Package 'biodbNcbi'

Title: biodbNcbi, a library for connecting to NCBI Databases.
Description: The biodbNcbi library provides access to the NCBI databases CCDS, Gene, Pubchem Comp and Pubchem Subst, using biodb package framework. It allows to retrieve entries by their accession number. Web services can be accessed for searching the database by name or mass.
Authors: Pierrick Roger [aut, cre]
Maintainer: Pierrick Roger <[email protected]>
License: AGPL-3
Version: 1.11.0
Built: 2024-10-30 04:22:44 UTC
Source: https://github.com/bioc/biodbNcbi

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biodbNcbi: biodbNcbi, a library for connecting to NCBI Databases.

Description

The biodbNcbi library provides access to the NCBI databases CCDS, Gene, Pubchem Comp and Pubchem Subst, using biodb package framework. It allows to retrieve entries by their accession number. Web services can be accessed for searching the database by name or mass.

Details

See vignette biodbNcbi:

vignette('biodbNcbi', package='biodbNcbi')

Author(s)

Maintainer: Pierrick Roger [email protected] (ORCID)

See Also

NcbiGeneConn, NcbiCcdsConn, NcbiPubchemCompConn and NcbiPubchemSubstConn.


NCBI CCDS connector class.

Description

Connector class for NCBI CCDS database.

Details

This is a concrete connector class. It must never be instantiated directly, but instead be instantiated through the factory BiodbFactory. Only specific methods are described here. See super classes for the description of inherited methods.

Super classes

biodb::BiodbConnBase -> biodb::BiodbConn -> NcbiCcdsConn

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
NcbiCcdsConn$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

BiodbConn.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Get a connector:
conn <- mybiodb$getFactory()$createConn('ncbi.ccds')

# Get the first entry
e <- conn$getEntry('CCDS12227.1')

# Terminate instance.
mybiodb$terminate()

NCBI CCDS entry class.

Description

Entry class for NCBI CCDS database.

Super classes

biodb::BiodbEntry -> biodb::BiodbXmlEntry -> biodb::BiodbHtmlEntry -> NcbiCcdsEntry

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
NcbiCcdsEntry$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

BiodbHtmlEntry.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Get a connector for CCDS database:
conn <- mybiodb$getFactory()$createConn('ncbi.ccds')

# Get the first entry
e <- conn$getEntry('CCDS12227.1')

# Terminate instance.
mybiodb$terminate()

NCBI Entrez connector abstract class.

Description

NCBI Entrez connector abstract class.

NCBI Entrez connector abstract class.

Details

This is an abstract class, mother class of all NCBI Entrez connector classes.

Note: the implementation of the getEntryIds() method uses a last resort solution. It returns only a small subset of Ncbi entries.

Super classes

biodb::BiodbConnBase -> biodb::BiodbConn -> NcbiEntrezConn

Methods

Public methods

Inherited methods

Method new()

New instance initializer. Connector classes must not be instantiated directly. Instead, you must use the createConn() method of the factory class.

Usage
NcbiEntrezConn$new(entrez.name, entrez.tag = NULL, entrez.id.tag = NULL, ...)
Arguments
entrez.name

Entrez database name (ex: "gene").

entrez.tag

Entrez database tag (ex: "Entrezgene").

entrez.id.tag

Entrez database ID tag (ex: "Gene-track_geneid").

...

All other parameters are passed to the super class initializer.

Returns

Nothing.


Method wsEfetch()

Calls Entrez efetch web service. See https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch.

Usage
NcbiEntrezConn$wsEfetch(
  id,
  rettype = NULL,
  retmode = NULL,
  retfmt = c("plain", "parsed", "request")
)
Arguments
id

A character vector of entry IDs.

rettype

The retrieval type. See NCBI documentation.

retmode

The retrieval mode. See NCBI documentation.

retfmt

Use to set the format of the returned value. 'plain' will return the raw results from the server, as a character value. 'parsed' will return the parsed results, as an XML object. 'request' will return a BiodbRequest object representing the request as it would have been sent.

Returns

Depending on retfmt parameter.


Method wsEsearch()

Calls Entrez esearch web service. See https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch.

Usage
NcbiEntrezConn$wsEsearch(
  term,
  field = NULL,
  retmax = NULL,
  retfmt = c("plain", "parsed", "request", "ids")
)
Arguments
term

Text query. See NCBI documentation.

field

Entrez field to which to limit the search. See NCBI documentation.

retmax

Maximum number of entry IDs to return.

retfmt

Use to set the format of the returned value. 'plain' will return the raw results from the server, as a character value. 'parsed' will return the parsed results, as an XML object. 'request' will return a BiodbRequest object representing the request as it would have been sent. 'ids' will return a character vector containing the IDs of the matching entries.

Returns

Depending on retfmt parameter.


Method wsEinfo()

Calls Entrez einfo web service, returning information about this database. See https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EInfo.

Usage
NcbiEntrezConn$wsEinfo(retfmt = c("plain", "request", "parsed"))
Arguments
retfmt

Use to set the format of the returned value. 'plain' will return the raw results from the server, as a character value. 'parsed' will return the parsed results, as an XML object. 'request' will return a BiodbRequest object representing the request as it would have been sent.

Returns

Depending on retfmt parameter.


Method clone()

The objects of this class are cloneable with this method.

Usage
NcbiEntrezConn$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

BiodbConn.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Create a connector
conn <- mybiodb$getFactory()$createConn('ncbi.gene')

# Get an entry
e <- conn$getEntry('2833')

# Terminate instance.
mybiodb$terminate()

NCBI Gene connector class.

Description

NCBI Gene connector class.

NCBI Gene connector class.

Details

This is the connector class for a NCBI Gene database.

Super classes

biodb::BiodbConnBase -> biodb::BiodbConn -> biodbNcbi::NcbiEntrezConn -> NcbiGeneConn

Methods

Public methods

Inherited methods

Method new()

New instance initializer.

Usage
NcbiGeneConn$new(...)
Arguments
...

All other parameters are passed to the super class initializer.

Returns

Nothing.


Method clone()

The objects of this class are cloneable with this method.

Usage
NcbiGeneConn$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

NcbiEntrezConn.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Create a connector
conn <- mybiodb$getFactory()$createConn('ncbi.gene')

# Get an entry
e <- conn$getEntry('2833')

# Terminate instance.
mybiodb$terminate()

NCBI Gene entry class.

Description

This is the entry class for a NCBI Gene database.

Super classes

biodb::BiodbEntry -> biodb::BiodbXmlEntry -> NcbiGeneEntry

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
NcbiGeneEntry$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Create a connector
conn <- mybiodb$getFactory()$createConn('ncbi.gene')

# Get an entry
e <- conn$getEntry('2833')

# Terminate instance.
mybiodb$terminate()

NCBI PubChem Compound connector class.

Description

NCBI PubChem Compound connector class.

NCBI PubChem Compound connector class.

Details

This is the connector class for a NCBI PubChen Compound database.

Super classes

biodb::BiodbConnBase -> biodb::BiodbConn -> biodbNcbi::NcbiEntrezConn -> biodbNcbi::NcbiPubchemConn -> NcbiPubchemCompConn

Methods

Public methods

Inherited methods

Method new()

New instance initializer. Connector classes must not be instantiated directly. Instead, you must use the createConn() method of the factory class.

Usage
NcbiPubchemCompConn$new(...)
Arguments
...

All other parameters are passed to the super class initializer.

Returns

Nothing.


Method clone()

The objects of this class are cloneable with this method.

Usage
NcbiPubchemCompConn$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Create a connector
conn <- mybiodb$getFactory()$createConn('ncbi.pubchem.comp')

# Get an entry
e <- conn$getEntry('2')

# Terminate instance.
mybiodb$terminate()

NCBI PubChem Compound entry class.

Description

This is the entry class for a NCBI PubChen Compound database.

Super classes

biodb::BiodbEntry -> biodb::BiodbXmlEntry -> biodbNcbi::NcbiPubchemEntry -> NcbiPubchemCompEntry

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
NcbiPubchemCompEntry$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Create a connector
conn <- mybiodb$getFactory()$createConn('ncbi.pubchem.comp')

# Get an entry
e <- conn$getEntry('2')

# Terminate instance.
mybiodb$terminate()

NCBI PubChem connector abstractclass.

Description

NCBI PubChem connector abstractclass.

NCBI PubChem connector abstractclass.

Details

This is an abstract class, mother class of all NCBI PubChem connector classes.

Super classes

biodb::BiodbConnBase -> biodb::BiodbConn -> biodbNcbi::NcbiEntrezConn -> NcbiPubchemConn

Methods

Public methods

Inherited methods

Method new()

New instance initializer. Connector classes must not be instantiated directly. Instead, you must use the createConn() method of the factory class.

Usage
NcbiPubchemConn$new(db.name, id.xmltag, entry.xmltag, id.urlfield, ...)
Arguments
db.name

PubChem database name.

id.xmltag

XML tag for ID.

entry.xmltag

XML tag for entry.

id.urlfield

Database ID to use when building URL.

...

All other parameters are passed to the super class initializer.

Returns

Nothing.


Method clone()

The objects of this class are cloneable with this method.

Usage
NcbiPubchemConn$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

NcbiEntrezConn.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Create a connector
conn <- mybiodb$getFactory()$createConn('ncbi.pubchem.comp')

# Get an entry
e <- conn$getEntry('2')

# Terminate instance.
mybiodb$terminate()

NCBI PubChem entry class.

Description

NCBI PubChem entry class.

NCBI PubChem entry class.

Details

This the abstract entry class for all NCBI PubChem entry classes.

Super classes

biodb::BiodbEntry -> biodb::BiodbXmlEntry -> NcbiPubchemEntry

Methods

Public methods

Inherited methods

Method new()

New instance initializer.

Usage
NcbiPubchemEntry$new(...)
Arguments
...

All other parameters are passed to the super class initializer.

Returns

Nothing.


Method clone()

The objects of this class are cloneable with this method.

Usage
NcbiPubchemEntry$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Create a connector
conn <- mybiodb$getFactory()$createConn('ncbi.pubchem.comp')

# Get an entry
e <- conn$getEntry('2')

# Terminate instance.
mybiodb$terminate()

NCBI PubChem Substance connector class.

Description

NCBI PubChem Substance connector class.

NCBI PubChem Substance connector class.

Details

This is the connector class for a NCBI PubChen Substance database.

Super classes

biodb::BiodbConnBase -> biodb::BiodbConn -> biodbNcbi::NcbiEntrezConn -> biodbNcbi::NcbiPubchemConn -> NcbiPubchemSubstConn

Methods

Public methods

Inherited methods

Method new()

New instance initializer. Connector classes must not be instantiated directly. Instead, you must use the createConn() method of the factory class.

Usage
NcbiPubchemSubstConn$new(...)
Arguments
...

All other parameters are passed to the super class initializer.

Returns

Nothing.


Method clone()

The objects of this class are cloneable with this method.

Usage
NcbiPubchemSubstConn$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Create a connector
conn <- mybiodb$getFactory()$createConn('ncbi.pubchem.subst')

# Get an entry
e <- conn$getEntry('2')

# Terminate instance.
mybiodb$terminate()

NCBI PubChem Substance entry class.

Description

This is the entry class for a NCBI PubChen Substance database.

Super classes

biodb::BiodbEntry -> biodb::BiodbXmlEntry -> biodbNcbi::NcbiPubchemEntry -> NcbiPubchemSubstEntry

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
NcbiPubchemSubstEntry$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Create a connector
conn <- mybiodb$getFactory()$createConn('ncbi.pubchem.subst')

# Get an entry
e <- conn$getEntry('2')

# Terminate instance.
mybiodb$terminate()