Package 'RISmed'...
MinutePmc
Extracts 'MinutePmc' from 'Medline' object.
MinutePmc-methods
~~ Methods for Function 'MinutePmc' in Package 'RISmed' ~~
MinutePpublish
Extracts 'MinutePpublish' from 'Medline' object.
MinutePpublish-methods
~~ Methods for Function 'MinutePpublish' in Package 'RISmed'...
MinutePubmed
Extracts 'MinutePubmed' from 'Medline' object.
MinutePubmed-methods
~~ Methods for Function 'MinutePubmed' in Package 'RISmed' ~~
MinuteReceived
Extracts 'MinuteReceived' from 'Medline' object.
MinuteReceived-methods
~~ Methods for Function 'MinuteReceived' in Package 'RISmed'...
MonthAccepted
Extracts 'MonthAccepted' from 'Medline' object.
MonthAccepted-methods
~~ Methods for Function 'MonthAccepted' in Package 'RISmed'...
MonthEpublish
Extracts 'MonthEpublish' from 'Medline' object.
MonthEpublish-methods
~~ Methods for Function 'MonthEpublish' in Package 'RISmed'...
MonthPmc
Extracts 'MonthPmc' from 'Medline' object.
MonthPmc-methods
~~ Methods for Function 'MonthPmc' in Package 'RISmed' ~~
MonthPpublish
Extracts 'MonthPpublish' from 'Medline' object.
MonthPpublish-methods
~~ Methods for Function 'MonthPpublish' in Package 'RISmed'...
MonthPubmed
Extracts 'MonthPubmed' from 'Medline' object.
MonthPubmed-methods
~~ Methods for Function 'MonthPubmed' in Package 'RISmed' ~~
MonthReceived
Extracts 'MonthReceived' from 'Medline' object.
MonthReceived-methods
~~ Methods for Function 'MonthReceived' in Package 'RISmed'...
myeloma
Example of results from 'EUtilsGet'
NlmUniqueID
Extracts 'NlmUniqueID' from 'Medline' object.
NlmUniqueID-methods
~~ Methods for Function 'NlmUniqueID' in Package 'RISmed' ~~
PMID
Extracts 'PMID' from 'Medline' object.
PMID-methods
~~ Methods for Function 'PMID' in Package 'RISmed' ~~
print
Print method for EUtilsSummary object
print-method
Print method for Medline object
PublicationStatus
Extracts 'PublicationStatus' from 'Medline' object.
PublicationStatus-methods
~~ Methods for Function 'PublicationStatus' in Package...
PublicationType
Extracts 'PublicationType' from 'Medline' object.
PublicationType-methods
~~ Methods for Function 'PublicationType' in Package 'RISmed'...
Query
Extract 'Query' from 'Medline' object.
Query-methods
~~ Methods for Function 'Query' in Package 'RISmed' ~~
RefSource
Extracts 'RefSource' from 'Medline' object.
RefSource-methods
~~ Methods for Function 'RefSource' in Package 'RISmed' ~~
RegistryNumber
Extracts 'RegistryNumber' from 'Medline' object.
RegistryNumber-methods
~~ Methods for Function 'RegistryNumber' in Package 'RISmed'...
RISmed-package
Download content from NCBI databases.
show-Medline-methods
Show method for Medline object
show-methods
Show method for EUtilsSummary object
summary-methods
Summary method for EUtilsSummary object
Title
Extracts 'Title' from 'Medline' object.
Title-methods
~~ Methods for Function 'Title' in Package 'RISmed' ~~
translation
Get the NCBI query translation from EUtilsQuery
Volume
Extracts 'Volume' from 'Medline' object.
Volume-methods
~~ Methods for Function 'Volume' in Package 'RISmed' ~~
YearAccepted
Extracts 'YearAccepted' from 'Medline' object.
YearAccepted-methods
~~ Methods for Function 'YearAccepted' in Package 'RISmed' ~~
YearEpublish
Extracts 'YearEpublish' from 'Medline' object.
YearEpublish-methods
~~ Methods for Function 'YearEpublish' in Package 'RISmed' ~~
YearPmc
Extracts 'YearPmc' from 'Medline' object.
YearPmc-methods
~~ Methods for Function 'YearPmc' in Package 'RISmed' ~~
YearPpublish
Extracts 'YearPpublish' from 'Medline' object.
YearPpublish-methods
~~ Methods for Function 'YearPpublish' in Package 'RISmed' ~~
YearPubmed
Extracts 'YearPubmed' from 'Medline' object.
YearPubmed-methods
~~ Methods for Function 'YearPubmed' in Package 'RISmed' ~~
YearReceived
Extracts 'YearReceived' from 'Medline' object.
YearReceived-methods
~~ Methods for Function 'YearReceived' in Package 'RISmed' ~~

Files in this package

RISmed
RISmed/inst
RISmed/inst/test
RISmed/inst/test/year_test.R
RISmed/NAMESPACE
RISmed/NEWS
RISmed/data
RISmed/data/myeloma.RData
RISmed/R
RISmed/R/AllGenerics.R
RISmed/R/MedlineC.R
RISmed/R/EUtils.R
RISmed/R/Cited.R
RISmed/R/EUtilsSummary.R
RISmed/R/Medline.R
RISmed/MD5
RISmed/DESCRIPTION
RISmed/man
RISmed/man/myeloma.Rd
RISmed/man/YearPubmed.Rd
RISmed/man/summary-methods.Rd
RISmed/man/DayPubmed-methods.Rd
RISmed/man/RefSource.Rd
RISmed/man/YearPmc-methods.Rd
RISmed/man/HourPubmed-methods.Rd
RISmed/man/MonthAccepted.Rd
RISmed/man/HourPubmed.Rd
RISmed/man/YearAccepted-methods.Rd
RISmed/man/Query.Rd
RISmed/man/DayPpublish.Rd
RISmed/man/Country-methods.Rd
RISmed/man/YearEpublish-methods.Rd
RISmed/man/MonthReceived.Rd
RISmed/man/Cited.Rd
RISmed/man/HourReceived-methods.Rd
RISmed/man/DayAccepted-methods.Rd
RISmed/man/NlmUniqueID-methods.Rd
RISmed/man/MonthPubmed-methods.Rd
RISmed/man/ArticleId.Rd
RISmed/man/DayPmc-methods.Rd
RISmed/man/EUtilsSummary-class.Rd
RISmed/man/HourPpublish.Rd
RISmed/man/DayAccepted.Rd
RISmed/man/MedlineTA-methods.Rd
RISmed/man/YearPpublish.Rd
RISmed/man/AbstractText.Rd
RISmed/man/PublicationStatus.Rd
RISmed/man/Author-methods.Rd
RISmed/man/CopyrightInformation.Rd
RISmed/man/Acronym.Rd
RISmed/man/Title.Rd
RISmed/man/Agency-methods.Rd
RISmed/man/YearPpublish-methods.Rd
RISmed/man/HourPmc-methods.Rd
RISmed/man/Issue.Rd
RISmed/man/NlmUniqueID.Rd
RISmed/man/MonthPpublish-methods.Rd
RISmed/man/id.Rd
RISmed/man/HourPpublish-methods.Rd
RISmed/man/RefSource-methods.Rd
RISmed/man/PublicationStatus-methods.Rd
RISmed/man/DayReceived-methods.Rd
RISmed/man/MinuteEpublish.Rd
RISmed/man/MonthPmc.Rd
RISmed/man/DayPmc.Rd
RISmed/man/MonthPmc-methods.Rd
RISmed/man/Title-methods.Rd
RISmed/man/MedlineTA.Rd
RISmed/man/ISSN-methods.Rd
RISmed/man/Volume.Rd
RISmed/man/Query-methods.Rd
RISmed/man/RegistryNumber.Rd
RISmed/man/MonthAccepted-methods.Rd
RISmed/man/Author.Rd
RISmed/man/MonthPubmed.Rd
RISmed/man/MinutePubmed-methods.Rd
RISmed/man/MinuteReceived.Rd
RISmed/man/DayEpublish-methods.Rd
RISmed/man/Cited-methods.Rd
RISmed/man/HourEpublish.Rd
RISmed/man/CollectiveName.Rd
RISmed/man/ELocationID.Rd
RISmed/man/MinutePubmed.Rd
RISmed/man/PublicationType-methods.Rd
RISmed/man/EUtilsGet.Rd
RISmed/man/show-Medline-methods.Rd
RISmed/man/EUtilsSummary.Rd
RISmed/man/ArticleTitle.Rd
RISmed/man/MinutePpublish.Rd
RISmed/man/YearReceived.Rd
RISmed/man/Country.Rd
RISmed/man/MinutePmc-methods.Rd
RISmed/man/Mesh.Rd
RISmed/man/DayReceived.Rd
RISmed/man/HourAccepted-methods.Rd
RISmed/man/HourAccepted.Rd
RISmed/man/Mesh-methods.Rd
RISmed/man/HourReceived.Rd
RISmed/man/YearReceived-methods.Rd
RISmed/man/MinuteAccepted-methods.Rd
RISmed/man/YearEpublish.Rd
RISmed/man/DayPubmed.Rd
RISmed/man/MinuteAccepted.Rd
RISmed/man/MinuteEpublish-methods.Rd
RISmed/man/MedlinePgn.Rd
RISmed/man/PMID.Rd
RISmed/man/MedlinePgn-methods.Rd
RISmed/man/Medline.Rd
RISmed/man/MonthEpublish.Rd
RISmed/man/Language-methods.Rd
RISmed/man/EUtilsQuery.Rd
RISmed/man/RegistryNumber-methods.Rd
RISmed/man/MinutePpublish-methods.Rd
RISmed/man/ISSN.Rd
RISmed/man/MonthPpublish.Rd
RISmed/man/Acronym-methods.Rd
RISmed/man/Affiliation.Rd
RISmed/man/c-methods.Rd
RISmed/man/ArticleId-methods.Rd
RISmed/man/Language.Rd
RISmed/man/RISmed-package.Rd
RISmed/man/Affiliation-methods.Rd
RISmed/man/MinutePmc.Rd
RISmed/man/DayPpublish-methods.Rd
RISmed/man/Issue-methods.Rd
RISmed/man/translation.Rd
RISmed/man/GrantID-methods.Rd
RISmed/man/print-method.Rd
RISmed/man/count.Rd
RISmed/man/YearAccepted.Rd
RISmed/man/Volume-methods.Rd
RISmed/man/MonthReceived-methods.Rd
RISmed/man/print.Rd
RISmed/man/AbstractText-methods.Rd
RISmed/man/ISSNLinking.Rd
RISmed/man/PMID-methods.Rd
RISmed/man/ISOAbbreviation-methods.Rd
RISmed/man/HourPmc.Rd
RISmed/man/MonthEpublish-methods.Rd
RISmed/man/MinuteReceived-methods.Rd
RISmed/man/YearPmc.Rd
RISmed/man/ArticleTitle-methods.Rd
RISmed/man/CollectiveName-methods.Rd
RISmed/man/CopyrightInformation-methods.Rd
RISmed/man/HourEpublish-methods.Rd
RISmed/man/GrantID.Rd
RISmed/man/ISOAbbreviation.Rd
RISmed/man/ISSNLinking-methods.Rd
RISmed/man/DayEpublish.Rd
RISmed/man/PublicationType.Rd
RISmed/man/ELocationID-methods.Rd
RISmed/man/YearPubmed-methods.Rd
RISmed/man/show-methods.Rd
RISmed/man/Agency.Rd