[med-svn] [r-bioc-go.db] 06/08: New upstream version 3.4.0
Andreas Tille
tille at debian.org
Mon Oct 2 12:14:56 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-bioc-go.db.
commit b69fda6f968ba4b8a34645514a5138eb23948567
Author: Andreas Tille <tille at debian.org>
Date: Mon Oct 2 13:56:18 2017 +0200
New upstream version 3.4.0
---
DESCRIPTION | 13 +++++
NAMESPACE | 14 ++++++
R/zzz.R | 37 ++++++++++++++
debian/README.test | 5 --
debian/changelog | 13 -----
debian/compat | 1 -
debian/control | 25 ---------
debian/copyright | 134 -------------------------------------------------
debian/rules | 4 --
debian/source/format | 1 -
debian/watch | 3 --
inst/extdata/GO.sqlite | Bin 0 -> 97032192 bytes
man/GOBASE.Rd | 35 +++++++++++++
man/GOBPANCESTOR.Rd | 54 ++++++++++++++++++++
man/GOBPCHILDREN.Rd | 61 ++++++++++++++++++++++
man/GOBPOFFSPRING.Rd | 55 ++++++++++++++++++++
man/GOBPPARENTS.Rd | 66 ++++++++++++++++++++++++
man/GOCCANCESTOR.Rd | 54 ++++++++++++++++++++
man/GOCCCHILDREN.Rd | 60 ++++++++++++++++++++++
man/GOCCOFFSPRING.Rd | 54 ++++++++++++++++++++
man/GOCCPARENTS.Rd | 64 +++++++++++++++++++++++
man/GOMAPCOUNTS.Rd | 51 +++++++++++++++++++
man/GOMFANCESTOR.Rd | 55 ++++++++++++++++++++
man/GOMFCHILDREN.Rd | 60 ++++++++++++++++++++++
man/GOMFOFFSPRING.Rd | 54 ++++++++++++++++++++
man/GOMFPARENTS.Rd | 66 ++++++++++++++++++++++++
man/GOOBSOLETE.Rd | 44 ++++++++++++++++
man/GOSYNONYM.Rd | 34 +++++++++++++
man/GOTERM.Rd | 60 ++++++++++++++++++++++
man/GO_dbconn.Rd | 87 ++++++++++++++++++++++++++++++++
30 files changed, 1078 insertions(+), 186 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
new file mode 100644
index 0000000..71fc253
--- /dev/null
+++ b/DESCRIPTION
@@ -0,0 +1,13 @@
+Package: GO.db
+Title: A set of annotation maps describing the entire Gene Ontology
+Description: A set of annotation maps describing the entire Gene Ontology assembled using data from GO
+Version: 3.4.0
+Author: Marc Carlson
+Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
+Depends: R (>= 2.7.0), methods, AnnotationDbi (>= 1.35.4)
+Imports: methods, AnnotationDbi
+Suggests: DBI
+License: Artistic-2.0
+biocViews: AnnotationData, FunctionalAnnotation
+NeedsCompilation: no
+Packaged: 2016-10-02 21:51:35 UTC; root
diff --git a/NAMESPACE b/NAMESPACE
new file mode 100644
index 0000000..de133c2
--- /dev/null
+++ b/NAMESPACE
@@ -0,0 +1,14 @@
+import(methods)
+import(AnnotationDbi)
+
+### Only put what is statically exported here. All the AnnObj instances
+### created at load time are dynamically exported (refer to R/zzz.R for
+### the details).
+export(
+ GO,
+ GO_dbconn,
+ GO_dbfile,
+ GO_dbschema,
+ GO_dbInfo
+)
+
diff --git a/R/zzz.R b/R/zzz.R
new file mode 100644
index 0000000..420a727
--- /dev/null
+++ b/R/zzz.R
@@ -0,0 +1,37 @@
+datacache <- new.env(hash=TRUE, parent=emptyenv())
+
+GO <- function() showQCData("GO", datacache)
+GO_dbconn <- function() dbconn(datacache)
+GO_dbfile <- function() dbfile(datacache)
+GO_dbschema <- function(file="", show.indices=FALSE) dbschema(datacache, file=file, show.indices=show.indices)
+GO_dbInfo <- function() dbInfo(datacache)
+
+.onLoad <- function(libname, pkgname)
+{
+ ## Connect to the SQLite DB
+ dbfile <- system.file("extdata", "GO.sqlite", package=pkgname, lib.loc=libname)
+ assign("dbfile", dbfile, envir=datacache)
+ dbconn <- dbFileConnect(dbfile)
+ assign("dbconn", dbconn, envir=datacache)
+
+ ## Create the OrgDb object
+ sPkgname <- sub(".db$","",pkgname)
+ txdb <- loadDb(system.file("extdata", paste(sPkgname,
+ ".sqlite",sep=""), package=pkgname, lib.loc=libname),
+ packageName=pkgname)
+ dbNewname <- AnnotationDbi:::dbObjectName(pkgname,"GODb")
+ ns <- asNamespace(pkgname)
+ assign(dbNewname, txdb, envir=ns)
+ namespaceExport(ns, dbNewname)
+
+ ## Create the AnnObj instances
+ ann_objs <- createAnnObjs.SchemaChoice("GO_DB", "GO", "GO", dbconn, datacache)
+ mergeToNamespaceAndExport(ann_objs, pkgname)
+ packageStartupMessage(AnnotationDbi:::annoStartupMessages("GO.db"))
+}
+
+.onUnload <- function(libpath)
+{
+ dbFileDisconnect(GO_dbconn())
+}
+
diff --git a/debian/README.test b/debian/README.test
deleted file mode 100644
index 149dd05..0000000
--- a/debian/README.test
+++ /dev/null
@@ -1,5 +0,0 @@
-Notes on how this package can be tested.
-────────────────────────────────────────
-
-This package can be tested by loading it into R with the command
-‘library(GO.db)’ in order to confirm its integrity.
diff --git a/debian/changelog b/debian/changelog
deleted file mode 100644
index 53e4cbd..0000000
--- a/debian/changelog
+++ /dev/null
@@ -1,13 +0,0 @@
-r-bioc-go.db (3.4.0-1) unstable; urgency=medium
-
- * New upstream version
- * Convert to dh-r
- * Generic BioConductor homepage
-
- -- Andreas Tille <tille at debian.org> Fri, 28 Oct 2016 08:59:52 +0200
-
-r-bioc-go.db (3.3.0-1) unstable; urgency=low
-
- * Initial release (closes: #824805)
-
- -- Andreas Tille <tille at debian.org> Fri, 20 May 2016 00:14:08 +0200
diff --git a/debian/compat b/debian/compat
deleted file mode 100644
index ec63514..0000000
--- a/debian/compat
+++ /dev/null
@@ -1 +0,0 @@
-9
diff --git a/debian/control b/debian/control
deleted file mode 100644
index 2269755..0000000
--- a/debian/control
+++ /dev/null
@@ -1,25 +0,0 @@
-Source: r-bioc-go.db
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
-Section: gnu-r
-Priority: optional
-Build-Depends: debhelper (>= 9),
- dh-r,
- r-base-dev,
- r-bioc-annotationdbi
-Standards-Version: 3.9.8
-Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-go.db/trunk/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-go.db/trunk/
-Homepage: https://bioconductor.org/packages/GO.db/
-
-Package: r-bioc-go.db
-Architecture: all
-Depends: ${R:Depends},
- ${misc:Depends}
-Recommends: ${R:Recommends}
-Suggests: ${R:Suggests}
-Description: annotation maps describing the entire Gene Ontology
- This package is part of BioConductor and provides a set of annotation
- maps describing the entire Gene Ontology assembled using data from GO.
- .
- The package helps running the test suites of some BioConductor packages.
diff --git a/debian/copyright b/debian/copyright
deleted file mode 100644
index e158644..0000000
--- a/debian/copyright
+++ /dev/null
@@ -1,134 +0,0 @@
-Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: GO.db
-Upstream-Contact: Bioconductor Package Maintainer <maintainer at bioconductor.org>
-Source: https://bioconductor.org/packages/GO.db/
-
-Files: *
-Copyright: 2006-2016 Marc Carlson
-License: Artistic-2.0
-
-Files: debian/*
-Copyright: 2016 Andreas Tille <tille at debian.org>
-License: Artistic-2.0
-
-License: Artistic-2.0
- Permission for Use and Modification Without Distribution
- .
- (1) You are permitted to use the Standard Version and create and use
- Modified Versions for any purpose without restriction, provided that you
- do not Distribute the Modified Version. Permissions for Redistribution
- of the Standard Version
- .
- (2) You may Distribute verbatim copies of the Source form of the
- Standard Version of this Package in any medium without restriction,
- either gratis or for a Distributor Fee, provided that you duplicate all
- of the original copyright notices and associated disclaimers. At your
- discretion, such verbatim copies may or may not include a Compiled form
- of the Package.
- .
- (3) You may apply any bug fixes, portability changes, and other
- modifications made available from the Copyright Holder. The resulting
- Package will still be considered the Standard Version, and as such will
- be subject to the Original License. Distribution of Modified Versions
- of the Package as Source
- .
- (4) You may Distribute your Modified Version as Source (either gratis
- or for a Distributor Fee, and with or without a Compiled form of the
- Modified Version) provided that you clearly document how it differs from
- the Standard Version, including, but not limited to, documenting any
- non-standard features, executables, or modules, and provided that you do
- at least ONE of the following:
- .
- (a) make the Modified Version available to the Copyright Holder of
- the Standard Version, under the Original License, so that the
- Copyright Holder may include your modifications in the Standard
- Version.
- (b) ensure that installation of your Modified Version does not
- prevent the user installing or running the Standard Version. In
- addition, the Modified Version must bear a name that is different
- from the name of the Standard Version.
- (c) allow anyone who receives a copy of the Modified Version to
- make the Source form of the Modified Version available to others
- under
- (i) the Original License or
- (ii) a license that permits the licensee to freely copy, modify
- and redistribute the Modified Version using the same licensing
- terms that apply to the copy that the licensee received, and
- requires that the Source form of the Modified Version, and of
- any works derived from it, be made freely available in that
- license fees are prohibited but Distributor Fees are allowed.
- .
- Distribution of Compiled Forms of the Standard Version or Modified Versions without the Source
- .
- (5) You may Distribute Compiled forms of the Standard Version without
- the Source, provided that you include complete instructions on how to
- get the Source of the Standard Version. Such instructions must be valid
- at the time of your distribution. If these instructions, at any time
- while you are carrying out such distribution, become invalid, you must
- provide new instructions on demand or cease further distribution. If you
- provide valid instructions or cease distribution within thirty days
- after you become aware that the instructions are invalid, then you do
- not forfeit any of your rights under this license.
- .
- (6) You may Distribute a Modified Version in Compiled form without the
- Source, provided that you comply with Section 4 with respect to the
- Source of the Modified Version.
- .
- Aggregating or Linking the Package
- .
- (7) You may aggregate the Package (either the Standard Version or
- Modified Version) with other packages and Distribute the resulting
- aggregation provided that you do not charge a licensing fee for the
- Package. Distributor Fees are permitted, and licensing fees for other
- components in the aggregation are permitted. The terms of this license
- apply to the use and Distribution of the Standard or Modified Versions
- as included in the aggregation.
- .
- (8) You are permitted to link Modified and Standard Versions with other
- works, to embed the Package in a larger work of your own, or to build
- stand-alone binary or bytecode versions of applications that include the
- Package, and Distribute the result without restriction, provided the
- result does not expose a direct interface to the Package.
- .
- Items That are Not Considered Part of a Modified Version
- .
- (9) Works (including, but not limited to, modules and scripts) that
- merely extend or make use of the Package, do not, by themselves, cause
- the Package to be a Modified Version. In addition, such works are not
- considered parts of the Package itself, and are not subject to the terms
- of this license.
- .
- General Provisions
- .
- (10) Any use, modification, and distribution of the Standard or
- Modified Versions is governed by this Artistic License. By using,
- modifying or distributing the Package, you accept this license. Do not
- use, modify, or distribute the Package, if you do not accept this
- license.
- .
- (11) If your Modified Version has been derived from a Modified Version
- made by someone other than you, you are nevertheless required to ensure
- that your Modified Version complies with the requirements of this
- license.
- .
- (12) This license does not grant you the right to use any trademark,
- service mark, tradename, or logo of the Copyright Holder.
- .
- (13) This license includes the non-exclusive, worldwide, free-of-charge
- patent license to make, have made, use, offer to sell, sell, import and
- otherwise transfer the Package with respect to any patent claims
- licensable by the Copyright Holder that are necessarily infringed by the
- Package. If you institute patent litigation (including a cross-claim or
- counterclaim) against any party alleging that the Package constitutes
- direct or contributory patent infringement, then this Artistic License
- to you shall terminate on the date that such litigation is filed.
- .
- (14) Disclaimer of Warranty: THE PACKAGE IS PROVIDED BY THE COPYRIGHT
- HOLDER AND CONTRIBUTORS "AS IS' AND WITHOUT ANY EXPRESS OR IMPLIED
- WARRANTIES. THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
- PARTICULAR PURPOSE, OR NON-INFRINGEMENT ARE DISCLAIMED TO THE EXTENT
- PERMITTED BY YOUR LOCAL LAW. UNLESS REQUIRED BY LAW, NO COPYRIGHT HOLDER
- OR CONTRIBUTOR WILL BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, OR
- CONSEQUENTIAL DAMAGES ARISING IN ANY WAY OUT OF THE USE OF THE PACKAGE,
- EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
diff --git a/debian/rules b/debian/rules
deleted file mode 100755
index 68d9a36..0000000
--- a/debian/rules
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/usr/bin/make -f
-
-%:
- dh $@ --buildsystem R
diff --git a/debian/source/format b/debian/source/format
deleted file mode 100644
index 163aaf8..0000000
--- a/debian/source/format
+++ /dev/null
@@ -1 +0,0 @@
-3.0 (quilt)
diff --git a/debian/watch b/debian/watch
deleted file mode 100644
index 4aa6006..0000000
--- a/debian/watch
+++ /dev/null
@@ -1,3 +0,0 @@
-version=3
-opts=downloadurlmangle=s?^(.*)\.\.?http:$1packages/release/data/annotation? \
- http://bioconductor.org/packages/release/data/annotation/html/GO.db.html .*/GO.db_([\d\.]+)\.tar\.gz
diff --git a/inst/extdata/GO.sqlite b/inst/extdata/GO.sqlite
new file mode 100644
index 0000000..172b0b0
Binary files /dev/null and b/inst/extdata/GO.sqlite differ
diff --git a/man/GOBASE.Rd b/man/GOBASE.Rd
new file mode 100644
index 0000000..5b2561f
--- /dev/null
+++ b/man/GOBASE.Rd
@@ -0,0 +1,35 @@
+\name{GO.db}
+\alias{GO.db}
+\alias{GO}
+\title{Bioconductor annotation data package}
+\description{
+
+ Welcome to the GO.db annotation Package. The purpose of this
+ package is to provide detailed information about the latest version of the
+ Gene Ontologies. This package is updated biannually.
+
+ Objects in this package are accessed using the \code{select()} interface.
+ See ?select in the AnnotationDbi package for details.
+}
+
+\seealso{
+ \itemize{
+ \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
+ \code{keys()}, \code{columns()} and \code{select()}.
+ }
+}
+
+\examples{
+## select() interface:
+## Objects in this package can be accessed using the select() interface
+## from the AnnotationDbi package. See ?select for details.
+columns(GO.db)
+
+## Bimap interface:
+## The 'old style' of interacting with these objects is manipulation as
+## bimaps. While this approach is still available we strongly encourage the
+## use of select().
+ls("package:GO.db")
+}
+\keyword{datasets}
+
diff --git a/man/GOBPANCESTOR.Rd b/man/GOBPANCESTOR.Rd
new file mode 100644
index 0000000..ed6b23e
--- /dev/null
+++ b/man/GOBPANCESTOR.Rd
@@ -0,0 +1,54 @@
+\name{GOBPANCESTOR}
+\alias{GOBPANCESTOR}
+\title{Annotation of GO Identifiers to their Biological Process Ancestors}
+\description{
+ This data set describes associations between GO Biological Process (BP)
+ terms and their ancestor BP terms, based on the directed acyclic
+ graph (DAG) defined by the Gene Ontology Consortium. The format is an R
+ object mapping the GO BP terms to all ancestor terms, where an
+ ancestor term is a more general GO term that precedes
+ the given GO term in the DAG (in other words, the parents, and all
+ their parents, etc.).
+}
+\details{
+ Each GO BP term is mapped to a vector of ancestor GO BP terms.
+
+ Biological process is defined as the broad biological goals, such as
+ mitosis or purine metabolism, that are accomplished by ordered
+ assemblies of molecular functions as defined by Gene Ontology
+ Consortium.
+
+ Mappings were based on data provided by: Gene Ontology
+ ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
+ With a date stamp from the source of: 2016-Sep21
+}
+
+\references{
+\url{http://www.geneontology.org/} and
+\url{https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene}
+}
+
+\seealso{
+ \itemize{
+ \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
+ the \code{select()} interface.
+ }
+}
+
+\examples{
+## select() interface:
+## Objects in this package can be accessed using the select() interface
+## from the AnnotationDbi package. See ?select for details.
+
+## Bimap interface:
+# Convert the object to a list
+xx <- as.list(GOBPANCESTOR)
+# Remove GO IDs that do not have any ancestor
+xx <- xx[!is.na(xx)]
+if(length(xx) > 0){
+ # Get the ancestor GO IDs for the first two elents of xx
+ goids <- xx[1:2]
+}
+}
+\keyword{datasets}
+
diff --git a/man/GOBPCHILDREN.Rd b/man/GOBPCHILDREN.Rd
new file mode 100644
index 0000000..4826024
--- /dev/null
+++ b/man/GOBPCHILDREN.Rd
@@ -0,0 +1,61 @@
+\name{GOBPCHILDREN}
+\alias{GOBPCHILDREN}
+\title{Annotation of GO Identifiers to their Biological Process Children}
+\description{
+This data set describes associations between GO molecular function (BP)
+ terms and their direct children BP terms, based on the directed acyclic
+ graph (DAG) defined by the Gene Ontology Consortium. The format is an R
+ object mapping the GO BP terms to all direct children terms, where a
+ direct child term is a more specific GO term that is immediately preceded
+ by the given GO term in the DAG.
+}
+\details{
+ Each GO BP term is mapped to a vector of children GO BP terms.
+
+ Biological process is defined as the broad biological goals, such as
+ mitosis or purine metabolism, that are accomplished by ordered
+ assemblies of molecular functions as defined by Gene Ontology
+ Consortium.
+
+ Mappings were based on data provided by: Gene Ontology
+ ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
+ With a date stamp from the source of: 2016-Sep21
+
+}
+
+\references{
+\url{http://www.geneontology.org/} and
+\url{https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene}
+}
+
+\seealso{
+ \itemize{
+ \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
+ the \code{select()} interface.
+ }
+}
+
+\examples{
+## select() interface:
+## Objects in this package can be accessed using the select() interface
+## from the AnnotationDbi package. See ?select for details.
+
+## Bimap interface:
+# Convert the object to a list
+xx <- as.list(GOBPCHILDREN)
+# Remove GO IDs that do not have any children
+xx <- xx[!is.na(xx)]
+if(length(xx) > 0){
+ # Get the parent GO IDs for the first elents of xx
+ goids <- xx[[1]]
+ # Find out the GO terms for the first parent goid
+ GOID(GOTERM[[goids[1]]])
+ Term(GOTERM[[goids[1]]])
+ Synonym(GOTERM[[goids[1]]])
+ Secondary(GOTERM[[goids[1]]])
+ Definition(GOTERM[[goids[1]]])
+ Ontology(GOTERM[[goids[1]]])
+}
+}
+\keyword{datasets}
+
diff --git a/man/GOBPOFFSPRING.Rd b/man/GOBPOFFSPRING.Rd
new file mode 100644
index 0000000..0eac23a
--- /dev/null
+++ b/man/GOBPOFFSPRING.Rd
@@ -0,0 +1,55 @@
+\name{GOBPOFFSPRING}
+\alias{GOBPOFFSPRING}
+\title{Annotation of GO Identifiers to their Biological Process Offspring}
+\description{
+ This data set describes associations between GO molecular function (BP)
+ terms and their offspring BP terms, based on the directed acyclic
+ graph (DAG) defined by the Gene Ontology Consortium. The format is an R
+ object mapping the GO BP terms to all offspring terms, where an
+ offspring term is a more specific GO term that is preceded
+ by the given GO term in the DAG (in other words, the children and all
+ their children, etc.).
+}
+
+\details{
+ Each GO BP term is mapped to a vector of offspring GO BP terms.
+
+ Biological process is defined as the broad biological goals, such as
+ mitosis or purine metabolism, that are accomplished by ordered
+ assemblies of molecular functions as defined by Gene Ontology
+ Consortium.
+
+ Mappings were based on data provided by: Gene Ontology
+ ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
+ With a date stamp from the source of: 2016-Sep21
+}
+
+\references{
+\url{http://www.geneontology.org/} and
+\url{https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene}
+}
+
+\seealso{
+ \itemize{
+ \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
+ the \code{select()} interface.
+ }
+}
+
+\examples{
+## select() interface:
+## Objects in this package can be accessed using the select() interface
+## from the AnnotationDbi package. See ?select for details.
+
+## Bimap interface:
+# Convert the object to a list
+xx <- as.list(GOBPOFFSPRING)
+# Remove GO IDs that do not have any offspring
+xx <- xx[!is.na(xx)]
+if(length(xx) > 0){
+ # Get the offspring GO IDs for the first two elents of xx
+ goids <- xx[1:2]
+}
+}
+\keyword{datasets}
+
diff --git a/man/GOBPPARENTS.Rd b/man/GOBPPARENTS.Rd
new file mode 100644
index 0000000..30abf9f
--- /dev/null
+++ b/man/GOBPPARENTS.Rd
@@ -0,0 +1,66 @@
+\name{GOBPPARENTS}
+\alias{GOBPPARENTS}
+\title{Annotation of GO Identifiers to their Biological Process Parents}
+\description{
+ This data set describes associations between GO molecular function (BP)
+ terms and their direct parent BP terms, based on the directed acyclic
+ graph (DAG) defined by the Gene Ontology Consortium. The format is an R
+ object mapping the GO BP terms to all direct parent terms, where a
+ direct parent term is a more general GO term that immediately precedes
+ the given GO term in the DAG.
+}
+\details{
+ Each GO BP term is mapped to a named vector of GO BP terms. The name
+ associated with the parent term will be either \emph{isa}, \emph{hasa} or \emph{partof},
+ where \emph{isa} indicates that the child term is a more specific version
+ of the parent, and \emph{hasa} and \emph{partof} indicate that the
+ child term is a part of the parent. For example, a telomere is part of
+ a chromosome.
+
+ Biological process is defined as the broad biological goals, such as
+ mitosis or purine metabolism, that are accomplished by ordered
+ assemblies of molecular functions as defined by Gene Ontology
+ Consortium.
+
+ Mappings were based on data provided: Gene Ontology
+ ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
+ With a date stamp from the source of: 2016-Sep21
+
+}
+
+\references{
+\url{http://www.geneontology.org/} and
+\url{https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene}
+}
+
+\seealso{
+ \itemize{
+ \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
+ the \code{select()} interface.
+ }
+}
+
+\examples{
+## select() interface:
+## Objects in this package can be accessed using the select() interface
+## from the AnnotationDbi package. See ?select for details.
+
+## Bimap interface:
+# Convert the object to a list
+xx <- as.list(GOBPPARENTS)
+# Remove GO IDs that do not have any parent
+xx <- xx[!is.na(xx)]
+if(length(xx) > 0){
+ # Get the children GO IDs for the first elents of xx
+ goids <- xx[[1]]
+ # Find out the GO terms for the first parent goid
+ GOID(GOTERM[[goids[1]]])
+ Term(GOTERM[[goids[1]]])
+ Synonym(GOTERM[[goids[1]]])
+ Secondary(GOTERM[[goids[1]]])
+ Definition(GOTERM[[goids[1]]])
+ Ontology(GOTERM[[goids[1]]])
+}
+}
+\keyword{datasets}
+
diff --git a/man/GOCCANCESTOR.Rd b/man/GOCCANCESTOR.Rd
new file mode 100644
index 0000000..c446c6b
--- /dev/null
+++ b/man/GOCCANCESTOR.Rd
@@ -0,0 +1,54 @@
+\name{GOCCANCESTOR}
+\alias{GOCCANCESTOR}
+\title{Annotation of GO Identifiers to their Cellular Component Ancestors}
+\description{
+ This data set describes associations between GO molecular function (CC)
+ terms and their ancestor CC terms, based on the directed acyclic
+ graph (DAG) defined by the Gene Ontology Consortium. The format is an R
+ object mapping the GO CC terms to all ancestor terms, where an
+ ancestor term is a more general GO term that precedes
+ the given GO term in the DAG (in other words, the parents, and all
+ their parents, etc.).
+}
+\details{
+ Each GO CC term is mapped to a vector of ancestor GO C terms.
+
+ Cellular component is defined as the subcellular structures,
+ locations, and macromolecular complexes; examples include nucleus,
+ telomere, and origin recognition complex as defined by Gene Ontology
+ Consortium.
+
+ Mappings were based on data provided: Gene Ontology
+ ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
+ With a date stamp from the source of: 2016-Sep21
+}
+
+\references{
+\url{http://www.geneontology.org/} and
+\url{https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene}
+}
+
+\seealso{
+ \itemize{
+ \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
+ the \code{select()} interface.
+ }
+}
+
+\examples{
+## select() interface:
+## Objects in this package can be accessed using the select() interface
+## from the AnnotationDbi package. See ?select for details.
+
+## Bimap interface:
+# Convert the object to a list
+xx <- as.list(GOCCANCESTOR)
+# Remove GO IDs that do not have any ancestor
+xx <- xx[!is.na(xx)]
+if(length(xx) > 0){
+ # Get the ancestor GO IDs for the first two elents of xx
+ goids <- xx[1:2]
+}
+}
+\keyword{datasets}
+
diff --git a/man/GOCCCHILDREN.Rd b/man/GOCCCHILDREN.Rd
new file mode 100644
index 0000000..398eb50
--- /dev/null
+++ b/man/GOCCCHILDREN.Rd
@@ -0,0 +1,60 @@
+\name{GOCCCHILDREN}
+\alias{GOCCCHILDREN}
+\title{Annotation of GO Identifiers to their Cellular Component Children}
+\description{
+ This data set describes associations between GO molecular function (CC)
+ terms and their direct children CC terms, based on the directed acyclic
+ graph (DAG) defined by the Gene Ontology Consortium. The format is an R
+ object mapping the GO CC terms to all direct children terms, where a
+ direct child term is a more specific GO term that is immediately preceded
+ by the given GO term in the DAG.
+}
+\details{
+ Each GO CC term is mapped to a vector of children GO CC terms.
+
+ Cellular component is defined as the subcellular structures,
+ locations, and macromolecular complexes; examples include nucleus,
+ telomere, and origin recognition complex as defined by Gene Ontology
+ Consortium.
+
+ Mappings were based on data provided: Gene Ontology
+ ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
+ With a date stamp from the source of: 2016-Sep21
+
+}
+
+\references{
+\url{http://www.geneontology.org/} and
+\url{https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene}
+}
+
+\seealso{
+ \itemize{
+ \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
+ the \code{select()} interface.
+ }
+}
+
+\examples{
+## select() interface:
+## Objects in this package can be accessed using the select() interface
+## from the AnnotationDbi package. See ?select for details.
+
+## Bimap interface:
+# Convert the object to a list
+xx <- as.list(GOCCCHILDREN)
+# Remove GO IDs that do not have any children
+xx <- xx[!is.na(xx)]
+if(length(xx) > 0){
+goids <- xx[[1]]
+# Find out the GO terms for the first parent goid
+GOID(GOTERM[[goids[1]]])
+Term(GOTERM[[goids[1]]])
+Synonym(GOTERM[[goids[1]]])
+Secondary(GOTERM[[goids[1]]])
+Definition(GOTERM[[goids[1]]])
+Ontology(GOTERM[[goids[1]]])
+}
+}
+\keyword{datasets}
+
diff --git a/man/GOCCOFFSPRING.Rd b/man/GOCCOFFSPRING.Rd
new file mode 100644
index 0000000..3e745d2
--- /dev/null
+++ b/man/GOCCOFFSPRING.Rd
@@ -0,0 +1,54 @@
+\name{GOCCOFFSPRING}
+\alias{GOCCOFFSPRING}
+\title{Annotation of GO Identifiers to their Cellular Component Offspring}
+\description{
+ This data set describes associations between GO molecular function (MF)
+ terms and their offspring MF terms, based on the directed acyclic
+ graph (DAG) defined by the Gene Ontology Consortium. The format is an R
+ object mapping the GO MF terms to all offspring terms, where an
+ offspring term is a more specific GO term that is preceded
+ by the given GO term in the DAG (in other words, the children and all
+ their children, etc.).
+}
+\details{
+ Each GO CC term is mapped to a vector of offspring GO MF terms.
+
+ Cellular component is defined as the subcellular structures,
+ locations, and macromolecular complexes; examples include nucleus,
+ telomere, and origin recognition complex as defined b y Gene Ontology
+ Consortium.
+
+ Mappings were based on data provided: Gene Ontology
+ ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
+ With a date stamp from the source of: 2016-Sep21
+}
+
+\references{
+\url{http://www.geneontology.org/} and
+\url{https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene}
+}
+
+\seealso{
+ \itemize{
+ \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
+ the \code{select()} interface.
+ }
+}
+
+\examples{
+## select() interface:
+## Objects in this package can be accessed using the select() interface
+## from the AnnotationDbi package. See ?select for details.
+
+## Bimap interface:
+# Convert the object to a list
+xx <- as.list(GOCCOFFSPRING)
+# Remove GO identifiers that do not have any offspring
+xx <- xx[!is.na(xx)]
+if(length(xx) > 0){
+ # Get the offspring GO identifiers for the first two elents of xx
+ goidentifiers <- xx[1:2]
+}
+}
+\keyword{datasets}
+
diff --git a/man/GOCCPARENTS.Rd b/man/GOCCPARENTS.Rd
new file mode 100644
index 0000000..c7c7a1e
--- /dev/null
+++ b/man/GOCCPARENTS.Rd
@@ -0,0 +1,64 @@
+\name{GOCCPARENTS}
+\alias{GOCCPARENTS}
+\title{Annotation of GO Identifiers to their Cellular Component Parents}
+\description{
+ This data set describes associations between GO molecular function (CC)
+ terms and their direct parent CC terms, based on the directed acyclic
+ graph (DAG) defined by the Gene Ontology Consortium. The format is an R
+ object mapping the GO CC terms to all direct parent terms, where a
+ direct parent term is a more general GO term that immediately precedes
+ the given GO term in the DAG.
+}
+\details{
+ Each GO CC term is mapped to a named vector of GO CC terms. The name
+ associated with the parent term will be either \emph{isa}, \emph{hasa} or \emph{partof},
+ where \emph{isa} indicates that the child term is a more specific version
+ of the parent, and \emph{hasa} and \emph{partof} indicate that the
+ child term is a part of the parent. For example, a telomere is part of
+ a chromosome.
+
+ Cellular component is defined as the subcellular structures,
+ locations, and macromolecular complexes; examples include nucleus,
+ telomere, and origin recognition complex as defined b y Gene Ontology
+ Consortium.
+
+ Mappings were based on data provided: Gene Ontology
+ ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
+ With a date stamp from the source of: 2016-Sep21
+}
+
+\references{
+\url{http://www.geneontology.org/} and
+\url{https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene}
+}
+
+\seealso{
+ \itemize{
+ \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
+ the \code{select()} interface.
+ }
+}
+
+\examples{
+## select() interface:
+## Objects in this package can be accessed using the select() interface
+## from the AnnotationDbi package. See ?select for details.
+
+## Bimap interface:
+# Convert the object to a list
+xx <- as.list(GOCCPARENTS)
+# Remove GO IDs that do not have any parent
+xx <- xx[!is.na(xx)]
+if(length(xx) > 0){
+ goids <- xx[[1]]
+ # Find out the GO terms for the first parent go ID
+ GOID(GOTERM[[goids[1]]])
+ Term(GOTERM[[goids[1]]])
+ Synonym(GOTERM[[goids[1]]])
+ Secondary(GOTERM[[goids[1]]])
+ Definition(GOTERM[[goids[1]]])
+ Ontology(GOTERM[[goids[1]]])
+}
+}
+\keyword{datasets}
+
diff --git a/man/GOMAPCOUNTS.Rd b/man/GOMAPCOUNTS.Rd
new file mode 100644
index 0000000..0c8218e
--- /dev/null
+++ b/man/GOMAPCOUNTS.Rd
@@ -0,0 +1,51 @@
+\name{GOMAPCOUNTS}
+
+\alias{GOMAPCOUNTS}
+
+
+\title{Number of mapped keys for the maps in package GO.db}
+
+\description{
+ GOMAPCOUNTS provides the "map count" (i.e. the
+ count of mapped keys) for each map in package GO.db.
+}
+
+\details{
+ This "map count" information is precalculated and stored in the
+ package annotation DB. This allows some quality control and is used by
+ the \code{\link[AnnotationDbi:AnnDbPkg-checker]{checkMAPCOUNTS}}
+ function defined in AnnotationDbi to compare and validate different
+ methods (like \code{count.mappedkeys(x)} or
+ \code{sum(!is.na(as.list(x)))}) for getting the "map count" of a given
+ map.
+}
+
+\seealso{
+ \itemize{
+ \item \code{\link[AnnotationDbi:Bimap-keys]{mappedkeys}},
+ \item \code{\link[AnnotationDbi:Bimap-keys]{count.mappedkeys}},
+ \item \code{\link[AnnotationDbi:AnnDbPkg-checker]{checkMAPCOUNTS}}
+ \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
+ the \code{select()} interface.
+ }
+}
+
+\examples{
+## select() interface:
+## Objects in this package can be accessed using the select() interface
+## from the AnnotationDbi package. See ?select for details.
+
+## Bimap interface:
+GOMAPCOUNTS
+mapnames <- names(GOMAPCOUNTS)
+GOMAPCOUNTS[mapnames[1]]
+x <- get(mapnames[1])
+sum(!is.na(as.list(x)))
+count.mappedkeys(x) # much faster!
+
+## Check the "map count" of all the maps in package GO.db
+checkMAPCOUNTS("GO.db")
+}
+
+\keyword{datasets}
+
diff --git a/man/GOMFANCESTOR.Rd b/man/GOMFANCESTOR.Rd
new file mode 100644
index 0000000..825dfd5
--- /dev/null
+++ b/man/GOMFANCESTOR.Rd
@@ -0,0 +1,55 @@
+\name{GOMFANCESTOR}
+\alias{GOMFANCESTOR}
+\title{Annotation of GO identifiers to their Molecular Function Ancestors}
+\description{
+ This data set describes associations between GO molecular function (MF)
+ terms and their ancestor MF terms, based on the directed acyclic
+ graph (DAG) defined by the Gene Ontology Consortium. The format is an R
+ object mapping the GO MF terms to all ancestor terms, where an
+ ancestor term is a more general GO term that precedes
+ the given GO term in the DAG (in other words, the parents, and all
+ their parents, etc.).
+}
+
+\details{
+ Each GO MF term is mapped to a vector of ancestor GO MF terms.
+
+ Molecular function is defined as the tasks performed by individual
+ gene products; examples are transcription factor and DNA helicase as
+ defined by Gene Ontology Consortium.
+
+ Mappings were based on data provided: Gene Ontology
+ ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
+ With a date stamp from the source of: 2016-Sep21
+
+}
+
+\references{
+\url{http://www.geneontology.org/} and
+\url{https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene}
+}
+
+\seealso{
+ \itemize{
+ \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
+ the \code{select()} interface.
+ }
+}
+
+\examples{
+## select() interface:
+## Objects in this package can be accessed using the select() interface
+## from the AnnotationDbi package. See ?select for details.
+
+## Bimap interface:
+# Convert the object to a list
+xx <- as.list(GOMFANCESTOR)
+# Remove GO identifiers that do not have any ancestor
+xx <- xx[!is.na(xx)]
+if(length(xx) > 0){
+ # Get the ancestor GO identifiers for the first two elents of xx
+ goids <- xx[1:2]
+}
+}
+\keyword{datasets}
+
diff --git a/man/GOMFCHILDREN.Rd b/man/GOMFCHILDREN.Rd
new file mode 100644
index 0000000..00d8b1f
--- /dev/null
+++ b/man/GOMFCHILDREN.Rd
@@ -0,0 +1,60 @@
+\name{GOMFCHILDREN}
+\alias{GOMFCHILDREN}
+\title{Annotation of GO Identifiers to their Molecular Function Children}
+\description{
+ This data set describes associations between GO molecular function (MF)
+ terms and their direct children MF terms, based on the directed acyclic
+ graph (DAG) defined by the Gene Ontology Consortium. The format is an R
+ object mapping the GO MF terms to all direct children terms, where a
+ direct child term is a more specific GO term that is immediately preceded
+ by the given GO term in the DAG.
+}
+\details{
+ Each GO MF term is mapped to a vector of children GO MF terms.
+
+ Molecular function is defined as the tasks performed by individual
+ gene products; examples are transcription factor and DNA helicase as
+ defined by Gene Ontology Consortium.
+
+ Mappings were based on data provided by: Gene Ontology
+ ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
+ With a date stamp from the source of: 2016-Sep21
+
+}
+
+\references{
+\url{http://www.geneontology.org/} and
+\url{https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene}
+}
+
+\seealso{
+ \itemize{
+ \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
+ the \code{select()} interface.
+ }
+}
+
+\examples{
+## select() interface:
+## Objects in this package can be accessed using the select() interface
+## from the AnnotationDbi package. See ?select for details.
+
+## Bimap interface:
+# Convert the object to a list
+xx <- as.list(GOMFCHILDREN)
+# Remove GO identifiers that do not have any children
+xx <- xx[!is.na(xx)]
+if(length(xx) > 0){
+ # Get the children GO identifiers for the first elents of xx
+ goids <- xx[[1]]
+ # Find out the GO terms for the first parent goid
+ GOID(GOTERM[[goids[1]]])
+ Term(GOTERM[[goids[1]]])
+ Synonym(GOTERM[[goids[1]]])
+ Secondary(GOTERM[[goids[1]]])
+ Definition(GOTERM[[goids[1]]])
+ Ontology(GOTERM[[goids[1]]])
+}
+}
+\keyword{datasets}
+
diff --git a/man/GOMFOFFSPRING.Rd b/man/GOMFOFFSPRING.Rd
new file mode 100644
index 0000000..09fa05d
--- /dev/null
+++ b/man/GOMFOFFSPRING.Rd
@@ -0,0 +1,54 @@
+\name{GOMFOFFSPRING}
+\alias{GOMFOFFSPRING}
+\title{Annotation of GO Identifiers to their Molecular Function Offspring}
+\description{
+ This data set describes associations between GO molecular function (MF)
+ terms and their offspring MF terms, based on the directed acyclic
+ graph (DAG) defined by the Gene Ontology Consortium. The format is an R
+ object mapping the GO MF terms to all offspring terms, where an
+ offspring term is a more specific GO term that is preceded
+ by the given GO term in the DAG (in other words, the children and all
+ their children, etc.).
+}
+\details{
+ Each GO MF term is mapped to a vector of offspring GO MF terms.
+
+ Molecular function is defined as the tasks performed by individual
+ gene products; examples are transcription factor and DNA helicase as
+ defined by Gene Ontology Consortium.
+
+ Mappings were based on data provided by: Gene Ontology
+ ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
+ With a date stamp from the source of: 2016-Sep21
+
+}
+
+\references{
+\url{http://www.geneontology.org/} and
+\url{https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene}
+}
+
+\seealso{
+ \itemize{
+ \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
+ the \code{select()} interface.
+ }
+}
+
+\examples{
+## select() interface:
+## Objects in this package can be accessed using the select() interface
+## from the AnnotationDbi package. See ?select for details.
+
+## Bimap interface:
+# Convert the object to a list
+xx <- as.list(GOMFOFFSPRING)
+# Remove GO identifiers that do not have any offspring
+xx <- xx[!is.na(xx)]
+if(length(xx) > 0){
+ # Get the offspring GO identifiers for the first two elents of xx
+goids <- xx[1:2]
+}
+}
+\keyword{datasets}
+
diff --git a/man/GOMFPARENTS.Rd b/man/GOMFPARENTS.Rd
new file mode 100644
index 0000000..ebd7a35
--- /dev/null
+++ b/man/GOMFPARENTS.Rd
@@ -0,0 +1,66 @@
+\name{GOMFPARENTS}
+\alias{GOMFPARENTS}
+\title{Annotation of GO Identifiers to their Molecular Function Parents}
+\description{
+ This data set describes associations between GO molecular function (MF)
+ terms and their direct parent MF terms, based on the directed acyclic
+ graph (DAG) defined by the Gene Ontology Consortium. The format is an R
+ object mapping the GO MF terms to all direct parent terms, where a
+ direct parent term is a more general GO term that immediately precedes
+ the given GO term in the DAG.
+}
+
+\details{
+ Each GO MF term is mapped to a named vector of GO MF terms. The name
+ associated with the parent term will be either \emph{isa}, \emph{hasa} or \emph{partof},
+ where \emph{isa} indicates that the child term is a more specific version
+ of the parent, and \emph{hasa} and \emph{partof} indicate that the
+ child term is a part of the parent. For example, a telomere is part of
+ a chromosome.
+
+ Molecular function is defined as the tasks performed by individual
+ gene products; examples are transcription factor and DNA helicase as
+ defined by the Gene Ontology Consortium.
+
+ Mappings were based on data provided by: Gene Ontology
+ ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
+ With a date stamp from the source of: 2016-Sep21
+
+}
+
+\references{
+ \url{http://www.geneontology.org/} and
+ \url{https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene}
+}
+
+\seealso{
+ \itemize{
+ \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
+ the \code{select()} interface.
+ }
+}
+
+\examples{
+## select() interface:
+## Objects in this package can be accessed using the select() interface
+## from the AnnotationDbi package. See ?select for details.
+
+## Bimap interface:
+# Convert the object to a list
+xx <- as.list(GOMFPARENTS)
+# Remove GO identifiers that do not have any parent
+xx <- xx[!is.na(xx)]
+if(length(xx) > 0){
+ # Get the parent GO identifiers for the first elents of xx
+ goids <- xx[[1]]
+ # Find out the GO terms for the first parent goid
+ GOID(GOTERM[[goids[1]]])
+ Term(GOTERM[[goids[1]]])
+ Synonym(GOTERM[[goids[1]]])
+ Secondary(GOTERM[[goids[1]]])
+ Definition(GOTERM[[goids[1]]])
+ Ontology(GOTERM[[goids[1]]])
+}
+}
+\keyword{datasets}
+
diff --git a/man/GOOBSOLETE.Rd b/man/GOOBSOLETE.Rd
new file mode 100644
index 0000000..6de9774
--- /dev/null
+++ b/man/GOOBSOLETE.Rd
@@ -0,0 +1,44 @@
+\name{GOOBSOLETE}
+\alias{GOOBSOLETE}
+\title{Annotation of GO identifiers by terms defined by Gene Ontology
+ Consortium and their status are obsolete}
+\description{
+This is an R object mapping GO identifiers to the specific
+terms in defined by Gene Ontology Consortium and their definition are obsolete
+}
+\details{
+ All the obsolete GO terms that are collected in this index will no longer exist
+ in other mapping objects.
+
+ Mappings were based on data provided by: Gene Ontology
+ ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
+ With a date stamp from the source of: 2016-Sep21
+
+}
+\references{
+ \url{https://www.ncib.nlm.nih.gov/LocusLink}
+}
+
+\seealso{
+ \itemize{
+ \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
+ the \code{select()} interface.
+ }
+}
+
+\examples{
+## select() interface:
+## Objects in this package can be accessed using the select() interface
+## from the AnnotationDbi package. See ?select for details.
+
+## Bimap interface:
+# Convert the object to a list
+xx <- as.list(GOTERM)
+if(length(xx) > 0){
+ # Get the TERMS for the first elent of xx
+ GOID(xx[[1]])
+ Ontology(xx[[1]])
+}
+}
+\keyword{datasets}
+
diff --git a/man/GOSYNONYM.Rd b/man/GOSYNONYM.Rd
new file mode 100644
index 0000000..cbb10ca
--- /dev/null
+++ b/man/GOSYNONYM.Rd
@@ -0,0 +1,34 @@
+\name{GOSYNONYM}
+\alias{GOSYNONYM}
+\title{Map from GO synonyms to GO terms}
+\description{
+ GOSYNONYM is an R object that provides mapping
+ from GO synonyms to GO terms
+}
+
+\details{
+ [TODO: Put some details here]
+}
+
+\seealso{
+ \itemize{
+ \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
+ the \code{select()} interface.
+ }
+}
+
+\examples{
+## select() interface:
+## Objects in this package can be accessed using the select() interface
+## from the AnnotationDbi package. See ?select for details.
+
+## Bimap interface:
+x <- GOSYNONYM
+sample(x, 3)
+# GO ID "GO:0009435" has a lot of synonyms
+GOTERM[["GO:0009435"]]
+# GO ID "GO:0006736" is a synonym of GO ID "GO:0009435"
+GOID(GOSYNONYM[["GO:0006736"]])
+}
+\keyword{datasets}
+
diff --git a/man/GOTERM.Rd b/man/GOTERM.Rd
new file mode 100644
index 0000000..2158484
--- /dev/null
+++ b/man/GOTERM.Rd
@@ -0,0 +1,60 @@
+\name{GOTERM}
+\alias{GOTERM}
+\title{Annotation of GO Identifiers to GO Terms}
+\description{
+ This data set gives mappings between GO identifiers and their respective terms.
+}
+\details{
+ Each GO identifier is mapped to a \code{GOTerms} object that has 6 slots:
+ GOID: GO Identifier
+ Term: The term for that GO id
+ Synonym: Synonymous terms
+ Secondary: Secondary terms that have been merged into this term
+ Definition: Further definition of the GO term
+ Ontology: One of MF - molecular function, BP - biological
+ process, or CC - cellular component
+
+ All the obsolete GO terms are under the nodes "obsolete molecular
+ function" (GO:0008369), "obsolete cellular component" (GO id
+ GO:0008370), and "obsolete biological process" (GO:0008371). Each of
+ these GO identifiers has a group of GO identifiers as their direct children with GO
+ terms that were defined by GO but are
+ deprecated in the current build. These deprecated GO terms were
+ appended by "(obsolete)" when the data package was built.
+
+ Mappings were based on data provided by: Gene Ontology
+ ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
+ With a date stamp from the source of: 2016-Sep21
+
+}
+\references{
+ \url{https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene}
+}
+
+\seealso{
+ \itemize{
+ \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
+ the \code{select()} interface.
+ }
+}
+
+\examples{
+## select() interface:
+## Objects in this package can be accessed using the select() interface
+## from the AnnotationDbi package. See ?select for details.
+
+## Bimap interface:
+# Convert the object to a list
+xx <- as.list(GOTERM)
+if(length(xx) > 0){
+ # Get the TERMS for the first elent of xx
+ GOID(xx[[1]])
+ Term(xx[[1]])
+ Synonym(xx[[1]])
+ Secondary(xx[[1]])
+ Definition(xx[[1]])
+ Ontology(xx[[1]])
+}
+}
+\keyword{datasets}
+
diff --git a/man/GO_dbconn.Rd b/man/GO_dbconn.Rd
new file mode 100644
index 0000000..1d27cc1
--- /dev/null
+++ b/man/GO_dbconn.Rd
@@ -0,0 +1,87 @@
+
+\name{GO_dbconn}
+
+\alias{GO_dbconn}
+\alias{GO_dbfile}
+\alias{GO_dbschema}
+\alias{GO_dbInfo}
+
+
+\title{Collect information about the package annotation DB}
+
+\description{
+ Some convenience functions for getting a connection object to (or collecting
+ information about) the package annotation DB.
+}
+
+\usage{
+ GO_dbconn()
+ GO_dbfile()
+ GO_dbschema(file="", show.indices=FALSE)
+ GO_dbInfo()
+}
+
+\arguments{
+ \item{file}{
+ A connection, or a character string naming the file to print to (see
+ the \code{file} argument of the \code{\link[base]{cat}} function for
+ the details).
+ }
+ \item{show.indices}{
+ The CREATE INDEX statements are not shown by default.
+ Use \code{show.indices=TRUE} to get them.
+ }
+}
+
+\details{
+ \code{GO_dbconn} returns a connection object to the
+ package annotation DB. IMPORTANT: Don't call
+ \code{\link[DBI:dbConnect]{dbDisconnect}} on the connection object
+ returned by \code{GO_dbconn} or you will break all the
+ \code{\link[AnnotationDbi:AnnDbObj-class]{AnnDbObj}} objects defined
+ in this package!
+
+ \code{GO_dbfile} returns the path (character string) to the
+ package annotation DB (this is an SQLite file).
+
+ \code{GO_dbschema} prints the schema definition of the
+ package annotation DB.
+
+ \code{GO_dbInfo} prints other information about the package
+ annotation DB.
+}
+
+\value{
+ \code{GO_dbconn}: a DBIConnection object representing an
+ open connection to the package annotation DB.
+
+ \code{GO_dbfile}: a character string with the path to the
+ package annotation DB.
+
+ \code{GO_dbschema}: none (invisible \code{NULL}).
+
+ \code{GO_dbInfo}: none (invisible \code{NULL}).
+}
+
+\seealso{
+ \code{\link[DBI:dbSendQuery]{dbGetQuery}},
+ \code{\link[DBI:dbConnect]{dbConnect}},
+ \code{\link[AnnotationDbi:AnnDbObj-class]{dbconn}},
+ \code{\link[AnnotationDbi:AnnDbObj-class]{dbfile}},
+ \code{\link[AnnotationDbi:AnnDbObj-class]{dbschema}},
+ \code{\link[AnnotationDbi:AnnDbObj-class]{dbInfo}}
+}
+
+\examples{
+ library(DBI)
+ ## Count the number of rows in the "go_term" table:
+ dbGetQuery(GO_dbconn(), "SELECT COUNT(*) FROM go_term")
+
+ GO_dbschema()
+
+ GO_dbInfo()
+}
+
+\keyword{utilities}
+\keyword{datasets}
+
--
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