# Using Bioconductor’s Annotation Libraries

# Overview

The Bioconductor project maintains a rich body of annotation data assembled into R libraries. The purpose of this vignette is to discuss the structure, contents, and usage of these annotation data libraries. Executable code is provided as examples.

# Contents

Bioconductor’s annotation data libraries are constructed by assembling data collected from various public data repositories using Bioconductor’s AnnotationDbi package and distributed as regular R libraries that can be installed and loaded in the same way an R library is installed/loaded. Each annotation library is an independent unit that can be used alone or in conjunction with other annotation libraries. Platform specific libraries are a group annotation libraries assembled specifically for given platforms (e. g. Affymetrix HG_U95Av2). `org.XX.eg.db` are libraries containing data assembled at genome level for specific organisms such as human, mouse, fly, or rat. KEGG.db1 and GO.db are source specific libraries containing generic data for various genomes.

Each annotation library, when installed, contains a sqlite database contained within the `extdata` along with a `man` subdirectory filled with documentation about the data. The data can be accessed using the standard methods that would work for the classic environment objects (hash table with key-value pairs) and act as if they were simple associations of annotation values to a set of keys. For each of these emulated environment objects (which we will refer to as mappings), there is a corresponding help file in the `man` directory with detail descriptions of the data file and usage. In addition to the traditional access to these data, these databases can also be accessed directly by using DBI interfaces which allow for powerful new combinations of these data.

Each platform specific library creates a series of these mapping objects named by following the convention of package name plus mapping name. The package name is in lower case letters and the mapping names are in capital letters. When a given mapping maps platform specific keys to annotation data, only the name of the annotation data is used for the name of the mapping. Otherwise, the mapping names have a pattern of key name and value name joined by a “2” in between. For example, `hgu95av2ENTREZID` maps probe ids on an Affymetrix human genome U95Av2 chip to EntrezGene IDs while `hgu95av2GO2PROBE` maps Gene Ontology IDs to probe IDs. Names of the mappings available in a platform specific data package are not listed here to save space but are easily accessible as shown later in the section for usage.

Genome level annotation libraries are named in the form of org.Xx.yy.db where Xx represents an abbreviation of the genus and species. Each of the organism wide genome annotation packages is based upon some type of widely used gene based identifier (such as an Entrez Gene id) that is mapped onto all the other features in the package. The yy part of the name corresponds to this designation, where eg means a package is an entrez gene package and sgd is a package based on the sgd database etc. In many cases the org packages will contain more different kinds of information that the platform based ones, since not all types of information are as widely sought after.

The KEGG.db library contains mappings between ids such as Entrez Gene IDs and GO to KEGG pathway ids and thus also to pathway names. The GO.db library maintain the directed acyclic graph structure of the original data from Gene Ontology Consortium by providing mappings of GO ids to their direct parents or children for each of the three categories (molecular function, cellular component, and biological process). Mappings between Entrez Gene and GO ids are also available to complement the GO.db package. These mappings are found within the organism wide packages mentioned above. These mappings are provided with evidence code that specifies the type of evidence that supports the annotation of a gene to a particular GO term.

# Usage

All the annotation libraries can be obtained from https://www.bioconductor.org. To illustrate their usages, we use the library for Affymetrix HG_U95Av2 chip hgu95av2.db as an example for platform specific data packages and the GO.db library for non-platform specific data packages. We assume that R and Bioconductor’s Biobase and annotation.

## Package installation

Download libraries hgu95av2.db and GO.db with `BiocManager::install()`.

Typing `library(library name)` in an R session will load the library into R. For example,

    library("annotate")
    library("hgu95av2.db")
    library("GO.db")

## Documentations

Each library contains documentation for the library in general and each of the individual mapping objects contained by the library. Two documents at the library level can be accessed by typing a library basename proceeded by a question mark (e. g. `?hgu95av2`) and the library basename followed by a pair of brackets (e. g. `hgu95av2()`), respectively. The former explains what the package is and details how a user can get more information, while the latter lists all the mappings contained by a library and provides information on the total number of keys within each of the maps contained by the library and how many of these keys are annotated. In addition, the latter will indicate the sources for the information provided by the package as well as the date that these sources claim to have last been updated.

The documentation for a given mapping object can be accessed by typing the name of a mapping object proceeded by a question mark (e. g. `hgu95av2GO`). The resulting documentation provides detail explanations to the mapping object, data source used to build the object, and example code for accessing annotation data.

## Accessing annotation data within a library

Annotation data of a given library are stored as mapping objects in the form of key (items to be annotated) and value (annotation for an key item) pairs. Each mapping object provides annotation for keys for a particular subject reflected by the name of the object. For example, `hgu95av2GO` annotates probes on the HGU95Av2 chip with ids of the Gene Ontology terms the probes correspond to.

The name of an mapping object consists of package basename (hgu95av2.db) and mapping name GO to avoid confusion when multiple libraries are loaded to the system at the same time. Data contained by an mapping can be accessed easily using Bioconductor’s existing functions. For example, the following code stores all the keys contained by the `hgu95av2GO` mapping object to variable `temp` and displays the first five keys on the screen:

    as.list(hgu95av2GO[5])

    ## $`1004_at`
    ## $`1004_at`$`GO:0006935`
    ## $`1004_at`$`GO:0006935`$GOID
    ## [1] "GO:0006935"
    ##
    ## $`1004_at`$`GO:0006935`$Evidence
    ## [1] "IEA"
    ##
    ## $`1004_at`$`GO:0006935`$Ontology
    ## [1] "BP"
    ##
    ##
    ## $`1004_at`$`GO:0006955`
    ## $`1004_at`$`GO:0006955`$GOID
    ## [1] "GO:0006955"
    ##
    ## $`1004_at`$`GO:0006955`$Evidence
    ## [1] "IBA"
    ##
    ## $`1004_at`$`GO:0006955`$Ontology
    ## [1] "BP"
    ##
    ##
    ## $`1004_at`$`GO:0006955`
    ## $`1004_at`$`GO:0006955`$GOID
    ## [1] "GO:0006955"
    ##
    ## $`1004_at`$`GO:0006955`$Evidence
    ## [1] "IEA"
    ##
    ## $`1004_at`$`GO:0006955`$Ontology
    ## [1] "BP"
    ##
    ##
    ## $`1004_at`$`GO:0007165`
    ## $`1004_at`$`GO:0007165`$GOID
    ## [1] "GO:0007165"
    ##
    ## $`1004_at`$`GO:0007165`$Evidence
    ## [1] "IEA"
    ##
    ## $`1004_at`$`GO:0007165`$Ontology
    ## [1] "BP"
    ##
    ##
    ## $`1004_at`$`GO:0007186`
    ## $`1004_at`$`GO:0007186`$GOID
    ## [1] "GO:0007186"
    ##
    ## $`1004_at`$`GO:0007186`$Evidence
    ## [1] "IEA"
    ##
    ## $`1004_at`$`GO:0007186`$Ontology
    ## [1] "BP"
    ##
    ##
    ## $`1004_at`$`GO:0007186`
    ## $`1004_at`$`GO:0007186`$GOID
    ## [1] "GO:0007186"
    ##
    ## $`1004_at`$`GO:0007186`$Evidence
    ## [1] "TAS"
    ##
    ## $`1004_at`$`GO:0007186`$Ontology
    ## [1] "BP"
    ##
    ##
    ## $`1004_at`$`GO:0007204`
    ## $`1004_at`$`GO:0007204`$GOID
    ## [1] "GO:0007204"
    ##
    ## $`1004_at`$`GO:0007204`$Evidence
    ## [1] "IBA"
    ##
    ## $`1004_at`$`GO:0007204`$Ontology
    ## [1] "BP"
    ##
    ##
    ## $`1004_at`$`GO:0019722`
    ## $`1004_at`$`GO:0019722`$GOID
    ## [1] "GO:0019722"
    ##
    ## $`1004_at`$`GO:0019722`$Evidence
    ## [1] "IBA"
    ##
    ## $`1004_at`$`GO:0019722`$Ontology
    ## [1] "BP"
    ##
    ##
    ## $`1004_at`$`GO:0030595`
    ## $`1004_at`$`GO:0030595`$GOID
    ## [1] "GO:0030595"
    ##
    ## $`1004_at`$`GO:0030595`$Evidence
    ## [1] "IEA"
    ##
    ## $`1004_at`$`GO:0030595`$Ontology
    ## [1] "BP"
    ##
    ##
    ## $`1004_at`$`GO:0032467`
    ## $`1004_at`$`GO:0032467`$GOID
    ## [1] "GO:0032467"
    ##
    ## $`1004_at`$`GO:0032467`$Evidence
    ## [1] "IMP"
    ##
    ## $`1004_at`$`GO:0032467`$Ontology
    ## [1] "BP"
    ##
    ##
    ## $`1004_at`$`GO:0042113`
    ## $`1004_at`$`GO:0042113`$GOID
    ## [1] "GO:0042113"
    ##
    ## $`1004_at`$`GO:0042113`$Evidence
    ## [1] "IEA"
    ##
    ## $`1004_at`$`GO:0042113`$Ontology
    ## [1] "BP"
    ##
    ##
    ## $`1004_at`$`GO:0048535`
    ## $`1004_at`$`GO:0048535`$GOID
    ## [1] "GO:0048535"
    ##
    ## $`1004_at`$`GO:0048535`$Evidence
    ## [1] "IEA"
    ##
    ## $`1004_at`$`GO:0048535`$Ontology
    ## [1] "BP"
    ##
    ##
    ## $`1004_at`$`GO:0060326`
    ## $`1004_at`$`GO:0060326`$GOID
    ## [1] "GO:0060326"
    ##
    ## $`1004_at`$`GO:0060326`$Evidence
    ## [1] "IBA"
    ##
    ## $`1004_at`$`GO:0060326`$Ontology
    ## [1] "BP"
    ##
    ##
    ## $`1004_at`$`GO:0070098`
    ## $`1004_at`$`GO:0070098`$GOID
    ## [1] "GO:0070098"
    ##
    ## $`1004_at`$`GO:0070098`$Evidence
    ## [1] "IEA"
    ##
    ## $`1004_at`$`GO:0070098`$Ontology
    ## [1] "BP"
    ##
    ##
    ## $`1004_at`$`GO:0005886`
    ## $`1004_at`$`GO:0005886`$GOID
    ## [1] "GO:0005886"
    ##
    ## $`1004_at`$`GO:0005886`$Evidence
    ## [1] "IEA"
    ##
    ## $`1004_at`$`GO:0005886`$Ontology
    ## [1] "CC"
    ##
    ##
    ## $`1004_at`$`GO:0005886`
    ## $`1004_at`$`GO:0005886`$GOID
    ## [1] "GO:0005886"
    ##
    ## $`1004_at`$`GO:0005886`$Evidence
    ## [1] "TAS"
    ##
    ## $`1004_at`$`GO:0005886`$Ontology
    ## [1] "CC"
    ##
    ##
    ## $`1004_at`$`GO:0009897`
    ## $`1004_at`$`GO:0009897`$GOID
    ## [1] "GO:0009897"
    ##
    ## $`1004_at`$`GO:0009897`$Evidence
    ## [1] "IBA"
    ##
    ## $`1004_at`$`GO:0009897`$Ontology
    ## [1] "CC"
    ##
    ##
    ## $`1004_at`$`GO:0009897`
    ## $`1004_at`$`GO:0009897`$GOID
    ## [1] "GO:0009897"
    ##
    ## $`1004_at`$`GO:0009897`$Evidence
    ## [1] "IEA"
    ##
    ## $`1004_at`$`GO:0009897`$Ontology
    ## [1] "CC"
    ##
    ##
    ## $`1004_at`$`GO:0016020`
    ## $`1004_at`$`GO:0016020`$GOID
    ## [1] "GO:0016020"
    ##
    ## $`1004_at`$`GO:0016020`$Evidence
    ## [1] "IEA"
    ##
    ## $`1004_at`$`GO:0016020`$Ontology
    ## [1] "CC"
    ##
    ##
    ## $`1004_at`$`GO:0004930`
    ## $`1004_at`$`GO:0004930`$GOID
    ## [1] "GO:0004930"
    ##
    ## $`1004_at`$`GO:0004930`$Evidence
    ## [1] "IEA"
    ##
    ## $`1004_at`$`GO:0004930`$Ontology
    ## [1] "MF"
    ##
    ##
    ## $`1004_at`$`GO:0004930`
    ## $`1004_at`$`GO:0004930`$GOID
    ## [1] "GO:0004930"
    ##
    ## $`1004_at`$`GO:0004930`$Evidence
    ## [1] "TAS"
    ##
    ## $`1004_at`$`GO:0004930`$Ontology
    ## [1] "MF"
    ##
    ##
    ## $`1004_at`$`GO:0005515`
    ## $`1004_at`$`GO:0005515`$GOID
    ## [1] "GO:0005515"
    ##
    ## $`1004_at`$`GO:0005515`$Evidence
    ## [1] "IPI"
    ##
    ## $`1004_at`$`GO:0005515`$Ontology
    ## [1] "MF"
    ##
    ##
    ## $`1004_at`$`GO:0016493`
    ## $`1004_at`$`GO:0016493`$GOID
    ## [1] "GO:0016493"
    ##
    ## $`1004_at`$`GO:0016493`$Evidence
    ## [1] "IBA"
    ##
    ## $`1004_at`$`GO:0016493`$Ontology
    ## [1] "MF"
    ##
    ##
    ## $`1004_at`$`GO:0016494`
    ## $`1004_at`$`GO:0016494`$GOID
    ## [1] "GO:0016494"
    ##
    ## $`1004_at`$`GO:0016494`$Evidence
    ## [1] "IEA"
    ##
    ## $`1004_at`$`GO:0016494`$Ontology
    ## [1] "MF"
    ##
    ##
    ## $`1004_at`$`GO:0019957`
    ## $`1004_at`$`GO:0019957`$GOID
    ## [1] "GO:0019957"
    ##
    ## $`1004_at`$`GO:0019957`$Evidence
    ## [1] "IBA"
    ##
    ## $`1004_at`$`GO:0019957`$Ontology
    ## [1] "MF"

To obtain annotation for a given set of keys, one may use the `mget` function. Suppose we have run an experiment using the HG_U95Av2 chip and found three genes represented by Affymetrix probe ids 738_at, 40840_at, and 41668_r_at interesting. To get the names of genes the three probe ids corresponding to, we do:

    mget(c("738_at", "40840_at", "41668_r_at"), hgu95av2GENENAME)

    ## $`738_at`
    ## [1] "5'-nucleotidase, cytosolic II"
    ##
    ## $`40840_at`
    ## [1] "peptidylprolyl isomerase F"
    ##
    ## $`41668_r_at`
    ## [1] "TDP-glucose 4,6-dehydratase"

Similarly, identifiers of Gene Ontology terms corrsponding to the three probes can be obtained as shown below:

    temp <- mget(c("41561_s_at", "40840_at", "41668_r_at"), hgu95av2GO)

In this case, the function `mget` returns a list of pre-defined S4 objects containing data for the ids, ontology, and evidence code of Gene Ontology terms corresponding to the three keys. The following code shows how to access the GO id, evidence code and ontology of the Gene Ontology term corresponding to probe id 40840_at:

    temp <- get("738_at", hgu95av2GO)
    names(temp)

    ##  [1] "GO:0000255" "GO:0000255" "GO:0006202" "GO:0006204" "GO:0009117"
    ##  [6] "GO:0043605" "GO:0046037" "GO:0046037" "GO:0046038" "GO:0046040"
    ## [11] "GO:0046040" "GO:0046054" "GO:0046054" "GO:0046055" "GO:0046085"
    ## [16] "GO:0050689" "GO:0070936" "GO:0140374" "GO:0005737" "GO:0005737"
    ## [21] "GO:0005829" "GO:0005829" "GO:0005829" "GO:0000166" "GO:0003824"
    ## [26] "GO:0005515" "GO:0005524" "GO:0005524" "GO:0008253" "GO:0008253"
    ## [31] "GO:0008253" "GO:0008253" "GO:0008253" "GO:0016740" "GO:0016787"
    ## [36] "GO:0042802" "GO:0046872" "GO:0050146" "GO:0050146" "GO:0061630"

    temp[["GO:0008253"]][["Evidence"]]

    ## [1] "IBA"

    temp[["GO:0008253"]][["Ontology"]]

    ## [1] "MF"

As shown above, probe 40840_at can be annotated by three Gene Ontology terms identified by GO:0005829, GO:0008253, and GO:0016787. The evidence code for GO:0008253 is TAS (traceable author statement) and it belongs to ontology MF (molecular function).

## Accessing annotation data across libraries

Often, data available in a given data package alone may not be sufficient and need to be sought across packages. Bioconductor’s annotation data packages are linked by common public data identifiers to allow traverse between packages. Using the example above, we know that probe id 738_at are annotated by three Gene Ontology ids GO:0005829, GO:0008253, and GO:0016787. The Gene Ontology terms for various Gene Ontology ids, however, are stored in another package named GO.db. As package hgu95av2.db and GO.db are linked by GO ids, one can annotate probe id 738_at with Gene Ontology terms by linking data in the two packages using GO id as shown below:

    mget(names(get("738_at", hgu95av2GO)), GOTERM)

    ## $`GO:0000255`
    ## GOID: GO:0000255
    ## Term: allantoin metabolic process
    ## Ontology: BP
    ## Definition: The chemical reactions and pathways involving allantoin,
    ##     (2,5-dioxo-4-imidazolidinyl)urea, an intermediate or end product of
    ##     purine catabolism.
    ## Synonym: allantoin metabolism
    ##
    ## $`GO:0000255`
    ## GOID: GO:0000255
    ## Term: allantoin metabolic process
    ## Ontology: BP
    ## Definition: The chemical reactions and pathways involving allantoin,
    ##     (2,5-dioxo-4-imidazolidinyl)urea, an intermediate or end product of
    ##     purine catabolism.
    ## Synonym: allantoin metabolism
    ##
    ## $`GO:0006202`
    ## GOID: GO:0006202
    ## Term: GMP catabolic process to guanine
    ## Ontology: BP
    ## Definition: The chemical reactions and pathways resulting in the
    ##     breakdown of guanosine monophosphate into other compounds,
    ##     including guanine.
    ## Synonym: GMP breakdown to guanine
    ## Synonym: GMP degradation to guanine
    ##
    ## $`GO:0006204`
    ## GOID: GO:0006204
    ## Term: IMP catabolic process
    ## Ontology: BP
    ## Definition: The chemical reactions and pathways resulting in the
    ##     breakdown of IMP, inosine monophosphate.
    ## Synonym: IMP breakdown
    ## Synonym: IMP catabolism
    ## Synonym: IMP degradation
    ##
    ## $`GO:0009117`
    ## GOID: GO:0009117
    ## Term: nucleotide metabolic process
    ## Ontology: BP
    ## Definition: The chemical reactions and pathways involving a nucleotide,
    ##     a nucleoside that is esterified with (ortho)phosphate or an
    ##     oligophosphate at any hydroxyl group on the glycose moiety; may be
    ##     mono-, di- or triphosphate; this definition includes cyclic
    ##     nucleotides (nucleoside cyclic phosphates).
    ## Synonym: nucleotide metabolism
    ##
    ## $`GO:0043605`
    ## GOID: GO:0043605
    ## Term: amide catabolic process
    ## Ontology: BP
    ## Definition: The chemical reactions and pathways resulting in the
    ##     breakdown of an amide, any derivative of an oxoacid in which an
    ##     acidic hydroxy group has been replaced by an amino or substituted
    ##     amino group.
    ## Synonym: cellular amide catabolic process
    ##
    ## $`GO:0046037`
    ## GOID: GO:0046037
    ## Term: GMP metabolic process
    ## Ontology: BP
    ## Definition: The chemical reactions and pathways involving GMP,
    ##     guanosine monophosphate.
    ## Synonym: GMP metabolism
    ##
    ## $`GO:0046037`
    ## GOID: GO:0046037
    ## Term: GMP metabolic process
    ## Ontology: BP
    ## Definition: The chemical reactions and pathways involving GMP,
    ##     guanosine monophosphate.
    ## Synonym: GMP metabolism
    ##
    ## $`GO:0046038`
    ## GOID: GO:0046038
    ## Term: GMP catabolic process
    ## Ontology: BP
    ## Definition: The chemical reactions and pathways resulting in the
    ##     breakdown of GMP, guanosine monophosphate.
    ## Synonym: GMP breakdown
    ## Synonym: GMP catabolism
    ## Synonym: GMP degradation
    ##
    ## $`GO:0046040`
    ## GOID: GO:0046040
    ## Term: IMP metabolic process
    ## Ontology: BP
    ## Definition: The chemical reactions and pathways involving IMP, inosine
    ##     monophosphate.
    ## Synonym: IMP metabolism
    ##
    ## $`GO:0046040`
    ## GOID: GO:0046040
    ## Term: IMP metabolic process
    ## Ontology: BP
    ## Definition: The chemical reactions and pathways involving IMP, inosine
    ##     monophosphate.
    ## Synonym: IMP metabolism
    ##
    ## $`GO:0046054`
    ## GOID: GO:0046054
    ## Term: dGMP metabolic process
    ## Ontology: BP
    ## Definition: The chemical reactions and pathways involving dGMP,
    ##     deoxyguanosine monophosphate (2'-deoxyguanosine 5'-phosphate).
    ## Synonym: dGMP metabolism
    ##
    ## $`GO:0046054`
    ## GOID: GO:0046054
    ## Term: dGMP metabolic process
    ## Ontology: BP
    ## Definition: The chemical reactions and pathways involving dGMP,
    ##     deoxyguanosine monophosphate (2'-deoxyguanosine 5'-phosphate).
    ## Synonym: dGMP metabolism
    ##
    ## $`GO:0046055`
    ## GOID: GO:0046055
    ## Term: dGMP catabolic process
    ## Ontology: BP
    ## Definition: The chemical reactions and pathways resulting in the
    ##     breakdown of dGMP, deoxyguanosine monophosphate (2'-deoxyguanosine
    ##     5'-phosphate).
    ## Synonym: dGMP breakdown
    ## Synonym: dGMP catabolism
    ## Synonym: dGMP degradation
    ##
    ## $`GO:0046085`
    ## GOID: GO:0046085
    ## Term: adenosine metabolic process
    ## Ontology: BP
    ## Definition: The chemical reactions and pathways involving adenosine,
    ##     adenine riboside, a ribonucleoside found widely distributed in
    ##     cells of every type as the free nucleoside and in combination in
    ##     nucleic acids and various nucleoside coenzymes.
    ## Synonym: adenosine metabolism
    ##
    ## $`GO:0050689`
    ## GOID: GO:0050689
    ## Term: negative regulation of defense response to virus by host
    ## Ontology: BP
    ## Definition: Any host process that results in the inhibition of
    ##     antiviral immune response mechanisms, thereby facilitating viral
    ##     replication. The host is defined as the larger of the organisms
    ##     involved in a symbiotic interaction.
    ## Synonym: down regulation of antiviral response by host
    ## Synonym: down-regulation of antiviral response by host
    ## Synonym: downregulation of antiviral response by host
    ## Synonym: negative regulation by host of antiviral response
    ## Synonym: negative regulation of antiviral response by host
    ## Synonym: inhibition of antiviral response by host
    ##
    ## $`GO:0070936`
    ## GOID: GO:0070936
    ## Term: protein K48-linked ubiquitination
    ## Ontology: BP
    ## Definition: A protein ubiquitination process in which a polymer of
    ##     ubiquitin, formed by linkages between lysine residues at position
    ##     48 of the ubiquitin monomers, is added to a protein. K48-linked
    ##     ubiquitination targets the substrate protein for degradation.
    ## Synonym: protein K48-linked polyubiquitination
    ##
    ## $`GO:0140374`
    ## GOID: GO:0140374
    ## Term: antiviral innate immune response
    ## Ontology: BP
    ## Definition: NA
    ##
    ## $`GO:0005737`
    ## GOID: GO:0005737
    ## Term: cytoplasm
    ## Ontology: CC
    ## Definition: The contents of a cell excluding the plasma membrane and
    ##     nucleus, but including other subcellular structures.
    ##
    ## $`GO:0005737`
    ## GOID: GO:0005737
    ## Term: cytoplasm
    ## Ontology: CC
    ## Definition: The contents of a cell excluding the plasma membrane and
    ##     nucleus, but including other subcellular structures.
    ##
    ## $`GO:0005829`
    ## GOID: GO:0005829
    ## Term: cytosol
    ## Ontology: CC
    ## Definition: The part of the cytoplasm that does not contain organelles
    ##     but which does contain other particulate matter, such as protein
    ##     complexes.
    ##
    ## $`GO:0005829`
    ## GOID: GO:0005829
    ## Term: cytosol
    ## Ontology: CC
    ## Definition: The part of the cytoplasm that does not contain organelles
    ##     but which does contain other particulate matter, such as protein
    ##     complexes.
    ##
    ## $`GO:0005829`
    ## GOID: GO:0005829
    ## Term: cytosol
    ## Ontology: CC
    ## Definition: The part of the cytoplasm that does not contain organelles
    ##     but which does contain other particulate matter, such as protein
    ##     complexes.
    ##
    ## $`GO:0000166`
    ## GOID: GO:0000166
    ## Term: nucleotide binding
    ## Ontology: MF
    ## Definition: Binding to a nucleotide, any compound consisting of a
    ##     nucleoside that is esterified with (ortho)phosphate or an
    ##     oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    ##
    ## $`GO:0003824`
    ## GOID: GO:0003824
    ## Term: catalytic activity
    ## Ontology: MF
    ## Definition: Catalysis of a biochemical reaction at physiological
    ##     temperatures. In biologically catalyzed reactions, the reactants
    ##     are known as substrates, and the catalysts are naturally occurring
    ##     macromolecular substances known as enzymes. Enzymes possess
    ##     specific binding sites for substrates, and are usually composed
    ##     wholly or largely of protein, but RNA that has catalytic activity
    ##     (ribozyme) is often also regarded as enzymatic.
    ## Synonym: enzyme activity
    ##
    ## $`GO:0005515`
    ## GOID: GO:0005515
    ## Term: protein binding
    ## Ontology: MF
    ## Definition: Binding to a protein.
    ## Synonym: GO:0001948
    ## Synonym: GO:0045308
    ## Synonym: protein amino acid binding
    ## Synonym: glycoprotein binding
    ## Secondary: GO:0001948
    ## Secondary: GO:0045308
    ##
    ## $`GO:0005524`
    ## GOID: GO:0005524
    ## Term: ATP binding
    ## Ontology: MF
    ## Definition: Binding to ATP, adenosine 5'-triphosphate, a universally
    ##     important coenzyme and enzyme regulator.
    ## Synonym: Mg-ATP binding
    ## Synonym: MgATP binding
    ##
    ## $`GO:0005524`
    ## GOID: GO:0005524
    ## Term: ATP binding
    ## Ontology: MF
    ## Definition: Binding to ATP, adenosine 5'-triphosphate, a universally
    ##     important coenzyme and enzyme regulator.
    ## Synonym: Mg-ATP binding
    ## Synonym: MgATP binding
    ##
    ## $`GO:0008253`
    ## GOID: GO:0008253
    ## Term: 5'-nucleotidase activity
    ## Ontology: MF
    ## Definition: Catalysis of the reaction: a 5'-ribonucleotide + H2O = a
    ##     ribonucleoside + phosphate.
    ## Synonym: 5' nucleotidase activity
    ## Synonym: 5'-mononucleotidase activity
    ## Synonym: 5'-ribonucleotide phosphohydrolase activity
    ## Synonym: 5'-adenylic phosphatase
    ## Synonym: 5'-AMP nucleotidase
    ## Synonym: 5'-AMPase
    ## Synonym: adenosine 5'-phosphatase
    ## Synonym: adenosine monophosphatase
    ## Synonym: AMP phosphatase
    ## Synonym: AMP phosphohydrolase
    ## Synonym: AMPase
    ## Synonym: snake venom 5'-nucleotidase
    ## Synonym: thimidine monophosphate nucleotidase
    ## Synonym: UMPase
    ## Synonym: uridine 5'-nucleotidase
    ##
    ## $`GO:0008253`
    ## GOID: GO:0008253
    ## Term: 5'-nucleotidase activity
    ## Ontology: MF
    ## Definition: Catalysis of the reaction: a 5'-ribonucleotide + H2O = a
    ##     ribonucleoside + phosphate.
    ## Synonym: 5' nucleotidase activity
    ## Synonym: 5'-mononucleotidase activity
    ## Synonym: 5'-ribonucleotide phosphohydrolase activity
    ## Synonym: 5'-adenylic phosphatase
    ## Synonym: 5'-AMP nucleotidase
    ## Synonym: 5'-AMPase
    ## Synonym: adenosine 5'-phosphatase
    ## Synonym: adenosine monophosphatase
    ## Synonym: AMP phosphatase
    ## Synonym: AMP phosphohydrolase
    ## Synonym: AMPase
    ## Synonym: snake venom 5'-nucleotidase
    ## Synonym: thimidine monophosphate nucleotidase
    ## Synonym: UMPase
    ## Synonym: uridine 5'-nucleotidase
    ##
    ## $`GO:0008253`
    ## GOID: GO:0008253
    ## Term: 5'-nucleotidase activity
    ## Ontology: MF
    ## Definition: Catalysis of the reaction: a 5'-ribonucleotide + H2O = a
    ##     ribonucleoside + phosphate.
    ## Synonym: 5' nucleotidase activity
    ## Synonym: 5'-mononucleotidase activity
    ## Synonym: 5'-ribonucleotide phosphohydrolase activity
    ## Synonym: 5'-adenylic phosphatase
    ## Synonym: 5'-AMP nucleotidase
    ## Synonym: 5'-AMPase
    ## Synonym: adenosine 5'-phosphatase
    ## Synonym: adenosine monophosphatase
    ## Synonym: AMP phosphatase
    ## Synonym: AMP phosphohydrolase
    ## Synonym: AMPase
    ## Synonym: snake venom 5'-nucleotidase
    ## Synonym: thimidine monophosphate nucleotidase
    ## Synonym: UMPase
    ## Synonym: uridine 5'-nucleotidase
    ##
    ## $`GO:0008253`
    ## GOID: GO:0008253
    ## Term: 5'-nucleotidase activity
    ## Ontology: MF
    ## Definition: Catalysis of the reaction: a 5'-ribonucleotide + H2O = a
    ##     ribonucleoside + phosphate.
    ## Synonym: 5' nucleotidase activity
    ## Synonym: 5'-mononucleotidase activity
    ## Synonym: 5'-ribonucleotide phosphohydrolase activity
    ## Synonym: 5'-adenylic phosphatase
    ## Synonym: 5'-AMP nucleotidase
    ## Synonym: 5'-AMPase
    ## Synonym: adenosine 5'-phosphatase
    ## Synonym: adenosine monophosphatase
    ## Synonym: AMP phosphatase
    ## Synonym: AMP phosphohydrolase
    ## Synonym: AMPase
    ## Synonym: snake venom 5'-nucleotidase
    ## Synonym: thimidine monophosphate nucleotidase
    ## Synonym: UMPase
    ## Synonym: uridine 5'-nucleotidase
    ##
    ## $`GO:0008253`
    ## GOID: GO:0008253
    ## Term: 5'-nucleotidase activity
    ## Ontology: MF
    ## Definition: Catalysis of the reaction: a 5'-ribonucleotide + H2O = a
    ##     ribonucleoside + phosphate.
    ## Synonym: 5' nucleotidase activity
    ## Synonym: 5'-mononucleotidase activity
    ## Synonym: 5'-ribonucleotide phosphohydrolase activity
    ## Synonym: 5'-adenylic phosphatase
    ## Synonym: 5'-AMP nucleotidase
    ## Synonym: 5'-AMPase
    ## Synonym: adenosine 5'-phosphatase
    ## Synonym: adenosine monophosphatase
    ## Synonym: AMP phosphatase
    ## Synonym: AMP phosphohydrolase
    ## Synonym: AMPase
    ## Synonym: snake venom 5'-nucleotidase
    ## Synonym: thimidine monophosphate nucleotidase
    ## Synonym: UMPase
    ## Synonym: uridine 5'-nucleotidase
    ##
    ## $`GO:0016740`
    ## GOID: GO:0016740
    ## Term: transferase activity
    ## Ontology: MF
    ## Definition: Catalysis of the transfer of a group, e.g. a methyl group,
    ##     glycosyl group, acyl group, phosphorus-containing, or other groups,
    ##     from one compound (generally regarded as the donor) to another
    ##     compound (generally regarded as the acceptor). Transferase is the
    ##     systematic name for any enzyme of EC class 2.
    ##
    ## $`GO:0016787`
    ## GOID: GO:0016787
    ## Term: hydrolase activity
    ## Ontology: MF
    ## Definition: Catalysis of the hydrolysis of various bonds, e.g. C-O,
    ##     C-N, C-C, phosphoric anhydride bonds, etc.
    ##
    ## $`GO:0042802`
    ## GOID: GO:0042802
    ## Term: identical protein binding
    ## Ontology: MF
    ## Definition: Binding to an identical protein or proteins.
    ## Synonym: isoform-specific homophilic binding
    ## Synonym: protein homopolymerization
    ##
    ## $`GO:0046872`
    ## GOID: GO:0046872
    ## Term: metal ion binding
    ## Ontology: MF
    ## Definition: Binding to a metal ion.
    ## Synonym: metal binding
    ## Synonym: heavy metal binding
    ##
    ## $`GO:0050146`
    ## GOID: GO:0050146
    ## Term: nucleoside phosphotransferase activity
    ## Ontology: MF
    ## Definition: Catalysis of the reaction: a nucleotide + a
    ##     2'-deoxynucleoside = a nucleoside + a 2'-deoxynucleoside
    ##     5'-monophosphate.
    ## Synonym: nonspecific nucleoside phosphotransferase activity
    ## Synonym: nucleotide:2'-nucleoside 5'-phosphotransferase activity
    ## Synonym: nucleotide:3'-deoxynucleoside 5'-phosphotransferase activity
    ## Synonym: nucleotide:nucleoside 5'-phosphotransferase activity
    ##
    ## $`GO:0050146`
    ## GOID: GO:0050146
    ## Term: nucleoside phosphotransferase activity
    ## Ontology: MF
    ## Definition: Catalysis of the reaction: a nucleotide + a
    ##     2'-deoxynucleoside = a nucleoside + a 2'-deoxynucleoside
    ##     5'-monophosphate.
    ## Synonym: nonspecific nucleoside phosphotransferase activity
    ## Synonym: nucleotide:2'-nucleoside 5'-phosphotransferase activity
    ## Synonym: nucleotide:3'-deoxynucleoside 5'-phosphotransferase activity
    ## Synonym: nucleotide:nucleoside 5'-phosphotransferase activity
    ##
    ## $`GO:0061630`
    ## GOID: GO:0061630
    ## Term: ubiquitin protein ligase activity
    ## Ontology: MF
    ## Definition: Catalysis of the transfer of ubiquitin to a substrate
    ##     protein via the reaction X-ubiquitin + S = X + S-ubiquitin, where X
    ##     is either an E2 or E3 enzyme, the X-ubiquitin linkage is a
    ##     thioester bond, and the S-ubiquitin linkage is an amide bond: an
    ##     isopeptide bond between the C-terminal glycine of ubiquitin and the
    ##     epsilon-amino group of lysine residues in the substrate or, in the
    ##     linear extension of ubiquitin chains, a peptide bond the between
    ##     the C-terminal glycine and N-terminal methionine of ubiquitin
    ##     residues.
    ## Synonym: GO:0090302
    ## Synonym: GO:0090622
    ## Synonym: GO:1904264
    ## Synonym: GO:1904822
    ## Synonym: protein ubiquitination activity
    ## Synonym: ubiquitin ligase activity
    ## Synonym: ER-associated E3 ligase
    ## Synonym: E3
    ## Secondary: GO:0090302
    ## Secondary: GO:0090622
    ## Secondary: GO:1904264
    ## Secondary: GO:1904822

It turns out that probe id 738_at (corresponding to GO:0008253, and GO:0016787) has molecular function (MF) 5’-nucleotidase activity and hydrolase activity.

# Session Information

The version number of R and packages loaded for generating the vignette were:

    ## R version 4.5.1 (2025-06-13)
    ## Platform: x86_64-pc-linux-gnu
    ## Running under: Ubuntu 24.04.3 LTS
    ##
    ## Matrix products: default
    ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
    ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
    ##
    ## locale:
    ##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
    ##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C
    ##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
    ##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
    ##  [9] LC_ADDRESS=C               LC_TELEPHONE=C
    ## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
    ##
    ## time zone: Etc/UTC
    ## tzcode source: system (glibc)
    ##
    ## attached base packages:
    ## [1] stats4    stats     graphics  grDevices utils     datasets  methods
    ## [8] base
    ##
    ## other attached packages:
    ##  [1] GO.db_3.22.0         hgu95av2.db_3.13.0   org.Hs.eg.db_3.22.0
    ##  [4] annotate_1.89.0      XML_3.99-0.19        AnnotationDbi_1.71.2
    ##  [7] IRanges_2.45.0       S4Vectors_0.49.0     Biobase_2.71.0
    ## [10] BiocGenerics_0.57.0  generics_0.1.4       BiocStyle_2.39.0
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] bit_4.6.0           jsonlite_2.0.0      compiler_4.5.1
    ##  [4] BiocManager_1.30.26 crayon_1.5.3        blob_1.2.4
    ##  [7] Biostrings_2.79.1   jquerylib_0.1.4     Seqinfo_1.1.0
    ## [10] png_0.1-8           yaml_2.3.10         fastmap_1.2.0
    ## [13] R6_2.6.1            XVector_0.51.0      knitr_1.50
    ## [16] maketools_1.3.2     DBI_1.2.3           bslib_0.9.0
    ## [19] rlang_1.1.6         KEGGREST_1.49.2     cachem_1.1.0
    ## [22] xfun_0.54           sass_0.4.10         sys_3.4.3
    ## [25] bit64_4.6.0-1       RSQLite_2.4.3       memoise_2.0.1
    ## [28] cli_3.6.5           digest_0.6.37       xtable_1.8-4
    ## [31] lifecycle_1.0.4     vctrs_0.6.5         evaluate_1.0.5
    ## [34] buildtools_1.0.0    rmarkdown_2.30      httr_1.4.7
    ## [37] pkgconfig_2.0.3     tools_4.5.1         htmltools_0.5.8.1

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